From 6af30d5f7fc2ea0d51f3748ef336e304f30ac07e Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 14:58:02 -0500 Subject: [PATCH 01/11] refactoring InstanceValidator code for readability. --- .../r5/validation/EnableWhenEvaluator.java | 3 +- .../fhir/r5/validation/ValidationEngine.java | 1 + .../InstanceValidator.java | 85 ++++++------------- .../InstanceValidatorFactory.java | 2 +- .../utils/ResolvedReference.java | 61 +++++++++++++ .../validation/tests/ValidationTestSuite.java | 2 +- 6 files changed, 92 insertions(+), 62 deletions(-) rename org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/{ => instancevalidator}/InstanceValidator.java (99%) rename org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/{ => instancevalidator}/InstanceValidatorFactory.java (95%) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java index 20d21d7d7..039938219 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java @@ -21,7 +21,6 @@ package org.hl7.fhir.r5.validation; */ import java.util.*; -import java.util.logging.Level; import java.util.stream.*; import org.hl7.fhir.exceptions.FHIRException; @@ -29,7 +28,7 @@ import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.model.*; import org.hl7.fhir.r5.model.Questionnaire.*; import org.hl7.fhir.r5.utils.FHIRPathEngine; -import org.hl7.fhir.r5.validation.InstanceValidator.ValidatorHostContext; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator.ValidatorHostContext; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java index 7f727fe38..411244049 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java @@ -22,6 +22,7 @@ import org.hl7.fhir.r5.terminologies.ConceptMapEngine; import org.hl7.fhir.r5.utils.*; import org.hl7.fhir.r5.utils.IResourceValidator.*; import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; import org.hl7.fhir.utilities.IniFile; import org.hl7.fhir.utilities.TextFile; import org.hl7.fhir.utilities.Utilities; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java similarity index 99% rename from org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java rename to org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 401d9ce5b..35735917d 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -1,4 +1,4 @@ -package org.hl7.fhir.r5.validation; +package org.hl7.fhir.r5.validation.instancevalidator; /*- * #%L @@ -35,9 +35,7 @@ import java.util.List; import java.util.Map; import java.util.Set; import java.util.UUID; -import java.util.stream.Collectors; -import ca.uhn.fhir.context.FhirContext; import org.apache.commons.lang3.NotImplementedException; import org.apache.commons.lang3.StringUtils; import org.hl7.fhir.r5.model.Reference; @@ -94,8 +92,6 @@ import org.hl7.fhir.r5.model.Extension; import org.hl7.fhir.r5.model.FhirPublication; import org.hl7.fhir.r5.model.HumanName; import org.hl7.fhir.r5.model.Identifier; -import org.hl7.fhir.r5.model.ImplementationGuide; -import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideGlobalComponent; import org.hl7.fhir.r5.model.InstantType; import org.hl7.fhir.r5.model.IntegerType; import org.hl7.fhir.r5.model.Period; @@ -130,11 +126,12 @@ import org.hl7.fhir.r5.utils.FHIRPathEngine; import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext; import org.hl7.fhir.r5.utils.IResourceValidator; import org.hl7.fhir.r5.utils.ToolingExtensions; +import org.hl7.fhir.r5.validation.BaseValidator; +import org.hl7.fhir.r5.validation.EnableWhenEvaluator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator.QStack; -import org.hl7.fhir.r5.validation.InstanceValidator.EntrySummary; -import org.hl7.fhir.r5.validation.InstanceValidator.ResolvedReference; +import org.hl7.fhir.r5.validation.XVerExtensionManager; +import org.hl7.fhir.r5.validation.instancevalidator.utils.ResolvedReference; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; -import org.hl7.fhir.utilities.TerminologyServiceOptions; import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities.DecimalStatus; import org.hl7.fhir.utilities.VersionUtilities; @@ -172,39 +169,7 @@ import ca.uhn.fhir.util.ObjectUtil; public class InstanceValidator extends BaseValidator implements IResourceValidator { - public class ResolvedReference { - - private Element resource; - private Element focus; - private boolean external; - private NodeStack stack; - - public String getType() { - return focus.fhirType(); - } - - public ValidatorHostContext hostContext(ValidatorHostContext hostContext, StructureDefinition profile) { - if (external) { - return hostContext.forRemoteReference(profile, resource); - } else { - return hostContext.forLocalReference(profile, resource); - } - } - - public Element getResource() { - return resource; - } - - public Element getFocus() { - return focus; - } - - public NodeStack getStack() { - return stack; - } - } - - public class ValidatorHostContext { + public class ValidatorHostContext { private Object appContext; private Element container; // bundle, or parameters private Element resource; @@ -2996,10 +2961,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat IndexedElement res = getContainedById(stack.getElement(), ref.substring(1)); if (res != null) { ResolvedReference rr = new ResolvedReference(); - rr.resource = stack.getElement(); - rr.focus = res.match; - rr.external = false; - rr.stack = stack.push(res.match, res.index, res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition()); + rr.setResource(stack.getElement()); + rr.setFocus(res.match); + rr.setExternal(false); + rr.setStack(stack.push(res.match, res.index, res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); return rr; } } @@ -3028,10 +2993,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return null; } else { ResolvedReference rr = new ResolvedReference(); - rr.resource = res.match; - rr.focus = res.match; - rr.external = false; - rr.stack = stack.push(res.entry, res.index, res.entry.getProperty().getDefinition(), res.entry.getProperty().getDefinition()).push(res.match, -1, res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition()); + rr.setResource(res.match); + rr.setFocus(res.match); + rr.setExternal(false); + rr.setStack(stack.push(res.entry, res.index, res.entry.getProperty().getDefinition(), + res.entry.getProperty().getDefinition()).push(res.match, -1, + res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); return rr; } } @@ -3047,10 +3014,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return null; } else { ResolvedReference rr = new ResolvedReference(); - rr.resource = res.match; - rr.focus = res.match; - rr.external = false; - rr.stack = new NodeStack(hostContext).push(res.entry, res.index, res.entry.getProperty().getDefinition(), res.entry.getProperty().getDefinition()).push(res.match, -1, res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition()); + rr.setResource(res.match); + rr.setFocus(res.match); + rr.setExternal(false); + rr.setStack(new NodeStack(hostContext).push(res.entry, res.index, res.entry.getProperty().getDefinition(), + res.entry.getProperty().getDefinition()).push(res.match, -1, + res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); return rr; } } @@ -3071,16 +3040,16 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat private ResolvedReference makeExternalRef(Element external, String path) { ResolvedReference res = new ResolvedReference(); - res.resource = external; - res.focus = external; - res.external = true; - res.stack = new NodeStack(external, path); + res.setResource(external); + res.setFocus(external); + res.setExternal(true); + res.setStack(new NodeStack(external, path)); return res; } private Element resolve(Object appContext, String ref, NodeStack stack, List errors, String path) throws IOException, FHIRException { - Element local = localResolve(ref, stack, errors, path, null, null).focus; + Element local = localResolve(ref, stack, errors, path, null, null).getFocus(); if (local!=null) return local; if (fetcher == null) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidatorFactory.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidatorFactory.java similarity index 95% rename from org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidatorFactory.java rename to org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidatorFactory.java index 539822357..90ef501a3 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidatorFactory.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidatorFactory.java @@ -1,4 +1,4 @@ -package org.hl7.fhir.r5.validation; +package org.hl7.fhir.r5.validation.instancevalidator; import org.hl7.fhir.exceptions.FHIRException; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java new file mode 100644 index 000000000..0d77dc288 --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java @@ -0,0 +1,61 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.elementmodel.Element; +import org.hl7.fhir.r5.model.StructureDefinition; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; + +public class ResolvedReference { + + private Element resource; + private Element focus; + private boolean external; + private InstanceValidator.NodeStack stack; + + public ResolvedReference setResource(Element resource) { + this.resource = resource; + return this; + } + + public Element getResource() { + return resource; + } + + public ResolvedReference setFocus(Element focus) { + this.focus = focus; + return this; + } + + public boolean isExternal() { + return external; + } + + public ResolvedReference setExternal(boolean external) { + this.external = external; + return this; + } + + public ResolvedReference setStack(InstanceValidator.NodeStack stack) { + this.stack = stack; + return this; + } + + public InstanceValidator.NodeStack getStack() { + return stack; + } + + public String getType() { + return focus.fhirType(); + } + + public Element getFocus() { + return focus; + } + + public InstanceValidator.ValidatorHostContext hostContext(InstanceValidator.ValidatorHostContext hostContext, StructureDefinition profile) { + if (external) { + return hostContext.forRemoteReference(profile, resource); + } else { + return hostContext.forLocalReference(profile, resource); + } + } +} diff --git a/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java b/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java index 66b5dd003..7b694f755 100644 --- a/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java +++ b/org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java @@ -26,7 +26,7 @@ import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext; import org.hl7.fhir.r5.utils.IResourceValidator; import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher; import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy; -import org.hl7.fhir.r5.validation.InstanceValidator; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; import org.hl7.fhir.r5.validation.ValidationEngine; import org.hl7.fhir.utilities.TextFile; import org.hl7.fhir.utilities.Utilities; From abd46acae3fec7b7d4e7f320f5e6e97c89536110 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:06:36 -0500 Subject: [PATCH 02/11] Indexed Element refactored. --- .../instancevalidator/InstanceValidator.java | 45 +++++++------------ .../utils/IndexedElement.java | 44 ++++++++++++++++++ 2 files changed, 60 insertions(+), 29 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/IndexedElement.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 35735917d..5692b2246 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -130,6 +130,7 @@ import org.hl7.fhir.r5.validation.BaseValidator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator.QStack; import org.hl7.fhir.r5.validation.XVerExtensionManager; +import org.hl7.fhir.r5.validation.instancevalidator.utils.IndexedElement; import org.hl7.fhir.r5.validation.instancevalidator.utils.ResolvedReference; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; import org.hl7.fhir.utilities.Utilities; @@ -2602,21 +2603,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return null; } - private class IndexedElement { - private int index; - private Element match; - private Element entry; - - public IndexedElement(int index, Element match, Element entry) { - super(); - this.index = index; - this.match = match; - this.entry = entry; - } - - } - - private IndexedElement getContainedById(Element container, String id) { + private IndexedElement getContainedById(Element container, String id) { List contained = new ArrayList(); container.getNamedChildren("contained", contained); for (int i = 0; i < contained.size(); i++) { @@ -2962,9 +2949,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat if (res != null) { ResolvedReference rr = new ResolvedReference(); rr.setResource(stack.getElement()); - rr.setFocus(res.match); + rr.setFocus(res.getMatch()); rr.setExternal(false); - rr.setStack(stack.push(res.match, res.index, res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); + rr.setStack(stack.push(res.getMatch(), res.getIndex(), res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); return rr; } } @@ -2993,12 +2980,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return null; } else { ResolvedReference rr = new ResolvedReference(); - rr.setResource(res.match); - rr.setFocus(res.match); + rr.setResource(res.getMatch()); + rr.setFocus(res.getMatch()); rr.setExternal(false); - rr.setStack(stack.push(res.entry, res.index, res.entry.getProperty().getDefinition(), - res.entry.getProperty().getDefinition()).push(res.match, -1, - res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); + rr.setStack(stack.push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), + res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, + res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); return rr; } } @@ -3014,12 +3001,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return null; } else { ResolvedReference rr = new ResolvedReference(); - rr.setResource(res.match); - rr.setFocus(res.match); + rr.setResource(res.getMatch()); + rr.setFocus(res.getMatch()); rr.setExternal(false); - rr.setStack(new NodeStack(hostContext).push(res.entry, res.index, res.entry.getProperty().getDefinition(), - res.entry.getProperty().getDefinition()).push(res.match, -1, - res.match.getProperty().getDefinition(), res.match.getProperty().getDefinition())); + rr.setStack(new NodeStack(hostContext).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), + res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, + res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); return rr; } } @@ -4564,8 +4551,8 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L for (String reference: references) { // We don't want errors when just retrieving the element as they will be caught (with better path info) in subsequent processing IndexedElement r = getFromBundle(stack.getElement(), reference, entry.getChildValue("fullUrl"), new ArrayList(), stack.addToLiteralPath("entry[" + candidateResources.indexOf(resource) + "]"), type, "transaction".equals(stack.getElement().getChildValue("type"))); - if (r!=null && !visitedResources.containsValue(r.match)) { - followResourceLinks(candidateEntries.get(r.match), visitedResources, candidateEntries, candidateResources, errors, stack, depth+1); + if (r!=null && !visitedResources.containsValue(r.getMatch())) { + followResourceLinks(candidateEntries.get(r.getMatch()), visitedResources, candidateEntries, candidateResources, errors, stack, depth+1); } } } diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/IndexedElement.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/IndexedElement.java new file mode 100644 index 000000000..feeb9d505 --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/IndexedElement.java @@ -0,0 +1,44 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.elementmodel.Element; + +public class IndexedElement { + private int index; + private Element match; + private Element entry; + + public int getIndex() { + return index; + } + + public IndexedElement setIndex(int index) { + this.index = index; + return this; + } + + public Element getMatch() { + return match; + } + + public IndexedElement setMatch(Element match) { + this.match = match; + return this; + } + + public Element getEntry() { + return entry; + } + + public IndexedElement setEntry(Element entry) { + this.entry = entry; + return this; + } + + public IndexedElement(int index, Element match, Element entry) { + super(); + this.index = index; + this.match = match; + this.entry = entry; + } + +} From a00c71bb320109483d9ef44e80bf81a0c670c6e5 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:18:44 -0500 Subject: [PATCH 03/11] ChildIterator refactored --- .../instancevalidator/InstanceValidator.java | 72 +---------- .../utils/ChildIterator.java | 112 ++++++++++++++++++ 2 files changed, 116 insertions(+), 68 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ChildIterator.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 5692b2246..6d13e8275 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -130,6 +130,7 @@ import org.hl7.fhir.r5.validation.BaseValidator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator.QStack; import org.hl7.fhir.r5.validation.XVerExtensionManager; +import org.hl7.fhir.r5.validation.instancevalidator.utils.ChildIterator; import org.hl7.fhir.r5.validation.instancevalidator.utils.IndexedElement; import org.hl7.fhir.r5.validation.instancevalidator.utils.ResolvedReference; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; @@ -2899,7 +2900,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return false; } - private boolean isPrimitiveType(String code) { + public boolean isPrimitiveType(String code) { StructureDefinition sd = context.fetchTypeDefinition(code); return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE; } @@ -5203,7 +5204,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L public List listChildren(Element element, NodeStack stack) { // 1. List the children, and remember their exact path (convenience) List children = new ArrayList(); - ChildIterator iter = new ChildIterator(stack.getLiteralPath(), element); + ChildIterator iter = new ChildIterator(this, stack.getLiteralPath(), element); while (iter.next()) children.add(new ElementInfo(iter.name(), iter.element(), iter.path(), iter.count())); return children; @@ -5496,72 +5497,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L return Calendar.getInstance().get(Calendar.YEAR); } - public class ChildIterator { - private String basePath; - private Element parent; - private int cursor; - private int lastCount; - - public ChildIterator(String path, Element element) { - parent = element; - basePath = path; - cursor = -1; - } - - public int count() { - String nb = cursor == 0 ? "--" : parent.getChildren().get(cursor-1).getName(); - String na = cursor >= parent.getChildren().size() - 1 ? "--" : parent.getChildren().get(cursor+1).getName(); - if (name().equals(nb) || name().equals(na) ) { - return lastCount; - } else - return -1; - } - - public Element element() { - return parent.getChildren().get(cursor); - } - - public String name() { - return element().getName(); - } - - public boolean next() { - if (cursor == -1) { - cursor++; - lastCount = 0; - } else { - String lastName = name(); - cursor++; - if (cursor < parent.getChildren().size() && name().equals(lastName)) - lastCount++; - else - lastCount = 0; - } - return cursor < parent.getChildren().size(); - } - - public String path() { - int i = count(); - String sfx = ""; - String n = name(); - String fn = ""; - if (element().getProperty().isChoice()) { - String en = element().getProperty().getName(); - en = en.substring(0, en.length()-3); - String t = n.substring(en.length()); - if (isPrimitiveType(Utilities.uncapitalize(t))) - t = Utilities.uncapitalize(t); - n = en; - fn = ".ofType("+t+")"; - } - if (i > -1 || (element().getSpecial() == null && element().isList())) { - sfx = "[" + Integer.toString(lastCount) + "]"; - } - return basePath + "." + n + sfx+fn; - } - } - - public class NodeStack { + public class NodeStack { private ElementDefinition definition; private Element element; private ElementDefinition extension; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ChildIterator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ChildIterator.java new file mode 100644 index 000000000..09e35d78c --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ChildIterator.java @@ -0,0 +1,112 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.elementmodel.Element; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; +import org.hl7.fhir.utilities.Utilities; + +public class ChildIterator { + private final InstanceValidator instanceValidator; + private String basePath; + private Element parent; + private int cursor; + private int lastCount; + + public ChildIterator(InstanceValidator instanceValidator, String path, Element element) { + this.instanceValidator = instanceValidator; + parent = element; + basePath = path; + cursor = -1; + } + + public InstanceValidator getInstanceValidator() { + return instanceValidator; + } + + public String getBasePath() { + return basePath; + } + + public ChildIterator setBasePath(String basePath) { + this.basePath = basePath; + return this; + } + + public Element getParent() { + return parent; + } + + public ChildIterator setParent(Element parent) { + this.parent = parent; + return this; + } + + public int getCursor() { + return cursor; + } + + public ChildIterator setCursor(int cursor) { + this.cursor = cursor; + return this; + } + + public int getLastCount() { + return lastCount; + } + + public ChildIterator setLastCount(int lastCount) { + this.lastCount = lastCount; + return this; + } + + public Element element() { + return parent.getChildren().get(cursor); + } + + public String name() { + return element().getName(); + } + + public int count() { + String nb = cursor == 0 ? "--" : parent.getChildren().get(cursor - 1).getName(); + String na = cursor >= parent.getChildren().size() - 1 ? "--" : parent.getChildren().get(cursor + 1).getName(); + if (name().equals(nb) || name().equals(na)) { + return lastCount; + } else + return -1; + } + + public boolean next() { + if (cursor == -1) { + cursor++; + lastCount = 0; + } else { + String lastName = name(); + cursor++; + if (cursor < parent.getChildren().size() && name().equals(lastName)) + lastCount++; + else + lastCount = 0; + } + return cursor < parent.getChildren().size(); + } + + public String path() { + int i = count(); + String sfx = ""; + String n = name(); + String fn = ""; + if (element().getProperty().isChoice()) { + String en = element().getProperty().getName(); + en = en.substring(0, en.length() - 3); + String t = n.substring(en.length()); + if (instanceValidator.isPrimitiveType(Utilities.uncapitalize(t))) + t = Utilities.uncapitalize(t); + n = en; + fn = ".ofType(" + t + ")"; + } + if (i > -1 || (element().getSpecial() == null && element().isList())) { + sfx = "[" + Integer.toString(lastCount) + "]"; + } + return basePath + "." + n + sfx + fn; + } +} From 4df9e568e6a117aa7bf72496b6306c7909d6cbc2 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:23:24 -0500 Subject: [PATCH 04/11] ChildIterator refactored --- .../instancevalidator/InstanceValidator.java | 39 ++----------------- 1 file changed, 3 insertions(+), 36 deletions(-) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 6d13e8275..8a3687225 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -131,6 +131,7 @@ import org.hl7.fhir.r5.validation.EnableWhenEvaluator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator.QStack; import org.hl7.fhir.r5.validation.XVerExtensionManager; import org.hl7.fhir.r5.validation.instancevalidator.utils.ChildIterator; +import org.hl7.fhir.r5.validation.instancevalidator.utils.ElementInfo; import org.hl7.fhir.r5.validation.instancevalidator.utils.IndexedElement; import org.hl7.fhir.r5.validation.instancevalidator.utils.ResolvedReference; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; @@ -5203,7 +5204,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L public List listChildren(Element element, NodeStack stack) { // 1. List the children, and remember their exact path (convenience) - List children = new ArrayList(); + List children = new ArrayList(); ChildIterator iter = new ChildIterator(this, stack.getLiteralPath(), element); while (iter.next()) children.add(new ElementInfo(iter.name(), iter.element(), iter.path(), iter.count())); @@ -5623,41 +5624,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } } - public class ElementInfo { - - public List sliceInfo; - public int index; // order of definition in overall order. all slices get the index of the slicing definition - public int sliceindex; // order of the definition in the slices (if slice != null) - public int count; - public ElementDefinition definition; - public ElementDefinition slice; - public boolean additionalSlice; // If true, indicates that this element is an additional slice - private Element element; - private String name; - private String path; - - public ElementInfo(String name, Element element, String path, int count) { - this.name = name; - this.element = element; - this.path = path; - this.count = count; - } - - public int col() { - return element.col(); - } - - public int line() { - return element.line(); - } - - @Override - public String toString() { - return path; - } - } - - public String reportTimes() { + public String reportTimes() { String s = String.format("Times (ms): overall = %d, tx = %d, sd = %d, load = %d, fpe = %d", overall / 1000000, txTime / 1000000, sdTime / 1000000, loadTime / 1000000, fpeTime / 1000000); overall = 0; txTime = 0; From ae30afdf53c91f26e9eea7a2b69696e4969f2b96 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:34:55 -0500 Subject: [PATCH 05/11] Refactored ElementInfo --- .../instancevalidator/InstanceValidator.java | 102 +++++++------- .../instancevalidator/utils/ElementInfo.java | 131 ++++++++++++++++++ 2 files changed, 181 insertions(+), 52 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ElementInfo.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 8a3687225..f5a6358aa 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -4805,7 +4805,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getWorkingCode())) { String prefix = tail(ei.definition.getPath()); assert prefix.endsWith("[x]"); - type = ei.name.substring(prefix.length() - 3); + type = ei.getName().substring(prefix.length() - 3); if (isPrimitiveType(type)) type = Utilities.uncapitalize(type); if (ei.definition.getType().get(0).hasProfile()) { @@ -4819,11 +4819,11 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L assert typesAreAllReference(ei.definition.getType()) || ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix; if (ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR)) - type = ei.element.getType(); + type = ei.getElement().getType(); else { prefix = prefix.substring(0, prefix.length() - 3); for (TypeRefComponent t : ei.definition.getType()) - if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.name)) { + if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) { type = t.getWorkingCode(); // Excluding reference is a kludge to get around versioning issues if (t.hasProfile() && !type.equals("Reference")) @@ -4836,7 +4836,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L type = "Reference"; else rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, - "The type of element " + ei.name + " is not known, which is illegal. Valid types at this point are " + describeTypes(ei.definition.getType())); + "The type of element " + ei.getName() + " is not known, which is illegal. Valid types at this point are " + describeTypes(ei.definition.getType())); } } else if (ei.definition.getContentReference() != null) { typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference()); @@ -4856,55 +4856,55 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L type = null; } } - NodeStack localStack = stack.push(ei.element, ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType())); + NodeStack localStack = stack.push(ei.getElement(), ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType())); if (debug) { System.out.println(" "+localStack.getLiteralPath()); } String localStackLiterapPath = localStack.getLiteralPath(); - String eiPath = ei.path; - assert(eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.path + " - localStack.getLiteralPath: " + localStackLiterapPath; + String eiPath = ei.getPath(); + assert(eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath; boolean thisIsCodeableConcept = false; String thisExtension = null; boolean checkDisplay = true; - checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.element, localStack, true); + checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.getElement(), localStack, true); - ei.element.markValidation(profile, ei.definition); + ei.getElement().markValidation(profile, ei.definition); boolean elementValidated = false; if (type != null) { if (isPrimitiveType(type)) { - checkPrimitive(hostContext, errors, ei.path, type, ei.definition, ei.element, profile, stack); + checkPrimitive(hostContext, errors, ei.getPath(), type, ei.definition, ei.getElement(), profile, stack); } else { if (ei.definition.hasFixed()) { - checkFixedValue(errors,ei.path, ei.element, ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null); + checkFixedValue(errors,ei.getPath(), ei.getElement(), ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null); } if (ei.definition.hasPattern()) { - checkFixedValue(errors,ei.path, ei.element, ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true); + checkFixedValue(errors,ei.getPath(), ei.getElement(), ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true); } } if (type.equals("Identifier")) { - checkIdentifier(errors, ei.path, ei.element, ei.definition); + checkIdentifier(errors, ei.getPath(), ei.getElement(), ei.definition); } else if (type.equals("Coding")) { - checkCoding(errors, ei.path, ei.element, profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack); + checkCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack); } else if (type.equals("CodeableConcept")) { - checkDisplay = checkCodeableConcept(errors, ei.path, ei.element, profile, ei.definition, stack); + checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack); thisIsCodeableConcept = true; } else if (type.equals("Reference")) { - checkReference(hostContext, errors, ei.path, ei.element, profile, ei.definition, actualType, localStack); + checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, ei.definition, actualType, localStack); // We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension } else if (type.equals("Extension")) { - Element eurl = ei.element.getNamedChild("url"); - if (rule(errors, IssueType.INVALID, ei.path, eurl != null, "Extension.url is required")) { + Element eurl = ei.getElement().getNamedChild("url"); + if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, "Extension.url is required")) { String url = eurl.primitiveValue(); thisExtension = url; - if (rule(errors, IssueType.INVALID, ei.path, !Utilities.noString(url), "Extension.url is required")) { - if (rule(errors, IssueType.INVALID, ei.path, (extensionUrl != null) || Utilities.isAbsoluteUrl(url), "Extension.url must be an absolute URL")) { - checkExtension(hostContext, errors, ei.path, resource, element, ei.element, ei.definition, profile, localStack, stack, extensionUrl); + if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), "Extension.url is required")) { + if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), "Extension.url must be an absolute URL")) { + checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), ei.definition, profile, localStack, stack, extensionUrl); } } } } else if (type.equals("Resource")) { - validateContains(hostContext, errors, ei.path, ei.definition, definition, resource, ei.element, localStack, idStatusForEntry(element, ei)); // if + validateContains(hostContext, errors, ei.getPath(), ei.definition, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if elementValidated = true; // (str.matches(".*([.,/])work\\1$")) } else if (Utilities.isAbsoluteUrl(type)) { @@ -4912,16 +4912,16 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) { List txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep()); if (txtype.contains("CodeableConcept")) { - checkTerminologyCodeableConcept(errors, ei.path, ei.element, profile, ei.definition, stack, defn); + checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack, defn); thisIsCodeableConcept = true; } else if (txtype.contains("Coding")) { - checkTerminologyCoding(errors, ei.path, ei.element, profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn); + checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn); } } } } else { - if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.name)) - validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.element, type, localStack, false, true, null); + if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.getName())) + validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, false, true, null); } StructureDefinition p = null; String tail = null; @@ -4936,7 +4936,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L // checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element); //} - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, p != null, "Unknown type " + type); + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown type " + type); } } else if (profiles.size()==1) { String url = profiles.get(0); @@ -4945,7 +4945,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L url = url.substring(0, url.indexOf("#")); } p = this.context.fetchResource(StructureDefinition.class, url); - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, p != null, "Unknown profile " + profiles.get(0)); + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + profiles.get(0)); } else { elementValidated = true; HashMap> goodProfiles = new HashMap>(); @@ -4958,9 +4958,9 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L url = url.substring(0, url.indexOf("#")); } p = this.context.fetchResource(StructureDefinition.class, typeProfile); - if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, p != null, "Unknown profile " + typeProfile)) { + if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + typeProfile)) { List profileErrors = new ArrayList(); - validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.element, type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); if (hasErrors(profileErrors)) badProfiles.put(typeProfile, profileErrors); else @@ -4970,7 +4970,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L if (goodProfiles.size()==1) { errors.addAll(goodProfiles.values().iterator().next()); } else if (goodProfiles.size()==0) { - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles)); + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles)); for (String m : badProfiles.keySet()) { p = this.context.fetchResource(StructureDefinition.class, m); for (ValidationMessage message : badProfiles.get(m)) { @@ -4979,7 +4979,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } } } else { - warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.path, false, "Found multiple matching profiles among choices: " + StringUtils.join("; ", goodProfiles.keySet())); + warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Found multiple matching profiles among choices: " + StringUtils.join("; ", goodProfiles.keySet())); for (String m : goodProfiles.keySet()) { p = this.context.fetchResource(StructureDefinition.class, m); for (ValidationMessage message : goodProfiles.get(m)) { @@ -4993,16 +4993,16 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L trackUsage(p, hostContext, element); if (!elementValidated) { - if (ei.element.getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.element.getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.element.getSpecial() == SpecialElement.PARAMETER ) - validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.element, ei.element, type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER ) + validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.getElement(), ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); else - validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.element, type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); } int index = profile.getSnapshot().getElement().indexOf(ei.definition); if (index < profile.getSnapshot().getElement().size() - 1) { String nextPath = profile.getSnapshot().getElement().get(index+1).getPath(); if (!nextPath.equals(ei.definition.getPath()) && nextPath.startsWith(ei.definition.getPath())) - validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.element, type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); } } } @@ -5065,13 +5065,11 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L profile.setUserData("usesMustSupport", usesMustSupport); } if (usesMustSupport.equals("Y")) { - String elementSupported = ei.element.getUserString("elementSupported"); + String elementSupported = ei.getElement().getUserString("elementSupported"); if (elementSupported==null || ei.definition.getMustSupport()) if (ei.definition.getMustSupport()) { - ei.element.setUserData("elementSupported", "Y"); + ei.getElement().setUserData("elementSupported", "Y"); } -// else -// ei.element.setUserData("elementSupported", "N"); } } @@ -5164,16 +5162,16 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L if (ei.additionalSlice && ei.definition != null) { if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPENATEND) && true /* TODO: replace "true" with condition to check that this element is at "end" */) { - slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.path, false, "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()), + slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()), "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()+": "+errorSummaryForSlicingAsHtml(ei.sliceInfo))); } else if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.CLOSED)) { - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, false, "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: "+errorSummaryForSlicing(ei.sliceInfo)), + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: "+errorSummaryForSlicing(ei.sliceInfo)), "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: "+errorSummaryForSlicingAsHtml(ei.sliceInfo))); } } else { // Don't raise this if we're in an abstract profile, like Resource if (!profile.getAbstract()) - rule(errors, IssueType.NOTSUPPORTED, ei.line(), ei.col(), ei.path, (ei.definition != null), "This element is not allowed by the profile "+profile.getUrl()); + rule(errors, IssueType.NOTSUPPORTED, ei.line(), ei.col(), ei.getPath(), (ei.definition != null), "This element is not allowed by the profile "+profile.getUrl()); } // TODO: Should get the order of elements correct when parsing elements that are XML attributes vs. elements boolean isXmlAttr = false; @@ -5188,10 +5186,10 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L if (!ToolingExtensions.readBoolExtension(profile, "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order")) { boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr; - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, ok, "As specified by profile " + profile.getUrl() + ", Element '"+ei.name+"' is out of order"); + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, "As specified by profile " + profile.getUrl() + ", Element '"+ei.getName()+"' is out of order"); } if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, (ei.definition == null) || (ei.sliceindex >= lastSlice) || isXmlAttr, "As specified by profile " + profile.getUrl() + ", Element '"+ei.name+"' is out of order in ordered slice"); + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), (ei.definition == null) || (ei.sliceindex >= lastSlice) || isXmlAttr, "As specified by profile " + profile.getUrl() + ", Element '"+ei.getName()+"' is out of order in ordered slice"); if (ei.definition == null || !isXmlAttr) last = ei.index; if (ei.slice != null) @@ -5220,11 +5218,11 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L boolean childUnsupportedSlicing, ElementInfo ei) { boolean match = false; if (slicer == null || slicer == ed) { - match = nameMatches(ei.name, tail(ed.getPath())); + match = nameMatches(ei.getName(), tail(ed.getPath())); } else { - if (nameMatches(ei.name, tail(ed.getPath()))) + if (nameMatches(ei.getName(), tail(ed.getPath()))) try { - match = sliceMatches(hostContext, ei.element, ei.path, slicer, ed, profile, errors, sliceInfo, stack); + match = sliceMatches(hostContext, ei.getElement(), ei.getPath(), slicer, ed, profile, errors, sliceInfo, stack); if (match) { ei.slice = slicer; @@ -5235,14 +5233,14 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L ei.additionalSlice = true; } } catch (FHIRException e) { - rule(errors, IssueType.PROCESSING, ei.line(), ei.col(), ei.path, false, e.getMessage()); + rule(errors, IssueType.PROCESSING, ei.line(), ei.col(), ei.getPath(), false, e.getMessage()); unsupportedSlicing = true; childUnsupportedSlicing = true; } } if (match) { boolean isOk = ei.definition == null || ei.definition == slicer || (ei.definition.getPath().endsWith("[x]") && ed.getPath().startsWith(ei.definition.getPath().replace("[x]", ""))); - if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.path, isOk, "Profile " + profile.getUrl() + ", Element matches more than one slice - " + (ei.definition==null || !ei.definition.hasSliceName() ? "" : ei.definition.getSliceName()) + ", " + (ed.hasSliceName() ? ed.getSliceName() : ""))) { + if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), isOk, "Profile " + profile.getUrl() + ", Element matches more than one slice - " + (ei.definition==null || !ei.definition.hasSliceName() ? "" : ei.definition.getSliceName()) + ", " + (ed.hasSliceName() ? ed.getSliceName() : ""))) { ei.definition = ed; if (ei.slice == null) { ei.index = i; @@ -5268,7 +5266,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } private IdStatus idStatusForEntry(Element ep, ElementInfo ei) { - if (isBundleEntry(ei.path)) { + if (isBundleEntry(ei.getPath())) { Element req = ep.getNamedChild("request"); Element resp = ep.getNamedChild("response"); Element fullUrl = ep.getNamedChild("fullUrl"); @@ -5299,7 +5297,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L else // actually, we should never get to here; a bundle entry with method get/delete should not have a resource return IdStatus.OPTIONAL; } - } else if (isParametersEntry(ei.path) || isBundleOutcome(ei.path)) + } else if (isParametersEntry(ei.getPath()) || isBundleOutcome(ei.getPath())) return IdStatus.OPTIONAL; else return IdStatus.REQUIRED; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ElementInfo.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ElementInfo.java new file mode 100644 index 000000000..b3f7b69b6 --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ElementInfo.java @@ -0,0 +1,131 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.elementmodel.Element; +import org.hl7.fhir.r5.model.ElementDefinition; +import org.hl7.fhir.utilities.validation.ValidationMessage; + +import java.util.List; + +public class ElementInfo { + + public List sliceInfo; + public int index; // order of definition in overall order. all slices get the index of the slicing definition + public int sliceindex; // order of the definition in the slices (if slice != null) + public int count; + public ElementDefinition definition; + public ElementDefinition slice; + public boolean additionalSlice; // If true, indicates that this element is an additional slice + private Element element; + private String name; + private String path; + + public ElementInfo(String name, Element element, String path, int count) { + this.name = name; + this.element = element; + this.path = path; + this.count = count; + } + + public List getSliceInfo() { + return sliceInfo; + } + + public ElementInfo setSliceInfo(List sliceInfo) { + this.sliceInfo = sliceInfo; + return this; + } + + public int getIndex() { + return index; + } + + public ElementInfo setIndex(int index) { + this.index = index; + return this; + } + + public int getSliceindex() { + return sliceindex; + } + + public ElementInfo setSliceindex(int sliceindex) { + this.sliceindex = sliceindex; + return this; + } + + public int getCount() { + return count; + } + + public ElementInfo setCount(int count) { + this.count = count; + return this; + } + + public ElementDefinition getDefinition() { + return definition; + } + + public ElementInfo setDefinition(ElementDefinition definition) { + this.definition = definition; + return this; + } + + public ElementDefinition getSlice() { + return slice; + } + + public ElementInfo setSlice(ElementDefinition slice) { + this.slice = slice; + return this; + } + + public boolean isAdditionalSlice() { + return additionalSlice; + } + + public ElementInfo setAdditionalSlice(boolean additionalSlice) { + this.additionalSlice = additionalSlice; + return this; + } + + public Element getElement() { + return element; + } + + public ElementInfo setElement(Element element) { + this.element = element; + return this; + } + + public String getName() { + return name; + } + + public ElementInfo setName(String name) { + this.name = name; + return this; + } + + public String getPath() { + return path; + } + + public ElementInfo setPath(String path) { + this.path = path; + return this; + } + + public int col() { + return element.col(); + } + + public int line() { + return element.line(); + } + + @Override + public String toString() { + return path; + } +} From eded933a2da1910dfe5b1daeea6fb355d64a15b2 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:43:15 -0500 Subject: [PATCH 06/11] Refactoring ResolvedReference --- .../r5/validation/EnableWhenEvaluator.java | 2 +- .../instancevalidator/InstanceValidator.java | 143 +++------------- .../ValidatorHostContext.java | 158 ++++++++++++++++++ .../utils/ResolvedReference.java | 3 +- 4 files changed, 184 insertions(+), 122 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java index 039938219..0ec899f69 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java @@ -28,7 +28,7 @@ import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.model.*; import org.hl7.fhir.r5.model.Questionnaire.*; import org.hl7.fhir.r5.utils.FHIRPathEngine; -import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator.ValidatorHostContext; +import org.hl7.fhir.r5.validation.instancevalidator.ValidatorHostContext; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index f5a6358aa..735d86cda 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -172,104 +172,7 @@ import ca.uhn.fhir.util.ObjectUtil; public class InstanceValidator extends BaseValidator implements IResourceValidator { - public class ValidatorHostContext { - private Object appContext; - private Element container; // bundle, or parameters - private Element resource; - private Element rootResource; - private StructureDefinition profile; // the profile that contains the content being validated - private boolean checkSpecials = true; - private Map> sliceRecords; - - public ValidatorHostContext(Object appContext) { - this.appContext = appContext; - } - - public ValidatorHostContext(Object appContext, Element element) { - this.appContext = appContext; - this.resource = element; - this.rootResource = element; - } - - public ValidatorHostContext forContained(Element element) { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.rootResource = resource; - res.resource = element; - res.container = resource; - res.profile = profile; - return res; - } - - public ValidatorHostContext forEntry(Element element) { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.rootResource = element; - res.resource = element; - res.container = resource; - res.profile = profile; - return res; - } - - public ValidatorHostContext forProfile(StructureDefinition profile) { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.resource = resource; - res.rootResource = rootResource; - res.container = container; - res.profile = profile; - res.sliceRecords = sliceRecords != null ? sliceRecords : new HashMap>(); - return res; - } - - public ValidatorHostContext forLocalReference(StructureDefinition profile, Element resource) { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.resource = resource; - res.rootResource = resource; - res.container = container; - res.profile = profile; - res.checkSpecials = false; - return res; - } - - public ValidatorHostContext forRemoteReference(StructureDefinition profile, Element resource) { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.resource = resource; - res.rootResource = resource; - res.container = resource; - res.profile = profile; - res.checkSpecials = false; - return res; - } - - public boolean isCheckSpecials() { - return checkSpecials; - } - - public void setCheckSpecials(boolean checkSpecials) { - this.checkSpecials = checkSpecials; - } - - public Base getResource() { - return resource; - } - - public void sliceNotes(String url, List record) { - sliceRecords.put(url, record); - } - - public ValidatorHostContext forSlicing() { - ValidatorHostContext res = new ValidatorHostContext(appContext); - res.resource = resource; - res.rootResource = resource; - res.container = resource; - res.profile = profile; - res.checkSpecials = false; - res.sliceRecords = new HashMap>(); - return res; - } - - - } - - private class ValidatorHostServices implements IEvaluationContext { + private class ValidatorHostServices implements IEvaluationContext { // private Stack>> @@ -277,7 +180,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException { ValidatorHostContext c = (ValidatorHostContext) appContext; if (externalHostServices != null) - return externalHostServices.resolveConstant(c.appContext, name, beforeContext); + return externalHostServices.resolveConstant(c.getAppContext(), name, beforeContext); else return null; } @@ -286,7 +189,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException { ValidatorHostContext c = (ValidatorHostContext) appContext; if (externalHostServices != null) - return externalHostServices.resolveConstantType(c.appContext, name); + return externalHostServices.resolveConstantType(c.getAppContext(), name); else return null; } @@ -322,24 +225,24 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return (Base) refContext.getUserData("validator.bundle.resolution"); } - if (c.appContext instanceof Element) { - Element bnd = (Element) c.appContext; + if (c.getAppContext() instanceof Element) { + Element bnd = (Element) c.getAppContext(); Base res = resolveInBundle(url, bnd); if (res != null) return res; } - Base res = resolveInBundle(url, c.resource); + Base res = resolveInBundle(url, c.getResource()); if (res != null) return res; - res = resolveInBundle(url, c.container); + res = resolveInBundle(url, c.getContainer()); if (res != null) return res; if (externalHostServices != null) - return externalHostServices.resolveReference(c.appContext, url, refContext); + return externalHostServices.resolveReference(c.getAppContext(), url, refContext); else if (fetcher != null) try { - return fetcher.fetch(c.appContext, url); + return fetcher.fetch(c.getAppContext(), url); } catch (IOException e) { throw new FHIRException(e); } @@ -380,14 +283,14 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat if (item instanceof Resource) { try { Element e = new ObjectConverter(context).convert((Resource) item); - self.validateResource(new ValidatorHostContext(ctxt.appContext, e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); + self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); } catch (IOException e1) { throw new FHIRException(e1); } } else if (item instanceof Element) { Element e = (Element) item; if (e.isResource()) { - self.validateResource(new ValidatorHostContext(ctxt.appContext, e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); + self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); } else { throw new FHIRException("Not supported yet"); } @@ -410,8 +313,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat @Override public ValueSet resolveValueSet(Object appContext, String url) { ValidatorHostContext c = (ValidatorHostContext) appContext; - if (c.profile != null && url.startsWith("#")) { - for (Resource r : c.profile.getContained()) { + if (c.getProfile() != null && url.startsWith("#")) { + for (Resource r : c.getProfile().getContained()) { if (r.getId().equals(url.substring(1))) { if (r instanceof ValueSet) return (ValueSet) r; @@ -1708,7 +1611,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat } else if (ctxt.getType() == ExtensionContextType.FHIRPATH) { contexts.append("p:"+ctxt.getExpression()); // The context is all elements that match the FHIRPath query found in the expression. - List res = fpe.evaluate(hostContext, resource, hostContext.rootResource, container, fpe.parse(ctxt.getExpression())); + List res = fpe.evaluate(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(ctxt.getExpression())); if (res.contains(container)) { ok = true; } @@ -1722,7 +1625,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat } else { if (definition.hasContextInvariant()) { for (StringType s : definition.getContextInvariant()) { - if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.rootResource, container, fpe.parse(s.getValue()))) { + if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) { rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, "The extension " + extUrl + " is not allowed to be used at this point (based on context invariant '"+s.getValue()+"')"); return false; @@ -2246,7 +2149,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat return; } - ResolvedReference we = localResolve(ref, stack, errors, path, (Element) hostContext.appContext, element); + ResolvedReference we = localResolve(ref, stack, errors, path, (Element) hostContext.getAppContext(), element); String refType; if (ref.startsWith("#")) { refType = "contained"; @@ -2257,7 +2160,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat refType = "bundled"; } } - ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundled") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.appContext, path, ref); + ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundled") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.getAppContext(), path, ref); if (pol.checkExists()) { if (we == null) { @@ -2270,7 +2173,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat ext = fetchCache.get(ref); } else { try { - ext = fetcher.fetch(hostContext.appContext, ref); + ext = fetcher.fetch(hostContext.getAppContext(), ref); } catch (IOException e) { throw new FHIRException(e); } @@ -3323,9 +3226,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat boolean pass = evaluateSlicingExpression(shc, element, path, profile, n); if (!pass) { slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Does not match slice'"+ed.getSliceName(), "discriminator = "+Utilities.escapeXml(n.toString())); - for (String url : shc.sliceRecords.keySet()) { + for (String url : shc.getSliceRecords().keySet()) { slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for "+stack.getLiteralPath()+" against profile "+url, - "Profile "+url+" does not match for "+stack.getLiteralPath()+" because of the following profile issues: "+errorSummaryForSlicingAsHtml(shc.sliceRecords.get(url))); + "Profile "+url+" does not match for "+stack.getLiteralPath()+" because of the following profile issues: "+errorSummaryForSlicingAsHtml(shc.getSliceRecords().get(url))); } } return pass; @@ -3336,7 +3239,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat boolean ok; try { long t = System.nanoTime(); - ok = fpe.evaluateToBoolean(hostContext.forProfile(profile), hostContext.resource, hostContext.rootResource, element, n); + ok = fpe.evaluateToBoolean(hostContext.forProfile(profile), hostContext.getResource(), hostContext.getRootResource(), element, n); fpeTime = fpeTime + (System.nanoTime() - t); msg = fpe.forLog(); } catch (Exception ex) { @@ -5010,7 +4913,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L private void trackUsage(StructureDefinition profile, ValidatorHostContext hostContext, Element element) { if (tracker != null) { - tracker.recordProfileUsage(profile, hostContext.appContext, element); + tracker.recordProfileUsage(profile, hostContext.getAppContext(), element); } } @@ -5343,7 +5246,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L boolean ok; try { long t = System.nanoTime(); - ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.rootResource, element, n); + ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n); fpeTime = fpeTime + (System.nanoTime() - t); msg = fpe.forLog(); } catch (Exception ex) { diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java new file mode 100644 index 000000000..f471e96cb --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java @@ -0,0 +1,158 @@ +package org.hl7.fhir.r5.validation.instancevalidator; + +import org.hl7.fhir.r5.elementmodel.Element; +import org.hl7.fhir.r5.model.Base; +import org.hl7.fhir.r5.model.StructureDefinition; +import org.hl7.fhir.utilities.validation.ValidationMessage; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +public class ValidatorHostContext { + + private Object appContext; + private Element container; // bundle, or parameters + private Element resource; + private Element rootResource; + private StructureDefinition profile; // the profile that contains the content being validated + private boolean checkSpecials = true; + private Map> sliceRecords; + + public ValidatorHostContext(Object appContext) { + this.appContext = appContext; + } + + public ValidatorHostContext(Object appContext, Element element) { + this.appContext = appContext; + this.resource = element; + this.rootResource = element; + } + + public Object getAppContext() { + return appContext; + } + + public ValidatorHostContext setAppContext(Object appContext) { + this.appContext = appContext; + return this; + } + + public Element getContainer() { + return container; + } + + public ValidatorHostContext setContainer(Element container) { + this.container = container; + return this; + } + + public ValidatorHostContext setResource(Element resource) { + this.resource = resource; + return this; + } + + public Element getRootResource() { + return rootResource; + } + + public ValidatorHostContext setRootResource(Element rootResource) { + this.rootResource = rootResource; + return this; + } + + public StructureDefinition getProfile() { + return profile; + } + + public ValidatorHostContext setProfile(StructureDefinition profile) { + this.profile = profile; + return this; + } + + public Map> getSliceRecords() { + return sliceRecords; + } + + public ValidatorHostContext setSliceRecords(Map> sliceRecords) { + this.sliceRecords = sliceRecords; + return this; + } + + public boolean isCheckSpecials() { + return checkSpecials; + } + + public void setCheckSpecials(boolean checkSpecials) { + this.checkSpecials = checkSpecials; + } + + public Element getResource() { + return resource; + } + + public void sliceNotes(String url, List record) { + sliceRecords.put(url, record); + } + + public ValidatorHostContext forContained(Element element) { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.rootResource = resource; + res.resource = element; + res.container = resource; + res.profile = profile; + return res; + } + + public ValidatorHostContext forEntry(Element element) { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.rootResource = element; + res.resource = element; + res.container = resource; + res.profile = profile; + return res; + } + + public ValidatorHostContext forProfile(StructureDefinition profile) { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.resource = resource; + res.rootResource = rootResource; + res.container = container; + res.profile = profile; + res.sliceRecords = sliceRecords != null ? sliceRecords : new HashMap>(); + return res; + } + + public ValidatorHostContext forLocalReference(StructureDefinition profile, Element resource) { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.resource = resource; + res.rootResource = resource; + res.container = container; + res.profile = profile; + res.checkSpecials = false; + return res; + } + + public ValidatorHostContext forRemoteReference(StructureDefinition profile, Element resource) { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.resource = resource; + res.rootResource = resource; + res.container = resource; + res.profile = profile; + res.checkSpecials = false; + return res; + } + + public ValidatorHostContext forSlicing() { + ValidatorHostContext res = new ValidatorHostContext(appContext); + res.resource = resource; + res.rootResource = resource; + res.container = resource; + res.profile = profile; + res.checkSpecials = false; + res.sliceRecords = new HashMap>(); + return res; + } + + +} diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java index 0d77dc288..30738889f 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java @@ -3,6 +3,7 @@ package org.hl7.fhir.r5.validation.instancevalidator.utils; import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; +import org.hl7.fhir.r5.validation.instancevalidator.ValidatorHostContext; public class ResolvedReference { @@ -51,7 +52,7 @@ public class ResolvedReference { return focus; } - public InstanceValidator.ValidatorHostContext hostContext(InstanceValidator.ValidatorHostContext hostContext, StructureDefinition profile) { + public ValidatorHostContext hostContext(ValidatorHostContext hostContext, StructureDefinition profile) { if (external) { return hostContext.forRemoteReference(profile, resource); } else { From 23677ca15502a0504cdcb5343e22e56137e81dff Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:52:01 -0500 Subject: [PATCH 07/11] Refactoring EntrySummary --- .../r5/validation/EnableWhenEvaluator.java | 2 +- .../instancevalidator/InstanceValidator.java | 32 ++++--------- .../instancevalidator/utils/EntrySummary.java | 46 +++++++++++++++++++ .../utils/ResolvedReference.java | 1 - .../{ => utils}/ValidatorHostContext.java | 3 +- 5 files changed, 57 insertions(+), 27 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/EntrySummary.java rename org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/{ => utils}/ValidatorHostContext.java (98%) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java index 0ec899f69..468b09647 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/EnableWhenEvaluator.java @@ -28,7 +28,7 @@ import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.model.*; import org.hl7.fhir.r5.model.Questionnaire.*; import org.hl7.fhir.r5.utils.FHIRPathEngine; -import org.hl7.fhir.r5.validation.instancevalidator.ValidatorHostContext; +import org.hl7.fhir.r5.validation.instancevalidator.utils.ValidatorHostContext; import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException; diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 735d86cda..a0a0026c4 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -130,10 +130,7 @@ import org.hl7.fhir.r5.validation.BaseValidator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator; import org.hl7.fhir.r5.validation.EnableWhenEvaluator.QStack; import org.hl7.fhir.r5.validation.XVerExtensionManager; -import org.hl7.fhir.r5.validation.instancevalidator.utils.ChildIterator; -import org.hl7.fhir.r5.validation.instancevalidator.utils.ElementInfo; -import org.hl7.fhir.r5.validation.instancevalidator.utils.IndexedElement; -import org.hl7.fhir.r5.validation.instancevalidator.utils.ResolvedReference; +import org.hl7.fhir.r5.validation.instancevalidator.utils.*; import org.hl7.fhir.utilities.CommaSeparatedStringBuilder; import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities.DecimalStatus; @@ -4357,18 +4354,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } } - public class EntrySummary { - Element entry; - Element resource; - List targets = new ArrayList<>(); - public EntrySummary(Element entry, Element resource) { - this.entry = entry; - this.resource = resource; - } - - } - - private void checkAllInterlinked(List errors, List entries, NodeStack stack, Element bundle, boolean isError) { + private void checkAllInterlinked(List errors, List entries, NodeStack stack, Element bundle, boolean isError) { List entryList = new ArrayList<>(); for (Element entry: entries) { Element r = entry.getNamedChild("resource"); @@ -4377,13 +4363,13 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L } } for (EntrySummary e : entryList) { - Set references = findReferences(e.entry); + Set references = findReferences(e.getEntry()); for (String ref : references) { - Element tgt = resolveInBundle(entries, ref, e.entry.getChildValue("fullUrl"), e.resource.fhirType(), e.resource.getIdBase()); + Element tgt = resolveInBundle(entries, ref, e.getEntry().getChildValue("fullUrl"), e.getResource().fhirType(), e.getResource().getIdBase()); if (tgt != null) { EntrySummary t = entryForTarget(entryList, tgt); if (t != null) { - e.targets.add(t); + e.getTargets().add(t); } } } @@ -4397,7 +4383,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L for (EntrySummary e : entryList) { if (!visited.contains(e)) { boolean add = false; - for (EntrySummary t : e.targets) { + for (EntrySummary t : e.getTargets()) { if (visited.contains(t)) { add = true; } @@ -4412,7 +4398,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L int i = 0; for (EntrySummary e : entryList) { - Element entry = e.entry; + Element entry = e.getEntry(); if (isError) { rule(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath("entry" + '[' + (i+1) + ']'), visited.contains(e), "Entry "+(entry.getChildValue("fullUrl") != null ? "'"+entry.getChildValue("fullUrl")+"'" : "")+" isn't reachable by traversing from first Bundle entry"); } else { @@ -4424,7 +4410,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L private EntrySummary entryForTarget(List entryList, Element tgt) { for (EntrySummary e : entryList) { - if (e.entry == tgt) { + if (e.getEntry() == tgt) { return e; } } @@ -4434,7 +4420,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L private void visitLinked(Set visited, EntrySummary t) { if (!visited.contains(t)) { visited.add(t); - for (EntrySummary e : t.targets) { + for (EntrySummary e : t.getTargets()) { visitLinked(visited, e); } } diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/EntrySummary.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/EntrySummary.java new file mode 100644 index 000000000..8457ead30 --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/EntrySummary.java @@ -0,0 +1,46 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.elementmodel.Element; +import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; + +import java.util.ArrayList; +import java.util.List; + +public class EntrySummary { + + Element entry; + Element resource; + List targets = new ArrayList<>(); + + public Element getEntry() { + return entry; + } + + public EntrySummary setEntry(Element entry) { + this.entry = entry; + return this; + } + + public Element getResource() { + return resource; + } + + public EntrySummary setResource(Element resource) { + this.resource = resource; + return this; + } + + public List getTargets() { + return targets; + } + + public EntrySummary setTargets(List targets) { + this.targets = targets; + return this; + } + + public EntrySummary(Element entry, Element resource) { + this.entry = entry; + this.resource = resource; + } +} diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java index 30738889f..7c619cd09 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResolvedReference.java @@ -3,7 +3,6 @@ package org.hl7.fhir.r5.validation.instancevalidator.utils; import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.validation.instancevalidator.InstanceValidator; -import org.hl7.fhir.r5.validation.instancevalidator.ValidatorHostContext; public class ResolvedReference { diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ValidatorHostContext.java similarity index 98% rename from org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java rename to org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ValidatorHostContext.java index f471e96cb..5eb22397c 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/ValidatorHostContext.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ValidatorHostContext.java @@ -1,7 +1,6 @@ -package org.hl7.fhir.r5.validation.instancevalidator; +package org.hl7.fhir.r5.validation.instancevalidator.utils; import org.hl7.fhir.r5.elementmodel.Element; -import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.utilities.validation.ValidationMessage; From 8c2679a20052575b52757e688dd7a51bf205b550 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 15:55:36 -0500 Subject: [PATCH 08/11] Refactoring EntrySummary --- .../instancevalidator/InstanceValidator.java | 169 +----------------- 1 file changed, 4 insertions(+), 165 deletions(-) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index a0a0026c4..44a586066 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -36,13 +36,11 @@ import java.util.Map; import java.util.Set; import java.util.UUID; -import org.apache.commons.lang3.NotImplementedException; import org.apache.commons.lang3.StringUtils; import org.hl7.fhir.r5.model.Reference; import org.hl7.fhir.convertors.*; import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.FHIRException; -import org.hl7.fhir.exceptions.PathEngineException; import org.hl7.fhir.exceptions.TerminologyServiceException; import org.hl7.fhir.r5.conformance.ProfileUtilities; import org.hl7.fhir.r5.context.IWorkerContext; @@ -116,7 +114,6 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule; import org.hl7.fhir.r5.model.TimeType; import org.hl7.fhir.r5.model.Timing; import org.hl7.fhir.r5.model.DataType; -import org.hl7.fhir.r5.model.TypeDetails; import org.hl7.fhir.r5.model.UriType; import org.hl7.fhir.r5.model.ValueSet; import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent; @@ -168,165 +165,7 @@ import ca.uhn.fhir.util.ObjectUtil; public class InstanceValidator extends BaseValidator implements IResourceValidator { - - private class ValidatorHostServices implements IEvaluationContext { - -// private Stack>> - - @Override - public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException { - ValidatorHostContext c = (ValidatorHostContext) appContext; - if (externalHostServices != null) - return externalHostServices.resolveConstant(c.getAppContext(), name, beforeContext); - else - return null; - } - - @Override - public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException { - ValidatorHostContext c = (ValidatorHostContext) appContext; - if (externalHostServices != null) - return externalHostServices.resolveConstantType(c.getAppContext(), name); - else - return null; - } - - @Override - public boolean log(String argument, List focus) { - if (externalHostServices != null) - return externalHostServices.log(argument, focus); - else - return false; - } - - @Override - public FunctionDetails resolveFunction(String functionName) { - throw new Error("Not done yet (ValidatorHostServices.resolveFunction): "+functionName); - } - - @Override - public TypeDetails checkFunction(Object appContext, String functionName, List parameters) throws PathEngineException { - throw new Error("Not done yet (ValidatorHostServices.checkFunction)"); - } - - @Override - public List executeFunction(Object appContext, String functionName, List> parameters) { - throw new Error("Not done yet (ValidatorHostServices.executeFunction)"); - } - - @Override - public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException { - ValidatorHostContext c = (ValidatorHostContext) appContext; - - if (refContext != null && refContext.hasUserData("validator.bundle.resolution")) { - return (Base) refContext.getUserData("validator.bundle.resolution"); - } - - if (c.getAppContext() instanceof Element) { - Element bnd = (Element) c.getAppContext(); - Base res = resolveInBundle(url, bnd); - if (res != null) - return res; - } - Base res = resolveInBundle(url, c.getResource()); - if (res != null) - return res; - res = resolveInBundle(url, c.getContainer()); - if (res != null) - return res; - - if (externalHostServices != null) - return externalHostServices.resolveReference(c.getAppContext(), url, refContext); - else if (fetcher != null) - try { - return fetcher.fetch(c.getAppContext(), url); - } catch (IOException e) { - throw new FHIRException(e); - } - else - throw new Error("Not done yet - resolve "+url+" locally (2)"); - - } - - public Base resolveInBundle(String url, Element bnd) { - if (bnd == null) - return null; - if (bnd.fhirType().equals("Bundle")) { - for (Element be : bnd.getChildrenByName("entry")) { - Element res = be.getNamedChild("resource"); - if (res != null) { - String fullUrl = be.getChildValue("fullUrl"); - String rt = res.fhirType(); - String id = res.getChildValue("id"); - if (url.equals(fullUrl)) - return res; - if (url.equals(rt+"/"+id)) - return res; - } - } - } - return null; - } - - @Override - public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException { - ValidatorHostContext ctxt = (ValidatorHostContext) appContext; - StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); - if (sd == null) { - throw new FHIRException("Unable to resolve "+url); - } - InstanceValidator self = InstanceValidator.this; - List valerrors = new ArrayList(); - if (item instanceof Resource) { - try { - Element e = new ObjectConverter(context).convert((Resource) item); - self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); - } catch (IOException e1) { - throw new FHIRException(e1); - } - } else if (item instanceof Element) { - Element e = (Element) item; - if (e.isResource()) { - self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL,new NodeStack(e)); - } else { - throw new FHIRException("Not supported yet"); - } - } else - throw new NotImplementedException("Not done yet (ValidatorHostServices.conformsToProfile), when item is not an element"); - boolean ok = true; - List record = new ArrayList<>(); - for (ValidationMessage v : valerrors) { - ok = ok && !v.getLevel().isError(); - if (v.getLevel().isError() || v.isSlicingHint()) { - record.add(v); - } - } - if (!ok && !record.isEmpty()) { - ctxt.sliceNotes(url, record); - } - return ok; - } - - @Override - public ValueSet resolveValueSet(Object appContext, String url) { - ValidatorHostContext c = (ValidatorHostContext) appContext; - if (c.getProfile() != null && url.startsWith("#")) { - for (Resource r : c.getProfile().getContained()) { - if (r.getId().equals(url.substring(1))) { - if (r instanceof ValueSet) - return (ValueSet) r; - else - throw new FHIRException("Reference "+url+" refers to a "+r.fhirType()+" not a ValueSet"); - } - } - return null; - } - return context.fetchResource(ValueSet.class, url); - } - - } - - /** + /** * The validator keeps one of these classes for each resource it validates (e.g. when chasing references) * * It keeps track of the state of resource validation - a given resrouce may be validated agaisnt multiple @@ -415,7 +254,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat this.context = theContext; this.externalHostServices = hostServices; fpe = new FHIRPathEngine(context); - validatorServices = new ValidatorHostServices(); + validatorServices = new ValidatorHostServices(this); fpe.setHostServices(validatorServices); if (theContext.getVersion().startsWith("3.0") || theContext.getVersion().startsWith("1.0")) fpe.setLegacyMode(true); @@ -5282,7 +5121,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L /* * The actual base entry point for internal use (re-entrant) */ - private void validateResource(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException { + public void validateResource(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException { assert stack != null; assert resource != null; boolean ok = true; @@ -5385,7 +5224,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L return Calendar.getInstance().get(Calendar.YEAR); } - public class NodeStack { + public static class NodeStack { private ElementDefinition definition; private Element element; private ElementDefinition extension; From e54d7556b19f934eaa5dc8fac57892c7603b6f40 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 16:09:13 -0500 Subject: [PATCH 09/11] Refactoring ResourceValidationTracker --- .../instancevalidator/InstanceValidator.java | 10395 ++++++++-------- .../utils/ResourceValidationTracker.java | 44 + 2 files changed, 5306 insertions(+), 5133 deletions(-) create mode 100644 org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResourceValidationTracker.java diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 44a586066..412210f65 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -9,9 +9,9 @@ package org.hl7.fhir.r5.validation.instancevalidator; * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at - * + * * http://www.apache.org/licenses/LICENSE-2.0 - * + * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. @@ -36,11 +36,13 @@ import java.util.Map; import java.util.Set; import java.util.UUID; +import org.apache.commons.lang3.NotImplementedException; import org.apache.commons.lang3.StringUtils; import org.hl7.fhir.r5.model.Reference; import org.hl7.fhir.convertors.*; import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.FHIRException; +import org.hl7.fhir.exceptions.PathEngineException; import org.hl7.fhir.exceptions.TerminologyServiceException; import org.hl7.fhir.r5.conformance.ProfileUtilities; import org.hl7.fhir.r5.context.IWorkerContext; @@ -114,6 +116,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule; import org.hl7.fhir.r5.model.TimeType; import org.hl7.fhir.r5.model.Timing; import org.hl7.fhir.r5.model.DataType; +import org.hl7.fhir.r5.model.TypeDetails; import org.hl7.fhir.r5.model.UriType; import org.hl7.fhir.r5.model.ValueSet; import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent; @@ -148,5324 +151,5450 @@ import ca.uhn.fhir.util.ObjectUtil; /** - * Thinking of using this in a java program? Don't! + * Thinking of using this in a java program? Don't! * You should use one of the wrappers instead. Either in HAPI, or use ValidationEngine - * + *

* Validation todo: * - support @default slices - * - * @author Grahame Grieve * + * @author Grahame Grieve */ -/* +/* * todo: * check urn's don't start oid: or uuid: - * check MetadataResource.url is absolute + * check MetadataResource.url is absolute */ public class InstanceValidator extends BaseValidator implements IResourceValidator { - /** - * The validator keeps one of these classes for each resource it validates (e.g. when chasing references) - * - * It keeps track of the state of resource validation - a given resrouce may be validated agaisnt multiple - * profiles during a single validation, and it may be valid against some, and invalid against others. - * - * We don't want to keep doing the same validation, so we remember the outcomes for each combination - * of resource + profile - * - * Additionally, profile validation may be circular - e.g. a Patient profile that applies the same profile - * to linked patients, and 2 patient resources that link to each other. So this class also tracks validation - * in process. - * - * If the validator comes back to the same point, and validates the same instance against the same profile - * while it's already validating, it assumes it's valid - it cannot have new errors that wouldn't already - * be found in the first iteration - in other words, there's no errors - * - * @author graha - * - */ - private class ResourceValidationTracker { - private Map> validations = new HashMap<>(); - - private void startValidating(StructureDefinition sd) { - validations.put(sd.getUrl(), new ArrayList()); - } - - private List getOutcomes(StructureDefinition sd) { - return validations.get(sd.getUrl()); - } + private class ValidatorHostServices implements IEvaluationContext { - public void storeOutcomes(StructureDefinition sd, List errors) { - validations.put(sd.getUrl(), errors); - } - } - - private IWorkerContext context; - private FHIRPathEngine fpe; - - // configuration items - private CheckDisplayOption checkDisplay; - private boolean anyExtensionsAllowed; - private boolean errorForUnknownProfiles; - private boolean noInvariantChecks; - private boolean noTerminologyChecks; - private boolean hintAboutNonMustSupport; - private boolean showMessagesFromReferences; - private BestPracticeWarningLevel bpWarnings; - private String validationLanguage; - private boolean baseOnly; - - private List extensionDomains = new ArrayList(); - - private IdStatus resourceIdRule; - private boolean allowXsiLocation; - - // used during the build process to keep the overall volume of messages down - private boolean suppressLoincSnomedMessages; - - // time tracking - private long overall = 0; - private long txTime = 0; - private long sdTime = 0; - private long loadTime = 0; - private long fpeTime = 0; - - private boolean noBindingMsgSuppressed; - private boolean debug; - private Map fetchCache = new HashMap<>(); - private HashMap resourceTracker = new HashMap<>(); - private IValidatorResourceFetcher fetcher; - long time = 0; - private IEvaluationContext externalHostServices; - private boolean noExtensibleWarnings; - private String serverBase; - - private EnableWhenEvaluator myEnableWhenEvaluator = new EnableWhenEvaluator(); - private String executionId; - private XVerExtensionManager xverManager; - private IValidationProfileUsageTracker tracker; - private ValidatorHostServices validatorServices; - private boolean assumeValidRestReferences; - private boolean allowExamples; - - public InstanceValidator(IWorkerContext theContext, IEvaluationContext hostServices) { - super(); - this.context = theContext; - this.externalHostServices = hostServices; - fpe = new FHIRPathEngine(context); - validatorServices = new ValidatorHostServices(this); - fpe.setHostServices(validatorServices); - if (theContext.getVersion().startsWith("3.0") || theContext.getVersion().startsWith("1.0")) - fpe.setLegacyMode(true); - source = Source.InstanceValidator; - } - - @Override - public boolean isNoExtensibleWarnings() { - return noExtensibleWarnings; - } - - @Override - public IResourceValidator setNoExtensibleWarnings(boolean noExtensibleWarnings) { - this.noExtensibleWarnings = noExtensibleWarnings; - return this; - } - - @Override - public boolean isShowMessagesFromReferences() { - return showMessagesFromReferences; - } - - @Override - public void setShowMessagesFromReferences(boolean showMessagesFromReferences) { - this.showMessagesFromReferences = showMessagesFromReferences; - } - - @Override - public boolean isNoInvariantChecks() { - return noInvariantChecks; - } - - @Override - public IResourceValidator setNoInvariantChecks(boolean value) { - this.noInvariantChecks = value; - return this; - } - - public IValidatorResourceFetcher getFetcher() { - return this.fetcher; - } - - public IResourceValidator setFetcher(IValidatorResourceFetcher value) { - this.fetcher = value; - return this; - } - - public IValidationProfileUsageTracker getTracker() { - return this.tracker; - } - - public IResourceValidator setTracker(IValidationProfileUsageTracker value) { - this.tracker = value; - return this; - } - - - public boolean isHintAboutNonMustSupport() { - return hintAboutNonMustSupport; - } - - public void setHintAboutNonMustSupport(boolean hintAboutNonMustSupport) { - this.hintAboutNonMustSupport = hintAboutNonMustSupport; - } - - public boolean isAssumeValidRestReferences() { - return this.assumeValidRestReferences; - } - - public void setAssumeValidRestReferences(boolean value) { - this.assumeValidRestReferences = value; - } - - public boolean isAllowExamples() { - return this.allowExamples; - } - - public void setAllowExamples(boolean value) { - this.allowExamples = value; - } - - - private boolean allowUnknownExtension(String url) { - if ((allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression")) - // Added structuredefinition-expression explicitly because it wasn't defined in the version of the spec it needs to be used with - return true; - for (String s : extensionDomains) - if (url.startsWith(s)) - return true; - return anyExtensionsAllowed; - } - - private boolean isKnownExtension(String url) { - // Added structuredefinition-expression and following extensions explicitly because they weren't defined in the version of the spec they need to be used with - if ((allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression") || url.equals(VersionConvertorConstants.IG_DEPENDSON_PACKAGE_EXTENSION)) - return true; - for (String s : extensionDomains) - if (url.startsWith(s)) - return true; - return false; - } - - private void bpCheck(List errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message) { - if (bpWarnings != null) { - switch (bpWarnings) { - case Error: - rule(errors, invalid, line, col, literalPath, test, message); - break; - case Warning: - warning(errors, invalid, line, col, literalPath, test, message); - break; - case Hint: - hint(errors, invalid, line, col, literalPath, test, message); - break; - default: // do nothing - break; - } - } - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format) throws FHIRException { - return validate(appContext, errors, stream, format, new ArrayList<>()); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - return validate(appContext, errors, stream, format, profiles); - } - - private StructureDefinition getSpecifiedProfile(String profile) { - StructureDefinition sd = context.fetchResource(StructureDefinition.class, profile); - if (sd == null) { - throw new FHIRException("Unable to locate the profile '"+profile+"' in order to validate against it"); - } - return sd; - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format, List profiles) throws FHIRException { - ParserBase parser = Manager.makeParser(context, format); - if (parser instanceof XmlParser) - ((XmlParser) parser).setAllowXsiLocation(allowXsiLocation); - parser.setupValidation(ValidationPolicy.EVERYTHING, errors); - long t = System.nanoTime(); - Element e; - try { - e = parser.parse(stream); - } catch (IOException e1) { - throw new FHIRException(e1); - } - loadTime = System.nanoTime() - t; - if (e != null) - validate(appContext, errors, e, profiles); - return e; - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource) throws FHIRException { - return validate(appContext, errors, resource, new ArrayList<>()); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - return validate(appContext, errors, resource, profiles); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource, List profiles) throws FHIRException { - long t = System.nanoTime(); - Element e; - try { - e = new ObjectConverter(context).convert(resource); - } catch (IOException e1) { - throw new FHIRException(e1); - } - loadTime = System.nanoTime() - t; - validate(appContext, errors, e, profiles); - return e; - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element) throws FHIRException { - return validate(appContext, errors, element, new ArrayList<>()); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - return validate(appContext, errors, element, profiles); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element, List profiles) throws FHIRException { - XmlParser parser = new XmlParser(context); - parser.setupValidation(ValidationPolicy.EVERYTHING, errors); - long t = System.nanoTime(); - Element e; - try { - e = parser.parse(element); - } catch (IOException e1) { - throw new FHIRException(e1); - } - loadTime = System.nanoTime() - t; - if (e != null) - validate(appContext, errors, e, profiles); - return e; - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document) throws FHIRException { - return validate(appContext, errors, document, new ArrayList<>()); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - return validate(appContext, errors, document, profiles); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document, List profiles) throws FHIRException { - XmlParser parser = new XmlParser(context); - parser.setupValidation(ValidationPolicy.EVERYTHING, errors); - long t = System.nanoTime(); - Element e; - try { - e = parser.parse(document); - } catch (IOException e1) { - throw new FHIRException(e1); - } - loadTime = System.nanoTime() - t; - if (e != null) - validate(appContext, errors, e, profiles); - return e; - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object) throws FHIRException { - return validate(appContext, errors, object, new ArrayList<>()); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - return validate(appContext, errors, object, profiles); - } - - @Override - public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object, List profiles) throws FHIRException { - JsonParser parser = new JsonParser(context); - parser.setupValidation(ValidationPolicy.EVERYTHING, errors); - long t = System.nanoTime(); - Element e = parser.parse(object); - loadTime = System.nanoTime() - t; - if (e != null) - validate(appContext, errors, e, profiles); - return e; - } - - @Override - public void validate(Object appContext, List errors, Element element) throws FHIRException { - validate(appContext, errors, element, new ArrayList<>()); - } - - @Override - public void validate(Object appContext, List errors, Element element, String profile) throws FHIRException { - ArrayList profiles = new ArrayList<>(); - if (profile != null) { - profiles.add(getSpecifiedProfile(profile)); - } - validate(appContext, errors, element, profiles); - } - - @Override - public void validate(Object appContext, List errors, Element element, List profiles) throws FHIRException { - // this is the main entry point; all the other public entry points end up here coming here... - // so the first thing to do is to clear the internal state - fetchCache.clear(); - fetchCache.put(element.fhirType()+"/"+element.getIdBase(), element); - resourceTracker.clear(); - executionId = UUID.randomUUID().toString(); - baseOnly = profiles.isEmpty(); - - long t = System.nanoTime(); - if (profiles == null || profiles.isEmpty()) { - validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, new NodeStack(element)); - } else { - for (StructureDefinition defn : profiles) { - validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, new NodeStack(element)); - } - } - if (hintAboutNonMustSupport) { - checkElementUsage(errors, element, new NodeStack(element)); - } - overall = System.nanoTime() - t; - } - - private void checkElementUsage(List errors, Element element, NodeStack stack) { - String elementUsage = element.getUserString("elementSupported"); - hint(errors, IssueType.INFORMATIONAL, element.line(),element.col(), stack.getLiteralPath(), elementUsage==null || elementUsage.equals("Y"), - "The element " + element.getName() + " is not marked as 'mustSupport' in the profile " + element.getProperty().getStructure().getUrl() + ". Consider not using the element, or marking the element as must-Support in the profile"); - - if (element.hasChildren()) { - String prevName = ""; - int elementCount = 0; - for (Element ce : element.getChildren()) { - if (ce.getName().equals(prevName)) - elementCount++; - else { - elementCount=1; - prevName = ce.getName(); + @Override + public Base resolveConstant(Object appContext, String name, boolean beforeContext) throws PathEngineException { + ValidatorHostContext c = (ValidatorHostContext) appContext; + if (externalHostServices != null) + return externalHostServices.resolveConstant(c.getAppContext(), name, beforeContext); + else + return null; } - checkElementUsage(errors, ce, stack.push(ce, elementCount, null, null)); - } + + @Override + public TypeDetails resolveConstantType(Object appContext, String name) throws PathEngineException { + ValidatorHostContext c = (ValidatorHostContext) appContext; + if (externalHostServices != null) + return externalHostServices.resolveConstantType(c.getAppContext(), name); + else + return null; + } + + @Override + public boolean log(String argument, List focus) { + if (externalHostServices != null) + return externalHostServices.log(argument, focus); + else + return false; + } + + @Override + public FunctionDetails resolveFunction(String functionName) { + throw new Error("Not done yet (ValidatorHostServices.resolveFunction): " + functionName); + } + + @Override + public TypeDetails checkFunction(Object appContext, String functionName, List parameters) throws PathEngineException { + throw new Error("Not done yet (ValidatorHostServices.checkFunction)"); + } + + @Override + public List executeFunction(Object appContext, String functionName, List> parameters) { + throw new Error("Not done yet (ValidatorHostServices.executeFunction)"); + } + + @Override + public Base resolveReference(Object appContext, String url, Base refContext) throws FHIRException { + ValidatorHostContext c = (ValidatorHostContext) appContext; + + if (refContext != null && refContext.hasUserData("validator.bundle.resolution")) { + return (Base) refContext.getUserData("validator.bundle.resolution"); + } + + if (c.getAppContext() instanceof Element) { + Element bnd = (Element) c.getAppContext(); + Base res = resolveInBundle(url, bnd); + if (res != null) + return res; + } + Base res = resolveInBundle(url, c.getResource()); + if (res != null) + return res; + res = resolveInBundle(url, c.getContainer()); + if (res != null) + return res; + + if (externalHostServices != null) + return externalHostServices.resolveReference(c.getAppContext(), url, refContext); + else if (fetcher != null) + try { + return fetcher.fetch(c.getAppContext(), url); + } catch (IOException e) { + throw new FHIRException(e); + } + else + throw new Error("Not done yet - resolve " + url + " locally (2)"); + + } + + public Base resolveInBundle(String url, Element bnd) { + if (bnd == null) + return null; + if (bnd.fhirType().equals("Bundle")) { + for (Element be : bnd.getChildrenByName("entry")) { + Element res = be.getNamedChild("resource"); + if (res != null) { + String fullUrl = be.getChildValue("fullUrl"); + String rt = res.fhirType(); + String id = res.getChildValue("id"); + if (url.equals(fullUrl)) + return res; + if (url.equals(rt + "/" + id)) + return res; + } + } + } + return null; + } + + @Override + public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException { + ValidatorHostContext ctxt = (ValidatorHostContext) appContext; + StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); + if (sd == null) { + throw new FHIRException("Unable to resolve " + url); + } + InstanceValidator self = InstanceValidator.this; + List valerrors = new ArrayList(); + if (item instanceof Resource) { + try { + Element e = new ObjectConverter(context).convert((Resource) item); + self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(e)); + } catch (IOException e1) { + throw new FHIRException(e1); + } + } else if (item instanceof Element) { + Element e = (Element) item; + if (e.isResource()) { + self.validateResource(new ValidatorHostContext(ctxt.getAppContext(), e), valerrors, e, e, sd, IdStatus.OPTIONAL, new NodeStack(e)); + } else { + throw new FHIRException("Not supported yet"); + } + } else + throw new NotImplementedException("Not done yet (ValidatorHostServices.conformsToProfile), when item is not an element"); + boolean ok = true; + List record = new ArrayList<>(); + for (ValidationMessage v : valerrors) { + ok = ok && !v.getLevel().isError(); + if (v.getLevel().isError() || v.isSlicingHint()) { + record.add(v); + } + } + if (!ok && !record.isEmpty()) { + ctxt.sliceNotes(url, record); + } + return ok; + } + + @Override + public ValueSet resolveValueSet(Object appContext, String url) { + ValidatorHostContext c = (ValidatorHostContext) appContext; + if (c.getProfile() != null && url.startsWith("#")) { + for (Resource r : c.getProfile().getContained()) { + if (r.getId().equals(url.substring(1))) { + if (r instanceof ValueSet) + return (ValueSet) r; + else + throw new FHIRException("Reference " + url + " refers to a " + r.fhirType() + " not a ValueSet"); + } + } + return null; + } + return context.fetchResource(ValueSet.class, url); + } + } - } - private boolean check(String v1, String v2) { - return v1 == null ? Utilities.noString(v1) : v1.equals(v2); - } + private IWorkerContext context; + private FHIRPathEngine fpe; - private void checkAddress(List errors, String path, Element focus, Address fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); - checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); - checkFixedValue(errors, path + ".city", focus.getNamedChild("city"), fixed.getCityElement(), fixedSource, "city", focus, pattern); - checkFixedValue(errors, path + ".state", focus.getNamedChild("state"), fixed.getStateElement(), fixedSource, "state", focus, pattern); - checkFixedValue(errors, path + ".country", focus.getNamedChild("country"), fixed.getCountryElement(), fixedSource, "country", focus, pattern); - checkFixedValue(errors, path + ".zip", focus.getNamedChild("zip"), fixed.getPostalCodeElement(), fixedSource, "postalCode", focus, pattern); + // configuration items + private CheckDisplayOption checkDisplay; + private boolean anyExtensionsAllowed; + private boolean errorForUnknownProfiles; + private boolean noInvariantChecks; + private boolean noTerminologyChecks; + private boolean hintAboutNonMustSupport; + private boolean showMessagesFromReferences; + private BestPracticeWarningLevel bpWarnings; + private String validationLanguage; + private boolean baseOnly; - List lines = new ArrayList(); - focus.getNamedChildren("line", lines); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, lines.size() == fixed.getLine().size(), - "Expected " + Integer.toString(fixed.getLine().size()) + " but found " + Integer.toString(lines.size()) + " line elements")) { - for (int i = 0; i < lines.size(); i++) - checkFixedValue(errors, path + ".coding", lines.get(i), fixed.getLine().get(i), fixedSource, "coding", focus, pattern); + private List extensionDomains = new ArrayList(); + + private IdStatus resourceIdRule; + private boolean allowXsiLocation; + + // used during the build process to keep the overall volume of messages down + private boolean suppressLoincSnomedMessages; + + // time tracking + private long overall = 0; + private long txTime = 0; + private long sdTime = 0; + private long loadTime = 0; + private long fpeTime = 0; + + private boolean noBindingMsgSuppressed; + private boolean debug; + private Map fetchCache = new HashMap<>(); + private HashMap resourceTracker = new HashMap<>(); + private IValidatorResourceFetcher fetcher; + long time = 0; + private IEvaluationContext externalHostServices; + private boolean noExtensibleWarnings; + private String serverBase; + + private EnableWhenEvaluator myEnableWhenEvaluator = new EnableWhenEvaluator(); + private String executionId; + private XVerExtensionManager xverManager; + private IValidationProfileUsageTracker tracker; + private ValidatorHostServices validatorServices; + private boolean assumeValidRestReferences; + private boolean allowExamples; + + public InstanceValidator(IWorkerContext theContext, IEvaluationContext hostServices) { + super(); + this.context = theContext; + this.externalHostServices = hostServices; + fpe = new FHIRPathEngine(context); + validatorServices = new ValidatorHostServices(); + fpe.setHostServices(validatorServices); + if (theContext.getVersion().startsWith("3.0") || theContext.getVersion().startsWith("1.0")) + fpe.setLegacyMode(true); + source = Source.InstanceValidator; } - } - private void checkAttachment(List errors, String path, Element focus, Attachment fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".contentType", focus.getNamedChild("contentType"), fixed.getContentTypeElement(), fixedSource, "contentType", focus, pattern); - checkFixedValue(errors, path + ".language", focus.getNamedChild("language"), fixed.getLanguageElement(), fixedSource, "language", focus, pattern); - checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), fixedSource, "data", focus, pattern); - checkFixedValue(errors, path + ".url", focus.getNamedChild("url"), fixed.getUrlElement(), fixedSource, "url", focus, pattern); - checkFixedValue(errors, path + ".size", focus.getNamedChild("size"), fixed.getSizeElement(), fixedSource, "size", focus, pattern); - checkFixedValue(errors, path + ".hash", focus.getNamedChild("hash"), fixed.getHashElement(), fixedSource, "hash", focus, pattern); - checkFixedValue(errors, path + ".title", focus.getNamedChild("title"), fixed.getTitleElement(), fixedSource, "title", focus, pattern); - } + @Override + public boolean isNoExtensibleWarnings() { + return noExtensibleWarnings; + } - // public API - private boolean checkCode(List errors, Element element, String path, String code, String system, String display, boolean checkDisplay, NodeStack stack) throws TerminologyServiceException { - long t = System.nanoTime(); - boolean ss = context.supportsSystem(system); - txTime = txTime + (System.nanoTime() - t); - if (ss) { - t = System.nanoTime(); - ValidationResult s = context.validateCode(new ValidationOptions(stack.workingLang), system, code, checkDisplay ? display : null); - txTime = txTime + (System.nanoTime() - t); - if (s == null) - return true; - if (s.isOk()) { - if (s.getMessage() != null) - txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); - return true; - } - if (s.getErrorClass() != null && s.getErrorClass().isInfrastructure()) - txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); - else if (s.getSeverity() == IssueSeverity.INFORMATION) - txHint(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); - else if (s.getSeverity() == IssueSeverity.WARNING) - txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); - else - return txRule(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()+" for '"+system+"#"+code+"'"); - return true; - } else if (system.startsWith("http://hl7.org/fhir")) { - if (Utilities.existsInList(system, "http://hl7.org/fhir/sid/icd-10", "http://hl7.org/fhir/sid/cvx", "http://hl7.org/fhir/sid/icd-10","http://hl7.org/fhir/sid/icd-10-cm","http://hl7.org/fhir/sid/icd-9","http://hl7.org/fhir/sid/ndc","http://hl7.org/fhir/sid/srt")) - return true; // else don't check these (for now) - else if (system.startsWith("http://hl7.org/fhir/test")) - return true; // we don't validate these - else { - CodeSystem cs = getCodeSystem(system); - if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs != null, "Unknown Code System '" + system+"'")) { - ConceptDefinitionComponent def = getCodeDefinition(cs, code); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, def != null, "Unknown Code (" + system + "#" + code + ")")) - return warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, display == null || display.equals(def.getDisplay()), "Display should be '" + def.getDisplay() + "'"); + @Override + public IResourceValidator setNoExtensibleWarnings(boolean noExtensibleWarnings) { + this.noExtensibleWarnings = noExtensibleWarnings; + return this; + } + + @Override + public boolean isShowMessagesFromReferences() { + return showMessagesFromReferences; + } + + @Override + public void setShowMessagesFromReferences(boolean showMessagesFromReferences) { + this.showMessagesFromReferences = showMessagesFromReferences; + } + + @Override + public boolean isNoInvariantChecks() { + return noInvariantChecks; + } + + @Override + public IResourceValidator setNoInvariantChecks(boolean value) { + this.noInvariantChecks = value; + return this; + } + + public IValidatorResourceFetcher getFetcher() { + return this.fetcher; + } + + public IResourceValidator setFetcher(IValidatorResourceFetcher value) { + this.fetcher = value; + return this; + } + + public IValidationProfileUsageTracker getTracker() { + return this.tracker; + } + + public IResourceValidator setTracker(IValidationProfileUsageTracker value) { + this.tracker = value; + return this; + } + + + public boolean isHintAboutNonMustSupport() { + return hintAboutNonMustSupport; + } + + public void setHintAboutNonMustSupport(boolean hintAboutNonMustSupport) { + this.hintAboutNonMustSupport = hintAboutNonMustSupport; + } + + public boolean isAssumeValidRestReferences() { + return this.assumeValidRestReferences; + } + + public void setAssumeValidRestReferences(boolean value) { + this.assumeValidRestReferences = value; + } + + public boolean isAllowExamples() { + return this.allowExamples; + } + + public void setAllowExamples(boolean value) { + this.allowExamples = value; + } + + + private boolean allowUnknownExtension(String url) { + if ((allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression")) + // Added structuredefinition-expression explicitly because it wasn't defined in the version of the spec it needs to be used with + return true; + for (String s : extensionDomains) + if (url.startsWith(s)) + return true; + return anyExtensionsAllowed; + } + + private boolean isKnownExtension(String url) { + // Added structuredefinition-expression and following extensions explicitly because they weren't defined in the version of the spec they need to be used with + if ((allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || url.contains("nema.org") || url.startsWith("http://hl7.org/fhir/tools/StructureDefinition/") || url.equals("http://hl7.org/fhir/StructureDefinition/structuredefinition-expression") || url.equals(VersionConvertorConstants.IG_DEPENDSON_PACKAGE_EXTENSION)) + return true; + for (String s : extensionDomains) + if (url.startsWith(s)) + return true; + return false; + } + + private void bpCheck(List errors, IssueType invalid, int line, int col, String literalPath, boolean test, String message) { + if (bpWarnings != null) { + switch (bpWarnings) { + case Error: + rule(errors, invalid, line, col, literalPath, test, message); + break; + case Warning: + warning(errors, invalid, line, col, literalPath, test, message); + break; + case Hint: + hint(errors, invalid, line, col, literalPath, test, message); + break; + default: // do nothing + break; + } + } + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format) throws FHIRException { + return validate(appContext, errors, stream, format, new ArrayList<>()); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + return validate(appContext, errors, stream, format, profiles); + } + + private StructureDefinition getSpecifiedProfile(String profile) { + StructureDefinition sd = context.fetchResource(StructureDefinition.class, profile); + if (sd == null) { + throw new FHIRException("Unable to locate the profile '" + profile + "' in order to validate against it"); + } + return sd; + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, InputStream stream, FhirFormat format, List profiles) throws FHIRException { + ParserBase parser = Manager.makeParser(context, format); + if (parser instanceof XmlParser) + ((XmlParser) parser).setAllowXsiLocation(allowXsiLocation); + parser.setupValidation(ValidationPolicy.EVERYTHING, errors); + long t = System.nanoTime(); + Element e; + try { + e = parser.parse(stream); + } catch (IOException e1) { + throw new FHIRException(e1); + } + loadTime = System.nanoTime() - t; + if (e != null) + validate(appContext, errors, e, profiles); + return e; + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource) throws FHIRException { + return validate(appContext, errors, resource, new ArrayList<>()); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + return validate(appContext, errors, resource, profiles); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Resource resource, List profiles) throws FHIRException { + long t = System.nanoTime(); + Element e; + try { + e = new ObjectConverter(context).convert(resource); + } catch (IOException e1) { + throw new FHIRException(e1); + } + loadTime = System.nanoTime() - t; + validate(appContext, errors, e, profiles); + return e; + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element) throws FHIRException { + return validate(appContext, errors, element, new ArrayList<>()); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + return validate(appContext, errors, element, profiles); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, org.w3c.dom.Element element, List profiles) throws FHIRException { + XmlParser parser = new XmlParser(context); + parser.setupValidation(ValidationPolicy.EVERYTHING, errors); + long t = System.nanoTime(); + Element e; + try { + e = parser.parse(element); + } catch (IOException e1) { + throw new FHIRException(e1); + } + loadTime = System.nanoTime() - t; + if (e != null) + validate(appContext, errors, e, profiles); + return e; + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document) throws FHIRException { + return validate(appContext, errors, document, new ArrayList<>()); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + return validate(appContext, errors, document, profiles); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, Document document, List profiles) throws FHIRException { + XmlParser parser = new XmlParser(context); + parser.setupValidation(ValidationPolicy.EVERYTHING, errors); + long t = System.nanoTime(); + Element e; + try { + e = parser.parse(document); + } catch (IOException e1) { + throw new FHIRException(e1); + } + loadTime = System.nanoTime() - t; + if (e != null) + validate(appContext, errors, e, profiles); + return e; + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object) throws FHIRException { + return validate(appContext, errors, object, new ArrayList<>()); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + return validate(appContext, errors, object, profiles); + } + + @Override + public org.hl7.fhir.r5.elementmodel.Element validate(Object appContext, List errors, JsonObject object, List profiles) throws FHIRException { + JsonParser parser = new JsonParser(context); + parser.setupValidation(ValidationPolicy.EVERYTHING, errors); + long t = System.nanoTime(); + Element e = parser.parse(object); + loadTime = System.nanoTime() - t; + if (e != null) + validate(appContext, errors, e, profiles); + return e; + } + + @Override + public void validate(Object appContext, List errors, Element element) throws FHIRException { + validate(appContext, errors, element, new ArrayList<>()); + } + + @Override + public void validate(Object appContext, List errors, Element element, String profile) throws FHIRException { + ArrayList profiles = new ArrayList<>(); + if (profile != null) { + profiles.add(getSpecifiedProfile(profile)); + } + validate(appContext, errors, element, profiles); + } + + @Override + public void validate(Object appContext, List errors, Element element, List profiles) throws FHIRException { + // this is the main entry point; all the other public entry points end up here coming here... + // so the first thing to do is to clear the internal state + fetchCache.clear(); + fetchCache.put(element.fhirType() + "/" + element.getIdBase(), element); + resourceTracker.clear(); + executionId = UUID.randomUUID().toString(); + baseOnly = profiles.isEmpty(); + + long t = System.nanoTime(); + if (profiles == null || profiles.isEmpty()) { + validateResource(new ValidatorHostContext(appContext, element), errors, element, element, null, resourceIdRule, new NodeStack(element)); + } else { + for (StructureDefinition defn : profiles) { + validateResource(new ValidatorHostContext(appContext, element), errors, element, element, defn, resourceIdRule, new NodeStack(element)); + } + } + if (hintAboutNonMustSupport) { + checkElementUsage(errors, element, new NodeStack(element)); + } + overall = System.nanoTime() - t; + } + + private void checkElementUsage(List errors, Element element, NodeStack stack) { + String elementUsage = element.getUserString("elementSupported"); + hint(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), elementUsage == null || elementUsage.equals("Y"), + "The element " + element.getName() + " is not marked as 'mustSupport' in the profile " + element.getProperty().getStructure().getUrl() + ". Consider not using the element, or marking the element as must-Support in the profile"); + + if (element.hasChildren()) { + String prevName = ""; + int elementCount = 0; + for (Element ce : element.getChildren()) { + if (ce.getName().equals(prevName)) + elementCount++; + else { + elementCount = 1; + prevName = ce.getName(); + } + checkElementUsage(errors, ce, stack.push(ce, elementCount, null, null)); + } + } + } + + private boolean check(String v1, String v2) { + return v1 == null ? Utilities.noString(v1) : v1.equals(v2); + } + + private void checkAddress(List errors, String path, Element focus, Address fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); + checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); + checkFixedValue(errors, path + ".city", focus.getNamedChild("city"), fixed.getCityElement(), fixedSource, "city", focus, pattern); + checkFixedValue(errors, path + ".state", focus.getNamedChild("state"), fixed.getStateElement(), fixedSource, "state", focus, pattern); + checkFixedValue(errors, path + ".country", focus.getNamedChild("country"), fixed.getCountryElement(), fixedSource, "country", focus, pattern); + checkFixedValue(errors, path + ".zip", focus.getNamedChild("zip"), fixed.getPostalCodeElement(), fixedSource, "postalCode", focus, pattern); + + List lines = new ArrayList(); + focus.getNamedChildren("line", lines); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, lines.size() == fixed.getLine().size(), + "Expected " + Integer.toString(fixed.getLine().size()) + " but found " + Integer.toString(lines.size()) + " line elements")) { + for (int i = 0; i < lines.size(); i++) + checkFixedValue(errors, path + ".coding", lines.get(i), fixed.getLine().get(i), fixedSource, "coding", focus, pattern); + } + } + + private void checkAttachment(List errors, String path, Element focus, Attachment fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".contentType", focus.getNamedChild("contentType"), fixed.getContentTypeElement(), fixedSource, "contentType", focus, pattern); + checkFixedValue(errors, path + ".language", focus.getNamedChild("language"), fixed.getLanguageElement(), fixedSource, "language", focus, pattern); + checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), fixedSource, "data", focus, pattern); + checkFixedValue(errors, path + ".url", focus.getNamedChild("url"), fixed.getUrlElement(), fixedSource, "url", focus, pattern); + checkFixedValue(errors, path + ".size", focus.getNamedChild("size"), fixed.getSizeElement(), fixedSource, "size", focus, pattern); + checkFixedValue(errors, path + ".hash", focus.getNamedChild("hash"), fixed.getHashElement(), fixedSource, "hash", focus, pattern); + checkFixedValue(errors, path + ".title", focus.getNamedChild("title"), fixed.getTitleElement(), fixedSource, "title", focus, pattern); + } + + // public API + private boolean checkCode(List errors, Element element, String path, String code, String system, String display, boolean checkDisplay, NodeStack stack) throws TerminologyServiceException { + long t = System.nanoTime(); + boolean ss = context.supportsSystem(system); + txTime = txTime + (System.nanoTime() - t); + if (ss) { + t = System.nanoTime(); + ValidationResult s = context.validateCode(new ValidationOptions(stack.workingLang), system, code, checkDisplay ? display : null); + txTime = txTime + (System.nanoTime() - t); + if (s == null) + return true; + if (s.isOk()) { + if (s.getMessage() != null) + txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); + return true; + } + if (s.getErrorClass() != null && s.getErrorClass().isInfrastructure()) + txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); + else if (s.getSeverity() == IssueSeverity.INFORMATION) + txHint(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); + else if (s.getSeverity() == IssueSeverity.WARNING) + txWarning(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage()); + else + return txRule(errors, s.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, s == null, s.getMessage() + " for '" + system + "#" + code + "'"); + return true; + } else if (system.startsWith("http://hl7.org/fhir")) { + if (Utilities.existsInList(system, "http://hl7.org/fhir/sid/icd-10", "http://hl7.org/fhir/sid/cvx", "http://hl7.org/fhir/sid/icd-10", "http://hl7.org/fhir/sid/icd-10-cm", "http://hl7.org/fhir/sid/icd-9", "http://hl7.org/fhir/sid/ndc", "http://hl7.org/fhir/sid/srt")) + return true; // else don't check these (for now) + else if (system.startsWith("http://hl7.org/fhir/test")) + return true; // we don't validate these + else { + CodeSystem cs = getCodeSystem(system); + if (rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, cs != null, "Unknown Code System '" + system + "'")) { + ConceptDefinitionComponent def = getCodeDefinition(cs, code); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, def != null, "Unknown Code (" + system + "#" + code + ")")) + return warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, display == null || display.equals(def.getDisplay()), "Display should be '" + def.getDisplay() + "'"); + } + return false; + } + } else if (context.isNoTerminologyServer() && Utilities.existsInList(system, "http://loinc.org", "http://unitsofmeasure.org", "http://snomed.info/sct", "http://www.nlm.nih.gov/research/umls/rxnorm")) { + return true; // no checks in this case + } else if (startsWithButIsNot(system, "http://snomed.info/sct", "http://loinc.org", "http://unitsofmeasure.org", "http://www.nlm.nih.gov/research/umls/rxnorm")) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: " + system); + return false; + } else { + try { + if (context.fetchResourceWithException(ValueSet.class, system) != null) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: " + system + " - cannot use a value set URI as a system"); + // Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur. Please talk to me before changing the code back. + } + hint(errors, IssueType.UNKNOWN, element.line(), element.col(), path, false, "Code System URI '" + system + "' is unknown so the code cannot be validated"); + return true; + } catch (Exception e) { + return true; + } + } + } + + private boolean startsWithButIsNot(String system, String... uri) { + for (String s : uri) + if (!system.equals(s) && system.startsWith(s)) + return true; + return false; + } + + + private boolean hasErrors(List errors) { + if (errors != null) { + for (ValidationMessage vm : errors) { + if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) { + return true; + } + } } return false; - } - } else if (context.isNoTerminologyServer() && Utilities.existsInList(system, "http://loinc.org", "http://unitsofmeasure.org", "http://snomed.info/sct", "http://www.nlm.nih.gov/research/umls/rxnorm")) { - return true; // no checks in this case - } else if (startsWithButIsNot(system, "http://snomed.info/sct", "http://loinc.org", "http://unitsofmeasure.org", "http://www.nlm.nih.gov/research/umls/rxnorm")) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: "+system); - return false; - } else { - try { - if (context.fetchResourceWithException(ValueSet.class, system) != null) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Invalid System URI: "+system+" - cannot use a value set URI as a system"); - // Lloyd: This error used to prohibit checking for downstream issues, but there are some cases where that checking needs to occur. Please talk to me before changing the code back. - } - hint(errors, IssueType.UNKNOWN, element.line(), element.col(), path, false, "Code System URI '"+system+"' is unknown so the code cannot be validated"); - return true; - } - catch (Exception e) { - return true; - } } - } - private boolean startsWithButIsNot(String system, String... uri) { - for (String s : uri) - if (!system.equals(s) && system.startsWith(s)) - return true; - return false; - } - - - private boolean hasErrors(List errors) { - if (errors!=null) { - for (ValidationMessage vm : errors) { - if (vm.getLevel() == IssueSeverity.FATAL || vm.getLevel() == IssueSeverity.ERROR) { - return true; - } - } - } - return false; - } - - private void checkCodeableConcept(List errors, String path, Element focus, CodeableConcept fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); - List codings = new ArrayList(); - focus.getNamedChildren("coding", codings); - if (pattern) { - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() >= fixed.getCoding().size(), - "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) - + " coding elements")) { - for (int i = 0; i < fixed.getCoding().size(); i++) { - Coding fixedCoding = fixed.getCoding().get(i); - boolean found = false; - List allErrorsFixed = new ArrayList<>(); - List errorsFixed; - for (int j = 0; j < codings.size() && !found; ++j) { - errorsFixed = new ArrayList<>(); - checkFixedValue(errorsFixed, path + ".coding", codings.get(j), fixedCoding, fixedSource, "coding", focus, pattern); - if (!hasErrors(errorsFixed)) { - found = true; - } else { - errorsFixed - .stream() - .filter(t->t.getLevel().ordinal() >= IssueSeverity.ERROR.ordinal()) - .forEach(t->allErrorsFixed.add(t)); - } - } - if (!found) { - // The argonaut DSTU2 labs profile requires userSelected=false on the category.coding and this - // needs to produce an understandable error message - String message = "Expected CodeableConcept "+(pattern ? "pattern" : "fixed value")+" not found for" + - " system: " + fixedCoding.getSystemElement().asStringValue() + - " code: " + fixedCoding.getCodeElement().asStringValue() + - " display: " + fixedCoding.getDisplayElement().asStringValue(); - if (fixedCoding.hasUserSelected()) { - message += " userSelected: " + fixedCoding.getUserSelected(); - } - message += " - Issues: " + allErrorsFixed; - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, message); - } - } - } - } else { - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(), - "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) - + " coding elements")) { - for (int i = 0; i < codings.size(); i++) - checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), fixedSource, "coding", focus); - } - } - } - - private boolean checkCodeableConcept(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, NodeStack stack) { - boolean res = true; - if (!noTerminologyChecks && theElementCntext != null && theElementCntext.hasBinding()) { - ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) { - if (binding.hasValueSet()) { - ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { - try { - CodeableConcept cc = ObjectConverter.readAsCodeableConcept(element); - if (!cc.hasCoding()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code must be provided from the value set " + describeReference(ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + " (max value set " + valueset.getUrl()+")"); - else - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+")"); + private void checkCodeableConcept(List errors, String path, Element focus, CodeableConcept fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); + List codings = new ArrayList(); + focus.getNamedChildren("coding", codings); + if (pattern) { + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() >= fixed.getCoding().size(), + "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) + + " coding elements")) { + for (int i = 0; i < fixed.getCoding().size(); i++) { + Coding fixedCoding = fixed.getCoding().get(i); + boolean found = false; + List allErrorsFixed = new ArrayList<>(); + List errorsFixed; + for (int j = 0; j < codings.size() && !found; ++j) { + errorsFixed = new ArrayList<>(); + checkFixedValue(errorsFixed, path + ".coding", codings.get(j), fixedCoding, fixedSource, "coding", focus, pattern); + if (!hasErrors(errorsFixed)) { + found = true; + } else { + errorsFixed + .stream() + .filter(t -> t.getLevel().ordinal() >= IssueSeverity.ERROR.ordinal()) + .forEach(t -> allErrorsFixed.add(t)); + } + } + if (!found) { + // The argonaut DSTU2 labs profile requires userSelected=false on the category.coding and this + // needs to produce an understandable error message + String message = "Expected CodeableConcept " + (pattern ? "pattern" : "fixed value") + " not found for" + + " system: " + fixedCoding.getSystemElement().asStringValue() + + " code: " + fixedCoding.getCodeElement().asStringValue() + + " display: " + fixedCoding.getDisplayElement().asStringValue(); + if (fixedCoding.hasUserSelected()) { + message += " userSelected: " + fixedCoding.getUserSelected(); + } + message += " - Issues: " + allErrorsFixed; + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, false, message); + } } - } else { - long t = System.nanoTime(); - - // Check whether the codes are appropriate for the type of binding we have - boolean bindingsOk = true; - if (binding.getStrength() != BindingStrength.EXAMPLE) { - boolean atLeastOneSystemIsSupported = false; - for (Coding nextCoding : cc.getCoding()) { - String nextSystem = nextCoding.getSystem(); - if (isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { - atLeastOneSystemIsSupported = true; - break; - } - } - - if (!atLeastOneSystemIsSupported && binding.getStrength() == BindingStrength.EXAMPLE) { - // ignore this since we can't validate but it doesn't matter.. - } else { - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang).checkValueSetOnly(), cc, valueset); // we're going to validate the codings directly, so only check the valueset - if (!vr.isOk()) { - bindingsOk = false; - if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code from this value set is required (class = "+vr.getErrorClass().toString()+")"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); - else if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code should come from this value set unless it has no suitable code (class = "+vr.getErrorClass().toString()+")"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code is recommended to come from this value set (class = "+vr.getErrorClass().toString()+")"); - } - } - } else { - if (binding.getStrength() == BindingStrength.REQUIRED) - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+", and a code from this value set is required) (codes = "+ccSummary(cc)+")"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); - if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code) (codes = "+ccSummary(cc)+")"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set) (codes = "+ccSummary(cc)+")"); - } - } - } - } else if (vr.getMessage()!=null) { - res = false; - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); - } else { - res = false; - } - } - // Then, for any codes that are in code systems we are able - // to validate, we'll validate that the codes actually exist - if (bindingsOk) { - for (Coding nextCoding : cc.getCoding()) { - if (isNotBlank(nextCoding.getCode()) && isNotBlank(nextCoding.getSystem()) && context.supportsSystem(nextCoding.getSystem())) { - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang).noCheckValueSetMembership(), nextCoding, valueset); - if (vr.getSeverity() != null) { - if (vr.getSeverity() == IssueSeverity.INFORMATION) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); - } else if (vr.getSeverity() == IssueSeverity.WARNING) { - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); - } else { - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); - } - } - } - } - } - txTime = txTime + (System.nanoTime() - t); - } - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept"); } - } - } else if (binding.hasValueSet()) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); - } else if (!noBindingMsgSuppressed) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); - } - } - } - return res; - } - - private boolean checkTerminologyCodeableConcept(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, NodeStack stack, StructureDefinition logical) { - boolean res = true; - if (!noTerminologyChecks && theElementCntext != null && theElementCntext.hasBinding()) { - ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) { - if (binding.hasValueSet()) { - ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { - try { - CodeableConcept cc = convertToCodeableConcept(element, logical); - if (!cc.hasCoding()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code must be provided from the value set " + describeReference(ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + " (max value set " + valueset.getUrl()+")"); - else - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+")"); - } - } else { - long t = System.nanoTime(); - - // Check whether the codes are appropriate for the type of binding we have - boolean bindingsOk = true; - if (binding.getStrength() != BindingStrength.EXAMPLE) { - boolean atLeastOneSystemIsSupported = false; - for (Coding nextCoding : cc.getCoding()) { - String nextSystem = nextCoding.getSystem(); - if (isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { - atLeastOneSystemIsSupported = true; - break; - } - } - - if (!atLeastOneSystemIsSupported && binding.getStrength() == BindingStrength.EXAMPLE) { - // ignore this since we can't validate but it doesn't matter.. - } else { - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), cc, valueset); // we're going to validate the codings directly - if (!vr.isOk()) { - bindingsOk = false; - if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code from this value set is required (class = "+vr.getErrorClass().toString()+")"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); - else if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code should come from this value set unless it has no suitable code (class = "+vr.getErrorClass().toString()+")"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code is recommended to come from this value set (class = "+vr.getErrorClass().toString()+")"); - } - } - } else { - if (binding.getStrength() == BindingStrength.REQUIRED) - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()+", and a code from this value set is required) (codes = "+ccSummary(cc)+")"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); - if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code) (codes = "+ccSummary(cc)+")"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set) (codes = "+ccSummary(cc)+")"); - } - } - } - } else if (vr.getMessage()!=null) { - res = false; - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); - } else { - res = false; - } - } - // Then, for any codes that are in code systems we are able - // to validate, we'll validate that the codes actually exist - if (bindingsOk) { - for (Coding nextCoding : cc.getCoding()) { - String nextCode = nextCoding.getCode(); - String nextSystem = nextCoding.getSystem(); - if (isNotBlank(nextCode) && isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), nextSystem, nextCode, null); - if (!vr.isOk()) { - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Code {0} is not a valid code in code system {1}", nextCode, nextSystem); - } - } - } - } - txTime = txTime + (System.nanoTime() - t); - } - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept"); - } - // special case: if the logical model has both CodeableConcept and Coding mappings, we'll also check the first coding. - if (getMapping("http://hl7.org/fhir/terminology-pattern", logical, logical.getSnapshot().getElementFirstRep()).contains("Coding")) { - checkTerminologyCoding(errors, path, element, profile, theElementCntext, true, true, stack, logical); - } - } - } else if (binding.hasValueSet()) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); - } else if (!noBindingMsgSuppressed) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); - } - } - } - return res; - } - - private void checkTerminologyCoding(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept, boolean checkDisplay, NodeStack stack, StructureDefinition logical) { - Coding c = convertToCoding(element, logical); - String code = c.getCode(); - String system = c.getSystem(); - String display = c.getDisplay(); - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Coding.system must be an absolute reference, not a local reference"); - - if (system != null && code != null && !noTerminologyChecks) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !isValueSet(system), "The Coding references a value set, not a code system (\""+system+"\")"); - try { - if (checkCode(errors, element, path, code, system, display, checkDisplay, stack)) - if (theElementCntext != null && theElementCntext.hasBinding()) { - ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) { - if (binding.hasValueSet()) { - ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { - try { - long t = System.nanoTime(); - ValidationResult vr = null; - if (binding.getStrength() != BindingStrength.EXAMPLE) { - vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); - } - txTime = txTime + (System.nanoTime() - t); - if (vr != null && !vr.isOk()) { - if (vr.IsNoService()) - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided could not be validated in the absence of a terminology server"); - else if (vr.getErrorClass() != null && !vr.getErrorClass().isInfrastructure()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code from this value set is required"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); - else if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set"); - } - } - } else if (binding.getStrength() == BindingStrength.REQUIRED) - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is required from this value set"+(vr.getMessage() != null ? " (error message = "+vr.getMessage()+")" : "")); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); - else - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code"+(vr.getMessage() != null ? " (error message = "+vr.getMessage()+")" : "")); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set"+(vr.getMessage() != null ? " (error message = "+vr.getMessage()+")" : "")); - } - } - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating Coding"); - } - } - } else if (binding.hasValueSet()) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); - } else if (!inCodeableConcept && !noBindingMsgSuppressed) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); - } - } - } - } catch (Exception e) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating Coding: " + e.toString()); - } - } - } - - private CodeableConcept convertToCodeableConcept(Element element, StructureDefinition logical) { - CodeableConcept res = new CodeableConcept(); - for (ElementDefinition ed : logical.getSnapshot().getElement()) { - if (Utilities.charCount(ed.getPath(), '.') == 1) { - List maps = getMapping("http://hl7.org/fhir/terminology-pattern", logical, ed); - for (String m : maps) { - String name = tail(ed.getPath()); - List list = new ArrayList<>(); - element.getNamedChildren(name, list); - if (!list.isEmpty()) { - if ("Coding.code".equals(m)) { - res.getCodingFirstRep().setCode(list.get(0).primitiveValue()); - } else if ("Coding.system[fmt:OID]".equals(m)) { - String oid = list.get(0).primitiveValue(); - String url = context.oid2Uri(oid); - if (url != null) { - res.getCodingFirstRep().setSystem(url); - } else { - res.getCodingFirstRep().setSystem("urn:oid:"+oid); - } - } else if ("Coding.version".equals(m)) { - res.getCodingFirstRep().setVersion(list.get(0).primitiveValue()); - } else if ("Coding.display".equals(m)) { - res.getCodingFirstRep().setDisplay(list.get(0).primitiveValue()); - } else if ("CodeableConcept.text".equals(m)) { - res.setText(list.get(0).primitiveValue()); - } else if ("CodeableConcept.coding".equals(m)) { - StructureDefinition c = context.fetchTypeDefinition(ed.getTypeFirstRep().getCode()); - for (Element e : list) { - res.addCoding(convertToCoding(e, c)); - } - } - } - } - } - } - return res; - } - - private Coding convertToCoding(Element element, StructureDefinition logical) { - Coding res = new Coding(); - for (ElementDefinition ed : logical.getSnapshot().getElement()) { - if (Utilities.charCount(ed.getPath(), '.') == 1) { - List maps = getMapping("http://hl7.org/fhir/terminology-pattern", logical, ed); - for (String m : maps) { - String name = tail(ed.getPath()); - List list = new ArrayList<>(); - element.getNamedChildren(name, list); - if (!list.isEmpty()) { - if ("Coding.code".equals(m)) { - res.setCode(list.get(0).primitiveValue()); - } else if ("Coding.system[fmt:OID]".equals(m)) { - String oid = list.get(0).primitiveValue(); - String url = context.oid2Uri(oid); - if (url != null) { - res.setSystem(url); - } else { - res.setSystem("urn:oid:"+oid); - } - } else if ("Coding.version".equals(m)) { - res.setVersion(list.get(0).primitiveValue()); - } else if ("Coding.display".equals(m)) { - res.setDisplay(list.get(0).primitiveValue()); - } - } - } - } - } - return res; - } - - private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, CodeableConcept cc, NodeStack stack) { - // TODO Auto-generated method stub - ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { - try { - long t = System.nanoTime(); - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), cc, valueset); - txTime = txTime + (System.nanoTime() - t); - if (!vr.isOk()) { - if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided could be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+"), (error = "+vr.getMessage()+")"); - else - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+", and a code from this value set is required) (codes = "+ccSummary(cc)+")"); - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept using maxValueSet"); - } - } - } - - private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, Coding c, NodeStack stack) { - // TODO Auto-generated method stub - ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { - try { - long t = System.nanoTime(); - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); - txTime = txTime + (System.nanoTime() - t); - if (!vr.isOk()) { - if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided could not be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+"), (error = "+vr.getMessage()+")"); - else - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided is not in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+", and a code from this value set is required) (code = "+c.getSystem()+"#"+c.getCode()+")"); - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept using maxValueSet"); - } - } - } - - private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, String value, NodeStack stack) { - // TODO Auto-generated method stub - ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { - try { - long t = System.nanoTime(); - ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), value, valueset); - txTime = txTime + (System.nanoTime() - t); - if (!vr.isOk()) { - if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided could not be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+"), (error = "+vr.getMessage()+")"); - else - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided is not in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl()+"), and a code from this value set is required) (code = "+value+"), (error = "+vr.getMessage()+")"); - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating CodeableConcept using maxValueSet"); - } - } - } - - private String ccSummary(CodeableConcept cc) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (Coding c : cc.getCoding()) - b.append(c.getSystem()+"#"+c.getCode()); - return b.toString(); - } - - private void checkCoding(List errors, String path, Element focus, Coding fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); - checkFixedValue(errors, path + ".version", focus.getNamedChild("version"), fixed.getVersionElement(), fixedSource, "version", focus, pattern); - checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), fixedSource, "code", focus, pattern); - checkFixedValue(errors, path + ".display", focus.getNamedChild("display"), fixed.getDisplayElement(), fixedSource, "display", focus, pattern); - checkFixedValue(errors, path + ".userSelected", focus.getNamedChild("userSelected"), fixed.getUserSelectedElement(), fixedSource, "userSelected", focus, pattern); - } - - private void checkCoding(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept, boolean checkDisplay, NodeStack stack) { - String code = element.getNamedChildValue("code"); - String system = element.getNamedChildValue("system"); - String display = element.getNamedChildValue("display"); - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Coding.system must be an absolute reference, not a local reference"); - - if (system != null && code != null && !noTerminologyChecks) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !isValueSet(system), "The Coding references a value set, not a code system (\""+system+"\")"); - try { - if (checkCode(errors, element, path, code, system, display, checkDisplay, stack)) - if (theElementCntext != null && theElementCntext.hasBinding()) { - ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) { - if (binding.hasValueSet()) { - ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { - try { - Coding c = ObjectConverter.readAsCoding(element); - long t = System.nanoTime(); - ValidationResult vr = null; - if (binding.getStrength() != BindingStrength.EXAMPLE) { - vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); - } - txTime = txTime + (System.nanoTime() - t); - if (vr != null && !vr.isOk()) { - if (vr.IsNoService()) - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided could not be validated in the absence of a terminology server"); - else if (vr.getErrorClass() != null && !vr.getErrorClass().isInfrastructure()) { - if (binding.getStrength() == BindingStrength.REQUIRED) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code from this value set is required"); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); - else if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code"); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set"); - } - } - } else if (binding.getStrength() == BindingStrength.REQUIRED) - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is required from this value set. "+getErrorMessage(vr.getMessage())); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); - else - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code. "+getErrorMessage(vr.getMessage())); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set. "+getErrorMessage(vr.getMessage())); - } - } - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating Coding"); - } - } - } else if (binding.hasValueSet()) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); - } else if (!inCodeableConcept && !noBindingMsgSuppressed) { - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); - } - } - } - } catch (Exception e) { - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error "+e.getMessage()+" validating Coding: " + e.toString()); - } - } - } - - private boolean isValueSet(String url) { - try { - ValueSet vs = context.fetchResourceWithException(ValueSet.class, url); - return vs != null; - } catch (Exception e) { - return false; - } - } - - private void checkContactPoint(List errors, String path, Element focus, ContactPoint fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); - checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); - checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); - checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); - - } - - private StructureDefinition checkExtension(ValidatorHostContext hostContext, List errors, String path, Element resource, Element container, Element element, ElementDefinition def, StructureDefinition profile, NodeStack stack, NodeStack containerStack, String extensionUrl) throws FHIRException { - String url = element.getNamedChildValue("url"); - boolean isModifier = element.getName().equals("modifierExtension"); - - long t = System.nanoTime(); - StructureDefinition ex = Utilities.isAbsoluteUrl(url) ? context.fetchResource(StructureDefinition.class, url) : null; - sdTime = sdTime + (System.nanoTime() - t); - if (ex == null) { - if (xverManager == null) { - xverManager = new XVerExtensionManager(context); - } - if (xverManager.matchingUrl(url)) { - switch (xverManager.status(url)) { - case BadVersion: - rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (invalidVersion \""+xverManager.getVersion(url)+"\")"); - break; - case Unknown: - rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (unknown Element id \""+xverManager.getElementId(url)+"\")"); - break; - case Invalid: - rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (Element id \""+xverManager.getElementId(url)+"\" is valid, but cannot be used in a cross-version paradigm because there has been no changes across the relevant versions)"); - break; - case Valid: - ex = xverManager.makeDefinition(url); - context.generateSnapshot(ex); - context.cacheResource(ex); - break; - default: - rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' evaluation state illegal"); - break; - } - } else if (extensionUrl != null && !isAbsolute(url)) { - if (extensionUrl.equals(profile.getUrl())) { - rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", hasExtensionSlice(profile, url), "Sub-extension url '" + url + "' is not defined by the Extension "+profile.getUrl()); - } - } else if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowUnknownExtension(url), "The extension " + url + " is unknown, and not allowed here")) { - hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, isKnownExtension(url), "Unknown extension " + url); - } - } - if (ex != null) { - trackUsage(ex, hostContext, element); - if (def.getIsModifier()) { - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(), - "Extension modifier mismatch: the extension element is labelled as a modifier, but the underlying extension is not"); - } else { - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(), - "Extension modifier mismatch: the extension element is not labelled as a modifier, but the underlying extension is"); - } - // two questions - // 1. can this extension be used here? - checkExtensionContext(errors, resource, container, ex, containerStack, hostContext); - - if (isModifier) - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(), - "The Extension '" + url + "' must be used as a modifierExtension"); - else - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(), - "The Extension '" + url + "' must not be used as an extension (it's a modifierExtension)"); - - // check the type of the extension: - Set allowedTypes = listExtensionTypes(ex); - String actualType = getExtensionType(element); - if (actualType == null) - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.isEmpty(), "The Extension '" + url + "' definition is for a simple extension, so it must contain a value, not extensions"); - else - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.contains(actualType), "The Extension '" + url + "' definition allows for the types "+allowedTypes.toString()+" but found type "+actualType); - - // 3. is the content of the extension valid? - validateElement(hostContext, errors, ex, ex.getSnapshot().getElement().get(0), null, null, resource, element, "Extension", stack, false, true, url); - - } - return ex; - } - - private boolean hasExtensionSlice(StructureDefinition profile, String sliceName) { - for (ElementDefinition ed : profile.getSnapshot().getElement()) { - if (ed.getPath().equals("Extension.extension.url") && ed.hasFixed() && sliceName.equals(ed.getFixed().primitiveValue())) { - return true; - } - } - return false; - } - - private String getExtensionType(Element element) { - for (Element e : element.getChildren()) { - if (e.getName().startsWith("value")) { - String tn = e.getName().substring(5); - String ltn = Utilities.uncapitalize(tn); - if (isPrimitiveType(ltn)) - return ltn; - else - return tn; - } - } - return null; - } - - private Set listExtensionTypes(StructureDefinition ex) { - ElementDefinition vd = null; - for (ElementDefinition ed : ex.getSnapshot().getElement()) { - if (ed.getPath().startsWith("Extension.value")) { - vd = ed; - break; - } - } - Set res = new HashSet(); - if (vd != null && !"0".equals(vd.getMax())) { - for (TypeRefComponent tr : vd.getType()) { - res.add(tr.getWorkingCode()); - } - } - return res; - } - - private boolean checkExtensionContext(List errors, Element resource, Element container, StructureDefinition definition, NodeStack stack, ValidatorHostContext hostContext) { - String extUrl = definition.getUrl(); - boolean ok = false; - CommaSeparatedStringBuilder contexts = new CommaSeparatedStringBuilder(); - List plist = new ArrayList<>(); - plist.add(stripIndexes(stack.getLiteralPath())); - for (String s : stack.getLogicalPaths()) { - String p = stripIndexes(s); - // all extensions are always allowed in ElementDefinition.example.value, and in fixed and pattern values. TODO: determine the logical paths from the path stated in the element definition.... - if (Utilities.existsInList(p, "ElementDefinition.example.value", "ElementDefinition.pattern", "ElementDefinition.fixed")) { - return true; - } - plist.add(p); - - } - - for (StructureDefinitionContextComponent ctxt : fixContexts(extUrl, definition.getContext())) { - if (ok) { break; } - if (ctxt.getType() == ExtensionContextType.ELEMENT) { - String en = ctxt.getExpression(); - contexts.append("e:"+en); - if ("Element".equals(en)) { - ok = true; - } else if (en.equals("Resource") && container.isResource()) { - ok = true; - } - for (String p : plist) { - if (ok) {break; } - if (p.equals(en)) { - ok = true; - } else { - String pn = p; - String pt = ""; - if (p.contains(".")) { - pn = p.substring(0, p.indexOf(".")); - pt = p.substring(p.indexOf(".")); - } - StructureDefinition sd = context.fetchTypeDefinition(pn); - while (sd != null) { - if ((sd.getType()+pt).equals(en)) { - ok = true; - break; - } - if (sd.getBaseDefinition() != null) { - sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition()); - } else { - sd = null; - } - } - } - } - } else if (ctxt.getType() == ExtensionContextType.EXTENSION) { - contexts.append("x:"+ctxt.getExpression()); - NodeStack estack = stack.parent; - if (estack != null && estack.getElement().fhirType().equals("Extension")) { - String ext = estack.element.getNamedChildValue("url"); - if (ctxt.getExpression().equals(ext)) { - ok = true; - } - } - } else if (ctxt.getType() == ExtensionContextType.FHIRPATH) { - contexts.append("p:"+ctxt.getExpression()); - // The context is all elements that match the FHIRPath query found in the expression. - List res = fpe.evaluate(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(ctxt.getExpression())); - if (res.contains(container)) { - ok = true; - } - } else { - throw new Error("Unrecognised extension context "+ctxt.getTypeElement().asStringValue()); - } - } - if (!ok) { - rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, "The extension " + extUrl + " is not allowed to be used at this point (allowed = "+ contexts.toString() + "; this element is ["+plist.toString()+")"); - return false; - } else { - if (definition.hasContextInvariant()) { - for (StringType s : definition.getContextInvariant()) { - if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) { - rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, - "The extension " + extUrl + " is not allowed to be used at this point (based on context invariant '"+s.getValue()+"')"); - return false; - } - } - } - return true; - } - } - - private List fixContexts(String extUrl, List list) { - List res = new ArrayList<>(); - for (StructureDefinitionContextComponent ctxt : list) { - res.add(ctxt.copy()); - } - if ("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type".equals(extUrl)) { - list.get(0).setExpression("ElementDefinition.type"); - } - if ("http://hl7.org/fhir/StructureDefinition/regex".equals(extUrl)) { - list.get(1).setExpression("ElementDefinition.type"); - } - return list; - } - - private String stripIndexes(String path) { - boolean skip = false; - StringBuilder b = new StringBuilder(); - for (char c : path.toCharArray()) { - if (skip) { - if (c == ']') { - skip = false; - } - } else if (c == '[') { - skip = true; - } else { - b.append(c); - } - } - return b.toString(); - } - - private void checkFixedValue(List errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent) { - checkFixedValue(errors, path, focus, fixed, fixedSource, propName, parent, false); - } - - @SuppressWarnings("rawtypes") - private void checkFixedValue(List errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent, boolean pattern) { - if ((fixed == null || fixed.isEmpty()) && focus == null) { - ; // this is all good - } else if ((fixed == null || fixed.isEmpty()) && focus != null) { - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, pattern, "The element " + focus.getName()+" is present in the instance but not allowed in the applicable "+(pattern ? "pattern" : "fixed value")+" specified in profile"); - } else if (fixed != null && !fixed.isEmpty() && focus == null) { - rule(errors, IssueType.VALUE, parent == null ? -1 : parent.line(), parent == null ? -1 : parent.col(), path, false, "Missing element '" + propName+"' - required by fixed value assigned in profile "+fixedSource); - } else { - String value = focus.primitiveValue(); - if (fixed instanceof org.hl7.fhir.r5.model.BooleanType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.BooleanType) fixed).asStringValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.BooleanType) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.IntegerType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.IntegerType) fixed).asStringValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.IntegerType) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.DecimalType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DecimalType) fixed).asStringValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DecimalType) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.Base64BinaryType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.Base64BinaryType) fixed).asStringValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.Base64BinaryType) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.InstantType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.InstantType) fixed).getValue().toString(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.InstantType) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.CodeType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.CodeType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.CodeType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.Enumeration) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.Enumeration) fixed).asStringValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.Enumeration) fixed).asStringValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.StringType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.StringType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.StringType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.UriType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.UriType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.UriType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.DateType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DateType) fixed).getValue().toString(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DateType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.DateTimeType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DateTimeType) fixed).getValue().toString(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DateTimeType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.OidType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.OidType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.OidType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.UuidType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.UuidType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.UuidType) fixed).getValue() + "'"); - else if (fixed instanceof org.hl7.fhir.r5.model.IdType) - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.IdType) fixed).getValue(), value), - "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.IdType) fixed).getValue() + "'"); - else if (fixed instanceof Quantity) - checkQuantity(errors, path, focus, (Quantity) fixed, fixedSource, pattern); - else if (fixed instanceof Address) - checkAddress(errors, path, focus, (Address) fixed, fixedSource, pattern); - else if (fixed instanceof ContactPoint) - checkContactPoint(errors, path, focus, (ContactPoint) fixed, fixedSource, pattern); - else if (fixed instanceof Attachment) - checkAttachment(errors, path, focus, (Attachment) fixed, fixedSource, pattern); - else if (fixed instanceof Identifier) - checkIdentifier(errors, path, focus, (Identifier) fixed, fixedSource, pattern); - else if (fixed instanceof Coding) - checkCoding(errors, path, focus, (Coding) fixed, fixedSource, pattern); - else if (fixed instanceof HumanName) - checkHumanName(errors, path, focus, (HumanName) fixed, fixedSource, pattern); - else if (fixed instanceof CodeableConcept) - checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed, fixedSource, pattern); - else if (fixed instanceof Timing) - checkTiming(errors, path, focus, (Timing) fixed, fixedSource, pattern); - else if (fixed instanceof Period) - checkPeriod(errors, path, focus, (Period) fixed, fixedSource, pattern); - else if (fixed instanceof Range) - checkRange(errors, path, focus, (Range) fixed, fixedSource, pattern); - else if (fixed instanceof Ratio) - checkRatio(errors, path, focus, (Ratio) fixed, fixedSource, pattern); - else if (fixed instanceof SampledData) - checkSampledData(errors, path, focus, (SampledData) fixed, fixedSource, pattern); - - else - rule(errors, IssueType.EXCEPTION, focus.line(), focus.col(), path, false, "Unhandled fixed value type " + fixed.getClass().getName()); - List extensions = new ArrayList(); - focus.getNamedChildren("extension", extensions); - if (fixed.getExtension().size() == 0) { - rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == 0, "No extensions allowed, as the specified fixed value doesn't contain any extensions"); - } else if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == fixed.getExtension().size(), - "Extensions count mismatch: expected " + Integer.toString(fixed.getExtension().size()) + " but found " + Integer.toString(extensions.size()))) { - for (Extension e : fixed.getExtension()) { - Element ex = getExtensionByUrl(extensions, e.getUrl()); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, ex != null, "Extension count mismatch: unable to find extension: " + e.getUrl())) { - checkFixedValue(errors, path, ex.getNamedChild("extension").getNamedChild("value"), e.getValue(), fixedSource, "extension.value", ex.getNamedChild("extension")); - } - } - } - } - } - - private void checkHumanName(List errors, String path, Element focus, HumanName fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); - checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); - checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); - - List parts = new ArrayList(); - focus.getNamedChildren("family", parts); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() > 0 == fixed.hasFamily(), - "Expected " + (fixed.hasFamily() ? "1" : "0") + " but found " + Integer.toString(parts.size()) + " family elements")) { - for (int i = 0; i < parts.size(); i++) - checkFixedValue(errors, path + ".family", parts.get(i), fixed.getFamilyElement(), fixedSource, "family", focus, pattern); - } - focus.getNamedChildren("given", parts); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getGiven().size(), - "Expected " + Integer.toString(fixed.getGiven().size()) + " but found " + Integer.toString(parts.size()) + " given elements")) { - for (int i = 0; i < parts.size(); i++) - checkFixedValue(errors, path + ".given", parts.get(i), fixed.getGiven().get(i), fixedSource, "given", focus, pattern); - } - focus.getNamedChildren("prefix", parts); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getPrefix().size(), - "Expected " + Integer.toString(fixed.getPrefix().size()) + " but found " + Integer.toString(parts.size()) + " prefix elements")) { - for (int i = 0; i < parts.size(); i++) - checkFixedValue(errors, path + ".prefix", parts.get(i), fixed.getPrefix().get(i), fixedSource, "prefix", focus, pattern); - } - focus.getNamedChildren("suffix", parts); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getSuffix().size(), - "Expected " + Integer.toString(fixed.getSuffix().size()) + " but found " + Integer.toString(parts.size()) + " suffix elements")) { - for (int i = 0; i < parts.size(); i++) - checkFixedValue(errors, path + ".suffix", parts.get(i), fixed.getSuffix().get(i), fixedSource, "suffix", focus, pattern); - } - } - - private void checkIdentifier(List errors, String path, Element element, ElementDefinition context) { - String system = element.getNamedChildValue("system"); - rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Identifier.system must be an absolute reference, not a local reference"); - } - - private void checkIdentifier(List errors, String path, Element focus, Identifier fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); - checkFixedValue(errors, path + ".type", focus.getNamedChild("type"), fixed.getType(), fixedSource, "type", focus, pattern); - checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); - checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); - checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); - checkFixedValue(errors, path + ".assigner", focus.getNamedChild("assigner"), fixed.getAssigner(), fixedSource, "assigner", focus, pattern); - } - - private void checkPeriod(List errors, String path, Element focus, Period fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".start", focus.getNamedChild("start"), fixed.getStartElement(), fixedSource, "start", focus, pattern); - checkFixedValue(errors, path + ".end", focus.getNamedChild("end"), fixed.getEndElement(), fixedSource, "end", focus, pattern); - } - - private void checkPrimitive(Object appContext, List errors, String path, String type, ElementDefinition context, Element e, StructureDefinition profile, NodeStack node) throws FHIRException { - if (isBlank(e.primitiveValue())) { - if (e.primitiveValue() == null) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types must have a value or must have child extensions"); - else if (e.primitiveValue().length() == 0) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types must have a value that is not empty"); - else if (StringUtils.isWhitespace(e.primitiveValue())) - warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types should not only be whitespace"); - return; - } - String regex = context.getExtensionString(ToolingExtensions.EXT_REGEX); - if (regex!=null) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().matches(regex), "Element value '" + e.primitiveValue() + "' does not meet regex '" + regex + "'"); - - if (type.equals("boolean")) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, "true".equals(e.primitiveValue()) || "false".equals(e.primitiveValue()), "boolean values must be 'true' or 'false'"); - } - if (type.equals("uri") || type.equals("oid") || type.equals("uuid") || type.equals("url") || type.equals("canonical")) { - String url = e.primitiveValue(); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("oid:"), "URI values cannot start with oid:"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("uuid:"), "URI values cannot start with uuid:"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.equals(url.trim().replace(" ", "")) - // work around an old invalid example in a core package - || "http://www.acme.com/identifiers/patient or urn:ietf:rfc:3986 if the Identifier.value itself is a full uri".equals(url), "URI values cannot have whitespace('"+url+"')"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || url.length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); - - if (type.equals("oid")) { - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.startsWith("urn:oid:"), "OIDs must start with urn:oid:")) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isOid(url.substring(8)), "OIDs must be valid"); - } - if (type.equals("uuid")) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.startsWith("urn:uuid:"), "UUIDs must start with urn:uuid:"); - try { - UUID.fromString(url.substring(8)); - } catch (Exception ex) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "UUIDs must be valid ("+ex.getMessage()+")"); - } - } - - // now, do we check the URI target? - if (fetcher != null) { - boolean found; - try { - found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || (url.startsWith("http://hl7.org/fhir/tools")) || fetcher.resolveURL(appContext, path, url); - } catch (IOException e1) { - found = false; - } - rule(errors, IssueType.INVALID, e.line(), e.col(), path, found, "URL value '"+url+"' does not resolve"); - } - } - if (type.equals("id")) { - // work around an old issue with ElementDefinition.id - if (!context.getPath().equals("ElementDefinition.id") && !VersionUtilities.versionsCompatible("1.4", this.context.getVersion())) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.isValidId(e.primitiveValue()), "id value '"+e.primitiveValue()+"' is not valid"); - } - } - if (type.equalsIgnoreCase("string") && e.hasPrimitiveValue()) { - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().length() > 0, "@value cannot be empty")) { - warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().trim().equals(e.primitiveValue()), "value should not start or finish with whitespace"); - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().length() <= 1048576, "value is longer than permitted maximum length of 1 MB (1048576 bytes)")) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); - } - } - } - if (type.equals("dateTime")) { - warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, - e.primitiveValue() - .matches("([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)(\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))?)?)?)?"), - "Not a valid date time"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !hasTime(e.primitiveValue()) || hasTimeZone(e.primitiveValue()), "if a date has a time, it must have a timezone"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); - try { - DateTimeType dt = new DateTimeType(e.primitiveValue()); - } catch (Exception ex) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid date/time ("+ex.getMessage()+")"); - } - } - if (type.equals("time")) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, - e.primitiveValue() - .matches("([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)"), - "Not a valid time"); - try { - TimeType dt = new TimeType(e.primitiveValue()); - } catch (Exception ex) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid time ("+ex.getMessage()+")"); - } - } - if (type.equals("date")) { - warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().matches("([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1]))?)?"), - "Not a valid date"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum value of " + context.getMaxLength()); - try { - DateType dt = new DateType(e.primitiveValue()); - } catch (Exception ex) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid date ("+ex.getMessage()+")"); - } - } - if (type.equals("base64Binary")) { - String encoded = e.primitiveValue(); - if (isNotBlank(encoded)) { - /* - * Technically this is not bulletproof as some invalid base64 won't be caught, - * but I think it's good enough. The original code used Java8 Base64 decoder - * but I've replaced it with a regex for 2 reasons: - * 1. This code will run on any version of Java - * 2. This code doesn't actually decode, which is much easier on memory use for big payloads - */ - int charCount = 0; - for (int i = 0; i < encoded.length(); i++) { - char nextChar = encoded.charAt(i); - if (Character.isWhitespace(nextChar)) { - continue; - } - if (Character.isLetterOrDigit(nextChar)) { - charCount++; - } - if (nextChar == '/' || nextChar == '=' || nextChar == '+') { - charCount++; - } - } - - if (charCount > 0 && charCount % 4 != 0) { - String value = encoded.length() < 100 ? encoded : "(snip)"; - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "The value \"{0}\" is not a valid Base64 value", value); - } - } - } - if (type.equals("integer") || type.equals("unsignedInt") || type.equals("positiveInt")) { - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isInteger(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is not a valid integer")) { - Integer v = new Integer(e.getValue()).intValue(); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxValueIntegerType() || !context.getMaxValueIntegerType().hasValue() || (context.getMaxValueIntegerType().getValue() >= v), "value is greater than permitted maximum value of " + (context.hasMaxValueIntegerType() ? context.getMaxValueIntegerType() : "")); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMinValueIntegerType() || !context.getMinValueIntegerType().hasValue() || (context.getMinValueIntegerType().getValue() <= v), "value is less than permitted minimum value of " + (context.hasMinValueIntegerType() ? context.getMinValueIntegerType() : "")); - if (type.equals("unsignedInt")) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, v >= 0, "value is less than permitted minimum value of 0"); - if (type.equals("positiveInt")) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, v > 0, "value is less than permitted minimum value of 1"); - } - } - if (type.equals("integer64")) { - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isLong(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is not a valid integer64")) { - Long v = new Long(e.getValue()).longValue(); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxValueInteger64Type() || !context.getMaxValueInteger64Type().hasValue() || (context.getMaxValueInteger64Type().getValue() >= v), "value is greater than permitted maximum value of " + (context.hasMaxValueInteger64Type() ? context.getMaxValueInteger64Type() : "")); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMinValueInteger64Type() || !context.getMinValueInteger64Type().hasValue() || (context.getMinValueInteger64Type().getValue() <= v), "value is less than permitted minimum value of " + (context.hasMinValueInteger64Type() ? context.getMinValueInteger64Type() : "")); - if (type.equals("unsignedInt")) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, v >= 0, "value is less than permitted minimum value of 0"); - if (type.equals("positiveInt")) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, v > 0, "value is less than permitted minimum value of 1"); - } - } - if (type.equals("decimal")) { - if (e.primitiveValue() != null) { - DecimalStatus ds = Utilities.checkDecimal(e.primitiveValue(), true, false); - if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, ds == DecimalStatus.OK || ds == DecimalStatus.RANGE, "The value '" + e.primitiveValue() + "' is not a valid decimal")) - warning(errors, IssueType.VALUE, e.line(), e.col(), path, ds != DecimalStatus.RANGE, "The value '" + e.primitiveValue() + "' is outside the range of commonly/reasonably supported decimals"); - } - } - if (type.equals("instant")) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, - e.primitiveValue().matches("-?[0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[1-2][0-9]|3[0-1])T([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)(\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))"), - "The instant '" + e.primitiveValue() + "' is not valid (by regex)"); - warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); - try { - InstantType dt = new InstantType(e.primitiveValue()); - } catch (Exception ex) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid instant ("+ex.getMessage()+")"); - } - } - - if (type.equals("code") && e.primitiveValue() != null) { - // Technically, a code is restricted to string which has at least one character and no leading or trailing whitespace, and where there is no whitespace - // other than single spaces in the contents - rule(errors, IssueType.INVALID, e.line(), e.col(), path, passesCodeWhitespaceRules(e.primitiveValue()), "The code '" + e.primitiveValue() + "' is not valid (whitespace rules)"); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength()==0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); - } - - if (context.hasBinding() && e.primitiveValue() != null) { - checkPrimitiveBinding(errors, path, type, context, e, profile, node); - } - - if (type.equals("xhtml")) { - XhtmlNode xhtml = e.getXhtml(); - if (xhtml != null) { // if it is null, this is an error already noted in the parsers - // check that the namespace is there and correct. - String ns = xhtml.getNsDecl(); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('"+ns+"', should be '"+FormatUtilities.XHTML_NS+"')"); - // check that inner namespaces are all correct - checkInnerNS(errors, e, path, xhtml.getChildNodes()); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, "div".equals(xhtml.getName()), "Wrong name on the XHTML ('"+ns+"') - must start with div"); - // check that no illegal elements and attributes have been used - checkInnerNames(errors, e, path, xhtml.getChildNodes()); - } - } - - if (context.hasFixed()) { - checkFixedValue(errors,path,e, context.getFixed(), profile.getUrl(), context.getSliceName(), null, false); - } - if (context.hasPattern()) { - checkFixedValue(errors, path, e, context.getPattern(), profile.getUrl(), context.getSliceName(), null, true); - } - - // for nothing to check - } - - private boolean isDefinitionURL(String url) { - return Utilities.existsInList(url, "http://hl7.org/fhirpath/System.Boolean", "http://hl7.org/fhirpath/System.String", "http://hl7.org/fhirpath/System.Integer", - "http://hl7.org/fhirpath/System.Decimal", "http://hl7.org/fhirpath/System.Date", "http://hl7.org/fhirpath/System.Time", "http://hl7.org/fhirpath/System.DateTime", "http://hl7.org/fhirpath/System.Quantity"); - } - - private void checkInnerNames(List errors, Element e, String path, List list) { - for (XhtmlNode node : list) { - if (node.getNodeType() == NodeType.Element) { - rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.existsInList(node.getName(), - "p", "br", "div", "h1", "h2", "h3", "h4", "h5", "h6", "a", "span", "b", "em", "i", "strong", - "small", "big", "tt", "small", "dfn", "q", "var", "abbr", "acronym", "cite", "blockquote", "hr", "address", "bdo", "kbd", "q", "sub", "sup", - "ul", "ol", "li", "dl", "dt", "dd", "pre", "table", "caption", "colgroup", "col", "thead", "tr", "tfoot", "tbody", "th", "td", - "code", "samp", "img", "map", "area" - - ), "Illegal element name in the XHTML ('"+node.getName()+"')"); - for (String an : node.getAttributes().keySet()) { - boolean ok = an.startsWith("xmlns") || Utilities.existsInList(an, - "title", "style", "class", "id", "lang", "xml:lang", "dir", "accesskey", "tabindex", - // tables - "span", "width", "align", "valign", "char", "charoff", "abbr", "axis", "headers", "scope", "rowspan", "colspan") || - - Utilities.existsInList(node.getName()+"."+an, "a.href", "a.name", "img.src", "img.border", "div.xmlns", "blockquote.cite", "q.cite", - "a.charset", "a.type", "a.name", "a.href", "a.hreflang", "a.rel", "a.rev", "a.shape", "a.coords", "img.src", - "img.alt", "img.longdesc", "img.height", "img.width", "img.usemap", "img.ismap", "map.name", "area.shape", - "area.coords", "area.href", "area.nohref", "area.alt", "table.summary", "table.width", "table.border", - "table.frame", "table.rules", "table.cellspacing", "table.cellpadding", "pre.space", "td.nowrap" - ); - if (!ok) - rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Illegal attribute name in the XHTML ('"+an+"' on '"+node.getName()+"')"); - } - checkInnerNames(errors, e, path, node.getChildNodes()); - } - } - } - - private void checkInnerNS(List errors, Element e, String path, List list) { - for (XhtmlNode node : list) { - if (node.getNodeType() == NodeType.Element) { - String ns = node.getNsDecl(); - rule(errors, IssueType.INVALID, e.line(), e.col(), path, ns == null || FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('"+ns+"', should be '"+FormatUtilities.XHTML_NS+"')"); - checkInnerNS(errors, e, path, node.getChildNodes()); - } - } - } - - private void checkPrimitiveBinding(List errors, String path, String type, ElementDefinition elementContext, Element element, StructureDefinition profile, NodeStack stack) { - // We ignore bindings that aren't on string, uri or code - if (!element.hasPrimitiveValue() || !("code".equals(type) || "string".equals(type) || "uri".equals(type) || "url".equals(type) || "canonical".equals(type))) { - return; - } - if (noTerminologyChecks) - return; - - String value = element.primitiveValue(); - // System.out.println("check "+value+" in "+path); - - // firstly, resolve the value set - ElementDefinitionBindingComponent binding = elementContext.getBinding(); - if (binding.hasValueSet()) { - ValueSet vs = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); - if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "ValueSet {0} not found by validator", describeReference(binding.getValueSet()))) { - long t = System.nanoTime(); - ValidationResult vr = null; - if (binding.getStrength() != BindingStrength.EXAMPLE) { - vr = context.validateCode(new ValidationOptions(stack.workingLang), value, vs); - } - txTime = txTime + (System.nanoTime() - t); - if (vr != null && !vr.isOk()) { - if (vr.IsNoService()) - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') could not be validated in the absence of a terminology server"); - else if (binding.getStrength() == BindingStrength.REQUIRED) - txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is required from this value set)"+getErrorMessage(vr.getMessage())); - else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { - if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) - checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), value, stack); - else if (!noExtensibleWarnings) - txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code should come from this value set unless it has no suitable code)"+getErrorMessage(vr.getMessage())); - } else if (binding.getStrength() == BindingStrength.PREFERRED) { - if (baseOnly) { - txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('"+value+"') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is recommended to come from this value set)"+getErrorMessage(vr.getMessage())); - } - } - } - } - } else if (!noBindingMsgSuppressed) - hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !type.equals("code"), "Binding has no source, so can't be checked"); - } - - private void checkQuantity(List errors, String path, Element focus, Quantity fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); - checkFixedValue(errors, path + ".comparator", focus.getNamedChild("comparator"), fixed.getComparatorElement(), fixedSource, "comparator", focus, pattern); - checkFixedValue(errors, path + ".units", focus.getNamedChild("unit"), fixed.getUnitElement(), fixedSource, "units", focus, pattern); - checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); - checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), fixedSource, "code", focus, pattern); - } - - // implementation - - private void checkRange(List errors, String path, Element focus, Range fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".low", focus.getNamedChild("low"), fixed.getLow(), fixedSource, "low", focus, pattern); - checkFixedValue(errors, path + ".high", focus.getNamedChild("high"), fixed.getHigh(), fixedSource, "high", focus, pattern); - - } - - private void checkRatio(List errors, String path, Element focus, Ratio fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".numerator", focus.getNamedChild("numerator"), fixed.getNumerator(), fixedSource, "numerator", focus, pattern); - checkFixedValue(errors, path + ".denominator", focus.getNamedChild("denominator"), fixed.getDenominator(), fixedSource, "denominator", focus, pattern); - } - - private void checkReference(ValidatorHostContext hostContext, List errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException { - Reference reference = ObjectConverter.readAsReference(element); - - String ref = reference.getReference(); - if (Utilities.noString(ref)) { - if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) { - warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference or identifier should have a display"); - } - return; - } else if (Utilities.existsInList(ref, "http://tools.ietf.org/html/bcp47")) { - // special known URLs that can't be validated but are known to be valid - return; - } - - ResolvedReference we = localResolve(ref, stack, errors, path, (Element) hostContext.getAppContext(), element); - String refType; - if (ref.startsWith("#")) { - refType = "contained"; - } else { - if (we == null) { - refType = "remote"; - } else { - refType = "bundled"; - } - } - ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundled") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.getAppContext(), path, ref); - - if (pol.checkExists()) { - if (we == null) { - if (fetcher == null) { - if (!refType.equals("contained")) - throw new FHIRException("Resource resolution services not provided"); } else { - Element ext = null; - if (fetchCache.containsKey(ref)) { - ext = fetchCache.get(ref); - } else { + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, codings.size() == fixed.getCoding().size(), + "Expected " + Integer.toString(fixed.getCoding().size()) + " but found " + Integer.toString(codings.size()) + + " coding elements")) { + for (int i = 0; i < codings.size(); i++) + checkFixedValue(errors, path + ".coding", codings.get(i), fixed.getCoding().get(i), fixedSource, "coding", focus); + } + } + } + + private boolean checkCodeableConcept(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, NodeStack stack) { + boolean res = true; + if (!noTerminologyChecks && theElementCntext != null && theElementCntext.hasBinding()) { + ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) { + if (binding.hasValueSet()) { + ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { + try { + CodeableConcept cc = ObjectConverter.readAsCodeableConcept(element); + if (!cc.hasCoding()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code must be provided from the value set " + describeReference(ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + " (max value set " + valueset.getUrl() + ")"); + else + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ")"); + } + } else { + long t = System.nanoTime(); + + // Check whether the codes are appropriate for the type of binding we have + boolean bindingsOk = true; + if (binding.getStrength() != BindingStrength.EXAMPLE) { + boolean atLeastOneSystemIsSupported = false; + for (Coding nextCoding : cc.getCoding()) { + String nextSystem = nextCoding.getSystem(); + if (isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { + atLeastOneSystemIsSupported = true; + break; + } + } + + if (!atLeastOneSystemIsSupported && binding.getStrength() == BindingStrength.EXAMPLE) { + // ignore this since we can't validate but it doesn't matter.. + } else { + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang).checkValueSetOnly(), cc, valueset); // we're going to validate the codings directly, so only check the valueset + if (!vr.isOk()) { + bindingsOk = false; + if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code from this value set is required (class = " + vr.getErrorClass().toString() + ")"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); + else if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code should come from this value set unless it has no suitable code (class = " + vr.getErrorClass().toString() + ")"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code is recommended to come from this value set (class = " + vr.getErrorClass().toString() + ")"); + } + } + } else { + if (binding.getStrength() == BindingStrength.REQUIRED) + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code from this value set is required) (codes = " + ccSummary(cc) + ")"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); + if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code) (codes = " + ccSummary(cc) + ")"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set) (codes = " + ccSummary(cc) + ")"); + } + } + } + } else if (vr.getMessage() != null) { + res = false; + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); + } else { + res = false; + } + } + // Then, for any codes that are in code systems we are able + // to validate, we'll validate that the codes actually exist + if (bindingsOk) { + for (Coding nextCoding : cc.getCoding()) { + if (isNotBlank(nextCoding.getCode()) && isNotBlank(nextCoding.getSystem()) && context.supportsSystem(nextCoding.getSystem())) { + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang).noCheckValueSetMembership(), nextCoding, valueset); + if (vr.getSeverity() != null) { + if (vr.getSeverity() == IssueSeverity.INFORMATION) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); + } else if (vr.getSeverity() == IssueSeverity.WARNING) { + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); + } else { + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); + } + } + } + } + } + txTime = txTime + (System.nanoTime() - t); + } + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating CodeableConcept"); + } + } + } else if (binding.hasValueSet()) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); + } else if (!noBindingMsgSuppressed) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); + } + } + } + return res; + } + + private boolean checkTerminologyCodeableConcept(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, NodeStack stack, StructureDefinition logical) { + boolean res = true; + if (!noTerminologyChecks && theElementCntext != null && theElementCntext.hasBinding()) { + ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing (cc)")) { + if (binding.hasValueSet()) { + ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { + try { + CodeableConcept cc = convertToCodeableConcept(element, logical); + if (!cc.hasCoding()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code is required from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl()); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code must be provided from the value set " + describeReference(ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + " (max value set " + valueset.getUrl() + ")"); + else + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "No code provided, and a code should be provided from the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ")"); + } + } else { + long t = System.nanoTime(); + + // Check whether the codes are appropriate for the type of binding we have + boolean bindingsOk = true; + if (binding.getStrength() != BindingStrength.EXAMPLE) { + boolean atLeastOneSystemIsSupported = false; + for (Coding nextCoding : cc.getCoding()) { + String nextSystem = nextCoding.getSystem(); + if (isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { + atLeastOneSystemIsSupported = true; + break; + } + } + + if (!atLeastOneSystemIsSupported && binding.getStrength() == BindingStrength.EXAMPLE) { + // ignore this since we can't validate but it doesn't matter.. + } else { + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), cc, valueset); // we're going to validate the codings directly + if (!vr.isOk()) { + bindingsOk = false; + if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code from this value set is required (class = " + vr.getErrorClass().toString() + ")"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); + else if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code should come from this value set unless it has no suitable code (class = " + vr.getErrorClass().toString() + ")"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet()) + " and a code is recommended to come from this value set (class = " + vr.getErrorClass().toString() + ")"); + } + } + } else { + if (binding.getStrength() == BindingStrength.REQUIRED) + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code from this value set is required) (codes = " + ccSummary(cc) + ")"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), cc, stack); + if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code should come from this value set unless it has no suitable code) (codes = " + ccSummary(cc) + ")"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the value set " + describeReference(binding.getValueSet()) + " (" + valueset.getUrl() + ", and a code is recommended to come from this value set) (codes = " + ccSummary(cc) + ")"); + } + } + } + } else if (vr.getMessage() != null) { + res = false; + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, vr.getMessage()); + } else { + res = false; + } + } + // Then, for any codes that are in code systems we are able + // to validate, we'll validate that the codes actually exist + if (bindingsOk) { + for (Coding nextCoding : cc.getCoding()) { + String nextCode = nextCoding.getCode(); + String nextSystem = nextCoding.getSystem(); + if (isNotBlank(nextCode) && isNotBlank(nextSystem) && context.supportsSystem(nextSystem)) { + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), nextSystem, nextCode, null); + if (!vr.isOk()) { + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Code {0} is not a valid code in code system {1}", nextCode, nextSystem); + } + } + } + } + txTime = txTime + (System.nanoTime() - t); + } + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating CodeableConcept"); + } + // special case: if the logical model has both CodeableConcept and Coding mappings, we'll also check the first coding. + if (getMapping("http://hl7.org/fhir/terminology-pattern", logical, logical.getSnapshot().getElementFirstRep()).contains("Coding")) { + checkTerminologyCoding(errors, path, element, profile, theElementCntext, true, true, stack, logical); + } + } + } else if (binding.hasValueSet()) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); + } else if (!noBindingMsgSuppressed) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); + } + } + } + return res; + } + + private void checkTerminologyCoding(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept, boolean checkDisplay, NodeStack stack, StructureDefinition logical) { + Coding c = convertToCoding(element, logical); + String code = c.getCode(); + String system = c.getSystem(); + String display = c.getDisplay(); + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Coding.system must be an absolute reference, not a local reference"); + + if (system != null && code != null && !noTerminologyChecks) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !isValueSet(system), "The Coding references a value set, not a code system (\"" + system + "\")"); try { - ext = fetcher.fetch(hostContext.getAppContext(), ref); - } catch (IOException e) { - throw new FHIRException(e); - } - if (ext != null) { - fetchCache.put(ref, ext); - } - } - we = ext == null ? null : makeExternalRef(ext, path); - } - } - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, (allowExamples && (ref.contains("example.org") || ref.contains("acme.com"))) || (we != null || pol == ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS), "Unable to resolve resource '"+ref+"'"); - } - - String ft; - if (we != null) - ft = we.getType(); - else - ft = tryParse(ref); - - if (reference.hasType()) { // R4 onwards... - // the type has to match the specified - String tu = isAbsolute(reference.getType()) ? reference.getType() : "http://hl7.org/fhir/StructureDefinition/"+reference.getType(); - TypeRefComponent containerType = container.getType("Reference"); - if (!containerType.hasTargetProfile(tu) && !containerType.hasTargetProfile("http://hl7.org/fhir/StructureDefinition/Resource")) { - boolean matchingResource = false; - for (CanonicalType target: containerType.getTargetProfile()) { - StructureDefinition sd = resolveProfile(profile, target.asStringValue()); - if (("http://hl7.org/fhir/StructureDefinition/" + sd.getType()).equals(tu)) { - matchingResource = true; - break; - } - } - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, matchingResource, - "The type '"+reference.getType()+"' is not a valid Target for this element (must be one of "+container.getType("Reference").getTargetProfile()+")"); - - } - // the type has to match the actual - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft==null || ft.equals(reference.getType()), "The specified type '"+reference.getType()+"' does not match the found type '"+ft+"'"); - } - - if (we != null && pol.checkType()) { - if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft!=null, "Unable to determine type of target resource")) { - // we validate as much as we can. First, can we infer a type from the profile? - boolean ok = false; - TypeRefComponent type = getReferenceTypeRef(container.getType()); - if (type.hasTargetProfile() && !type.hasTargetProfile("http://hl7.org/fhir/StructureDefinition/Resource")) { - Set types = new HashSet<>(); - List profiles = new ArrayList<>(); - for (UriType u : type.getTargetProfile()) { - StructureDefinition sd = resolveProfile(profile, u.getValue()); - if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, sd != null, "Unable to resolve the profile reference '" + u.getValue() + "'")) { - types.add(sd.getType()); - if (ft.equals(sd.getType())) { - ok = true; - profiles.add(sd); - } - } - } - if (!pol.checkValid()) { - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, profiles.size() > 0, "Unable to find matching profile for "+ref+" (by type) among choices: " + StringUtils.join("; ", type.getTargetProfile())); - } else { - Map> badProfiles = new HashMap>(); - Map> goodProfiles = new HashMap>(); - int goodCount = 0; - for (StructureDefinition pr: profiles) { - List profileErrors = new ArrayList(); - validateResource(we.hostContext(hostContext, pr), profileErrors, we.getResource(), we.getFocus(), pr, IdStatus.OPTIONAL, we.getStack()); - if (!hasErrors(profileErrors)) { - goodCount++; - goodProfiles.put(pr, profileErrors); - trackUsage(pr, hostContext, element); - } else { - badProfiles.put(pr, profileErrors); - } - } - if (goodCount == 1) { - if (showMessagesFromReferences) { - for (ValidationMessage vm : goodProfiles.values().iterator().next()) { - if (!errors.contains(vm)) { - errors.add(vm); - } - } - } - - } else if (goodProfiles.size()==0) { - if (!isShowMessagesFromReferences()) { - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, areAllBaseProfiles(profiles), "Unable to find matching profile for "+ref+" among choices: " + asList(type.getTargetProfile())); - for (StructureDefinition sd : badProfiles.keySet()) { - slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for "+ref+" matching against Profile"+sd.getUrl(), errorSummaryForSlicingAsHtml(badProfiles.get(sd))); - } - } else { - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, profiles.size()==1, "Unable to find matching profile for "+ref+" among choices: " + asList(type.getTargetProfile())); - for (List messages : badProfiles.values()) { - for (ValidationMessage vm : messages) { - if (!errors.contains(vm)) { - errors.add(vm); + if (checkCode(errors, element, path, code, system, display, checkDisplay, stack)) + if (theElementCntext != null && theElementCntext.hasBinding()) { + ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) { + if (binding.hasValueSet()) { + ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { + try { + long t = System.nanoTime(); + ValidationResult vr = null; + if (binding.getStrength() != BindingStrength.EXAMPLE) { + vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); + } + txTime = txTime + (System.nanoTime() - t); + if (vr != null && !vr.isOk()) { + if (vr.IsNoService()) + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided could not be validated in the absence of a terminology server"); + else if (vr.getErrorClass() != null && !vr.getErrorClass().isInfrastructure()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code from this value set is required"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); + else if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set"); + } + } + } else if (binding.getStrength() == BindingStrength.REQUIRED) + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is required from this value set" + (vr.getMessage() != null ? " (error message = " + vr.getMessage() + ")" : "")); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); + else + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code" + (vr.getMessage() != null ? " (error message = " + vr.getMessage() + ")" : "")); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set" + (vr.getMessage() != null ? " (error message = " + vr.getMessage() + ")" : "")); + } + } + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating Coding"); + } + } + } else if (binding.hasValueSet()) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); + } else if (!inCodeableConcept && !noBindingMsgSuppressed) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); + } + } + } + } catch (Exception e) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating Coding: " + e.toString()); + } + } + } + + private CodeableConcept convertToCodeableConcept(Element element, StructureDefinition logical) { + CodeableConcept res = new CodeableConcept(); + for (ElementDefinition ed : logical.getSnapshot().getElement()) { + if (Utilities.charCount(ed.getPath(), '.') == 1) { + List maps = getMapping("http://hl7.org/fhir/terminology-pattern", logical, ed); + for (String m : maps) { + String name = tail(ed.getPath()); + List list = new ArrayList<>(); + element.getNamedChildren(name, list); + if (!list.isEmpty()) { + if ("Coding.code".equals(m)) { + res.getCodingFirstRep().setCode(list.get(0).primitiveValue()); + } else if ("Coding.system[fmt:OID]".equals(m)) { + String oid = list.get(0).primitiveValue(); + String url = context.oid2Uri(oid); + if (url != null) { + res.getCodingFirstRep().setSystem(url); + } else { + res.getCodingFirstRep().setSystem("urn:oid:" + oid); + } + } else if ("Coding.version".equals(m)) { + res.getCodingFirstRep().setVersion(list.get(0).primitiveValue()); + } else if ("Coding.display".equals(m)) { + res.getCodingFirstRep().setDisplay(list.get(0).primitiveValue()); + } else if ("CodeableConcept.text".equals(m)) { + res.setText(list.get(0).primitiveValue()); + } else if ("CodeableConcept.coding".equals(m)) { + StructureDefinition c = context.fetchTypeDefinition(ed.getTypeFirstRep().getCode()); + for (Element e : list) { + res.addCoding(convertToCoding(e, c)); + } + } } - } } - } + } + } + return res; + } + + private Coding convertToCoding(Element element, StructureDefinition logical) { + Coding res = new Coding(); + for (ElementDefinition ed : logical.getSnapshot().getElement()) { + if (Utilities.charCount(ed.getPath(), '.') == 1) { + List maps = getMapping("http://hl7.org/fhir/terminology-pattern", logical, ed); + for (String m : maps) { + String name = tail(ed.getPath()); + List list = new ArrayList<>(); + element.getNamedChildren(name, list); + if (!list.isEmpty()) { + if ("Coding.code".equals(m)) { + res.setCode(list.get(0).primitiveValue()); + } else if ("Coding.system[fmt:OID]".equals(m)) { + String oid = list.get(0).primitiveValue(); + String url = context.oid2Uri(oid); + if (url != null) { + res.setSystem(url); + } else { + res.setSystem("urn:oid:" + oid); + } + } else if ("Coding.version".equals(m)) { + res.setVersion(list.get(0).primitiveValue()); + } else if ("Coding.display".equals(m)) { + res.setDisplay(list.get(0).primitiveValue()); + } + } + } + } + } + return res; + } + + private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, CodeableConcept cc, NodeStack stack) { + // TODO Auto-generated method stub + ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { + try { + long t = System.nanoTime(); + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), cc, valueset); + txTime = txTime + (System.nanoTime() - t); + if (!vr.isOk()) { + if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided could be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + "), (error = " + vr.getMessage() + ")"); + else + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "None of the codes provided are in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + ", and a code from this value set is required) (codes = " + ccSummary(cc) + ")"); + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating CodeableConcept using maxValueSet"); + } + } + } + + private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, Coding c, NodeStack stack) { + // TODO Auto-generated method stub + ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { + try { + long t = System.nanoTime(); + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); + txTime = txTime + (System.nanoTime() - t); + if (!vr.isOk()) { + if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided could not be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + "), (error = " + vr.getMessage() + ")"); + else + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided is not in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + ", and a code from this value set is required) (code = " + c.getSystem() + "#" + c.getCode() + ")"); + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating CodeableConcept using maxValueSet"); + } + } + } + + private void checkMaxValueSet(List errors, String path, Element element, StructureDefinition profile, String maxVSUrl, String value, NodeStack stack) { + // TODO Auto-generated method stub + ValueSet valueset = resolveBindingReference(profile, maxVSUrl, profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(maxVSUrl) + " not found by validator")) { + try { + long t = System.nanoTime(); + ValidationResult vr = context.validateCode(new ValidationOptions(stack.workingLang), value, valueset); + txTime = txTime + (System.nanoTime() - t); + if (!vr.isOk()) { + if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided could not be validated against the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + "), (error = " + vr.getMessage() + ")"); + else + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The code provided is not in the maximum value set " + describeReference(maxVSUrl) + " (" + valueset.getUrl() + "), and a code from this value set is required) (code = " + value + "), (error = " + vr.getMessage() + ")"); + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating CodeableConcept using maxValueSet"); + } + } + } + + private String ccSummary(CodeableConcept cc) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (Coding c : cc.getCoding()) + b.append(c.getSystem() + "#" + c.getCode()); + return b.toString(); + } + + private void checkCoding(List errors, String path, Element focus, Coding fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); + checkFixedValue(errors, path + ".version", focus.getNamedChild("version"), fixed.getVersionElement(), fixedSource, "version", focus, pattern); + checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), fixedSource, "code", focus, pattern); + checkFixedValue(errors, path + ".display", focus.getNamedChild("display"), fixed.getDisplayElement(), fixedSource, "display", focus, pattern); + checkFixedValue(errors, path + ".userSelected", focus.getNamedChild("userSelected"), fixed.getUserSelectedElement(), fixedSource, "userSelected", focus, pattern); + } + + private void checkCoding(List errors, String path, Element element, StructureDefinition profile, ElementDefinition theElementCntext, boolean inCodeableConcept, boolean checkDisplay, NodeStack stack) { + String code = element.getNamedChildValue("code"); + String system = element.getNamedChildValue("system"); + String display = element.getNamedChildValue("display"); + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Coding.system must be an absolute reference, not a local reference"); + + if (system != null && code != null && !noTerminologyChecks) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !isValueSet(system), "The Coding references a value set, not a code system (\"" + system + "\")"); + try { + if (checkCode(errors, element, path, code, system, display, checkDisplay, stack)) + if (theElementCntext != null && theElementCntext.hasBinding()) { + ElementDefinitionBindingComponent binding = theElementCntext.getBinding(); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, binding != null, "Binding for " + path + " missing")) { + if (binding.hasValueSet()) { + ValueSet valueset = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, valueset != null, "ValueSet " + describeReference(binding.getValueSet()) + " not found by validator")) { + try { + Coding c = ObjectConverter.readAsCoding(element); + long t = System.nanoTime(); + ValidationResult vr = null; + if (binding.getStrength() != BindingStrength.EXAMPLE) { + vr = context.validateCode(new ValidationOptions(stack.workingLang), c, valueset); + } + txTime = txTime + (System.nanoTime() - t); + if (vr != null && !vr.isOk()) { + if (vr.IsNoService()) + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided could not be validated in the absence of a terminology server"); + else if (vr.getErrorClass() != null && !vr.getErrorClass().isInfrastructure()) { + if (binding.getStrength() == BindingStrength.REQUIRED) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code from this value set is required"); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); + else if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code"); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "Could not confirm that the codes provided are in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set"); + } + } + } else if (binding.getStrength() == BindingStrength.REQUIRED) + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is required from this value set. " + getErrorMessage(vr.getMessage())); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), c, stack); + else + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code should come from this value set unless it has no suitable code. " + getErrorMessage(vr.getMessage())); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The Coding provided is not in the value set " + describeReference(binding.getValueSet(), valueset) + ", and a code is recommended to come from this value set. " + getErrorMessage(vr.getMessage())); + } + } + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating Coding"); + } + } + } else if (binding.hasValueSet()) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding by URI reference cannot be checked"); + } else if (!inCodeableConcept && !noBindingMsgSuppressed) { + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Binding for path " + path + " has no source, so can't be checked"); + } + } + } + } catch (Exception e) { + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, "Error " + e.getMessage() + " validating Coding: " + e.toString()); + } + } + } + + private boolean isValueSet(String url) { + try { + ValueSet vs = context.fetchResourceWithException(ValueSet.class, url); + return vs != null; + } catch (Exception e) { + return false; + } + } + + private void checkContactPoint(List errors, String path, Element focus, ContactPoint fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); + checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); + checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); + checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); + + } + + private StructureDefinition checkExtension(ValidatorHostContext hostContext, List errors, String path, Element resource, Element container, Element element, ElementDefinition def, StructureDefinition profile, NodeStack stack, NodeStack containerStack, String extensionUrl) throws FHIRException { + String url = element.getNamedChildValue("url"); + boolean isModifier = element.getName().equals("modifierExtension"); + + long t = System.nanoTime(); + StructureDefinition ex = Utilities.isAbsoluteUrl(url) ? context.fetchResource(StructureDefinition.class, url) : null; + sdTime = sdTime + (System.nanoTime() - t); + if (ex == null) { + if (xverManager == null) { + xverManager = new XVerExtensionManager(context); + } + if (xverManager.matchingUrl(url)) { + switch (xverManager.status(url)) { + case BadVersion: + rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (invalidVersion \"" + xverManager.getVersion(url) + "\")"); + break; + case Unknown: + rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (unknown Element id \"" + xverManager.getElementId(url) + "\")"); + break; + case Invalid: + rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' is not valid (Element id \"" + xverManager.getElementId(url) + "\" is valid, but cannot be used in a cross-version paradigm because there has been no changes across the relevant versions)"); + break; + case Valid: + ex = xverManager.makeDefinition(url); + context.generateSnapshot(ex); + context.cacheResource(ex); + break; + default: + rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", false, "Extension url '" + url + "' evaluation state illegal"); + break; + } + } else if (extensionUrl != null && !isAbsolute(url)) { + if (extensionUrl.equals(profile.getUrl())) { + rule(errors, IssueType.INVALID, element.line(), element.col(), path + "[url='" + url + "']", hasExtensionSlice(profile, url), "Sub-extension url '" + url + "' is not defined by the Extension " + profile.getUrl()); + } + } else if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowUnknownExtension(url), "The extension " + url + " is unknown, and not allowed here")) { + hint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, isKnownExtension(url), "Unknown extension " + url); + } + } + if (ex != null) { + trackUsage(ex, hostContext, element); + if (def.getIsModifier()) { + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(), + "Extension modifier mismatch: the extension element is labelled as a modifier, but the underlying extension is not"); } else { - if (!isShowMessagesFromReferences()) { - warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Found multiple matching profiles for "+ref+" among choices: " + asListByUrl(goodProfiles.keySet())); - for (StructureDefinition sd : badProfiles.keySet()) { - slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for "+ref+" matching against Profile"+sd.getUrl(), errorSummaryForSlicingAsHtml(badProfiles.get(sd))); - } - } else { - warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Found multiple matching profiles for "+ref+" among choices: " + asListByUrl(goodProfiles.keySet())); - for (List messages : goodProfiles.values()) { - for (ValidationMessage vm : messages) { - if (!errors.contains(vm)) { - errors.add(vm); - } - } - } - } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(), + "Extension modifier mismatch: the extension element is not labelled as a modifier, but the underlying extension is"); } - } - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ok, "Invalid Resource target type. Found " + ft + ", but expected one of (" + types.toString() + ")"); - } - if (type.hasAggregation()) { - boolean modeOk = false; - for (Enumeration mode : type.getAggregation()) { - if (mode.getValue().equals(AggregationMode.CONTAINED) && refType.equals("contained")) - modeOk = true; - else if (mode.getValue().equals(AggregationMode.BUNDLED) && refType.equals("bundled")) - modeOk = true; - else if (mode.getValue().equals(AggregationMode.REFERENCED) && (refType.equals("bundled")||refType.equals("remote"))) - modeOk = true; - } - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, modeOk, "Reference is " + refType + " which isn't supported by the specified aggregation mode(s) for the reference"); + // two questions + // 1. can this extension be used here? + checkExtensionContext(errors, resource, container, ex, containerStack, hostContext); + + if (isModifier) + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", ex.getSnapshot().getElement().get(0).getIsModifier(), + "The Extension '" + url + "' must be used as a modifierExtension"); + else + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path + "[url='" + url + "']", !ex.getSnapshot().getElement().get(0).getIsModifier(), + "The Extension '" + url + "' must not be used as an extension (it's a modifierExtension)"); + + // check the type of the extension: + Set allowedTypes = listExtensionTypes(ex); + String actualType = getExtensionType(element); + if (actualType == null) + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.isEmpty(), "The Extension '" + url + "' definition is for a simple extension, so it must contain a value, not extensions"); + else + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, allowedTypes.contains(actualType), "The Extension '" + url + "' definition allows for the types " + allowedTypes.toString() + " but found type " + actualType); + + // 3. is the content of the extension valid? + validateElement(hostContext, errors, ex, ex.getSnapshot().getElement().get(0), null, null, resource, element, "Extension", stack, false, true, url); + } - } + return ex; } - if (we == null) { - TypeRefComponent type = getReferenceTypeRef(container.getType()); - boolean okToRef = !type.hasAggregation() || type.hasAggregation(AggregationMode.REFERENCED); - rule(errors, IssueType.REQUIRED, -1, -1, path, okToRef, "Bundled or contained reference not found within the bundle/resource " + ref); - } - if (we == null && ft != null && assumeValidRestReferences) { - // if we == null, we inferred ft from the reference. if we are told to treat this as gospel - TypeRefComponent type = getReferenceTypeRef(container.getType()); - Set types = new HashSet<>(); - for (CanonicalType tp : type.getTargetProfile()) { - StructureDefinition sd = context.fetchResource(StructureDefinition.class, tp.getValue()); - if (sd != null) { - types.add(sd.getType()); + + private boolean hasExtensionSlice(StructureDefinition profile, String sliceName) { + for (ElementDefinition ed : profile.getSnapshot().getElement()) { + if (ed.getPath().equals("Extension.extension.url") && ed.hasFixed() && sliceName.equals(ed.getFixed().primitiveValue())) { + return true; + } } - } - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, types.isEmpty() || types.contains(ft), "The type '"+ft+"' implied by the reference URL "+ref+" is not a valid Target for this element (must be one of "+types+")"); - + return false; } - if (pol == ReferenceValidationPolicy.CHECK_VALID) { - // todo.... - } - } - private String asListByUrl(Collection list) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (StructureDefinition sd : list) { - b.append(sd.getUrl()); - } - return b.toString(); - } - - private String asList(Collection list) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (CanonicalType c : list) { - b.append(c.getValue()); - } - return b.toString(); - } - - private boolean areAllBaseProfiles(List profiles) { - for (StructureDefinition sd : profiles) { - if (!sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/")) { - return false; - } - } - return true; - } - - private String errorSummaryForSlicing(List list) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (ValidationMessage vm : list) { - if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL || vm.isSlicingHint()) { - b.append(vm.getLocation()+": "+vm.getMessage()); - } - } - return b.toString(); - } - - private String errorSummaryForSlicingAsHtml(List list) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (ValidationMessage vm : list) { - if (vm.isSlicingHint()) { - b.append("

  • "+vm.getLocation()+": "+vm.getSliceHtml()+"
    • "); - } else if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL ) { - b.append("
  • "+vm.getLocation()+": "+vm.getHtml()+"
    • "); - } - } - return "
      "+b.toString()+"
    "; - } - - private TypeRefComponent getReferenceTypeRef(List types) { - for (TypeRefComponent tr : types) { - if ("Reference".equals(tr.getCode())) { - return tr; - } - } - return null; - } - - private String checkResourceType(String type) { - long t = System.nanoTime(); - try { - if (context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + type) != null) - return type; - else + private String getExtensionType(Element element) { + for (Element e : element.getChildren()) { + if (e.getName().startsWith("value")) { + String tn = e.getName().substring(5); + String ltn = Utilities.uncapitalize(tn); + if (isPrimitiveType(ltn)) + return ltn; + else + return tn; + } + } return null; - } finally { - sdTime = sdTime + (System.nanoTime() - t); } - } - private void checkSampledData(List errors, String path, Element focus, SampledData fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".origin", focus.getNamedChild("origin"), fixed.getOrigin(), fixedSource, "origin", focus, pattern); - checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriodElement(), fixedSource, "period", focus, pattern); - checkFixedValue(errors, path + ".factor", focus.getNamedChild("factor"), fixed.getFactorElement(), fixedSource, "factor", focus, pattern); - checkFixedValue(errors, path + ".lowerLimit", focus.getNamedChild("lowerLimit"), fixed.getLowerLimitElement(), fixedSource, "lowerLimit", focus, pattern); - checkFixedValue(errors, path + ".upperLimit", focus.getNamedChild("upperLimit"), fixed.getUpperLimitElement(), fixedSource, "upperLimit", focus, pattern); - checkFixedValue(errors, path + ".dimensions", focus.getNamedChild("dimensions"), fixed.getDimensionsElement(), fixedSource, "dimensions", focus, pattern); - checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), fixedSource, "data", focus, pattern); - } - - private void checkTiming(List errors, String path, Element focus, Timing fixed, String fixedSource, boolean pattern) { - checkFixedValue(errors, path + ".repeat", focus.getNamedChild("repeat"), fixed.getRepeat(), fixedSource, "value", focus, pattern); - - List events = new ArrayList(); - focus.getNamedChildren("event", events); - if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, events.size() == fixed.getEvent().size(), - "Expected " + Integer.toString(fixed.getEvent().size()) + " but found " + Integer.toString(events.size()) + " event elements")) { - for (int i = 0; i < events.size(); i++) - checkFixedValue(errors, path + ".event", events.get(i), fixed.getEvent().get(i), fixedSource, "event", focus, pattern); + private Set listExtensionTypes(StructureDefinition ex) { + ElementDefinition vd = null; + for (ElementDefinition ed : ex.getSnapshot().getElement()) { + if (ed.getPath().startsWith("Extension.value")) { + vd = ed; + break; + } + } + Set res = new HashSet(); + if (vd != null && !"0".equals(vd.getMax())) { + for (TypeRefComponent tr : vd.getType()) { + res.add(tr.getWorkingCode()); + } + } + return res; } - } - private boolean codeinExpansion(ValueSetExpansionContainsComponent cnt, String system, String code) { - for (ValueSetExpansionContainsComponent c : cnt.getContains()) { - if (code.equals(c.getCode()) && system.equals(c.getSystem().toString())) - return true; - if (codeinExpansion(c, system, code)) + private boolean checkExtensionContext(List errors, Element resource, Element container, StructureDefinition definition, NodeStack stack, ValidatorHostContext hostContext) { + String extUrl = definition.getUrl(); + boolean ok = false; + CommaSeparatedStringBuilder contexts = new CommaSeparatedStringBuilder(); + List plist = new ArrayList<>(); + plist.add(stripIndexes(stack.getLiteralPath())); + for (String s : stack.getLogicalPaths()) { + String p = stripIndexes(s); + // all extensions are always allowed in ElementDefinition.example.value, and in fixed and pattern values. TODO: determine the logical paths from the path stated in the element definition.... + if (Utilities.existsInList(p, "ElementDefinition.example.value", "ElementDefinition.pattern", "ElementDefinition.fixed")) { + return true; + } + plist.add(p); + + } + + for (StructureDefinitionContextComponent ctxt : fixContexts(extUrl, definition.getContext())) { + if (ok) { + break; + } + if (ctxt.getType() == ExtensionContextType.ELEMENT) { + String en = ctxt.getExpression(); + contexts.append("e:" + en); + if ("Element".equals(en)) { + ok = true; + } else if (en.equals("Resource") && container.isResource()) { + ok = true; + } + for (String p : plist) { + if (ok) { + break; + } + if (p.equals(en)) { + ok = true; + } else { + String pn = p; + String pt = ""; + if (p.contains(".")) { + pn = p.substring(0, p.indexOf(".")); + pt = p.substring(p.indexOf(".")); + } + StructureDefinition sd = context.fetchTypeDefinition(pn); + while (sd != null) { + if ((sd.getType() + pt).equals(en)) { + ok = true; + break; + } + if (sd.getBaseDefinition() != null) { + sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition()); + } else { + sd = null; + } + } + } + } + } else if (ctxt.getType() == ExtensionContextType.EXTENSION) { + contexts.append("x:" + ctxt.getExpression()); + NodeStack estack = stack.parent; + if (estack != null && estack.getElement().fhirType().equals("Extension")) { + String ext = estack.element.getNamedChildValue("url"); + if (ctxt.getExpression().equals(ext)) { + ok = true; + } + } + } else if (ctxt.getType() == ExtensionContextType.FHIRPATH) { + contexts.append("p:" + ctxt.getExpression()); + // The context is all elements that match the FHIRPath query found in the expression. + List res = fpe.evaluate(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(ctxt.getExpression())); + if (res.contains(container)) { + ok = true; + } + } else { + throw new Error("Unrecognised extension context " + ctxt.getTypeElement().asStringValue()); + } + } + if (!ok) { + rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, "The extension " + extUrl + " is not allowed to be used at this point (allowed = " + contexts.toString() + "; this element is [" + plist.toString() + ")"); + return false; + } else { + if (definition.hasContextInvariant()) { + for (StringType s : definition.getContextInvariant()) { + if (!fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), container, fpe.parse(s.getValue()))) { + rule(errors, IssueType.STRUCTURE, container.line(), container.col(), stack.literalPath, false, + "The extension " + extUrl + " is not allowed to be used at this point (based on context invariant '" + s.getValue() + "')"); + return false; + } + } + } + return true; + } + } + + private List fixContexts(String extUrl, List list) { + List res = new ArrayList<>(); + for (StructureDefinitionContextComponent ctxt : list) { + res.add(ctxt.copy()); + } + if ("http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type".equals(extUrl)) { + list.get(0).setExpression("ElementDefinition.type"); + } + if ("http://hl7.org/fhir/StructureDefinition/regex".equals(extUrl)) { + list.get(1).setExpression("ElementDefinition.type"); + } + return list; + } + + private String stripIndexes(String path) { + boolean skip = false; + StringBuilder b = new StringBuilder(); + for (char c : path.toCharArray()) { + if (skip) { + if (c == ']') { + skip = false; + } + } else if (c == '[') { + skip = true; + } else { + b.append(c); + } + } + return b.toString(); + } + + private void checkFixedValue(List errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent) { + checkFixedValue(errors, path, focus, fixed, fixedSource, propName, parent, false); + } + + @SuppressWarnings("rawtypes") + private void checkFixedValue(List errors, String path, Element focus, org.hl7.fhir.r5.model.Element fixed, String fixedSource, String propName, Element parent, boolean pattern) { + if ((fixed == null || fixed.isEmpty()) && focus == null) { + ; // this is all good + } else if ((fixed == null || fixed.isEmpty()) && focus != null) { + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, pattern, "The element " + focus.getName() + " is present in the instance but not allowed in the applicable " + (pattern ? "pattern" : "fixed value") + " specified in profile"); + } else if (fixed != null && !fixed.isEmpty() && focus == null) { + rule(errors, IssueType.VALUE, parent == null ? -1 : parent.line(), parent == null ? -1 : parent.col(), path, false, "Missing element '" + propName + "' - required by fixed value assigned in profile " + fixedSource); + } else { + String value = focus.primitiveValue(); + if (fixed instanceof org.hl7.fhir.r5.model.BooleanType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.BooleanType) fixed).asStringValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.BooleanType) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.IntegerType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.IntegerType) fixed).asStringValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.IntegerType) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.DecimalType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DecimalType) fixed).asStringValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DecimalType) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.Base64BinaryType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.Base64BinaryType) fixed).asStringValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.Base64BinaryType) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.InstantType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.InstantType) fixed).getValue().toString(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.InstantType) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.CodeType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.CodeType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.CodeType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.Enumeration) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.Enumeration) fixed).asStringValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.Enumeration) fixed).asStringValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.StringType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.StringType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.StringType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.UriType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.UriType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.UriType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.DateType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DateType) fixed).getValue().toString(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DateType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.DateTimeType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.DateTimeType) fixed).getValue().toString(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.DateTimeType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.OidType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.OidType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.OidType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.UuidType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.UuidType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.UuidType) fixed).getValue() + "'"); + else if (fixed instanceof org.hl7.fhir.r5.model.IdType) + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, check(((org.hl7.fhir.r5.model.IdType) fixed).getValue(), value), + "Value is '" + value + "' but must be '" + ((org.hl7.fhir.r5.model.IdType) fixed).getValue() + "'"); + else if (fixed instanceof Quantity) + checkQuantity(errors, path, focus, (Quantity) fixed, fixedSource, pattern); + else if (fixed instanceof Address) + checkAddress(errors, path, focus, (Address) fixed, fixedSource, pattern); + else if (fixed instanceof ContactPoint) + checkContactPoint(errors, path, focus, (ContactPoint) fixed, fixedSource, pattern); + else if (fixed instanceof Attachment) + checkAttachment(errors, path, focus, (Attachment) fixed, fixedSource, pattern); + else if (fixed instanceof Identifier) + checkIdentifier(errors, path, focus, (Identifier) fixed, fixedSource, pattern); + else if (fixed instanceof Coding) + checkCoding(errors, path, focus, (Coding) fixed, fixedSource, pattern); + else if (fixed instanceof HumanName) + checkHumanName(errors, path, focus, (HumanName) fixed, fixedSource, pattern); + else if (fixed instanceof CodeableConcept) + checkCodeableConcept(errors, path, focus, (CodeableConcept) fixed, fixedSource, pattern); + else if (fixed instanceof Timing) + checkTiming(errors, path, focus, (Timing) fixed, fixedSource, pattern); + else if (fixed instanceof Period) + checkPeriod(errors, path, focus, (Period) fixed, fixedSource, pattern); + else if (fixed instanceof Range) + checkRange(errors, path, focus, (Range) fixed, fixedSource, pattern); + else if (fixed instanceof Ratio) + checkRatio(errors, path, focus, (Ratio) fixed, fixedSource, pattern); + else if (fixed instanceof SampledData) + checkSampledData(errors, path, focus, (SampledData) fixed, fixedSource, pattern); + + else + rule(errors, IssueType.EXCEPTION, focus.line(), focus.col(), path, false, "Unhandled fixed value type " + fixed.getClass().getName()); + List extensions = new ArrayList(); + focus.getNamedChildren("extension", extensions); + if (fixed.getExtension().size() == 0) { + rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == 0, "No extensions allowed, as the specified fixed value doesn't contain any extensions"); + } else if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, extensions.size() == fixed.getExtension().size(), + "Extensions count mismatch: expected " + Integer.toString(fixed.getExtension().size()) + " but found " + Integer.toString(extensions.size()))) { + for (Extension e : fixed.getExtension()) { + Element ex = getExtensionByUrl(extensions, e.getUrl()); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, ex != null, "Extension count mismatch: unable to find extension: " + e.getUrl())) { + checkFixedValue(errors, path, ex.getNamedChild("extension").getNamedChild("value"), e.getValue(), fixedSource, "extension.value", ex.getNamedChild("extension")); + } + } + } + } + } + + private void checkHumanName(List errors, String path, Element focus, HumanName fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); + checkFixedValue(errors, path + ".text", focus.getNamedChild("text"), fixed.getTextElement(), fixedSource, "text", focus, pattern); + checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); + + List parts = new ArrayList(); + focus.getNamedChildren("family", parts); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() > 0 == fixed.hasFamily(), + "Expected " + (fixed.hasFamily() ? "1" : "0") + " but found " + Integer.toString(parts.size()) + " family elements")) { + for (int i = 0; i < parts.size(); i++) + checkFixedValue(errors, path + ".family", parts.get(i), fixed.getFamilyElement(), fixedSource, "family", focus, pattern); + } + focus.getNamedChildren("given", parts); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getGiven().size(), + "Expected " + Integer.toString(fixed.getGiven().size()) + " but found " + Integer.toString(parts.size()) + " given elements")) { + for (int i = 0; i < parts.size(); i++) + checkFixedValue(errors, path + ".given", parts.get(i), fixed.getGiven().get(i), fixedSource, "given", focus, pattern); + } + focus.getNamedChildren("prefix", parts); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getPrefix().size(), + "Expected " + Integer.toString(fixed.getPrefix().size()) + " but found " + Integer.toString(parts.size()) + " prefix elements")) { + for (int i = 0; i < parts.size(); i++) + checkFixedValue(errors, path + ".prefix", parts.get(i), fixed.getPrefix().get(i), fixedSource, "prefix", focus, pattern); + } + focus.getNamedChildren("suffix", parts); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, parts.size() == fixed.getSuffix().size(), + "Expected " + Integer.toString(fixed.getSuffix().size()) + " but found " + Integer.toString(parts.size()) + " suffix elements")) { + for (int i = 0; i < parts.size(); i++) + checkFixedValue(errors, path + ".suffix", parts.get(i), fixed.getSuffix().get(i), fixedSource, "suffix", focus, pattern); + } + } + + private void checkIdentifier(List errors, String path, Element element, ElementDefinition context) { + String system = element.getNamedChildValue("system"); + rule(errors, IssueType.CODEINVALID, element.line(), element.col(), path, isAbsolute(system), "Identifier.system must be an absolute reference, not a local reference"); + } + + private void checkIdentifier(List errors, String path, Element focus, Identifier fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".use", focus.getNamedChild("use"), fixed.getUseElement(), fixedSource, "use", focus, pattern); + checkFixedValue(errors, path + ".type", focus.getNamedChild("type"), fixed.getType(), fixedSource, "type", focus, pattern); + checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); + checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); + checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriod(), fixedSource, "period", focus, pattern); + checkFixedValue(errors, path + ".assigner", focus.getNamedChild("assigner"), fixed.getAssigner(), fixedSource, "assigner", focus, pattern); + } + + private void checkPeriod(List errors, String path, Element focus, Period fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".start", focus.getNamedChild("start"), fixed.getStartElement(), fixedSource, "start", focus, pattern); + checkFixedValue(errors, path + ".end", focus.getNamedChild("end"), fixed.getEndElement(), fixedSource, "end", focus, pattern); + } + + private void checkPrimitive(Object appContext, List errors, String path, String type, ElementDefinition context, Element e, StructureDefinition profile, NodeStack node) throws FHIRException { + if (isBlank(e.primitiveValue())) { + if (e.primitiveValue() == null) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types must have a value or must have child extensions"); + else if (e.primitiveValue().length() == 0) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types must have a value that is not empty"); + else if (StringUtils.isWhitespace(e.primitiveValue())) + warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.hasChildren(), "Primitive types should not only be whitespace"); + return; + } + String regex = context.getExtensionString(ToolingExtensions.EXT_REGEX); + if (regex != null) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().matches(regex), "Element value '" + e.primitiveValue() + "' does not meet regex '" + regex + "'"); + + if (type.equals("boolean")) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, "true".equals(e.primitiveValue()) || "false".equals(e.primitiveValue()), "boolean values must be 'true' or 'false'"); + } + if (type.equals("uri") || type.equals("oid") || type.equals("uuid") || type.equals("url") || type.equals("canonical")) { + String url = e.primitiveValue(); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("oid:"), "URI values cannot start with oid:"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !url.startsWith("uuid:"), "URI values cannot start with uuid:"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.equals(url.trim().replace(" ", "")) + // work around an old invalid example in a core package + || "http://www.acme.com/identifiers/patient or urn:ietf:rfc:3986 if the Identifier.value itself is a full uri".equals(url), "URI values cannot have whitespace('" + url + "')"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || url.length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); + + if (type.equals("oid")) { + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.startsWith("urn:oid:"), "OIDs must start with urn:oid:")) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isOid(url.substring(8)), "OIDs must be valid"); + } + if (type.equals("uuid")) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, url.startsWith("urn:uuid:"), "UUIDs must start with urn:uuid:"); + try { + UUID.fromString(url.substring(8)); + } catch (Exception ex) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "UUIDs must be valid (" + ex.getMessage() + ")"); + } + } + + // now, do we check the URI target? + if (fetcher != null) { + boolean found; + try { + found = isDefinitionURL(url) || (allowExamples && (url.contains("example.org") || url.contains("acme.com"))) || (url.startsWith("http://hl7.org/fhir/tools")) || fetcher.resolveURL(appContext, path, url); + } catch (IOException e1) { + found = false; + } + rule(errors, IssueType.INVALID, e.line(), e.col(), path, found, "URL value '" + url + "' does not resolve"); + } + } + if (type.equals("id")) { + // work around an old issue with ElementDefinition.id + if (!context.getPath().equals("ElementDefinition.id") && !VersionUtilities.versionsCompatible("1.4", this.context.getVersion())) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.isValidId(e.primitiveValue()), "id value '" + e.primitiveValue() + "' is not valid"); + } + } + if (type.equalsIgnoreCase("string") && e.hasPrimitiveValue()) { + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().length() > 0, "@value cannot be empty")) { + warning(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue() == null || e.primitiveValue().trim().equals(e.primitiveValue()), "value should not start or finish with whitespace"); + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().length() <= 1048576, "value is longer than permitted maximum length of 1 MB (1048576 bytes)")) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); + } + } + } + if (type.equals("dateTime")) { + warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, + e.primitiveValue() + .matches("([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)(\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))?)?)?)?"), + "Not a valid date time"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !hasTime(e.primitiveValue()) || hasTimeZone(e.primitiveValue()), "if a date has a time, it must have a timezone"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); + try { + DateTimeType dt = new DateTimeType(e.primitiveValue()); + } catch (Exception ex) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid date/time (" + ex.getMessage() + ")"); + } + } + if (type.equals("time")) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, + e.primitiveValue() + .matches("([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)"), + "Not a valid time"); + try { + TimeType dt = new TimeType(e.primitiveValue()); + } catch (Exception ex) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid time (" + ex.getMessage() + ")"); + } + } + if (type.equals("date")) { + warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, e.primitiveValue().matches("([0-9]([0-9]([0-9][1-9]|[1-9]0)|[1-9]00)|[1-9]000)(-(0[1-9]|1[0-2])(-(0[1-9]|[1-2][0-9]|3[0-1]))?)?"), + "Not a valid date"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum value of " + context.getMaxLength()); + try { + DateType dt = new DateType(e.primitiveValue()); + } catch (Exception ex) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid date (" + ex.getMessage() + ")"); + } + } + if (type.equals("base64Binary")) { + String encoded = e.primitiveValue(); + if (isNotBlank(encoded)) { + /* + * Technically this is not bulletproof as some invalid base64 won't be caught, + * but I think it's good enough. The original code used Java8 Base64 decoder + * but I've replaced it with a regex for 2 reasons: + * 1. This code will run on any version of Java + * 2. This code doesn't actually decode, which is much easier on memory use for big payloads + */ + int charCount = 0; + for (int i = 0; i < encoded.length(); i++) { + char nextChar = encoded.charAt(i); + if (Character.isWhitespace(nextChar)) { + continue; + } + if (Character.isLetterOrDigit(nextChar)) { + charCount++; + } + if (nextChar == '/' || nextChar == '=' || nextChar == '+') { + charCount++; + } + } + + if (charCount > 0 && charCount % 4 != 0) { + String value = encoded.length() < 100 ? encoded : "(snip)"; + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "The value \"{0}\" is not a valid Base64 value", value); + } + } + } + if (type.equals("integer") || type.equals("unsignedInt") || type.equals("positiveInt")) { + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isInteger(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is not a valid integer")) { + Integer v = new Integer(e.getValue()).intValue(); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxValueIntegerType() || !context.getMaxValueIntegerType().hasValue() || (context.getMaxValueIntegerType().getValue() >= v), "value is greater than permitted maximum value of " + (context.hasMaxValueIntegerType() ? context.getMaxValueIntegerType() : "")); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMinValueIntegerType() || !context.getMinValueIntegerType().hasValue() || (context.getMinValueIntegerType().getValue() <= v), "value is less than permitted minimum value of " + (context.hasMinValueIntegerType() ? context.getMinValueIntegerType() : "")); + if (type.equals("unsignedInt")) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, v >= 0, "value is less than permitted minimum value of 0"); + if (type.equals("positiveInt")) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, v > 0, "value is less than permitted minimum value of 1"); + } + } + if (type.equals("integer64")) { + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isLong(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is not a valid integer64")) { + Long v = new Long(e.getValue()).longValue(); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxValueInteger64Type() || !context.getMaxValueInteger64Type().hasValue() || (context.getMaxValueInteger64Type().getValue() >= v), "value is greater than permitted maximum value of " + (context.hasMaxValueInteger64Type() ? context.getMaxValueInteger64Type() : "")); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMinValueInteger64Type() || !context.getMinValueInteger64Type().hasValue() || (context.getMinValueInteger64Type().getValue() <= v), "value is less than permitted minimum value of " + (context.hasMinValueInteger64Type() ? context.getMinValueInteger64Type() : "")); + if (type.equals("unsignedInt")) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, v >= 0, "value is less than permitted minimum value of 0"); + if (type.equals("positiveInt")) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, v > 0, "value is less than permitted minimum value of 1"); + } + } + if (type.equals("decimal")) { + if (e.primitiveValue() != null) { + DecimalStatus ds = Utilities.checkDecimal(e.primitiveValue(), true, false); + if (rule(errors, IssueType.INVALID, e.line(), e.col(), path, ds == DecimalStatus.OK || ds == DecimalStatus.RANGE, "The value '" + e.primitiveValue() + "' is not a valid decimal")) + warning(errors, IssueType.VALUE, e.line(), e.col(), path, ds != DecimalStatus.RANGE, "The value '" + e.primitiveValue() + "' is outside the range of commonly/reasonably supported decimals"); + } + } + if (type.equals("instant")) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, + e.primitiveValue().matches("-?[0-9]{4}-(0[1-9]|1[0-2])-(0[1-9]|[1-2][0-9]|3[0-1])T([01][0-9]|2[0-3]):[0-5][0-9]:([0-5][0-9]|60)(\\.[0-9]+)?(Z|(\\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00))"), + "The instant '" + e.primitiveValue() + "' is not valid (by regex)"); + warning(errors, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), "The value '" + e.primitiveValue() + "' is outside the range of reasonable years - check for data entry error"); + try { + InstantType dt = new InstantType(e.primitiveValue()); + } catch (Exception ex) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Not a valid instant (" + ex.getMessage() + ")"); + } + } + + if (type.equals("code") && e.primitiveValue() != null) { + // Technically, a code is restricted to string which has at least one character and no leading or trailing whitespace, and where there is no whitespace + // other than single spaces in the contents + rule(errors, IssueType.INVALID, e.line(), e.col(), path, passesCodeWhitespaceRules(e.primitiveValue()), "The code '" + e.primitiveValue() + "' is not valid (whitespace rules)"); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, !context.hasMaxLength() || context.getMaxLength() == 0 || e.primitiveValue().length() <= context.getMaxLength(), "value is longer than permitted maximum length of " + context.getMaxLength()); + } + + if (context.hasBinding() && e.primitiveValue() != null) { + checkPrimitiveBinding(errors, path, type, context, e, profile, node); + } + + if (type.equals("xhtml")) { + XhtmlNode xhtml = e.getXhtml(); + if (xhtml != null) { // if it is null, this is an error already noted in the parsers + // check that the namespace is there and correct. + String ns = xhtml.getNsDecl(); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('" + ns + "', should be '" + FormatUtilities.XHTML_NS + "')"); + // check that inner namespaces are all correct + checkInnerNS(errors, e, path, xhtml.getChildNodes()); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, "div".equals(xhtml.getName()), "Wrong name on the XHTML ('" + ns + "') - must start with div"); + // check that no illegal elements and attributes have been used + checkInnerNames(errors, e, path, xhtml.getChildNodes()); + } + } + + if (context.hasFixed()) { + checkFixedValue(errors, path, e, context.getFixed(), profile.getUrl(), context.getSliceName(), null, false); + } + if (context.hasPattern()) { + checkFixedValue(errors, path, e, context.getPattern(), profile.getUrl(), context.getSliceName(), null, true); + } + + // for nothing to check + } + + private boolean isDefinitionURL(String url) { + return Utilities.existsInList(url, "http://hl7.org/fhirpath/System.Boolean", "http://hl7.org/fhirpath/System.String", "http://hl7.org/fhirpath/System.Integer", + "http://hl7.org/fhirpath/System.Decimal", "http://hl7.org/fhirpath/System.Date", "http://hl7.org/fhirpath/System.Time", "http://hl7.org/fhirpath/System.DateTime", "http://hl7.org/fhirpath/System.Quantity"); + } + + private void checkInnerNames(List errors, Element e, String path, List list) { + for (XhtmlNode node : list) { + if (node.getNodeType() == NodeType.Element) { + rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.existsInList(node.getName(), + "p", "br", "div", "h1", "h2", "h3", "h4", "h5", "h6", "a", "span", "b", "em", "i", "strong", + "small", "big", "tt", "small", "dfn", "q", "var", "abbr", "acronym", "cite", "blockquote", "hr", "address", "bdo", "kbd", "q", "sub", "sup", + "ul", "ol", "li", "dl", "dt", "dd", "pre", "table", "caption", "colgroup", "col", "thead", "tr", "tfoot", "tbody", "th", "td", + "code", "samp", "img", "map", "area" + + ), "Illegal element name in the XHTML ('" + node.getName() + "')"); + for (String an : node.getAttributes().keySet()) { + boolean ok = an.startsWith("xmlns") || Utilities.existsInList(an, + "title", "style", "class", "id", "lang", "xml:lang", "dir", "accesskey", "tabindex", + // tables + "span", "width", "align", "valign", "char", "charoff", "abbr", "axis", "headers", "scope", "rowspan", "colspan") || + + Utilities.existsInList(node.getName() + "." + an, "a.href", "a.name", "img.src", "img.border", "div.xmlns", "blockquote.cite", "q.cite", + "a.charset", "a.type", "a.name", "a.href", "a.hreflang", "a.rel", "a.rev", "a.shape", "a.coords", "img.src", + "img.alt", "img.longdesc", "img.height", "img.width", "img.usemap", "img.ismap", "map.name", "area.shape", + "area.coords", "area.href", "area.nohref", "area.alt", "table.summary", "table.width", "table.border", + "table.frame", "table.rules", "table.cellspacing", "table.cellpadding", "pre.space", "td.nowrap" + ); + if (!ok) + rule(errors, IssueType.INVALID, e.line(), e.col(), path, false, "Illegal attribute name in the XHTML ('" + an + "' on '" + node.getName() + "')"); + } + checkInnerNames(errors, e, path, node.getChildNodes()); + } + } + } + + private void checkInnerNS(List errors, Element e, String path, List list) { + for (XhtmlNode node : list) { + if (node.getNodeType() == NodeType.Element) { + String ns = node.getNsDecl(); + rule(errors, IssueType.INVALID, e.line(), e.col(), path, ns == null || FormatUtilities.XHTML_NS.equals(ns), "Wrong namespace on the XHTML ('" + ns + "', should be '" + FormatUtilities.XHTML_NS + "')"); + checkInnerNS(errors, e, path, node.getChildNodes()); + } + } + } + + private void checkPrimitiveBinding(List errors, String path, String type, ElementDefinition elementContext, Element element, StructureDefinition profile, NodeStack stack) { + // We ignore bindings that aren't on string, uri or code + if (!element.hasPrimitiveValue() || !("code".equals(type) || "string".equals(type) || "uri".equals(type) || "url".equals(type) || "canonical".equals(type))) { + return; + } + if (noTerminologyChecks) + return; + + String value = element.primitiveValue(); + // System.out.println("check "+value+" in "+path); + + // firstly, resolve the value set + ElementDefinitionBindingComponent binding = elementContext.getBinding(); + if (binding.hasValueSet()) { + ValueSet vs = resolveBindingReference(profile, binding.getValueSet(), profile.getUrl()); + if (warning(errors, IssueType.CODEINVALID, element.line(), element.col(), path, vs != null, "ValueSet {0} not found by validator", describeReference(binding.getValueSet()))) { + long t = System.nanoTime(); + ValidationResult vr = null; + if (binding.getStrength() != BindingStrength.EXAMPLE) { + vr = context.validateCode(new ValidationOptions(stack.workingLang), value, vs); + } + txTime = txTime + (System.nanoTime() - t); + if (vr != null && !vr.isOk()) { + if (vr.IsNoService()) + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('" + value + "') could not be validated in the absence of a terminology server"); + else if (binding.getStrength() == BindingStrength.REQUIRED) + txRule(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('" + value + "') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is required from this value set)" + getErrorMessage(vr.getMessage())); + else if (binding.getStrength() == BindingStrength.EXTENSIBLE) { + if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) + checkMaxValueSet(errors, path, element, profile, ToolingExtensions.readStringExtension(binding, "http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"), value, stack); + else if (!noExtensibleWarnings) + txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('" + value + "') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code should come from this value set unless it has no suitable code)" + getErrorMessage(vr.getMessage())); + } else if (binding.getStrength() == BindingStrength.PREFERRED) { + if (baseOnly) { + txHint(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, "The value provided ('" + value + "') is not in the value set " + describeReference(binding.getValueSet()) + " (" + vs.getUrl() + ", and a code is recommended to come from this value set)" + getErrorMessage(vr.getMessage())); + } + } + } + } + } else if (!noBindingMsgSuppressed) + hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, !type.equals("code"), "Binding has no source, so can't be checked"); + } + + private void checkQuantity(List errors, String path, Element focus, Quantity fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".value", focus.getNamedChild("value"), fixed.getValueElement(), fixedSource, "value", focus, pattern); + checkFixedValue(errors, path + ".comparator", focus.getNamedChild("comparator"), fixed.getComparatorElement(), fixedSource, "comparator", focus, pattern); + checkFixedValue(errors, path + ".units", focus.getNamedChild("unit"), fixed.getUnitElement(), fixedSource, "units", focus, pattern); + checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), fixedSource, "system", focus, pattern); + checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), fixedSource, "code", focus, pattern); + } + + // implementation + + private void checkRange(List errors, String path, Element focus, Range fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".low", focus.getNamedChild("low"), fixed.getLow(), fixedSource, "low", focus, pattern); + checkFixedValue(errors, path + ".high", focus.getNamedChild("high"), fixed.getHigh(), fixedSource, "high", focus, pattern); + + } + + private void checkRatio(List errors, String path, Element focus, Ratio fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".numerator", focus.getNamedChild("numerator"), fixed.getNumerator(), fixedSource, "numerator", focus, pattern); + checkFixedValue(errors, path + ".denominator", focus.getNamedChild("denominator"), fixed.getDenominator(), fixedSource, "denominator", focus, pattern); + } + + private void checkReference(ValidatorHostContext hostContext, List errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException { + Reference reference = ObjectConverter.readAsReference(element); + + String ref = reference.getReference(); + if (Utilities.noString(ref)) { + if (Utilities.noString(reference.getIdentifier().getSystem()) && Utilities.noString(reference.getIdentifier().getValue())) { + warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference or identifier should have a display"); + } + return; + } else if (Utilities.existsInList(ref, "http://tools.ietf.org/html/bcp47")) { + // special known URLs that can't be validated but are known to be valid + return; + } + + ResolvedReference we = localResolve(ref, stack, errors, path, (Element) hostContext.getAppContext(), element); + String refType; + if (ref.startsWith("#")) { + refType = "contained"; + } else { + if (we == null) { + refType = "remote"; + } else { + refType = "bundled"; + } + } + ReferenceValidationPolicy pol = refType.equals("contained") || refType.equals("bundled") ? ReferenceValidationPolicy.CHECK_VALID : fetcher == null ? ReferenceValidationPolicy.IGNORE : fetcher.validationPolicy(hostContext.getAppContext(), path, ref); + + if (pol.checkExists()) { + if (we == null) { + if (fetcher == null) { + if (!refType.equals("contained")) + throw new FHIRException("Resource resolution services not provided"); + } else { + Element ext = null; + if (fetchCache.containsKey(ref)) { + ext = fetchCache.get(ref); + } else { + try { + ext = fetcher.fetch(hostContext.getAppContext(), ref); + } catch (IOException e) { + throw new FHIRException(e); + } + if (ext != null) { + fetchCache.put(ref, ext); + } + } + we = ext == null ? null : makeExternalRef(ext, path); + } + } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, (allowExamples && (ref.contains("example.org") || ref.contains("acme.com"))) || (we != null || pol == ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS), "Unable to resolve resource '" + ref + "'"); + } + + String ft; + if (we != null) + ft = we.getType(); + else + ft = tryParse(ref); + + if (reference.hasType()) { // R4 onwards... + // the type has to match the specified + String tu = isAbsolute(reference.getType()) ? reference.getType() : "http://hl7.org/fhir/StructureDefinition/" + reference.getType(); + TypeRefComponent containerType = container.getType("Reference"); + if (!containerType.hasTargetProfile(tu) && !containerType.hasTargetProfile("http://hl7.org/fhir/StructureDefinition/Resource")) { + boolean matchingResource = false; + for (CanonicalType target : containerType.getTargetProfile()) { + StructureDefinition sd = resolveProfile(profile, target.asStringValue()); + if (("http://hl7.org/fhir/StructureDefinition/" + sd.getType()).equals(tu)) { + matchingResource = true; + break; + } + } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, matchingResource, + "The type '" + reference.getType() + "' is not a valid Target for this element (must be one of " + container.getType("Reference").getTargetProfile() + ")"); + + } + // the type has to match the actual + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft == null || ft.equals(reference.getType()), "The specified type '" + reference.getType() + "' does not match the found type '" + ft + "'"); + } + + if (we != null && pol.checkType()) { + if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ft != null, "Unable to determine type of target resource")) { + // we validate as much as we can. First, can we infer a type from the profile? + boolean ok = false; + TypeRefComponent type = getReferenceTypeRef(container.getType()); + if (type.hasTargetProfile() && !type.hasTargetProfile("http://hl7.org/fhir/StructureDefinition/Resource")) { + Set types = new HashSet<>(); + List profiles = new ArrayList<>(); + for (UriType u : type.getTargetProfile()) { + StructureDefinition sd = resolveProfile(profile, u.getValue()); + if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, sd != null, "Unable to resolve the profile reference '" + u.getValue() + "'")) { + types.add(sd.getType()); + if (ft.equals(sd.getType())) { + ok = true; + profiles.add(sd); + } + } + } + if (!pol.checkValid()) { + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, profiles.size() > 0, "Unable to find matching profile for " + ref + " (by type) among choices: " + StringUtils.join("; ", type.getTargetProfile())); + } else { + Map> badProfiles = new HashMap>(); + Map> goodProfiles = new HashMap>(); + int goodCount = 0; + for (StructureDefinition pr : profiles) { + List profileErrors = new ArrayList(); + validateResource(we.hostContext(hostContext, pr), profileErrors, we.getResource(), we.getFocus(), pr, IdStatus.OPTIONAL, we.getStack()); + if (!hasErrors(profileErrors)) { + goodCount++; + goodProfiles.put(pr, profileErrors); + trackUsage(pr, hostContext, element); + } else { + badProfiles.put(pr, profileErrors); + } + } + if (goodCount == 1) { + if (showMessagesFromReferences) { + for (ValidationMessage vm : goodProfiles.values().iterator().next()) { + if (!errors.contains(vm)) { + errors.add(vm); + } + } + } + + } else if (goodProfiles.size() == 0) { + if (!isShowMessagesFromReferences()) { + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, areAllBaseProfiles(profiles), "Unable to find matching profile for " + ref + " among choices: " + asList(type.getTargetProfile())); + for (StructureDefinition sd : badProfiles.keySet()) { + slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for " + ref + " matching against Profile" + sd.getUrl(), errorSummaryForSlicingAsHtml(badProfiles.get(sd))); + } + } else { + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, profiles.size() == 1, "Unable to find matching profile for " + ref + " among choices: " + asList(type.getTargetProfile())); + for (List messages : badProfiles.values()) { + for (ValidationMessage vm : messages) { + if (!errors.contains(vm)) { + errors.add(vm); + } + } + } + } + } else { + if (!isShowMessagesFromReferences()) { + warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Found multiple matching profiles for " + ref + " among choices: " + asListByUrl(goodProfiles.keySet())); + for (StructureDefinition sd : badProfiles.keySet()) { + slicingHint(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for " + ref + " matching against Profile" + sd.getUrl(), errorSummaryForSlicingAsHtml(badProfiles.get(sd))); + } + } else { + warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Found multiple matching profiles for " + ref + " among choices: " + asListByUrl(goodProfiles.keySet())); + for (List messages : goodProfiles.values()) { + for (ValidationMessage vm : messages) { + if (!errors.contains(vm)) { + errors.add(vm); + } + } + } + } + } + } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, ok, "Invalid Resource target type. Found " + ft + ", but expected one of (" + types.toString() + ")"); + } + if (type.hasAggregation()) { + boolean modeOk = false; + for (Enumeration mode : type.getAggregation()) { + if (mode.getValue().equals(AggregationMode.CONTAINED) && refType.equals("contained")) + modeOk = true; + else if (mode.getValue().equals(AggregationMode.BUNDLED) && refType.equals("bundled")) + modeOk = true; + else if (mode.getValue().equals(AggregationMode.REFERENCED) && (refType.equals("bundled") || refType.equals("remote"))) + modeOk = true; + } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, modeOk, "Reference is " + refType + " which isn't supported by the specified aggregation mode(s) for the reference"); + } + } + } + if (we == null) { + TypeRefComponent type = getReferenceTypeRef(container.getType()); + boolean okToRef = !type.hasAggregation() || type.hasAggregation(AggregationMode.REFERENCED); + rule(errors, IssueType.REQUIRED, -1, -1, path, okToRef, "Bundled or contained reference not found within the bundle/resource " + ref); + } + if (we == null && ft != null && assumeValidRestReferences) { + // if we == null, we inferred ft from the reference. if we are told to treat this as gospel + TypeRefComponent type = getReferenceTypeRef(container.getType()); + Set types = new HashSet<>(); + for (CanonicalType tp : type.getTargetProfile()) { + StructureDefinition sd = context.fetchResource(StructureDefinition.class, tp.getValue()); + if (sd != null) { + types.add(sd.getType()); + } + } + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), path, types.isEmpty() || types.contains(ft), "The type '" + ft + "' implied by the reference URL " + ref + " is not a valid Target for this element (must be one of " + types + ")"); + + } + if (pol == ReferenceValidationPolicy.CHECK_VALID) { + // todo.... + } + } + + private String asListByUrl(Collection list) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (StructureDefinition sd : list) { + b.append(sd.getUrl()); + } + return b.toString(); + } + + private String asList(Collection list) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (CanonicalType c : list) { + b.append(c.getValue()); + } + return b.toString(); + } + + private boolean areAllBaseProfiles(List profiles) { + for (StructureDefinition sd : profiles) { + if (!sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/")) { + return false; + } + } return true; } - return false; - } - private boolean codeInExpansion(ValueSet vs, String system, String code) { - for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) { - if (code.equals(c.getCode()) && (system == null || system.equals(c.getSystem()))) - return true; - if (codeinExpansion(c, system, code)) - return true; + private String errorSummaryForSlicing(List list) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (ValidationMessage vm : list) { + if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL || vm.isSlicingHint()) { + b.append(vm.getLocation() + ": " + vm.getMessage()); + } + } + return b.toString(); } - return false; - } - private String describeReference(String reference) { - if (reference == null) - return "null"; - return reference; - } - - private String describeReference(String reference, CanonicalResource target) { - if (reference == null && target == null) - return "null"; - if (reference == null) { - return target.getUrl(); + private String errorSummaryForSlicingAsHtml(List list) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (ValidationMessage vm : list) { + if (vm.isSlicingHint()) { + b.append("
  • " + vm.getLocation() + ": " + vm.getSliceHtml() + "
    • "); + } else if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL) { + b.append("
  • " + vm.getLocation() + ": " + vm.getHtml() + "
    • "); + } + } + return "
      " + b.toString() + "
    "; } - if (target == null) { - return reference; - } - if (reference.equals(target.getUrl())) { - return reference; - } - return reference+"(which actually refers to "+target.getUrl()+")"; - } - private String describeTypes(List types) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - for (TypeRefComponent t : types) { - b.append(t.getWorkingCode()); + private TypeRefComponent getReferenceTypeRef(List types) { + for (TypeRefComponent tr : types) { + if ("Reference".equals(tr.getCode())) { + return tr; + } + } + return null; } - return b.toString(); - } - protected ElementDefinition findElement(StructureDefinition profile, String name) { - for (ElementDefinition c : profile.getSnapshot().getElement()) { - if (c.getPath().equals(name)) { - return c; - } + private String checkResourceType(String type) { + long t = System.nanoTime(); + try { + if (context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + type) != null) + return type; + else + return null; + } finally { + sdTime = sdTime + (System.nanoTime() - t); + } } - return null; - } - public BestPracticeWarningLevel getBestPracticeWarningLevel() { - return bpWarnings; - } - - @Override - public CheckDisplayOption getCheckDisplay() { - return checkDisplay; - } - - private ConceptDefinitionComponent getCodeDefinition(ConceptDefinitionComponent c, String code) { - if (code.equals(c.getCode())) - return c; - for (ConceptDefinitionComponent g : c.getConcept()) { - ConceptDefinitionComponent r = getCodeDefinition(g, code); - if (r != null) - return r; + private void checkSampledData(List errors, String path, Element focus, SampledData fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".origin", focus.getNamedChild("origin"), fixed.getOrigin(), fixedSource, "origin", focus, pattern); + checkFixedValue(errors, path + ".period", focus.getNamedChild("period"), fixed.getPeriodElement(), fixedSource, "period", focus, pattern); + checkFixedValue(errors, path + ".factor", focus.getNamedChild("factor"), fixed.getFactorElement(), fixedSource, "factor", focus, pattern); + checkFixedValue(errors, path + ".lowerLimit", focus.getNamedChild("lowerLimit"), fixed.getLowerLimitElement(), fixedSource, "lowerLimit", focus, pattern); + checkFixedValue(errors, path + ".upperLimit", focus.getNamedChild("upperLimit"), fixed.getUpperLimitElement(), fixedSource, "upperLimit", focus, pattern); + checkFixedValue(errors, path + ".dimensions", focus.getNamedChild("dimensions"), fixed.getDimensionsElement(), fixedSource, "dimensions", focus, pattern); + checkFixedValue(errors, path + ".data", focus.getNamedChild("data"), fixed.getDataElement(), fixedSource, "data", focus, pattern); } - return null; - } - private ConceptDefinitionComponent getCodeDefinition(CodeSystem cs, String code) { - for (ConceptDefinitionComponent c : cs.getConcept()) { - ConceptDefinitionComponent r = getCodeDefinition(c, code); - if (r != null) - return r; + private void checkTiming(List errors, String path, Element focus, Timing fixed, String fixedSource, boolean pattern) { + checkFixedValue(errors, path + ".repeat", focus.getNamedChild("repeat"), fixed.getRepeat(), fixedSource, "value", focus, pattern); + + List events = new ArrayList(); + focus.getNamedChildren("event", events); + if (rule(errors, IssueType.VALUE, focus.line(), focus.col(), path, events.size() == fixed.getEvent().size(), + "Expected " + Integer.toString(fixed.getEvent().size()) + " but found " + Integer.toString(events.size()) + " event elements")) { + for (int i = 0; i < events.size(); i++) + checkFixedValue(errors, path + ".event", events.get(i), fixed.getEvent().get(i), fixedSource, "event", focus, pattern); + } + } + + private boolean codeinExpansion(ValueSetExpansionContainsComponent cnt, String system, String code) { + for (ValueSetExpansionContainsComponent c : cnt.getContains()) { + if (code.equals(c.getCode()) && system.equals(c.getSystem().toString())) + return true; + if (codeinExpansion(c, system, code)) + return true; + } + return false; + } + + private boolean codeInExpansion(ValueSet vs, String system, String code) { + for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) { + if (code.equals(c.getCode()) && (system == null || system.equals(c.getSystem()))) + return true; + if (codeinExpansion(c, system, code)) + return true; + } + return false; + } + + private String describeReference(String reference) { + if (reference == null) + return "null"; + return reference; + } + + private String describeReference(String reference, CanonicalResource target) { + if (reference == null && target == null) + return "null"; + if (reference == null) { + return target.getUrl(); + } + if (target == null) { + return reference; + } + if (reference.equals(target.getUrl())) { + return reference; + } + return reference + "(which actually refers to " + target.getUrl() + ")"; + } + + private String describeTypes(List types) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + for (TypeRefComponent t : types) { + b.append(t.getWorkingCode()); + } + return b.toString(); + } + + protected ElementDefinition findElement(StructureDefinition profile, String name) { + for (ElementDefinition c : profile.getSnapshot().getElement()) { + if (c.getPath().equals(name)) { + return c; + } + } + return null; + } + + public BestPracticeWarningLevel getBestPracticeWarningLevel() { + return bpWarnings; + } + + @Override + public CheckDisplayOption getCheckDisplay() { + return checkDisplay; + } + + private ConceptDefinitionComponent getCodeDefinition(ConceptDefinitionComponent c, String code) { + if (code.equals(c.getCode())) + return c; + for (ConceptDefinitionComponent g : c.getConcept()) { + ConceptDefinitionComponent r = getCodeDefinition(g, code); + if (r != null) + return r; + } + return null; + } + + private ConceptDefinitionComponent getCodeDefinition(CodeSystem cs, String code) { + for (ConceptDefinitionComponent c : cs.getConcept()) { + ConceptDefinitionComponent r = getCodeDefinition(c, code); + if (r != null) + return r; + } + return null; } - return null; - } private IndexedElement getContainedById(Element container, String id) { - List contained = new ArrayList(); - container.getNamedChildren("contained", contained); - for (int i = 0; i < contained.size(); i++) { - Element we = contained.get(i); - if (id.equals(we.getNamedChildValue("id"))) { - return new IndexedElement(i, we, null); - } - } - return null; - } - - public IWorkerContext getContext() { - return context; - } - - private List getCriteriaForDiscriminator(String path, ElementDefinition element, String discriminator, StructureDefinition profile, boolean removeResolve) throws FHIRException { - List elements = new ArrayList(); - if ("value".equals(discriminator) && element.hasFixed()) { - elements.add(element); - return elements; - } - - if (removeResolve) { // if we're doing profile slicing, we don't want to walk into the last resolve.. we need the profile on the source not the target - if (discriminator.equals("resolve()")) { - elements.add(element); - return elements; - } - if (discriminator.endsWith(".resolve()")) - discriminator = discriminator.substring(0, discriminator.length() - 10); - } - - ElementDefinition ed = null; - ExpressionNode expr = fpe.parse(fixExpr(discriminator)); - long t2 = System.nanoTime(); - ed = fpe.evaluateDefinition(expr, profile, element); - sdTime = sdTime + (System.nanoTime() - t2); - if (ed!= null) - elements.add(ed); - - for (TypeRefComponent type: element.getType()) { - for (CanonicalType p: type.getProfile()) { - String id = p.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT) ? p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT) : null; - StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue()); - if (sd == null) - throw new DefinitionException("Unable to resolve profile "+p); - profile = sd; - if (id == null) - element = sd.getSnapshot().getElementFirstRep(); - else { - element = null; - for (ElementDefinition t : sd.getSnapshot().getElement()) { - if (id.equals(t.getId())) - element = t; - } - if (element == null) - throw new DefinitionException("Unable to resolve element "+id+" in profile "+p); + List contained = new ArrayList(); + container.getNamedChildren("contained", contained); + for (int i = 0; i < contained.size(); i++) { + Element we = contained.get(i); + if (id.equals(we.getNamedChildValue("id"))) { + return new IndexedElement(i, we, null); + } } - expr = fpe.parse(fixExpr(discriminator)); - t2 = System.nanoTime(); + return null; + } + + public IWorkerContext getContext() { + return context; + } + + private List getCriteriaForDiscriminator(String path, ElementDefinition element, String discriminator, StructureDefinition profile, boolean removeResolve) throws FHIRException { + List elements = new ArrayList(); + if ("value".equals(discriminator) && element.hasFixed()) { + elements.add(element); + return elements; + } + + if (removeResolve) { // if we're doing profile slicing, we don't want to walk into the last resolve.. we need the profile on the source not the target + if (discriminator.equals("resolve()")) { + elements.add(element); + return elements; + } + if (discriminator.endsWith(".resolve()")) + discriminator = discriminator.substring(0, discriminator.length() - 10); + } + + ElementDefinition ed = null; + ExpressionNode expr = fpe.parse(fixExpr(discriminator)); + long t2 = System.nanoTime(); ed = fpe.evaluateDefinition(expr, profile, element); sdTime = sdTime + (System.nanoTime() - t2); if (ed != null) - elements.add(ed); - } - } - return elements; - } + elements.add(ed); - - private Element getExtensionByUrl(List extensions, String urlSimple) { - for (Element e : extensions) { - if (urlSimple.equals(e.getNamedChildValue("url"))) - return e; - } - return null; - } - - public List getExtensionDomains() { - return extensionDomains; - } - - private IndexedElement getFromBundle(Element bundle, String ref, String fullUrl, List errors, String path, String type, boolean isTransaction) { - String targetUrl = null; - String version = ""; - String resourceType = null; - if (ref.startsWith("http") || ref.startsWith("urn")) { - // We've got an absolute reference, no need to calculate - if (ref.contains("/_history/")) { - targetUrl = ref.substring(0, ref.indexOf("/_history/") - 1); - version = ref.substring(ref.indexOf("/_history/") + 10); - } else - targetUrl = ref; - - } else if (fullUrl == null) { - //This isn't a problem for signatures - if it's a signature, we won't have a resolution for a relative reference. For anything else, this is an error - // but this rule doesn't apply for batches or transactions - rule(errors, IssueType.REQUIRED, -1, -1, path, Utilities.existsInList(type, "batch-response", "transaction-response") || path.startsWith("Bundle.signature"), "Relative Reference appears inside Bundle whose entry is missing a fullUrl"); - return null; - - } else if (ref.split("/").length!=2 && ref.split("/").length!=4) { - if (isTransaction) { - rule(errors, IssueType.INVALID, -1, -1, path, isSearchUrl(ref), "Relative URLs must be of the format [ResourceName]/[id], or a search ULR is allowed ([type]?parameters. Encountered " + ref); - } else { - rule(errors, IssueType.INVALID, -1, -1, path, false, "Relative URLs must be of the format [ResourceName]/[id]. Encountered " + ref); - } - return null; - - } else { - String base = ""; - if (fullUrl.startsWith("urn")) { - String[] parts = fullUrl.split("\\:"); - for (int i=0; i < parts.length-1; i++) { - base = base + parts[i] + ":"; - } - } else { - String[] parts; - parts = fullUrl.split("/"); - for (int i=0; i < parts.length-2; i++) { - base = base + parts[i] + "/"; - } - } - - String id = null; - if (ref.contains("/_history/")) { - version = ref.substring(ref.indexOf("/_history/") + 10); - String[] refBaseParts = ref.substring(0, ref.indexOf("/_history/")).split("/"); - resourceType = refBaseParts[0]; - id = refBaseParts[1]; - } else if (base.startsWith("urn")) { - resourceType = ref.split("/")[0]; - id = ref.split("/")[1]; - } else - id = ref; - - targetUrl = base + id; - } - - List entries = new ArrayList(); - bundle.getNamedChildren("entry", entries); - Element match = null; - int matchIndex = -1; - for (int i = 0; i < entries.size(); i++) { - Element we = entries.get(i); - if (targetUrl.equals(we.getChildValue("fullUrl"))) { - Element r = we.getNamedChild("resource"); - if (version.isEmpty()) { - rule(errors, IssueType.FORBIDDEN, -1, -1, path, match==null, "Multiple matches in bundle for reference " + ref); - match = r; - matchIndex = i; - } else { - try { - if (version.equals(r.getChildren("meta").get(0).getChildValue("versionId"))) { - rule(errors, IssueType.FORBIDDEN, -1, -1, path, match==null, "Multiple matches in bundle for reference " + ref); - match = r; - matchIndex = i; + for (TypeRefComponent type : element.getType()) { + for (CanonicalType p : type.getProfile()) { + String id = p.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT) ? p.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT) : null; + StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue()); + if (sd == null) + throw new DefinitionException("Unable to resolve profile " + p); + profile = sd; + if (id == null) + element = sd.getSnapshot().getElementFirstRep(); + else { + element = null; + for (ElementDefinition t : sd.getSnapshot().getElement()) { + if (id.equals(t.getId())) + element = t; + } + if (element == null) + throw new DefinitionException("Unable to resolve element " + id + " in profile " + p); + } + expr = fpe.parse(fixExpr(discriminator)); + t2 = System.nanoTime(); + ed = fpe.evaluateDefinition(expr, profile, element); + sdTime = sdTime + (System.nanoTime() - t2); + if (ed != null) + elements.add(ed); } - } catch (Exception e) { - warning(errors, IssueType.REQUIRED, -1, -1, path, r.getChildren("meta").size()==1 && r.getChildren("meta").get(0).getChildValue("versionId")!=null, "Entries matching fullURL " + targetUrl + " should declare meta/versionId because there are version-specific references"); - // If one of these things is null - } } - } + return elements; } - if (match!=null && resourceType!=null) - rule(errors, IssueType.REQUIRED, -1, -1, path, match.getType().equals(resourceType), "Matching reference for reference " + ref + " has resourceType " + match.getType()); - if (match == null) - warning(errors, IssueType.REQUIRED, -1, -1, path, !ref.startsWith("urn"), "URN reference is not locally contained within the bundle " + ref); - return match == null ? null : new IndexedElement(matchIndex, match, entries.get(matchIndex)); - } - private boolean isSearchUrl(String ref) { - if (Utilities.noString(ref) || !ref.contains("?")) { - return false; - } - String tn = ref.substring(0, ref.indexOf("?")); - String q = ref.substring(ref.indexOf("?")+1); - if (!context.getResourceNames().contains(tn)) { - return false; - } else { - return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*"); - } - } - - private StructureDefinition getProfileForType(String type, List list) { - for (TypeRefComponent tr : list) { - String url = tr.getWorkingCode(); - if (!Utilities.isAbsoluteUrl(url)) - url = "http://hl7.org/fhir/StructureDefinition/" + url; - long t = System.nanoTime(); - StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); - sdTime = sdTime + (System.nanoTime() - t); - if (sd != null && (sd.getType().equals(type) || sd.getUrl().equals(type)) && sd.hasSnapshot()) - return sd; - } - return null; - } - - private Element getValueForDiscriminator(Object appContext, List errors, Element element, String discriminator, ElementDefinition criteria, NodeStack stack) throws FHIRException, IOException { - String p = stack.getLiteralPath()+"."+element.getName(); - Element focus = element; - String[] dlist = discriminator.split("\\."); - for (String d : dlist) { - if (focus.fhirType().equals("Reference") && d.equals("reference")) { - String url = focus.getChildValue("reference"); - if (Utilities.noString(url)) - throw new FHIRException("No reference resolving discriminator "+discriminator+" from "+element.getProperty().getName()); - // Note that we use the passed in stack here. This might be a problem if the discriminator is deep enough? - Element target = resolve(appContext, url, stack, errors, p); - if (target == null) - throw new FHIRException("Unable to find resource "+url+" at "+d+" resolving discriminator "+discriminator+" from "+element.getProperty().getName()); - focus = target; - } else if (d.equals("value") && focus.isPrimitive()) { - return focus; - } else { - List children = focus.getChildren(d); - if (children.isEmpty()) - throw new FHIRException("Unable to find "+d+" resolving discriminator "+discriminator+" from "+element.getProperty().getName()); - if (children.size() > 1) - throw new FHIRException("Found "+Integer.toString(children.size())+" items for "+d+" resolving discriminator "+discriminator+" from "+element.getProperty().getName()); - focus = children.get(0); - p = p + "."+d; - } - } - return focus; - } - - private CodeSystem getCodeSystem(String system) { - long t = System.nanoTime(); - try { - return context.fetchCodeSystem(system); - } finally { - txTime = txTime + (System.nanoTime() - t); - } - } - - private boolean hasTime(String fmt) { - return fmt.contains("T"); - } - - private boolean hasTimeZone(String fmt) { - return fmt.length() > 10 && (fmt.substring(10).contains("-") || fmt.substring(10).contains("+") || fmt.substring(10).contains("Z")); - } - - private boolean isAbsolute(String uri) { - return Utilities.noString(uri) || uri.startsWith("http:") || uri.startsWith("https:") || uri.startsWith("urn:uuid:") || uri.startsWith("urn:oid:") || uri.startsWith("urn:ietf:") - || uri.startsWith("urn:iso:") || uri.startsWith("urn:iso-astm:") || isValidFHIRUrn(uri); - } - - private boolean isValidFHIRUrn(String uri) { - return (uri.equals("urn:x-fhir:uk:id:nhs-number")) || uri.startsWith("urn:"); // Anyone can invent a URN, so why should we complain? - } - - public boolean isAnyExtensionsAllowed() { - return anyExtensionsAllowed; - } - - public boolean isErrorForUnknownProfiles() { - return errorForUnknownProfiles; - } - - public void setErrorForUnknownProfiles(boolean errorForUnknownProfiles) { - this.errorForUnknownProfiles = errorForUnknownProfiles; - } - - private boolean isParametersEntry(String path) { - String[] parts = path.split("\\."); - return parts.length > 2 && parts[parts.length - 1].equals("resource") && (pathEntryHasName(parts[parts.length - 2], "parameter") || pathEntryHasName(parts[parts.length - 2], "part")); - } - - private boolean isBundleEntry(String path) { - String[] parts = path.split("\\."); - return parts.length > 2 && parts[parts.length - 1].equals("resource") && pathEntryHasName(parts[parts.length - 2], "entry"); - } - - private boolean isBundleOutcome(String path) { - String[] parts = path.split("\\."); - return parts.length > 2 && parts[parts.length - 1].equals("outcome") && pathEntryHasName(parts[parts.length - 2], "response"); - } - - - private static boolean pathEntryHasName(String thePathEntry, String theName) { - if (thePathEntry.equals(theName)) { - return true; - } - if (thePathEntry.length() >= theName.length() + 3) { - if (thePathEntry.startsWith(theName)) { - if (thePathEntry.charAt(theName.length()) == '[') { - return true; - } - } - } - return false; - } - - public boolean isPrimitiveType(String code) { - StructureDefinition sd = context.fetchTypeDefinition(code); - return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE; - } - - private String getErrorMessage(String message) { - return message != null ? " (error message = " + message + ")" : ""; - } - - public boolean isSuppressLoincSnomedMessages() { - return suppressLoincSnomedMessages; - } - - private boolean nameMatches(String name, String tail) { - if (tail.endsWith("[x]")) - return name.startsWith(tail.substring(0, tail.length() - 3)); - else - return (name.equals(tail)); - } - - private boolean passesCodeWhitespaceRules(String v) { - if (!v.trim().equals(v)) - return false; - boolean lastWasSpace = true; - for (char c : v.toCharArray()) { - if (c == ' ') { - if (lastWasSpace) - return false; - else - lastWasSpace = true; - } else if (Character.isWhitespace(c)) - return false; - else - lastWasSpace = false; - } - return true; - } - - private ResolvedReference localResolve(String ref, NodeStack stack, List errors, String path, Element hostContext, Element source) { - if (ref.startsWith("#")) { - // work back through the parent list. - // really, there should only be one level for this (contained resources cannot contain - // contained resources), but we'll leave that to some other code to worry about - while (stack != null && stack.getElement() != null) { - if (stack.getElement().getProperty().isResource()) { - // ok, we'll try to find the contained reference - IndexedElement res = getContainedById(stack.getElement(), ref.substring(1)); - if (res != null) { - ResolvedReference rr = new ResolvedReference(); - rr.setResource(stack.getElement()); - rr.setFocus(res.getMatch()); - rr.setExternal(false); - rr.setStack(stack.push(res.getMatch(), res.getIndex(), res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); - return rr; - } - } - if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY) { - return null; // we don't try to resolve contained references across this boundary - } - stack = stack.parent; - } - return null; - } else { - // work back through the parent list - if any of them are bundles, try to resolve - // the resource in the bundle - String fullUrl = null; // we're going to try to work this out as we go up - while (stack != null && stack.getElement() != null) { - if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY && fullUrl==null && stack.parent != null && stack.parent.getElement().getName().equals("entry")) { - String type = stack.parent.parent.element.getChildValue("type"); - fullUrl = stack.parent.getElement().getChildValue("fullUrl"); // we don't try to resolve contained references across this boundary - if (fullUrl==null) - rule(errors, IssueType.REQUIRED, stack.parent.getElement().line(), stack.parent.getElement().col(), stack.parent.getLiteralPath(), - Utilities.existsInList(type, "batch-response", "transaction-response") || fullUrl!=null, "Bundle entry missing fullUrl"); - } - if ("Bundle".equals(stack.getElement().getType())) { - String type = stack.getElement().getChildValue("type"); - IndexedElement res = getFromBundle(stack.getElement(), ref, fullUrl, errors, path, type, "transaction".equals(type)); - if (res == null) { - return null; - } else { - ResolvedReference rr = new ResolvedReference(); - rr.setResource(res.getMatch()); - rr.setFocus(res.getMatch()); - rr.setExternal(false); - rr.setStack(stack.push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), - res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, - res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); - return rr; - } - } - stack = stack.parent; - } - // we can get here if we got called via FHIRPath conformsTo which breaks the stack continuity. - if (hostContext != null && "Bundle".equals(hostContext.fhirType())) { - String type = hostContext.getChildValue("type"); - Element entry = getEntryForSource(hostContext, source); - fullUrl = entry.getChildValue("fullUrl"); - IndexedElement res = getFromBundle(hostContext, ref, fullUrl, errors, path, type, "transaction".equals(type)); - if (res == null) { - return null; - } else { - ResolvedReference rr = new ResolvedReference(); - rr.setResource(res.getMatch()); - rr.setFocus(res.getMatch()); - rr.setExternal(false); - rr.setStack(new NodeStack(hostContext).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), - res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, - res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); - return rr; - } - } - } - return null; - } - - private Element getEntryForSource(Element bundle, Element element) { - List entries = new ArrayList(); - bundle.getNamedChildren("entry", entries); - for (Element entry : entries) { - if (entry.hasDescendant(element)) { - return entry; - } - } - return null; - } - - private ResolvedReference makeExternalRef(Element external, String path) { - ResolvedReference res = new ResolvedReference(); - res.setResource(external); - res.setFocus(external); - res.setExternal(true); - res.setStack(new NodeStack(external, path)); - return res; - } - - - private Element resolve(Object appContext, String ref, NodeStack stack, List errors, String path) throws IOException, FHIRException { - Element local = localResolve(ref, stack, errors, path, null, null).getFocus(); - if (local!=null) - return local; - if (fetcher == null) - return null; - if (fetchCache.containsKey(ref)) { - return fetchCache.get(ref); - } else { - Element res = fetcher.fetch(appContext, ref); - fetchCache.put(ref, res); - return res; - } - } - - private ValueSet resolveBindingReference(DomainResource ctxt, String reference, String uri) { - if (reference != null) { - if (reference.startsWith("#")) { - for (Resource c : ctxt.getContained()) { - if (c.getId().equals(reference.substring(1)) && (c instanceof ValueSet)) - return (ValueSet) c; + private Element getExtensionByUrl(List extensions, String urlSimple) { + for (Element e : extensions) { + if (urlSimple.equals(e.getNamedChildValue("url"))) + return e; } return null; - } else { - long t = System.nanoTime(); - ValueSet fr = context.fetchResource(ValueSet.class, reference); - if (fr == null) { - if (!Utilities.isAbsoluteUrl(reference)) { - reference = resolve(uri, reference); - fr = context.fetchResource(ValueSet.class, reference); - } - } - if (fr == null) - fr = ValueSetUtilities.generateImplicitValueSet(reference); - txTime = txTime + (System.nanoTime() - t); - return fr; - } - } else - return null; - } - - private String resolve(String uri, String ref) { - if (isBlank(uri)) { - return ref; } - String[] up = uri.split("\\/"); - String[] rp = ref.split("\\/"); - if (context.getResourceNames().contains(up[up.length-2]) && context.getResourceNames().contains(rp[0])) { - StringBuilder b = new StringBuilder(); - for (int i = 0; i < up.length-2; i++) { - b.append(up[i]); - b.append("/"); - } - b.append(ref); - return b.toString(); - } else - return ref; - } - private Element resolveInBundle(List entries, String ref, String fullUrl, String type, String id) { - if (Utilities.isAbsoluteUrl(ref)) { - // if the reference is absolute, then you resolve by fullUrl. No other thinking is required. - for (Element entry : entries) { - String fu = entry.getNamedChildValue("fullUrl"); - if (ref.equals(fu)) - return entry; - } - return null; - } else { - // split into base, type, and id - String u = null; - if (fullUrl != null && fullUrl.endsWith(type+"/"+id)) - // fullUrl = complex - u = fullUrl.substring(0, fullUrl.length() - (type+"/"+id).length())+ref; -// u = fullUrl.substring((type+"/"+id).length())+ref; - String[] parts = ref.split("\\/"); - if (parts.length >= 2) { - String t = parts[0]; - String i = parts[1]; + public List getExtensionDomains() { + return extensionDomains; + } + + private IndexedElement getFromBundle(Element bundle, String ref, String fullUrl, List errors, String path, String type, boolean isTransaction) { + String targetUrl = null; + String version = ""; + String resourceType = null; + if (ref.startsWith("http") || ref.startsWith("urn")) { + // We've got an absolute reference, no need to calculate + if (ref.contains("/_history/")) { + targetUrl = ref.substring(0, ref.indexOf("/_history/") - 1); + version = ref.substring(ref.indexOf("/_history/") + 10); + } else + targetUrl = ref; + + } else if (fullUrl == null) { + //This isn't a problem for signatures - if it's a signature, we won't have a resolution for a relative reference. For anything else, this is an error + // but this rule doesn't apply for batches or transactions + rule(errors, IssueType.REQUIRED, -1, -1, path, Utilities.existsInList(type, "batch-response", "transaction-response") || path.startsWith("Bundle.signature"), "Relative Reference appears inside Bundle whose entry is missing a fullUrl"); + return null; + + } else if (ref.split("/").length != 2 && ref.split("/").length != 4) { + if (isTransaction) { + rule(errors, IssueType.INVALID, -1, -1, path, isSearchUrl(ref), "Relative URLs must be of the format [ResourceName]/[id], or a search ULR is allowed ([type]?parameters. Encountered " + ref); + } else { + rule(errors, IssueType.INVALID, -1, -1, path, false, "Relative URLs must be of the format [ResourceName]/[id]. Encountered " + ref); + } + return null; + + } else { + String base = ""; + if (fullUrl.startsWith("urn")) { + String[] parts = fullUrl.split("\\:"); + for (int i = 0; i < parts.length - 1; i++) { + base = base + parts[i] + ":"; + } + } else { + String[] parts; + parts = fullUrl.split("/"); + for (int i = 0; i < parts.length - 2; i++) { + base = base + parts[i] + "/"; + } + } + + String id = null; + if (ref.contains("/_history/")) { + version = ref.substring(ref.indexOf("/_history/") + 10); + String[] refBaseParts = ref.substring(0, ref.indexOf("/_history/")).split("/"); + resourceType = refBaseParts[0]; + id = refBaseParts[1]; + } else if (base.startsWith("urn")) { + resourceType = ref.split("/")[0]; + id = ref.split("/")[1]; + } else + id = ref; + + targetUrl = base + id; + } + + List entries = new ArrayList(); + bundle.getNamedChildren("entry", entries); + Element match = null; + int matchIndex = -1; + for (int i = 0; i < entries.size(); i++) { + Element we = entries.get(i); + if (targetUrl.equals(we.getChildValue("fullUrl"))) { + Element r = we.getNamedChild("resource"); + if (version.isEmpty()) { + rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, "Multiple matches in bundle for reference " + ref); + match = r; + matchIndex = i; + } else { + try { + if (version.equals(r.getChildren("meta").get(0).getChildValue("versionId"))) { + rule(errors, IssueType.FORBIDDEN, -1, -1, path, match == null, "Multiple matches in bundle for reference " + ref); + match = r; + matchIndex = i; + } + } catch (Exception e) { + warning(errors, IssueType.REQUIRED, -1, -1, path, r.getChildren("meta").size() == 1 && r.getChildren("meta").get(0).getChildValue("versionId") != null, "Entries matching fullURL " + targetUrl + " should declare meta/versionId because there are version-specific references"); + // If one of these things is null + } + } + } + } + + if (match != null && resourceType != null) + rule(errors, IssueType.REQUIRED, -1, -1, path, match.getType().equals(resourceType), "Matching reference for reference " + ref + " has resourceType " + match.getType()); + if (match == null) + warning(errors, IssueType.REQUIRED, -1, -1, path, !ref.startsWith("urn"), "URN reference is not locally contained within the bundle " + ref); + return match == null ? null : new IndexedElement(matchIndex, match, entries.get(matchIndex)); + } + + private boolean isSearchUrl(String ref) { + if (Utilities.noString(ref) || !ref.contains("?")) { + return false; + } + String tn = ref.substring(0, ref.indexOf("?")); + String q = ref.substring(ref.indexOf("?") + 1); + if (!context.getResourceNames().contains(tn)) { + return false; + } else { + return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*"); + } + } + + private StructureDefinition getProfileForType(String type, List list) { + for (TypeRefComponent tr : list) { + String url = tr.getWorkingCode(); + if (!Utilities.isAbsoluteUrl(url)) + url = "http://hl7.org/fhir/StructureDefinition/" + url; + long t = System.nanoTime(); + StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); + sdTime = sdTime + (System.nanoTime() - t); + if (sd != null && (sd.getType().equals(type) || sd.getUrl().equals(type)) && sd.hasSnapshot()) + return sd; + } + return null; + } + + private Element getValueForDiscriminator(Object appContext, List errors, Element element, String discriminator, ElementDefinition criteria, NodeStack stack) throws FHIRException, IOException { + String p = stack.getLiteralPath() + "." + element.getName(); + Element focus = element; + String[] dlist = discriminator.split("\\."); + for (String d : dlist) { + if (focus.fhirType().equals("Reference") && d.equals("reference")) { + String url = focus.getChildValue("reference"); + if (Utilities.noString(url)) + throw new FHIRException("No reference resolving discriminator " + discriminator + " from " + element.getProperty().getName()); + // Note that we use the passed in stack here. This might be a problem if the discriminator is deep enough? + Element target = resolve(appContext, url, stack, errors, p); + if (target == null) + throw new FHIRException("Unable to find resource " + url + " at " + d + " resolving discriminator " + discriminator + " from " + element.getProperty().getName()); + focus = target; + } else if (d.equals("value") && focus.isPrimitive()) { + return focus; + } else { + List children = focus.getChildren(d); + if (children.isEmpty()) + throw new FHIRException("Unable to find " + d + " resolving discriminator " + discriminator + " from " + element.getProperty().getName()); + if (children.size() > 1) + throw new FHIRException("Found " + Integer.toString(children.size()) + " items for " + d + " resolving discriminator " + discriminator + " from " + element.getProperty().getName()); + focus = children.get(0); + p = p + "." + d; + } + } + return focus; + } + + private CodeSystem getCodeSystem(String system) { + long t = System.nanoTime(); + try { + return context.fetchCodeSystem(system); + } finally { + txTime = txTime + (System.nanoTime() - t); + } + } + + private boolean hasTime(String fmt) { + return fmt.contains("T"); + } + + private boolean hasTimeZone(String fmt) { + return fmt.length() > 10 && (fmt.substring(10).contains("-") || fmt.substring(10).contains("+") || fmt.substring(10).contains("Z")); + } + + private boolean isAbsolute(String uri) { + return Utilities.noString(uri) || uri.startsWith("http:") || uri.startsWith("https:") || uri.startsWith("urn:uuid:") || uri.startsWith("urn:oid:") || uri.startsWith("urn:ietf:") + || uri.startsWith("urn:iso:") || uri.startsWith("urn:iso-astm:") || isValidFHIRUrn(uri); + } + + private boolean isValidFHIRUrn(String uri) { + return (uri.equals("urn:x-fhir:uk:id:nhs-number")) || uri.startsWith("urn:"); // Anyone can invent a URN, so why should we complain? + } + + public boolean isAnyExtensionsAllowed() { + return anyExtensionsAllowed; + } + + public boolean isErrorForUnknownProfiles() { + return errorForUnknownProfiles; + } + + public void setErrorForUnknownProfiles(boolean errorForUnknownProfiles) { + this.errorForUnknownProfiles = errorForUnknownProfiles; + } + + private boolean isParametersEntry(String path) { + String[] parts = path.split("\\."); + return parts.length > 2 && parts[parts.length - 1].equals("resource") && (pathEntryHasName(parts[parts.length - 2], "parameter") || pathEntryHasName(parts[parts.length - 2], "part")); + } + + private boolean isBundleEntry(String path) { + String[] parts = path.split("\\."); + return parts.length > 2 && parts[parts.length - 1].equals("resource") && pathEntryHasName(parts[parts.length - 2], "entry"); + } + + private boolean isBundleOutcome(String path) { + String[] parts = path.split("\\."); + return parts.length > 2 && parts[parts.length - 1].equals("outcome") && pathEntryHasName(parts[parts.length - 2], "response"); + } + + + private static boolean pathEntryHasName(String thePathEntry, String theName) { + if (thePathEntry.equals(theName)) { + return true; + } + if (thePathEntry.length() >= theName.length() + 3) { + if (thePathEntry.startsWith(theName)) { + if (thePathEntry.charAt(theName.length()) == '[') { + return true; + } + } + } + return false; + } + + public boolean isPrimitiveType(String code) { + StructureDefinition sd = context.fetchTypeDefinition(code); + return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE; + } + + private String getErrorMessage(String message) { + return message != null ? " (error message = " + message + ")" : ""; + } + + public boolean isSuppressLoincSnomedMessages() { + return suppressLoincSnomedMessages; + } + + private boolean nameMatches(String name, String tail) { + if (tail.endsWith("[x]")) + return name.startsWith(tail.substring(0, tail.length() - 3)); + else + return (name.equals(tail)); + } + + private boolean passesCodeWhitespaceRules(String v) { + if (!v.trim().equals(v)) + return false; + boolean lastWasSpace = true; + for (char c : v.toCharArray()) { + if (c == ' ') { + if (lastWasSpace) + return false; + else + lastWasSpace = true; + } else if (Character.isWhitespace(c)) + return false; + else + lastWasSpace = false; + } + return true; + } + + private ResolvedReference localResolve(String ref, NodeStack stack, List errors, String path, Element hostContext, Element source) { + if (ref.startsWith("#")) { + // work back through the parent list. + // really, there should only be one level for this (contained resources cannot contain + // contained resources), but we'll leave that to some other code to worry about + while (stack != null && stack.getElement() != null) { + if (stack.getElement().getProperty().isResource()) { + // ok, we'll try to find the contained reference + IndexedElement res = getContainedById(stack.getElement(), ref.substring(1)); + if (res != null) { + ResolvedReference rr = new ResolvedReference(); + rr.setResource(stack.getElement()); + rr.setFocus(res.getMatch()); + rr.setExternal(false); + rr.setStack(stack.push(res.getMatch(), res.getIndex(), res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); + return rr; + } + } + if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY) { + return null; // we don't try to resolve contained references across this boundary + } + stack = stack.parent; + } + return null; + } else { + // work back through the parent list - if any of them are bundles, try to resolve + // the resource in the bundle + String fullUrl = null; // we're going to try to work this out as we go up + while (stack != null && stack.getElement() != null) { + if (stack.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY && fullUrl == null && stack.parent != null && stack.parent.getElement().getName().equals("entry")) { + String type = stack.parent.parent.element.getChildValue("type"); + fullUrl = stack.parent.getElement().getChildValue("fullUrl"); // we don't try to resolve contained references across this boundary + if (fullUrl == null) + rule(errors, IssueType.REQUIRED, stack.parent.getElement().line(), stack.parent.getElement().col(), stack.parent.getLiteralPath(), + Utilities.existsInList(type, "batch-response", "transaction-response") || fullUrl != null, "Bundle entry missing fullUrl"); + } + if ("Bundle".equals(stack.getElement().getType())) { + String type = stack.getElement().getChildValue("type"); + IndexedElement res = getFromBundle(stack.getElement(), ref, fullUrl, errors, path, type, "transaction".equals(type)); + if (res == null) { + return null; + } else { + ResolvedReference rr = new ResolvedReference(); + rr.setResource(res.getMatch()); + rr.setFocus(res.getMatch()); + rr.setExternal(false); + rr.setStack(stack.push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), + res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, + res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); + return rr; + } + } + stack = stack.parent; + } + // we can get here if we got called via FHIRPath conformsTo which breaks the stack continuity. + if (hostContext != null && "Bundle".equals(hostContext.fhirType())) { + String type = hostContext.getChildValue("type"); + Element entry = getEntryForSource(hostContext, source); + fullUrl = entry.getChildValue("fullUrl"); + IndexedElement res = getFromBundle(hostContext, ref, fullUrl, errors, path, type, "transaction".equals(type)); + if (res == null) { + return null; + } else { + ResolvedReference rr = new ResolvedReference(); + rr.setResource(res.getMatch()); + rr.setFocus(res.getMatch()); + rr.setExternal(false); + rr.setStack(new NodeStack(hostContext).push(res.getEntry(), res.getIndex(), res.getEntry().getProperty().getDefinition(), + res.getEntry().getProperty().getDefinition()).push(res.getMatch(), -1, + res.getMatch().getProperty().getDefinition(), res.getMatch().getProperty().getDefinition())); + return rr; + } + } + } + return null; + } + + private Element getEntryForSource(Element bundle, Element element) { + List entries = new ArrayList(); + bundle.getNamedChildren("entry", entries); for (Element entry : entries) { - String fu = entry.getNamedChildValue("fullUrl"); - if (fu != null && fu.equals(u)) - return entry; - if (u == null) { - Element resource = entry.getNamedChild("resource"); - if (resource != null) { - String et = resource.getType(); - String eid = resource.getNamedChildValue("id"); - if (t.equals(et) && i.equals(eid)) + if (entry.hasDescendant(element)) { return entry; } - } } - } - return null; + return null; } - } - private ElementDefinition resolveNameReference(StructureDefinitionSnapshotComponent snapshot, String contentReference) { - for (ElementDefinition ed : snapshot.getElement()) - if (contentReference.equals("#"+ed.getId())) - return ed; - return null; - } - - private StructureDefinition resolveProfile(StructureDefinition profile, String pr) { - if (pr.startsWith("#")) { - for (Resource r : profile.getContained()) { - if (r.getId().equals(pr.substring(1)) && r instanceof StructureDefinition) - return (StructureDefinition) r; - } - return null; - } else { - long t = System.nanoTime(); - StructureDefinition fr = context.fetchResource(StructureDefinition.class, pr); - sdTime = sdTime + (System.nanoTime() - t); - return fr; + private ResolvedReference makeExternalRef(Element external, String path) { + ResolvedReference res = new ResolvedReference(); + res.setResource(external); + res.setFocus(external); + res.setExternal(true); + res.setStack(new NodeStack(external, path)); + return res; } - } - - private ElementDefinition resolveType(String type, List list) { - for (TypeRefComponent tr : list) { - String url = tr.getWorkingCode(); - if (!Utilities.isAbsoluteUrl(url)) - url = "http://hl7.org/fhir/StructureDefinition/" + url; - long t = System.nanoTime(); - StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); - sdTime = sdTime + (System.nanoTime() - t); - if (sd != null && (sd.getType().equals(type) || sd.getUrl().equals(type)) && sd.hasSnapshot()) - return sd.getSnapshot().getElement().get(0); - } - return null; - } - - public void setAnyExtensionsAllowed(boolean anyExtensionsAllowed) { - this.anyExtensionsAllowed = anyExtensionsAllowed; - } - - public IResourceValidator setBestPracticeWarningLevel(BestPracticeWarningLevel value) { - bpWarnings = value; - return this; - } - - @Override - public void setCheckDisplay(CheckDisplayOption checkDisplay) { - this.checkDisplay = checkDisplay; - } - - public void setSuppressLoincSnomedMessages(boolean suppressLoincSnomedMessages) { - this.suppressLoincSnomedMessages = suppressLoincSnomedMessages; - } - - public IdStatus getResourceIdRule() { - return resourceIdRule; - } - - public void setResourceIdRule(IdStatus resourceIdRule) { - this.resourceIdRule = resourceIdRule; - } - public boolean isAllowXsiLocation() { - return allowXsiLocation; - } - - public void setAllowXsiLocation(boolean allowXsiLocation) { - this.allowXsiLocation = allowXsiLocation; - } - - /** - * - * @param element - * - the candidate that might be in the slice - * @param path - * - for reporting any errors. the XPath for the element - * @param slicer - * - the definition of how slicing is determined - * @param ed - * - the slice for which to test membership - * @param errors - * @param stack - * @return - * @throws DefinitionException - * @throws DefinitionException - * @throws IOException - * @throws FHIRException - */ - private boolean sliceMatches(ValidatorHostContext hostContext, Element element, String path, ElementDefinition slicer, ElementDefinition ed, StructureDefinition profile, List errors, List sliceInfo, NodeStack stack) throws DefinitionException, FHIRException { - if (!slicer.getSlicing().hasDiscriminator()) - return false; // cannot validate in this case - - ExpressionNode n = (ExpressionNode) ed.getUserData("slice.expression.cache"); - if (n == null) { - long t = System.nanoTime(); - // GG: this approach is flawed because it treats discriminators individually rather than collectively - StringBuilder expression = new StringBuilder("true"); - boolean anyFound = false; - Set discriminators = new HashSet<>(); - for (ElementDefinitionSlicingDiscriminatorComponent s : slicer.getSlicing().getDiscriminator()) { - String discriminator = s.getPath(); - discriminators.add(discriminator); - - List criteriaElements = getCriteriaForDiscriminator(path, ed, discriminator, profile, s.getType() == DiscriminatorType.PROFILE); - boolean found = false; - for (ElementDefinition criteriaElement : criteriaElements) { - found = true; - if (s.getType() == DiscriminatorType.TYPE) { - String type = null; - if (!criteriaElement.getPath().contains("[") && discriminator.contains("[")) { - discriminator = discriminator.substring(0, discriminator.indexOf('[')); - String lastNode = tail(discriminator); - type = tail(criteriaElement.getPath()).substring(lastNode.length()); - type = type.substring(0,1).toLowerCase() + type.substring(1); - } else if (!criteriaElement.hasType() || criteriaElement.getType().size()==1) { - if (discriminator.contains("[")) - discriminator = discriminator.substring(0, discriminator.indexOf('[')); - type = criteriaElement.getType().get(0).getWorkingCode(); - } else if (criteriaElement.getType().size() > 1) { - throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " in "+profile.getUrl()+" has multiple types: "+criteriaElement.typeSummary()); - } else - throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " in "+profile.getUrl()+" has no types"); - if (discriminator.isEmpty()) - expression.append(" and $this is " + type); - else - expression.append(" and " + discriminator + " is " + type); - } else if (s.getType() == DiscriminatorType.PROFILE) { - if (criteriaElement.getType().size() == 0) { - throw new DefinitionException("Profile based discriminators must have a type ("+criteriaElement.getId()+" in profile "+profile.getUrl()+")"); - } - if (criteriaElement.getType().size() != 1) { - throw new DefinitionException("Profile based discriminators must have only one type ("+criteriaElement.getId()+" in profile "+profile.getUrl()+")"); - } - List list = discriminator.endsWith(".resolve()") || discriminator.equals("resolve()") ? criteriaElement.getType().get(0).getTargetProfile() : criteriaElement.getType().get(0).getProfile(); - if (list.size() == 0) { - throw new DefinitionException("Profile based discriminators must have a type with a profile ("+criteriaElement.getId()+" in profile "+profile.getUrl()+")"); - } else if (list.size() > 1) { - CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(" or "); - for (CanonicalType c : list) { - b.append(discriminator+".conformsTo('"+c.getValue()+"')"); - } - expression.append(" and ("+b+")"); - } else { - expression.append(" and "+discriminator+".conformsTo('"+list.get(0).getValue()+"')"); - } - } else if (s.getType() == DiscriminatorType.EXISTS) { - if (criteriaElement.hasMin() && criteriaElement.getMin()>=1) - expression.append(" and (" + discriminator + ".exists())"); - else if (criteriaElement.hasMax() && criteriaElement.getMax().equals("0")) - expression.append(" and (" + discriminator + ".exists().not())"); - else - throw new FHIRException("Discriminator (" + discriminator + ") is based on element existence, but slice " + ed.getId() + " neither sets min>=1 or max=0"); - } else if (criteriaElement.hasFixed()) { - buildFixedExpression(ed, expression, discriminator, criteriaElement); - } else if (criteriaElement.hasPattern()) { - buildPattternExpression(ed, expression, discriminator, criteriaElement); - } else if (criteriaElement.hasBinding() && criteriaElement.getBinding().hasStrength() && criteriaElement.getBinding().getStrength().equals(BindingStrength.REQUIRED) && criteriaElement.getBinding().hasValueSet()) { - expression.append(" and (" + discriminator + " memberOf '" + criteriaElement.getBinding().getValueSet() + "')"); - } else { - found = false; - } - if (found) - break; + private Element resolve(Object appContext, String ref, NodeStack stack, List errors, String path) throws IOException, FHIRException { + Element local = localResolve(ref, stack, errors, path, null, null).getFocus(); + if (local != null) + return local; + if (fetcher == null) + return null; + if (fetchCache.containsKey(ref)) { + return fetchCache.get(ref); + } else { + Element res = fetcher.fetch(appContext, ref); + fetchCache.put(ref, res); + return res; } - if (found) - anyFound = true; - } - if (!anyFound) { - if (slicer.getSlicing().getDiscriminator().size() > 1) - throw new DefinitionException("Could not match any discriminators (" + discriminators + ") for slice " + ed.getId() + " in profile " + profile.getUrl() + " - None of the discriminator " + discriminators + " have fixed value, binding or existence assertions"); - else - throw new DefinitionException("Could not match discriminator (" + discriminators + ") for slice " + ed.getId() + " in profile " + profile.getUrl() + " - the discriminator " + discriminators + " does not have fixed value, binding or existence assertions"); - } - - try { - n = fpe.parse(fixExpr(expression.toString())); - } catch (FHIRLexerException e) { - throw new FHIRException("Problem processing expression "+expression +" in profile " + profile.getUrl() + " path " + path + ": " + e.getMessage()); - } - fpeTime = fpeTime + (System.nanoTime() - t); - ed.setUserData("slice.expression.cache", n); } - ValidatorHostContext shc = hostContext.forSlicing(); - boolean pass = evaluateSlicingExpression(shc, element, path, profile, n); - if (!pass) { - slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Does not match slice'"+ed.getSliceName(), "discriminator = "+Utilities.escapeXml(n.toString())); - for (String url : shc.getSliceRecords().keySet()) { - slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for "+stack.getLiteralPath()+" against profile "+url, - "Profile "+url+" does not match for "+stack.getLiteralPath()+" because of the following profile issues: "+errorSummaryForSlicingAsHtml(shc.getSliceRecords().get(url))); - } - } - return pass; - } - - public boolean evaluateSlicingExpression(ValidatorHostContext hostContext, Element element, String path, StructureDefinition profile, ExpressionNode n) throws FHIRException { - String msg; - boolean ok; - try { - long t = System.nanoTime(); - ok = fpe.evaluateToBoolean(hostContext.forProfile(profile), hostContext.getResource(), hostContext.getRootResource(), element, n); - fpeTime = fpeTime + (System.nanoTime() - t); - msg = fpe.forLog(); - } catch (Exception ex) { - ex.printStackTrace(); - throw new FHIRException("Problem evaluating slicing expression for element in profile " + profile.getUrl() + " path " + path + " (fhirPath = "+n+"): " + ex.getMessage()); - } - return ok; - } - - private void buildPattternExpression(ElementDefinition ed, StringBuilder expression, String discriminator, ElementDefinition criteriaElement) throws DefinitionException { - DataType pattern = criteriaElement.getPattern(); - if (pattern instanceof CodeableConcept) { - CodeableConcept cc = (CodeableConcept) pattern; - expression.append(" and "); - buildCodeableConceptExpression(ed, expression, discriminator, cc); - } else if (pattern instanceof Identifier) { - Identifier ii = (Identifier) pattern; - expression.append(" and "); - buildIdentifierExpression(ed, expression, discriminator, ii); - } else - throw new DefinitionException("Unsupported fixed pattern type for discriminator(" + discriminator + ") for slice " + ed.getId() + ": " + pattern.getClass().getName()); - } - - private void buildIdentifierExpression(ElementDefinition ed, StringBuilder expression, String discriminator, Identifier ii) - throws DefinitionException { - if (ii.hasExtension()) - throw new DefinitionException("Unsupported Identifier pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); - boolean first = true; - expression.append(discriminator + ".where("); - if (ii.hasSystem()) { - first = false; - expression.append("system = '"+ii.getSystem()+"'"); - } - if (ii.hasValue()) { - if (first) - first = false; - else - expression.append(" and "); - expression.append("value = '"+ii.getValue()+"'"); - } - if (ii.hasUse()) { - if (first) - first = false; - else - expression.append(" and "); - expression.append("use = '"+ii.getUse()+"'"); - } - if (ii.hasType()) { - if (first) - first = false; - else - expression.append(" and "); - buildCodeableConceptExpression(ed, expression, "type", ii.getType()); - } - expression.append(").exists()"); - } - - private void buildCodeableConceptExpression(ElementDefinition ed, StringBuilder expression, String discriminator, CodeableConcept cc) - throws DefinitionException { - if (cc.hasText()) - throw new DefinitionException("Unsupported CodeableConcept pattern - using text - for discriminator(" + discriminator + ") for slice " + ed.getId()); - if (!cc.hasCoding()) - throw new DefinitionException("Unsupported CodeableConcept pattern - must have at least one coding - for discriminator(" + discriminator + ") for slice " + ed.getId()); - if (cc.hasExtension()) - throw new DefinitionException("Unsupported CodeableConcept pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); - boolean firstCoding = true; - for(Coding c : cc.getCoding()) { - if (c.hasExtension()) - throw new DefinitionException("Unsupported CodeableConcept pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); - if (firstCoding) firstCoding = false; else expression.append(" and "); - expression.append(discriminator + ".coding.where("); - boolean first = true; - if (c.hasSystem()) { - first = false; - expression.append("system = '"+c.getSystem()+"'"); - } - if (c.hasVersion()) { - if (first) first = false; else expression.append(" and "); - expression.append("version = '"+c.getVersion()+"'"); - } - if (c.hasCode()) { - if (first) first = false; else expression.append(" and "); - expression.append("code = '"+c.getCode()+"'"); - } - if (c.hasDisplay()) { - if (first) first = false; else expression.append(" and "); - expression.append("display = '"+c.getDisplay()+"'"); - } - expression.append(").exists()"); - } - } - - private void buildFixedExpression(ElementDefinition ed, StringBuilder expression, String discriminator, ElementDefinition criteriaElement) throws DefinitionException { - DataType fixed = criteriaElement.getFixed(); - if (fixed instanceof CodeableConcept) { - CodeableConcept cc = (CodeableConcept) fixed; - expression.append(" and "); - buildCodeableConceptExpression(ed, expression, discriminator, cc); - } else if (fixed instanceof Identifier) { - Identifier ii = (Identifier) fixed; - expression.append(" and "); - buildIdentifierExpression(ed, expression, discriminator, ii); - } else { - expression.append(" and ("); - if (fixed instanceof StringType) { - Gson gson = new Gson(); - String json = gson.toJson((StringType)fixed); - String escapedString = json.substring(json.indexOf(":")+2); - escapedString = escapedString.substring(0, escapedString.indexOf(",\"myStringValue")-1); - expression.append("'" + escapedString + "'"); - } else if (fixed instanceof UriType) { - expression.append("'" + ((UriType)fixed).asStringValue() + "'"); - } else if (fixed instanceof IntegerType) { - expression.append(((IntegerType)fixed).asStringValue()); - } else if (fixed instanceof DecimalType) { - expression.append(((IntegerType)fixed).asStringValue()); - } else if (fixed instanceof BooleanType) { - expression.append(((BooleanType)fixed).asStringValue()); - } else - throw new DefinitionException("Unsupported fixed value type for discriminator(" + discriminator + ") for slice " + ed.getId() + ": " + fixed.getClass().getName()); - expression.append(" in " + discriminator +")"); - } - } - - // checkSpecials = we're only going to run these tests if we are actually validating this content (as opposed to we looked it up) - private void start(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, NodeStack stack) throws FHIRException { - checkLang(resource, stack); - - if ("Bundle".equals(element.fhirType())) { - resolveBundleReferences(element, new ArrayList()); - } - startInner(hostContext, errors, resource, element, defn, stack, hostContext.isCheckSpecials()); - - List res = new ArrayList<>(); - Element meta = element.getNamedChild("meta"); - if (meta != null) { - List profiles = new ArrayList(); - meta.getNamedChildren("profile", profiles); - int i = 0; - for (Element profile : profiles) { - StructureDefinition sd = context.fetchResource(StructureDefinition.class, profile.primitiveValue()); - if (!defn.getUrl().equals(profile.primitiveValue())) { - if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath()+".meta.profile["+i+"]", sd != null, "Profile reference '"+profile.primitiveValue()+"' could not be resolved, so has not been checked")) { - startInner(hostContext, errors, resource, element, sd, stack, false); - } - } - i++; - } - } - } - - private void resolveBundleReferences(Element element, List bundles) { - if (!element.hasUserData("validator.bundle.resolved")) { - element.setUserData("validator.bundle.resolved", true); - List list = new ArrayList(); - list.addAll(bundles); - list.add(0, element); - List entries = element.getChildrenByName("entry"); - for (Element entry : entries) { - String fu = entry.getChildValue("fullUrl"); - Element r = entry.getNamedChild("resource"); - if (r != null) { - resolveBundleReferencesInResource(list, r, fu); - } - } - } - } - - private void resolveBundleReferencesInResource(List bundles, Element r, String fu) { - r.setUserData("validator.bundle.resolution-resource", null); - if ("Bundle".equals(r.fhirType())) { - resolveBundleReferences(r, bundles); - } else { - for (Element child : r.getChildren()) { - resolveBundleReferencesForElement(bundles, r, fu, child); - } - } - } - - private void resolveBundleReferencesForElement(List bundles, Element resource, String fu, Element element) { - if ("Reference".equals(element.fhirType())) { - String ref = element.getChildValue("reference"); - if (!Utilities.noString(ref)) { - for (Element bundle : bundles) { - List entries = bundle.getChildren("entry"); - Element tgt = resolveInBundle(entries, ref, fu, resource.fhirType(), resource.getIdBase()); - if (tgt != null) { - element.setUserData("validator.bundle.resolution", tgt.getNamedChild("resource")); - return; - } - } - element.setUserData("validator.bundle.resolution-failed", ref); - } - } else { - element.setUserData("validator.bundle.resolution-noref", null); - for (Element child : element.getChildren()) { - resolveBundleReferencesForElement(bundles, resource, fu, child); - } - } - - } - - public void startInner(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, NodeStack stack, boolean checkSpecials) { - // the first piece of business is to see if we've validated this resource against this profile before. - // if we have (*or if we still are*), then we'll just return our existing errors - ResourceValidationTracker resTracker = getResourceTracker(element); - List cachedErrors = resTracker.getOutcomes(defn); - if (cachedErrors != null) { - for (ValidationMessage vm : cachedErrors) { - if (!errors.contains(vm)) { - errors.add(vm); - } - } - return; - } - if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), defn.hasSnapshot(), "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) { - List localErrors = new ArrayList(); - resTracker.startValidating(defn); - trackUsage(defn, hostContext, element); - validateElement(hostContext, localErrors, defn, defn.getSnapshot().getElement().get(0), null, null, resource, element, element.getName(), stack, false, true, null); - resTracker.storeOutcomes(defn, localErrors); - for (ValidationMessage vm : localErrors) { - if (!errors.contains(vm)) { - errors.add(vm); - } - } - } - if (checkSpecials) { - checkSpecials(hostContext, errors, element, stack, checkSpecials); - validateResourceRules(errors, element, stack); - } - } - - public void checkSpecials(ValidatorHostContext hostContext, List errors, Element element, NodeStack stack, boolean checkSpecials) { - // specific known special validations - if (element.getType().equals("Bundle")) { - validateBundle(errors, element, stack, checkSpecials); - } else if (element.getType().equals("Observation")) { - validateObservation(errors, element, stack); - } else if (element.getType().equals("Questionnaire")) { - ArrayList parents = new ArrayList<>(); - parents.add(element); - validateQuestionannaireItem(errors, element, element, stack, parents); - } else if (element.getType().equals("QuestionnaireResponse")) { - validateQuestionannaireResponse(hostContext, errors, element, stack); - } else if (element.getType().equals("CapabilityStatement")) { - validateCapabilityStatement(errors, element, stack); - } else if (element.getType().equals("CodeSystem")) { - validateCodeSystem(errors, element, stack); - } - } - - private ResourceValidationTracker getResourceTracker(Element element) { - ResourceValidationTracker res = resourceTracker.get(element); - if (res == null) { - res = new ResourceValidationTracker(); - resourceTracker.put(element, res); - } - return res; - } - - private void validateQuestionannaireItem(List errors, Element element, Element questionnaire, NodeStack stack, List parents) { - List list = getItems(element); - for (int i = 0; i < list.size(); i++) { - Element e = list.get(i); - NodeStack ns = stack.push(e, i, e.getProperty().getDefinition(), e.getProperty().getDefinition()); - validateQuestionnaireElement(errors, ns, questionnaire, e, parents); - List np = new ArrayList(); - np.add(e); - np.addAll(parents); - validateQuestionannaireItem(errors, e, questionnaire, ns, np); - } - } - - private void validateQuestionnaireElement(List errors, NodeStack ns, Element questionnaire, Element item, List parents) { - // R4+ - if (FHIRVersion.isR4Plus(context.getVersion())) { - if (item.hasChildren("enableWhen")) { - List ewl = item.getChildren("enableWhen"); - for (Element ew : ewl) { -// Element ew = item.getNamedChild("enableWhen"); - String ql = ew.getNamedChildValue("question"); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, ql != null, "Questions with an enableWhen must have a value for the question link")) { - Element tgt = getQuestionById(item, ql); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt == null, "Questions with an enableWhen cannot refer to an inner question for it's enableWhen condition")) { - tgt = getQuestionById(questionnaire, ql); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != null, "Unable to find target '"+ql+"' for this question enableWhen")) { - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != item, "Target for this question enableWhen can't reference itself")) { - if (!isBefore(item, tgt, parents)) { - warning(errors, IssueType.BUSINESSRULE, ns.literalPath, false, "The target of this enableWhen rule ("+ql+") comes after the question itself"); - } + private ValueSet resolveBindingReference(DomainResource ctxt, String reference, String uri) { + if (reference != null) { + if (reference.startsWith("#")) { + for (Resource c : ctxt.getContained()) { + if (c.getId().equals(reference.substring(1)) && (c instanceof ValueSet)) + return (ValueSet) c; } - } - } - } - } - } - } - } - - private boolean isBefore(Element item, Element tgt, List parents) { - // we work up the list, looking for tgt in the children of the parents - if (parents.contains(tgt)) { - // actually, if the target is a parent, that's automatically ok - return true; - } - for (Element p : parents) { - int i = findIndex(p, item); - int t = findIndex(p, tgt); - if (i > -1 && t > -1) { - return i > t; - } - } - return false; // unsure... shouldn't ever get to this point; - } - - - private int findIndex(Element parent, Element descendant) { - for (int i = 0; i < parent.getChildren().size(); i++) { - if (parent.getChildren().get(i) == descendant || isChild(parent.getChildren().get(i), descendant)) - return i; - } - return -1; - } - - private boolean isChild(Element element, Element descendant) { - for (Element e : element.getChildren()) { - if (e == descendant) - return true; - if (isChild(e, descendant)) - return true; - } - return false; - } - - private Element getQuestionById(Element focus, String ql) { - List list = getItems(focus); - for (Element item : list) { - String v = item.getNamedChildValue("linkId"); - if (ql.equals(v)) - return item; - Element tgt = getQuestionById(item, ql); - if (tgt != null) - return tgt; - } - return null; - - } - - private List getItems(Element element) { - List list = new ArrayList<>(); - element.getNamedChildren("item", list); - return list; - } - - private void checkLang(Element resource, NodeStack stack) { - String lang = resource.getNamedChildValue("language"); - if (!Utilities.noString(lang)) - stack.workingLang = lang; - } - - private void validateResourceRules(List errors, Element element, NodeStack stack) { - String lang = element.getNamedChildValue("language"); - Element text = element.getNamedChild("text"); - if (text != null) { - Element div = text.getNamedChild("div"); - if (lang != null && div != null) { - XhtmlNode xhtml = div.getXhtml(); - String l = xhtml.getAttribute("lang"); - String xl = xhtml.getAttribute("xml:lang"); - if (l == null && xl == null) { - warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have an lang or an xml:lang tag (needs both - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); - } else { - if (l == null) { - warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have a lang tag (needs both lang and xml:lang - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); - } else if (!l.equals(lang)) { - warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language ("+lang+"), and the XHTML has a lang ("+l+"), but they differ "); - } - if (xl == null) { - warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have an xml:lang tag (needs both lang and xml:lang - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); - } else if (!xl.equals(lang)) { - warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language ("+lang+"), and the XHTML has an xml:lang ("+xl+"), but they differ "); - } - } - } - } - // security tags are a set (system|code) - Element meta = element.getNamedChild("meta"); - if (meta != null) { - Set tags = new HashSet<>(); - List list = new ArrayList<>(); - meta.getNamedChildren("security", list); - int i = 0; - for (Element e : list) { - String s = e.getNamedChildValue("system") + "#" + e.getNamedChildValue("code"); - rule(errors, IssueType.BUSINESSRULE, e.line(), e.col(), stack.getLiteralPath()+".meta.profile["+Integer.toString(i)+"]", !tags.contains(s), "Duplicate Security Label "+s); - tags.add(s); - i++; - } - } - } - - private void validateCapabilityStatement(List errors, Element cs, NodeStack stack) { - int iRest = 0; - for (Element rest : cs.getChildrenByName("rest")) { - int iResource = 0; - for (Element resource : rest.getChildrenByName("resource")) { - int iSP = 0; - for (Element searchParam : resource.getChildrenByName("searchParam")) { - String ref = searchParam.getChildValue("definition"); - String type = searchParam.getChildValue("type"); - if (!Utilities.noString(ref)) { - SearchParameter sp = context.fetchResource(SearchParameter.class, ref); - if (sp != null) { - rule(errors, IssueType.INVALID, searchParam.line(), searchParam.col(), stack.literalPath+".rest["+iRest+"].resource["+iResource+"].searchParam["+iSP+"]", - sp.getType().toCode().equals(type), "Type mismatch - SearchParameter '"+sp.getUrl()+"' type is "+sp.getType().toCode()+", but type here is "+type); + return null; + } else { + long t = System.nanoTime(); + ValueSet fr = context.fetchResource(ValueSet.class, reference); + if (fr == null) { + if (!Utilities.isAbsoluteUrl(reference)) { + reference = resolve(uri, reference); + fr = context.fetchResource(ValueSet.class, reference); + } + } + if (fr == null) + fr = ValueSetUtilities.generateImplicitValueSet(reference); + txTime = txTime + (System.nanoTime() - t); + return fr; } - } - iSP++; - } - iResource++; - } - iRest++; + } else + return null; } - } - private void validateCodeSystem(List errors, Element cs, NodeStack stack) { - String url = cs.getNamedChildValue("url"); - String vsu = cs.getNamedChildValue("valueSet"); - if (!Utilities.noString(vsu)) { - ValueSet vs; - try { - vs = context.fetchResourceWithException(ValueSet.class, vsu); - } catch (FHIRException e) { - vs = null; - } - if (vs != null) { - if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose() && !vs.hasExpansion(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but it is an expansion")) - if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 1, "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have a single include")) - if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().get(0).getSystem().equals(url), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but doesn't have a matching system ("+vs.getCompose().getInclude().get(0).getSystem()+")")) { - rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasValueSet() - && !vs.getCompose().getInclude().get(0).hasConcept() && !vs.getCompose().getInclude().get(0).hasFilter(), "CodeSystem "+url+" has a 'all system' value set of "+vsu+", but the include has extra details"); + + private String resolve(String uri, String ref) { + if (isBlank(uri)) { + return ref; + } + String[] up = uri.split("\\/"); + String[] rp = ref.split("\\/"); + if (context.getResourceNames().contains(up[up.length - 2]) && context.getResourceNames().contains(rp[0])) { + StringBuilder b = new StringBuilder(); + for (int i = 0; i < up.length - 2; i++) { + b.append(up[i]); + b.append("/"); } - } - } // todo... try getting the value set the other way... - } - - private void validateQuestionannaireResponse(ValidatorHostContext hostContext, List errors, Element element, NodeStack stack) throws FHIRException { - Element q = element.getNamedChild("questionnaire"); - String questionnaire = null; - if (q != null) { - /* - * q.getValue() is correct for R4 content, but we'll also accept the second - * option just in case we're validating raw STU3 content. Being lenient here - * isn't the end of the world since if someone is actually doing the reference - * wrong in R4 content it'll get flagged elsewhere by the validator too - */ - if (isNotBlank(q.getValue())) { - questionnaire = q.getValue(); - } else if (isNotBlank(q.getChildValue("reference"))) { - questionnaire = q.getChildValue("reference"); - } - } - if (hint(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), questionnaire != null, "No questionnaire is identified, so no validation can be performed against the base questionnaire")) { - long t = System.nanoTime(); - Questionnaire qsrc = questionnaire.startsWith("#") ? loadQuestionnaire(element, questionnaire.substring(1)) : context.fetchResource(Questionnaire.class, questionnaire); - sdTime = sdTime + (System.nanoTime() - t); - if (warning(errors, IssueType.REQUIRED, q.line(), q.col(), stack.getLiteralPath(), qsrc != null, "The questionnaire \""+questionnaire+"\" could not be resolved, so no validation can be performed against the base questionnaire")) { - boolean inProgress = "in-progress".equals(element.getNamedChildValue("status")); - validateQuestionannaireResponseItems(hostContext, qsrc, qsrc.getItem(), errors, element, stack, inProgress, element, new QStack(qsrc, element)); - } - } - } - - private Questionnaire loadQuestionnaire(Element resource, String id) throws FHIRException { - try { - for (Element contained : resource.getChildren("contained")) { - if (contained.getIdBase().equals(id)) { - FhirPublication v = FhirPublication.fromCode(context.getVersion()); - ByteArrayOutputStream bs = new ByteArrayOutputStream(); - new JsonParser(context).compose(contained, bs, OutputStyle.NORMAL, id); - byte[] json = bs.toByteArray(); - switch (v) { - case DSTU1: throw new FHIRException("Unsupported version R1"); - case DSTU2: - org.hl7.fhir.dstu2.model.Resource r2 = new org.hl7.fhir.dstu2.formats.JsonParser().parse(json); - Resource r5 = VersionConvertor_10_50.convertResource(r2); - if (r5 instanceof Questionnaire) - return (Questionnaire) r5; - else - return null; - case DSTU2016May: - org.hl7.fhir.dstu2016may.model.Resource r2a = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(json); - r5 = VersionConvertor_14_50.convertResource(r2a); - if (r5 instanceof Questionnaire) - return (Questionnaire) r5; - else - return null; - case STU3: - org.hl7.fhir.dstu3.model.Resource r3 = new org.hl7.fhir.dstu3.formats.JsonParser().parse(json); - r5 = VersionConvertor_30_50.convertResource(r3, false); - if (r5 instanceof Questionnaire) - return (Questionnaire) r5; - else - return null; - case R4: - org.hl7.fhir.r4.model.Resource r4 = new org.hl7.fhir.r4.formats.JsonParser().parse(json); - r5 = VersionConvertor_40_50.convertResource(r4); - if (r5 instanceof Questionnaire) - return (Questionnaire) r5; - else - return null; - case R5: - r5 = new org.hl7.fhir.r5.formats.JsonParser().parse(json); - if (r5 instanceof Questionnaire) - return (Questionnaire) r5; - else - return null; - } - } - } - return null; - } catch (IOException e) { - throw new FHIRException(e); - } - } - - private void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, Questionnaire qsrc, QuestionnaireItemComponent qItem, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { - String text = element.getNamedChildValue("text"); - rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), Utilities.noString(text) || text.equals(qItem.getText()), "If text exists, it must match the questionnaire definition for linkId "+qItem.getLinkId()); - - List answers = new ArrayList(); - element.getNamedChildren("answer", answers); - if (inProgress) - warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item "+qItem.getLinkId()); - else if (myEnableWhenEvaluator.isQuestionEnabled(hostContext, qItem, qstack, fpe)) { - rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item "+qItem.getLinkId()); - } else if (!answers.isEmpty()) { // items without answers should be allowed, but not items with answers to questions that are disabled - // it appears that this is always a duplicate error - it will always already have beeb reported, so no need to report it again? - // GDG 2019-07-13 -// rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), !isAnswerRequirementFulfilled(qItem, answers), "Item has answer (2), even though it is not enabled "+qItem.getLinkId()); + b.append(ref); + return b.toString(); + } else + return ref; } - if (answers.size() > 1) - rule(errors, IssueType.INVALID, answers.get(1).line(), answers.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response answer item with this linkId allowed"); - - for (Element answer : answers) { - NodeStack ns = stack.push(answer, -1, null, null); - if (qItem.getType() != null) { - switch (qItem.getType()) { - case GROUP: - rule(errors, IssueType.STRUCTURE, answer.line(), answer.col(), stack.getLiteralPath(), false, "Items of type group should not have answers"); - break; - case DISPLAY: // nothing - break; - case BOOLEAN: - validateQuestionnaireResponseItemType(errors, answer, ns, "boolean"); - break; - case DECIMAL: - validateQuestionnaireResponseItemType(errors, answer, ns, "decimal"); - break; - case INTEGER: - validateQuestionnaireResponseItemType(errors, answer, ns, "integer"); - break; - case DATE: - validateQuestionnaireResponseItemType(errors, answer, ns, "date"); - break; - case DATETIME: - validateQuestionnaireResponseItemType(errors, answer, ns, "dateTime"); - break; - case TIME: - validateQuestionnaireResponseItemType(errors, answer, ns, "time"); - break; - case STRING: - validateQuestionnaireResponseItemType(errors, answer, ns, "string"); - break; - case TEXT: - validateQuestionnaireResponseItemType(errors, answer, ns, "text"); - break; - case URL: - validateQuestionnaireResponseItemType(errors, answer, ns, "uri"); - break; - case ATTACHMENT: - validateQuestionnaireResponseItemType(errors, answer, ns, "Attachment"); - break; - case REFERENCE: - validateQuestionnaireResponseItemType(errors, answer, ns, "Reference"); - break; - case QUANTITY: - if ("Quantity".equals(validateQuestionnaireResponseItemType(errors, answer, ns, "Quantity"))) - if (qItem.hasExtension("???")) - validateQuestionnaireResponseItemQuantity(errors, answer, ns); - break; - case CHOICE: - String itemType = validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string"); - if (itemType != null) { - if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, false); - else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date"); - else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time"); - else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer"); - else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string"); + private Element resolveInBundle(List entries, String ref, String fullUrl, String type, String id) { + if (Utilities.isAbsoluteUrl(ref)) { + // if the reference is absolute, then you resolve by fullUrl. No other thinking is required. + for (Element entry : entries) { + String fu = entry.getNamedChildValue("fullUrl"); + if (ref.equals(fu)) + return entry; } - break; - case OPENCHOICE: - itemType = validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string"); - if (itemType != null) { - if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, true); - else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date"); - else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time"); - else if (itemType.equals("integer")) checkOption(errors, answer, ns, qsrc, qItem, "integer"); - else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string", true); - } - break; -// case QUESTION: - case NULL: - // no validation - break; - } - } - validateQuestionannaireResponseItems(hostContext, qsrc, qItem.getItem(), errors, answer, stack, inProgress, questionnaireResponseRoot, qstack); - } - if (qItem.getType() == null) { - fail(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, "Definition for item "+qItem.getLinkId() + " does not contain a type"); - } else if (qItem.getType() == QuestionnaireItemType.DISPLAY) { - List items = new ArrayList(); - element.getNamedChildren("item", items); - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), items.isEmpty(), "Items not of type DISPLAY should not have items - linkId {0}", qItem.getLinkId()); - } else { - validateQuestionannaireResponseItems(hostContext, qsrc, qItem.getItem(), errors, element, stack, inProgress, questionnaireResponseRoot, qstack); - } - } - -private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, List answers) { - return !answers.isEmpty() || !qItem.getRequired() || qItem.getType() == QuestionnaireItemType.GROUP; -} - - private void validateQuestionnaireResponseItem(ValidatorHostContext hostcontext, Questionnaire qsrc, QuestionnaireItemComponent qItem, List errors, List elements, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { - if (elements.size() > 1) - rule(errors, IssueType.INVALID, elements.get(1).line(), elements.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response item with this linkId allowed - " + qItem.getLinkId()); - int i = 0; - for (Element element : elements) { - NodeStack ns = stack.push(element, i, null, null); - validateQuestionnaireResponseItem(hostcontext, qsrc, qItem, errors, element, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, element)); - i++; - } - } - - private int getLinkIdIndex(List qItems, String linkId) { - for (int i = 0; i < qItems.size(); i++) { - if (linkId.equals(qItems.get(i).getLinkId())) - return i; - } - return -1; - } - - private void validateQuestionannaireResponseItems(ValidatorHostContext hostContext, Questionnaire qsrc, List qItems, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { - List items = new ArrayList(); - element.getNamedChildren("item", items); - // now, sort into stacks - Map> map = new HashMap>(); - int lastIndex = -1; - for (Element item : items) { - String linkId = item.getNamedChildValue("linkId"); - if (rule(errors, IssueType.REQUIRED, item.line(), item.col(), stack.getLiteralPath(), !Utilities.noString(linkId), "No LinkId, so can't be validated")) { - int index = getLinkIdIndex(qItems, linkId); - if (index == -1) { - QuestionnaireItemComponent qItem = findQuestionnaireItem(qsrc, linkId); - if (qItem != null) { - rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, misplacedItemError(qItem)); - NodeStack ns = stack.push(item, -1, null, null); - validateQuestionnaireResponseItem(hostContext, qsrc, qItem, errors, item, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, item)); - } - else - rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, "LinkId \""+linkId+"\" not found in questionnaire"); - } - else - { - rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index >= lastIndex, "Structural Error: items are out of order"); - lastIndex = index; - - // If an item has a child called "linkId" but no child called "answer", - // we'll treat it as not existing for the purposes of enableWhen validation - if (item.hasChildren("answer") || item.hasChildren("item")) { - List mapItem = map.computeIfAbsent(linkId, key -> new ArrayList<>()); - mapItem.add(item); - } - } - } - } - - // ok, now we have a list of known items, grouped by linkId. We've made an error for anything out of order - for (QuestionnaireItemComponent qItem : qItems) { - List mapItem = map.get(qItem.getLinkId()); - validateQuestionnaireResponseItem(hostContext, qsrc, errors, element, stack, inProgress, questionnaireResponseRoot, qItem, mapItem, qstack); - } - } - - public void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, Questionnaire qsrc, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QuestionnaireItemComponent qItem, List mapItem, QStack qstack) { - boolean enabled = myEnableWhenEvaluator.isQuestionEnabled(hostContext, qItem, qstack, fpe); - if (mapItem != null){ - if (!enabled) { - int i = 0; - for (Element e : mapItem) { - NodeStack ns = stack.push(e, i, e.getProperty().getDefinition(), e.getProperty().getDefinition()); - rule(errors, IssueType.INVALID, e.line(), e.col(), ns.getLiteralPath(), enabled, "Item has answer, even though it is not enabled (item id = '"+qItem.getLinkId()+"')"); - i++; - } - } - - // Recursively validate child items - validateQuestionnaireResponseItem(hostContext, qsrc, qItem, errors, mapItem, stack, inProgress, questionnaireResponseRoot, qstack); - - } else { - - // item is missing, is the question enabled? - if (enabled && qItem.getRequired()) { - String message = "No response found for required item with id = '" + qItem.getLinkId() + "'"; - if (inProgress) { - warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, message); + return null; } else { - rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, message); + // split into base, type, and id + String u = null; + if (fullUrl != null && fullUrl.endsWith(type + "/" + id)) + // fullUrl = complex + u = fullUrl.substring(0, fullUrl.length() - (type + "/" + id).length()) + ref; +// u = fullUrl.substring((type+"/"+id).length())+ref; + String[] parts = ref.split("\\/"); + if (parts.length >= 2) { + String t = parts[0]; + String i = parts[1]; + for (Element entry : entries) { + String fu = entry.getNamedChildValue("fullUrl"); + if (fu != null && fu.equals(u)) + return entry; + if (u == null) { + Element resource = entry.getNamedChild("resource"); + if (resource != null) { + String et = resource.getType(); + String eid = resource.getNamedChildValue("id"); + if (t.equals(et) && i.equals(eid)) + return entry; + } + } + } + } + return null; + } + } + + private ElementDefinition resolveNameReference(StructureDefinitionSnapshotComponent snapshot, String contentReference) { + for (ElementDefinition ed : snapshot.getElement()) + if (contentReference.equals("#" + ed.getId())) + return ed; + return null; + } + + private StructureDefinition resolveProfile(StructureDefinition profile, String pr) { + if (pr.startsWith("#")) { + for (Resource r : profile.getContained()) { + if (r.getId().equals(pr.substring(1)) && r instanceof StructureDefinition) + return (StructureDefinition) r; + } + return null; + } else { + long t = System.nanoTime(); + StructureDefinition fr = context.fetchResource(StructureDefinition.class, pr); + sdTime = sdTime + (System.nanoTime() - t); + return fr; + } + } + + private ElementDefinition resolveType(String type, List list) { + for (TypeRefComponent tr : list) { + String url = tr.getWorkingCode(); + if (!Utilities.isAbsoluteUrl(url)) + url = "http://hl7.org/fhir/StructureDefinition/" + url; + long t = System.nanoTime(); + StructureDefinition sd = context.fetchResource(StructureDefinition.class, url); + sdTime = sdTime + (System.nanoTime() - t); + if (sd != null && (sd.getType().equals(type) || sd.getUrl().equals(type)) && sd.hasSnapshot()) + return sd.getSnapshot().getElement().get(0); + } + return null; + } + + public void setAnyExtensionsAllowed(boolean anyExtensionsAllowed) { + this.anyExtensionsAllowed = anyExtensionsAllowed; + } + + public IResourceValidator setBestPracticeWarningLevel(BestPracticeWarningLevel value) { + bpWarnings = value; + return this; + } + + @Override + public void setCheckDisplay(CheckDisplayOption checkDisplay) { + this.checkDisplay = checkDisplay; + } + + public void setSuppressLoincSnomedMessages(boolean suppressLoincSnomedMessages) { + this.suppressLoincSnomedMessages = suppressLoincSnomedMessages; + } + + public IdStatus getResourceIdRule() { + return resourceIdRule; + } + + public void setResourceIdRule(IdStatus resourceIdRule) { + this.resourceIdRule = resourceIdRule; + } + + + public boolean isAllowXsiLocation() { + return allowXsiLocation; + } + + public void setAllowXsiLocation(boolean allowXsiLocation) { + this.allowXsiLocation = allowXsiLocation; + } + + /** + * @param element - the candidate that might be in the slice + * @param path - for reporting any errors. the XPath for the element + * @param slicer - the definition of how slicing is determined + * @param ed - the slice for which to test membership + * @param errors + * @param stack + * @return + * @throws DefinitionException + * @throws DefinitionException + * @throws IOException + * @throws FHIRException + */ + private boolean sliceMatches(ValidatorHostContext hostContext, Element element, String path, ElementDefinition slicer, ElementDefinition ed, StructureDefinition profile, List errors, List sliceInfo, NodeStack stack) throws DefinitionException, FHIRException { + if (!slicer.getSlicing().hasDiscriminator()) + return false; // cannot validate in this case + + ExpressionNode n = (ExpressionNode) ed.getUserData("slice.expression.cache"); + if (n == null) { + long t = System.nanoTime(); + // GG: this approach is flawed because it treats discriminators individually rather than collectively + StringBuilder expression = new StringBuilder("true"); + boolean anyFound = false; + Set discriminators = new HashSet<>(); + for (ElementDefinitionSlicingDiscriminatorComponent s : slicer.getSlicing().getDiscriminator()) { + String discriminator = s.getPath(); + discriminators.add(discriminator); + + List criteriaElements = getCriteriaForDiscriminator(path, ed, discriminator, profile, s.getType() == DiscriminatorType.PROFILE); + boolean found = false; + for (ElementDefinition criteriaElement : criteriaElements) { + found = true; + if (s.getType() == DiscriminatorType.TYPE) { + String type = null; + if (!criteriaElement.getPath().contains("[") && discriminator.contains("[")) { + discriminator = discriminator.substring(0, discriminator.indexOf('[')); + String lastNode = tail(discriminator); + type = tail(criteriaElement.getPath()).substring(lastNode.length()); + type = type.substring(0, 1).toLowerCase() + type.substring(1); + } else if (!criteriaElement.hasType() || criteriaElement.getType().size() == 1) { + if (discriminator.contains("[")) + discriminator = discriminator.substring(0, discriminator.indexOf('[')); + type = criteriaElement.getType().get(0).getWorkingCode(); + } else if (criteriaElement.getType().size() > 1) { + throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " in " + profile.getUrl() + " has multiple types: " + criteriaElement.typeSummary()); + } else + throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " in " + profile.getUrl() + " has no types"); + if (discriminator.isEmpty()) + expression.append(" and $this is " + type); + else + expression.append(" and " + discriminator + " is " + type); + } else if (s.getType() == DiscriminatorType.PROFILE) { + if (criteriaElement.getType().size() == 0) { + throw new DefinitionException("Profile based discriminators must have a type (" + criteriaElement.getId() + " in profile " + profile.getUrl() + ")"); + } + if (criteriaElement.getType().size() != 1) { + throw new DefinitionException("Profile based discriminators must have only one type (" + criteriaElement.getId() + " in profile " + profile.getUrl() + ")"); + } + List list = discriminator.endsWith(".resolve()") || discriminator.equals("resolve()") ? criteriaElement.getType().get(0).getTargetProfile() : criteriaElement.getType().get(0).getProfile(); + if (list.size() == 0) { + throw new DefinitionException("Profile based discriminators must have a type with a profile (" + criteriaElement.getId() + " in profile " + profile.getUrl() + ")"); + } else if (list.size() > 1) { + CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(" or "); + for (CanonicalType c : list) { + b.append(discriminator + ".conformsTo('" + c.getValue() + "')"); + } + expression.append(" and (" + b + ")"); + } else { + expression.append(" and " + discriminator + ".conformsTo('" + list.get(0).getValue() + "')"); + } + } else if (s.getType() == DiscriminatorType.EXISTS) { + if (criteriaElement.hasMin() && criteriaElement.getMin() >= 1) + expression.append(" and (" + discriminator + ".exists())"); + else if (criteriaElement.hasMax() && criteriaElement.getMax().equals("0")) + expression.append(" and (" + discriminator + ".exists().not())"); + else + throw new FHIRException("Discriminator (" + discriminator + ") is based on element existence, but slice " + ed.getId() + " neither sets min>=1 or max=0"); + } else if (criteriaElement.hasFixed()) { + buildFixedExpression(ed, expression, discriminator, criteriaElement); + } else if (criteriaElement.hasPattern()) { + buildPattternExpression(ed, expression, discriminator, criteriaElement); + } else if (criteriaElement.hasBinding() && criteriaElement.getBinding().hasStrength() && criteriaElement.getBinding().getStrength().equals(BindingStrength.REQUIRED) && criteriaElement.getBinding().hasValueSet()) { + expression.append(" and (" + discriminator + " memberOf '" + criteriaElement.getBinding().getValueSet() + "')"); + } else { + found = false; + } + if (found) + break; + } + if (found) + anyFound = true; + } + if (!anyFound) { + if (slicer.getSlicing().getDiscriminator().size() > 1) + throw new DefinitionException("Could not match any discriminators (" + discriminators + ") for slice " + ed.getId() + " in profile " + profile.getUrl() + " - None of the discriminator " + discriminators + " have fixed value, binding or existence assertions"); + else + throw new DefinitionException("Could not match discriminator (" + discriminators + ") for slice " + ed.getId() + " in profile " + profile.getUrl() + " - the discriminator " + discriminators + " does not have fixed value, binding or existence assertions"); + } + + try { + n = fpe.parse(fixExpr(expression.toString())); + } catch (FHIRLexerException e) { + throw new FHIRException("Problem processing expression " + expression + " in profile " + profile.getUrl() + " path " + path + ": " + e.getMessage()); + } + fpeTime = fpeTime + (System.nanoTime() - t); + ed.setUserData("slice.expression.cache", n); + } + + ValidatorHostContext shc = hostContext.forSlicing(); + boolean pass = evaluateSlicingExpression(shc, element, path, profile, n); + if (!pass) { + slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Does not match slice'" + ed.getSliceName(), "discriminator = " + Utilities.escapeXml(n.toString())); + for (String url : shc.getSliceRecords().keySet()) { + slicingHint(sliceInfo, IssueType.STRUCTURE, element.line(), element.col(), path, false, "Details for " + stack.getLiteralPath() + " against profile " + url, + "Profile " + url + " does not match for " + stack.getLiteralPath() + " because of the following profile issues: " + errorSummaryForSlicingAsHtml(shc.getSliceRecords().get(url))); + } + } + return pass; + } + + public boolean evaluateSlicingExpression(ValidatorHostContext hostContext, Element element, String path, StructureDefinition profile, ExpressionNode n) throws FHIRException { + String msg; + boolean ok; + try { + long t = System.nanoTime(); + ok = fpe.evaluateToBoolean(hostContext.forProfile(profile), hostContext.getResource(), hostContext.getRootResource(), element, n); + fpeTime = fpeTime + (System.nanoTime() - t); + msg = fpe.forLog(); + } catch (Exception ex) { + ex.printStackTrace(); + throw new FHIRException("Problem evaluating slicing expression for element in profile " + profile.getUrl() + " path " + path + " (fhirPath = " + n + "): " + ex.getMessage()); + } + return ok; + } + + private void buildPattternExpression(ElementDefinition ed, StringBuilder expression, String discriminator, ElementDefinition criteriaElement) throws DefinitionException { + DataType pattern = criteriaElement.getPattern(); + if (pattern instanceof CodeableConcept) { + CodeableConcept cc = (CodeableConcept) pattern; + expression.append(" and "); + buildCodeableConceptExpression(ed, expression, discriminator, cc); + } else if (pattern instanceof Identifier) { + Identifier ii = (Identifier) pattern; + expression.append(" and "); + buildIdentifierExpression(ed, expression, discriminator, ii); + } else + throw new DefinitionException("Unsupported fixed pattern type for discriminator(" + discriminator + ") for slice " + ed.getId() + ": " + pattern.getClass().getName()); + } + + private void buildIdentifierExpression(ElementDefinition ed, StringBuilder expression, String discriminator, Identifier ii) + throws DefinitionException { + if (ii.hasExtension()) + throw new DefinitionException("Unsupported Identifier pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); + boolean first = true; + expression.append(discriminator + ".where("); + if (ii.hasSystem()) { + first = false; + expression.append("system = '" + ii.getSystem() + "'"); + } + if (ii.hasValue()) { + if (first) + first = false; + else + expression.append(" and "); + expression.append("value = '" + ii.getValue() + "'"); + } + if (ii.hasUse()) { + if (first) + first = false; + else + expression.append(" and "); + expression.append("use = '" + ii.getUse() + "'"); + } + if (ii.hasType()) { + if (first) + first = false; + else + expression.append(" and "); + buildCodeableConceptExpression(ed, expression, "type", ii.getType()); + } + expression.append(").exists()"); + } + + private void buildCodeableConceptExpression(ElementDefinition ed, StringBuilder expression, String discriminator, CodeableConcept cc) + throws DefinitionException { + if (cc.hasText()) + throw new DefinitionException("Unsupported CodeableConcept pattern - using text - for discriminator(" + discriminator + ") for slice " + ed.getId()); + if (!cc.hasCoding()) + throw new DefinitionException("Unsupported CodeableConcept pattern - must have at least one coding - for discriminator(" + discriminator + ") for slice " + ed.getId()); + if (cc.hasExtension()) + throw new DefinitionException("Unsupported CodeableConcept pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); + boolean firstCoding = true; + for (Coding c : cc.getCoding()) { + if (c.hasExtension()) + throw new DefinitionException("Unsupported CodeableConcept pattern - extensions are not allowed - for discriminator(" + discriminator + ") for slice " + ed.getId()); + if (firstCoding) firstCoding = false; + else expression.append(" and "); + expression.append(discriminator + ".coding.where("); + boolean first = true; + if (c.hasSystem()) { + first = false; + expression.append("system = '" + c.getSystem() + "'"); + } + if (c.hasVersion()) { + if (first) first = false; + else expression.append(" and "); + expression.append("version = '" + c.getVersion() + "'"); + } + if (c.hasCode()) { + if (first) first = false; + else expression.append(" and "); + expression.append("code = '" + c.getCode() + "'"); + } + if (c.hasDisplay()) { + if (first) first = false; + else expression.append(" and "); + expression.append("display = '" + c.getDisplay() + "'"); + } + expression.append(").exists()"); + } + } + + private void buildFixedExpression(ElementDefinition ed, StringBuilder expression, String discriminator, ElementDefinition criteriaElement) throws DefinitionException { + DataType fixed = criteriaElement.getFixed(); + if (fixed instanceof CodeableConcept) { + CodeableConcept cc = (CodeableConcept) fixed; + expression.append(" and "); + buildCodeableConceptExpression(ed, expression, discriminator, cc); + } else if (fixed instanceof Identifier) { + Identifier ii = (Identifier) fixed; + expression.append(" and "); + buildIdentifierExpression(ed, expression, discriminator, ii); + } else { + expression.append(" and ("); + if (fixed instanceof StringType) { + Gson gson = new Gson(); + String json = gson.toJson((StringType) fixed); + String escapedString = json.substring(json.indexOf(":") + 2); + escapedString = escapedString.substring(0, escapedString.indexOf(",\"myStringValue") - 1); + expression.append("'" + escapedString + "'"); + } else if (fixed instanceof UriType) { + expression.append("'" + ((UriType) fixed).asStringValue() + "'"); + } else if (fixed instanceof IntegerType) { + expression.append(((IntegerType) fixed).asStringValue()); + } else if (fixed instanceof DecimalType) { + expression.append(((IntegerType) fixed).asStringValue()); + } else if (fixed instanceof BooleanType) { + expression.append(((BooleanType) fixed).asStringValue()); + } else + throw new DefinitionException("Unsupported fixed value type for discriminator(" + discriminator + ") for slice " + ed.getId() + ": " + fixed.getClass().getName()); + expression.append(" in " + discriminator + ")"); + } + } + + // checkSpecials = we're only going to run these tests if we are actually validating this content (as opposed to we looked it up) + private void start(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, NodeStack stack) throws FHIRException { + checkLang(resource, stack); + + if ("Bundle".equals(element.fhirType())) { + resolveBundleReferences(element, new ArrayList()); + } + startInner(hostContext, errors, resource, element, defn, stack, hostContext.isCheckSpecials()); + + List res = new ArrayList<>(); + Element meta = element.getNamedChild("meta"); + if (meta != null) { + List profiles = new ArrayList(); + meta.getNamedChildren("profile", profiles); + int i = 0; + for (Element profile : profiles) { + StructureDefinition sd = context.fetchResource(StructureDefinition.class, profile.primitiveValue()); + if (!defn.getUrl().equals(profile.primitiveValue())) { + if (warning(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath() + ".meta.profile[" + i + "]", sd != null, "Profile reference '" + profile.primitiveValue() + "' could not be resolved, so has not been checked")) { + startInner(hostContext, errors, resource, element, sd, stack, false); + } + } + i++; + } + } + } + + private void resolveBundleReferences(Element element, List bundles) { + if (!element.hasUserData("validator.bundle.resolved")) { + element.setUserData("validator.bundle.resolved", true); + List list = new ArrayList(); + list.addAll(bundles); + list.add(0, element); + List entries = element.getChildrenByName("entry"); + for (Element entry : entries) { + String fu = entry.getChildValue("fullUrl"); + Element r = entry.getNamedChild("resource"); + if (r != null) { + resolveBundleReferencesInResource(list, r, fu); + } + } + } + } + + private void resolveBundleReferencesInResource(List bundles, Element r, String fu) { + r.setUserData("validator.bundle.resolution-resource", null); + if ("Bundle".equals(r.fhirType())) { + resolveBundleReferences(r, bundles); + } else { + for (Element child : r.getChildren()) { + resolveBundleReferencesForElement(bundles, r, fu, child); + } + } + } + + private void resolveBundleReferencesForElement(List bundles, Element resource, String fu, Element element) { + if ("Reference".equals(element.fhirType())) { + String ref = element.getChildValue("reference"); + if (!Utilities.noString(ref)) { + for (Element bundle : bundles) { + List entries = bundle.getChildren("entry"); + Element tgt = resolveInBundle(entries, ref, fu, resource.fhirType(), resource.getIdBase()); + if (tgt != null) { + element.setUserData("validator.bundle.resolution", tgt.getNamedChild("resource")); + return; + } + } + element.setUserData("validator.bundle.resolution-failed", ref); + } + } else { + element.setUserData("validator.bundle.resolution-noref", null); + for (Element child : element.getChildren()) { + resolveBundleReferencesForElement(bundles, resource, fu, child); + } } - } } - } - - private String misplacedItemError(QuestionnaireItemComponent qItem) { - return qItem.hasLinkId() ? String.format("Structural Error: item with linkid %s is in the wrong place", qItem.getLinkId()) : "Structural Error: item is in the wrong place"; - } - - private void validateQuestionnaireResponseItemQuantity( List errors, Element answer, NodeStack stack) { - - } - - private String validateQuestionnaireResponseItemType(List errors, Element element, NodeStack stack, String... types) { - List values = new ArrayList(); - element.getNamedChildrenWithWildcard("value[x]", values); - for (int i = 0; i < types.length; i++) { - if (types[i].equals("text")) { - types[i] = "string"; - } - } - if (values.size() > 0) { - NodeStack ns = stack.push(values.get(0), -1, null, null); - CommaSeparatedStringBuilder l = new CommaSeparatedStringBuilder(); - for (String s : types) { - l.append(s); - if (values.get(0).getName().equals("value"+Utilities.capitalize(s))) - return(s); - } - if (types.length == 1) - rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be of type "+types[0]); - else - rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be one of the types "+l.toString()); - } - return null; - } - - private QuestionnaireItemComponent findQuestionnaireItem(Questionnaire qSrc, String linkId) { - return findItem(qSrc.getItem(), linkId); - } - - private QuestionnaireItemComponent findItem(List list, String linkId) { - for (QuestionnaireItemComponent item : list) { - if (linkId.equals(item.getLinkId())) - return item; - QuestionnaireItemComponent result = findItem(item.getItem(), linkId); - if (result != null) - return result; - } - return null; - } - - private void validateAnswerCode(List errors, Element value, NodeStack stack, Questionnaire qSrc, String ref, boolean theOpenChoice) { - ValueSet vs = resolveBindingReference(qSrc, ref, qSrc.getUrl()); - if (warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), vs != null, "ValueSet " + describeReference(ref) + " not found by validator")) { - try { - Coding c = ObjectConverter.readAsCoding(value); - if (isBlank(c.getCode()) && isBlank(c.getSystem()) && isNotBlank(c.getDisplay())) { - if (theOpenChoice) { + public void startInner(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, NodeStack stack, boolean checkSpecials) { + // the first piece of business is to see if we've validated this resource against this profile before. + // if we have (*or if we still are*), then we'll just return our existing errors + ResourceValidationTracker resTracker = getResourceTracker(element); + List cachedErrors = resTracker.getOutcomes(defn); + if (cachedErrors != null) { + for (ValidationMessage vm : cachedErrors) { + if (!errors.contains(vm)) { + errors.add(vm); + } + } return; - } } - - long t = System.nanoTime(); - ValidationResult res = context.validateCode(new ValidationOptions(stack.workingLang), c, vs); - txTime = txTime + (System.nanoTime() - t); - if (!res.isOk()) { - txRule(errors, res.getTxLink(), IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "The value provided (" + c.getSystem() + "::" + c.getCode() + ") is not in the options value set in the questionnaire"); - } else if (res.getSeverity() != null) { - super.addValidationMessage(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), res.getMessage(), res.getSeverity(), Source.TerminologyEngine); - } - } catch (Exception e) { - warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "Error " + e.getMessage() + " validating Coding against Questionnaire Options"); - } - } - } - - private void validateAnswerCode( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean theOpenChoice) { - Element v = answer.getNamedChild("valueCoding"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) - checkCodingOption(errors, answer, stack, qSrc, qItem, theOpenChoice); - // validateAnswerCode(errors, v, stack, qItem.getOption()); - else if (qItem.hasAnswerValueSet()) - validateAnswerCode(errors, v, stack, qSrc, qItem.getAnswerValueSet(), theOpenChoice); - else - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate options because no option or options are provided"); - } - - private void checkOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type) { - checkOption(errors, answer, stack, qSrc, qItem, type, false); - } - - private void checkOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type, boolean openChoice) { - if (type.equals("integer")) checkIntegerOption(errors, answer, stack, qSrc, qItem, openChoice); - else if (type.equals("date")) checkDateOption(errors, answer, stack, qSrc, qItem, openChoice); - else if (type.equals("time")) checkTimeOption(errors, answer, stack, qSrc, qItem, openChoice); - else if (type.equals("string")) checkStringOption(errors, answer, stack, qSrc, qItem, openChoice); - else if (type.equals("Coding")) checkCodingOption(errors, answer, stack, qSrc, qItem, openChoice); - } - - private void checkIntegerOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { - Element v = answer.getNamedChild("valueInteger"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) { - List list = new ArrayList(); - for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { - try { - list.add(components.getValueIntegerType()); - } catch (FHIRException e) { - // If it's the wrong type, just keep going - } - } - if (list.isEmpty() && !openChoice) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type integer"); - } else { - boolean found = false; - for (IntegerType item : list) { - if (item.getValue() == Integer.parseInt(v.primitiveValue())) { - found = true; - break; - } - } - if (!found) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The integer "+v.primitiveValue()+" is not a valid option"); - } - } - } else - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate integer answer option because no option list is provided"); - } - - private void checkDateOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { - Element v = answer.getNamedChild("valueDate"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) { - List list = new ArrayList(); - for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { - try { - list.add(components.getValueDateType()); - } catch (FHIRException e) { - // If it's the wrong type, just keep going - } - } - if (list.isEmpty() && !openChoice) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type date"); - } else { - boolean found = false; - for (DateType item : list) { - if (item.getValue().equals(v.primitiveValue())) { - found = true; - break; - } - } - if (!found) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The date "+v.primitiveValue()+" is not a valid option"); - } - } - } else - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate date answer option because no option list is provided"); - } - - private void checkTimeOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { - Element v = answer.getNamedChild("valueTime"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) { - List list = new ArrayList(); - for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { - try { - list.add(components.getValueTimeType()); - } catch (FHIRException e) { - // If it's the wrong type, just keep going - } - } - if (list.isEmpty() && !openChoice) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type time"); - } else { - boolean found = false; - for (TimeType item : list) { - if (item.getValue().equals(v.primitiveValue())) { - found = true; - break; - } - } - if (!found) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The time "+v.primitiveValue()+" is not a valid option"); - } - } - } else - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate time answer option because no option list is provided"); - } - - private void checkStringOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { - Element v = answer.getNamedChild("valueString"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) { - List list = new ArrayList(); - for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { - try { - if (components.getValue() != null) { - list.add(components.getValueStringType()); - } - } catch (FHIRException e) { - // If it's the wrong type, just keep going - } - } - if (!openChoice) { - if (list.isEmpty()) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type string"); - } else { - boolean found = false; - for (StringType item : list) { - if (item.getValue().equals((v.primitiveValue()))) { - found = true; - break; + if (rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), defn.hasSnapshot(), "StructureDefinition has no snapshot - validation is against the snapshot, so it must be provided")) { + List localErrors = new ArrayList(); + resTracker.startValidating(defn); + trackUsage(defn, hostContext, element); + validateElement(hostContext, localErrors, defn, defn.getSnapshot().getElement().get(0), null, null, resource, element, element.getName(), stack, false, true, null); + resTracker.storeOutcomes(defn, localErrors); + for (ValidationMessage vm : localErrors) { + if (!errors.contains(vm)) { + errors.add(vm); + } } - } - if (!found) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The string " + v.primitiveValue() + " is not a valid option"); - } } - } - } else { - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate string answer option because no option list is provided"); + if (checkSpecials) { + checkSpecials(hostContext, errors, element, stack, checkSpecials); + validateResourceRules(errors, element, stack); + } } - } - private void checkCodingOption( List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { - Element v = answer.getNamedChild("valueCoding"); - String system = v.getNamedChildValue("system"); - String code = v.getNamedChildValue("code"); - NodeStack ns = stack.push(v, -1, null, null); - if (qItem.getAnswerOption().size() > 0) { - List list = new ArrayList(); - for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { - try { - if (components.getValue() != null) { - list.add(components.getValueCoding()); - } - } catch (FHIRException e) { - // If it's the wrong type, just keep going + public void checkSpecials(ValidatorHostContext hostContext, List errors, Element element, NodeStack stack, boolean checkSpecials) { + // specific known special validations + if (element.getType().equals("Bundle")) { + validateBundle(errors, element, stack, checkSpecials); + } else if (element.getType().equals("Observation")) { + validateObservation(errors, element, stack); + } else if (element.getType().equals("Questionnaire")) { + ArrayList parents = new ArrayList<>(); + parents.add(element); + validateQuestionannaireItem(errors, element, element, stack, parents); + } else if (element.getType().equals("QuestionnaireResponse")) { + validateQuestionannaireResponse(hostContext, errors, element, stack); + } else if (element.getType().equals("CapabilityStatement")) { + validateCapabilityStatement(errors, element, stack); + } else if (element.getType().equals("CodeSystem")) { + validateCodeSystem(errors, element, stack); } - } - if (list.isEmpty() && !openChoice) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type coding"); - } else { - boolean found = false; - for (Coding item : list) { - if (ObjectUtil.equals(item.getSystem(), system) && ObjectUtil.equals(item.getCode(), code)) { - found = true; - break; - } - } - if (!found) { - rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The code "+system+"::"+code+" is not a valid option"); - } - } - } else - hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate Coding option because no option list is provided"); - } - - private String tail(String path) { - return path.substring(path.lastIndexOf(".") + 1); - } - - private String tryParse(String ref) { - String[] parts = ref.split("\\/"); - switch (parts.length) { - case 1: - return null; - case 2: - return checkResourceType(parts[0]); - default: - if (parts[parts.length - 2].equals("_history")) - return checkResourceType(parts[parts.length - 4]); - else - return checkResourceType(parts[parts.length - 2]); } - } - private boolean typesAreAllReference(List theType) { - for (TypeRefComponent typeRefComponent : theType) { - if (typeRefComponent.getCode().equals("Reference") == false) { + private ResourceValidationTracker getResourceTracker(Element element) { + ResourceValidationTracker res = resourceTracker.get(element); + if (res == null) { + res = new ResourceValidationTracker(); + resourceTracker.put(element, res); + } + return res; + } + + private void validateQuestionannaireItem(List errors, Element element, Element questionnaire, NodeStack stack, List parents) { + List list = getItems(element); + for (int i = 0; i < list.size(); i++) { + Element e = list.get(i); + NodeStack ns = stack.push(e, i, e.getProperty().getDefinition(), e.getProperty().getDefinition()); + validateQuestionnaireElement(errors, ns, questionnaire, e, parents); + List np = new ArrayList(); + np.add(e); + np.addAll(parents); + validateQuestionannaireItem(errors, e, questionnaire, ns, np); + } + } + + private void validateQuestionnaireElement(List errors, NodeStack ns, Element questionnaire, Element item, List parents) { + // R4+ + if (FHIRVersion.isR4Plus(context.getVersion())) { + if (item.hasChildren("enableWhen")) { + List ewl = item.getChildren("enableWhen"); + for (Element ew : ewl) { +// Element ew = item.getNamedChild("enableWhen"); + String ql = ew.getNamedChildValue("question"); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, ql != null, "Questions with an enableWhen must have a value for the question link")) { + Element tgt = getQuestionById(item, ql); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt == null, "Questions with an enableWhen cannot refer to an inner question for it's enableWhen condition")) { + tgt = getQuestionById(questionnaire, ql); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != null, "Unable to find target '" + ql + "' for this question enableWhen")) { + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != item, "Target for this question enableWhen can't reference itself")) { + if (!isBefore(item, tgt, parents)) { + warning(errors, IssueType.BUSINESSRULE, ns.literalPath, false, "The target of this enableWhen rule (" + ql + ") comes after the question itself"); + } + } + } + } + } + } + } + } + } + + private boolean isBefore(Element item, Element tgt, List parents) { + // we work up the list, looking for tgt in the children of the parents + if (parents.contains(tgt)) { + // actually, if the target is a parent, that's automatically ok + return true; + } + for (Element p : parents) { + int i = findIndex(p, item); + int t = findIndex(p, tgt); + if (i > -1 && t > -1) { + return i > t; + } + } + return false; // unsure... shouldn't ever get to this point; + } + + + private int findIndex(Element parent, Element descendant) { + for (int i = 0; i < parent.getChildren().size(); i++) { + if (parent.getChildren().get(i) == descendant || isChild(parent.getChildren().get(i), descendant)) + return i; + } + return -1; + } + + private boolean isChild(Element element, Element descendant) { + for (Element e : element.getChildren()) { + if (e == descendant) + return true; + if (isChild(e, descendant)) + return true; + } return false; - } } - return true; - } - private void validateBundle(List errors, Element bundle, NodeStack stack, boolean checkSpecials) { - List entries = new ArrayList(); - bundle.getNamedChildren("entry", entries); - String type = bundle.getNamedChildValue("type"); - type = StringUtils.defaultString(type); - - if (entries.size() == 0) { - rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals("document") || type.equals("message")), "Documents or Messages must contain at least one entry"); - } else { - // Get the first entry, the MessageHeader - Element firstEntry = entries.get(0); - // Get the stack of the first entry - NodeStack firstStack = stack.push(firstEntry, 1, null, null); - - String fullUrl = firstEntry.getNamedChildValue("fullUrl"); - - if (type.equals("document")) { - Element resource = firstEntry.getNamedChild("resource"); - String id = resource.getNamedChildValue("id"); - if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath("entry", ":0"), resource != null, "No resource on first entry")) { - validateDocument(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id); + private Element getQuestionById(Element focus, String ql) { + List list = getItems(focus); + for (Element item : list) { + String v = item.getNamedChildValue("linkId"); + if (ql.equals(v)) + return item; + Element tgt = getQuestionById(item, ql); + if (tgt != null) + return tgt; } - checkAllInterlinked(errors, entries, stack, bundle, true); - } - if (type.equals("message")) { - Element resource = firstEntry.getNamedChild("resource"); - String id = resource.getNamedChildValue("id"); - if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath("entry", ":0"), resource != null, "No resource on first entry")) { - validateMessage(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id); + return null; + + } + + private List getItems(Element element) { + List list = new ArrayList<>(); + element.getNamedChildren("item", list); + return list; + } + + private void checkLang(Element resource, NodeStack stack) { + String lang = resource.getNamedChildValue("language"); + if (!Utilities.noString(lang)) + stack.workingLang = lang; + } + + private void validateResourceRules(List errors, Element element, NodeStack stack) { + String lang = element.getNamedChildValue("language"); + Element text = element.getNamedChild("text"); + if (text != null) { + Element div = text.getNamedChild("div"); + if (lang != null && div != null) { + XhtmlNode xhtml = div.getXhtml(); + String l = xhtml.getAttribute("lang"); + String xl = xhtml.getAttribute("xml:lang"); + if (l == null && xl == null) { + warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have an lang or an xml:lang tag (needs both - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); + } else { + if (l == null) { + warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have a lang tag (needs both lang and xml:lang - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); + } else if (!l.equals(lang)) { + warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language (" + lang + "), and the XHTML has a lang (" + l + "), but they differ "); + } + if (xl == null) { + warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language, but the XHTML does not have an xml:lang tag (needs both lang and xml:lang - see https://www.w3.org/TR/i18n-html-tech-lang/#langvalues)"); + } else if (!xl.equals(lang)) { + warning(errors, IssueType.BUSINESSRULE, div.line(), div.col(), stack.getLiteralPath(), false, "Resource has a language (" + lang + "), and the XHTML has an xml:lang (" + xl + "), but they differ "); + } + } + } + } + // security tags are a set (system|code) + Element meta = element.getNamedChild("meta"); + if (meta != null) { + Set tags = new HashSet<>(); + List list = new ArrayList<>(); + meta.getNamedChildren("security", list); + int i = 0; + for (Element e : list) { + String s = e.getNamedChildValue("system") + "#" + e.getNamedChildValue("code"); + rule(errors, IssueType.BUSINESSRULE, e.line(), e.col(), stack.getLiteralPath() + ".meta.profile[" + Integer.toString(i) + "]", !tags.contains(s), "Duplicate Security Label " + s); + tags.add(s); + i++; + } } - checkAllInterlinked(errors, entries, stack, bundle, VersionUtilities.isR5Ver(context.getVersion())); - } - // We do not yet have rules requiring that the id and fullUrl match when dealing with messaging Bundles - // validateResourceIds(errors, entries, stack); } - for (Element entry : entries) { - String fullUrl = entry.getNamedChildValue("fullUrl"); - String url = getCanonicalURLForEntry(entry); - String id = getIdForEntry(entry); - if (url != null) { - if (!(!url.equals(fullUrl) || (url.matches(uriRegexForVersion()) && url.endsWith("/"+id))) && !isV3orV2Url(url)) - rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry", ":0"), false, "The canonical URL ("+url+") cannot match the fullUrl ("+fullUrl+") unless the resource id ("+id+") also matches"); - rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry", ":0"), !url.equals(fullUrl) || serverBase == null || (url.equals(Utilities.pathURL(serverBase, entry.getNamedChild("resource").fhirType(), id))), "The canonical URL ("+url+") cannot match the fullUrl ("+fullUrl+") unless on the canonical server itself"); - } - // todo: check specials + + private void validateCapabilityStatement(List errors, Element cs, NodeStack stack) { + int iRest = 0; + for (Element rest : cs.getChildrenByName("rest")) { + int iResource = 0; + for (Element resource : rest.getChildrenByName("resource")) { + int iSP = 0; + for (Element searchParam : resource.getChildrenByName("searchParam")) { + String ref = searchParam.getChildValue("definition"); + String type = searchParam.getChildValue("type"); + if (!Utilities.noString(ref)) { + SearchParameter sp = context.fetchResource(SearchParameter.class, ref); + if (sp != null) { + rule(errors, IssueType.INVALID, searchParam.line(), searchParam.col(), stack.literalPath + ".rest[" + iRest + "].resource[" + iResource + "].searchParam[" + iSP + "]", + sp.getType().toCode().equals(type), "Type mismatch - SearchParameter '" + sp.getUrl() + "' type is " + sp.getType().toCode() + ", but type here is " + type); + } + } + iSP++; + } + iResource++; + } + iRest++; + } } - } - // hack for pre-UTG v2/v3 - private boolean isV3orV2Url(String url) { - return url.startsWith("http://hl7.org/fhir/v3/") || url.startsWith("http://hl7.org/fhir/v2/"); - } + private void validateCodeSystem(List errors, Element cs, NodeStack stack) { + String url = cs.getNamedChildValue("url"); + String vsu = cs.getNamedChildValue("valueSet"); + if (!Utilities.noString(vsu)) { + ValueSet vs; + try { + vs = context.fetchResourceWithException(ValueSet.class, vsu); + } catch (FHIRException e) { + vs = null; + } + if (vs != null) { + if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.hasCompose() && !vs.hasExpansion(), "CodeSystem " + url + " has a 'all system' value set of " + vsu + ", but it is an expansion")) + if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().size() == 1, "CodeSystem " + url + " has a 'all system' value set of " + vsu + ", but doesn't have a single include")) + if (rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), vs.getCompose().getInclude().get(0).getSystem().equals(url), "CodeSystem " + url + " has a 'all system' value set of " + vsu + ", but doesn't have a matching system (" + vs.getCompose().getInclude().get(0).getSystem() + ")")) { + rule(errors, IssueType.BUSINESSRULE, stack.getLiteralPath(), !vs.getCompose().getInclude().get(0).hasValueSet() + && !vs.getCompose().getInclude().get(0).hasConcept() && !vs.getCompose().getInclude().get(0).hasFilter(), "CodeSystem " + url + " has a 'all system' value set of " + vsu + ", but the include has extra details"); + } + } + } // todo... try getting the value set the other way... + } - public final static String URI_REGEX3 = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AllergyIntolerance|AdverseEvent|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BodySite|Bundle|CapabilityStatement|CarePlan|CareTeam|ChargeItem|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition (aka Problem)|Consent|Contract|Coverage|DataElement|DetectedIssue|Device|DeviceComponent|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EligibilityRequest|EligibilityResponse|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|ExpansionProfile|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingManifest|ImagingStudy|Immunization|ImmunizationRecommendation|ImplementationGuide|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationRequest|MedicationStatement|MessageDefinition|MessageHeader|NamingSystem|NutritionOrder|Observation|OperationDefinition|OperationOutcome|Organization|Parameters|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|ProcedureRequest|ProcessRequest|ProcessResponse|Provenance|Questionnaire|QuestionnaireResponse|ReferralRequest|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|Sequence|ServiceDefinition|Slot|Specimen|StructureDefinition|StructureMap|Subscription|Substance|SupplyDelivery|SupplyRequest|Task|TestScript|TestReport|ValueSet|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?"; - private static final String EXECUTED_CONSTRAINT_LIST = "validator.executed.invariant.list"; - private static final String EXECUTION_ID = "validator.execution.id"; + private void validateQuestionannaireResponse(ValidatorHostContext hostContext, List errors, Element element, NodeStack stack) throws FHIRException { + Element q = element.getNamedChild("questionnaire"); + String questionnaire = null; + if (q != null) { + /* + * q.getValue() is correct for R4 content, but we'll also accept the second + * option just in case we're validating raw STU3 content. Being lenient here + * isn't the end of the world since if someone is actually doing the reference + * wrong in R4 content it'll get flagged elsewhere by the validator too + */ + if (isNotBlank(q.getValue())) { + questionnaire = q.getValue(); + } else if (isNotBlank(q.getChildValue("reference"))) { + questionnaire = q.getChildValue("reference"); + } + } + if (hint(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), questionnaire != null, "No questionnaire is identified, so no validation can be performed against the base questionnaire")) { + long t = System.nanoTime(); + Questionnaire qsrc = questionnaire.startsWith("#") ? loadQuestionnaire(element, questionnaire.substring(1)) : context.fetchResource(Questionnaire.class, questionnaire); + sdTime = sdTime + (System.nanoTime() - t); + if (warning(errors, IssueType.REQUIRED, q.line(), q.col(), stack.getLiteralPath(), qsrc != null, "The questionnaire \"" + questionnaire + "\" could not be resolved, so no validation can be performed against the base questionnaire")) { + boolean inProgress = "in-progress".equals(element.getNamedChildValue("status")); + validateQuestionannaireResponseItems(hostContext, qsrc, qsrc.getItem(), errors, element, stack, inProgress, element, new QStack(qsrc, element)); + } + } + } - private String uriRegexForVersion() { - if (VersionUtilities.isR3Ver(context.getVersion())) - return URI_REGEX3; - else - return Constants.URI_REGEX; - } + private Questionnaire loadQuestionnaire(Element resource, String id) throws FHIRException { + try { + for (Element contained : resource.getChildren("contained")) { + if (contained.getIdBase().equals(id)) { + FhirPublication v = FhirPublication.fromCode(context.getVersion()); + ByteArrayOutputStream bs = new ByteArrayOutputStream(); + new JsonParser(context).compose(contained, bs, OutputStyle.NORMAL, id); + byte[] json = bs.toByteArray(); + switch (v) { + case DSTU1: + throw new FHIRException("Unsupported version R1"); + case DSTU2: + org.hl7.fhir.dstu2.model.Resource r2 = new org.hl7.fhir.dstu2.formats.JsonParser().parse(json); + Resource r5 = VersionConvertor_10_50.convertResource(r2); + if (r5 instanceof Questionnaire) + return (Questionnaire) r5; + else + return null; + case DSTU2016May: + org.hl7.fhir.dstu2016may.model.Resource r2a = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(json); + r5 = VersionConvertor_14_50.convertResource(r2a); + if (r5 instanceof Questionnaire) + return (Questionnaire) r5; + else + return null; + case STU3: + org.hl7.fhir.dstu3.model.Resource r3 = new org.hl7.fhir.dstu3.formats.JsonParser().parse(json); + r5 = VersionConvertor_30_50.convertResource(r3, false); + if (r5 instanceof Questionnaire) + return (Questionnaire) r5; + else + return null; + case R4: + org.hl7.fhir.r4.model.Resource r4 = new org.hl7.fhir.r4.formats.JsonParser().parse(json); + r5 = VersionConvertor_40_50.convertResource(r4); + if (r5 instanceof Questionnaire) + return (Questionnaire) r5; + else + return null; + case R5: + r5 = new org.hl7.fhir.r5.formats.JsonParser().parse(json); + if (r5 instanceof Questionnaire) + return (Questionnaire) r5; + else + return null; + } + } + } + return null; + } catch (IOException e) { + throw new FHIRException(e); + } + } - private String getCanonicalURLForEntry(Element entry) { - Element e = entry.getNamedChild("resource"); - if (e == null) - return null; - return e.getNamedChildValue("url"); - } + private void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, Questionnaire qsrc, QuestionnaireItemComponent qItem, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { + String text = element.getNamedChildValue("text"); + rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), Utilities.noString(text) || text.equals(qItem.getText()), "If text exists, it must match the questionnaire definition for linkId " + qItem.getLinkId()); - private String getIdForEntry(Element entry) { - Element e = entry.getNamedChild("resource"); - if (e == null) - return null; - return e.getNamedChildValue("id"); - } + List answers = new ArrayList(); + element.getNamedChildren("answer", answers); + if (inProgress) + warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item " + qItem.getLinkId()); + else if (myEnableWhenEvaluator.isQuestionEnabled(hostContext, qItem, qstack, fpe)) { + rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), isAnswerRequirementFulfilled(qItem, answers), "No response answer found for required item " + qItem.getLinkId()); + } else if (!answers.isEmpty()) { // items without answers should be allowed, but not items with answers to questions that are disabled + // it appears that this is always a duplicate error - it will always already have beeb reported, so no need to report it again? + // GDG 2019-07-13 +// rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), !isAnswerRequirementFulfilled(qItem, answers), "Item has answer (2), even though it is not enabled "+qItem.getLinkId()); + } - /** - * Check each resource entry to ensure that the entry's fullURL includes the resource's id - * value. Adds an ERROR ValidationMessge to errors List for a given entry if it references - * a resource and fullURL does not include the resource's id. - * @param errors List of ValidationMessage objects that new errors will be added to. - * @param entries List of entry Element objects to be checked. - * @param stack Current NodeStack used to create path names in error detail messages. - */ - private void validateResourceIds(List errors, List entries, NodeStack stack) { - // TODO: Need to handle _version - int i = 1; - for(Element entry : entries) { - String fullUrl = entry.getNamedChildValue("fullUrl"); - Element resource = entry.getNamedChild("resource"); - String id = resource != null?resource.getNamedChildValue("id"):null; - if (id != null && fullUrl != null) { - String urlId = null; - if (fullUrl.startsWith("https://") || fullUrl.startsWith("http://")) { - urlId = fullUrl.substring(fullUrl.lastIndexOf('/')+1); - } else if (fullUrl.startsWith("urn:uuid") || fullUrl.startsWith("urn:oid")) { - urlId = fullUrl.substring(fullUrl.lastIndexOf(':')+1); - } - rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry["+i+"]"), urlId.equals(id), - "Resource ID does not match the ID in the entry full URL ('"+id+"' vs '"+fullUrl+"') "); - } - i++; - } - } + if (answers.size() > 1) + rule(errors, IssueType.INVALID, answers.get(1).line(), answers.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response answer item with this linkId allowed"); + + for (Element answer : answers) { + NodeStack ns = stack.push(answer, -1, null, null); + if (qItem.getType() != null) { + switch (qItem.getType()) { + case GROUP: + rule(errors, IssueType.STRUCTURE, answer.line(), answer.col(), stack.getLiteralPath(), false, "Items of type group should not have answers"); + break; + case DISPLAY: // nothing + break; + case BOOLEAN: + validateQuestionnaireResponseItemType(errors, answer, ns, "boolean"); + break; + case DECIMAL: + validateQuestionnaireResponseItemType(errors, answer, ns, "decimal"); + break; + case INTEGER: + validateQuestionnaireResponseItemType(errors, answer, ns, "integer"); + break; + case DATE: + validateQuestionnaireResponseItemType(errors, answer, ns, "date"); + break; + case DATETIME: + validateQuestionnaireResponseItemType(errors, answer, ns, "dateTime"); + break; + case TIME: + validateQuestionnaireResponseItemType(errors, answer, ns, "time"); + break; + case STRING: + validateQuestionnaireResponseItemType(errors, answer, ns, "string"); + break; + case TEXT: + validateQuestionnaireResponseItemType(errors, answer, ns, "text"); + break; + case URL: + validateQuestionnaireResponseItemType(errors, answer, ns, "uri"); + break; + case ATTACHMENT: + validateQuestionnaireResponseItemType(errors, answer, ns, "Attachment"); + break; + case REFERENCE: + validateQuestionnaireResponseItemType(errors, answer, ns, "Reference"); + break; + case QUANTITY: + if ("Quantity".equals(validateQuestionnaireResponseItemType(errors, answer, ns, "Quantity"))) + if (qItem.hasExtension("???")) + validateQuestionnaireResponseItemQuantity(errors, answer, ns); + break; + case CHOICE: + String itemType = validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string"); + if (itemType != null) { + if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, false); + else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date"); + else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time"); + else if (itemType.equals("integer")) + checkOption(errors, answer, ns, qsrc, qItem, "integer"); + else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string"); + } + break; + case OPENCHOICE: + itemType = validateQuestionnaireResponseItemType(errors, answer, ns, "Coding", "date", "time", "integer", "string"); + if (itemType != null) { + if (itemType.equals("Coding")) validateAnswerCode(errors, answer, ns, qsrc, qItem, true); + else if (itemType.equals("date")) checkOption(errors, answer, ns, qsrc, qItem, "date"); + else if (itemType.equals("time")) checkOption(errors, answer, ns, qsrc, qItem, "time"); + else if (itemType.equals("integer")) + checkOption(errors, answer, ns, qsrc, qItem, "integer"); + else if (itemType.equals("string")) + checkOption(errors, answer, ns, qsrc, qItem, "string", true); + } + break; +// case QUESTION: + case NULL: + // no validation + break; + } + } + validateQuestionannaireResponseItems(hostContext, qsrc, qItem.getItem(), errors, answer, stack, inProgress, questionnaireResponseRoot, qstack); + } + if (qItem.getType() == null) { + fail(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, "Definition for item " + qItem.getLinkId() + " does not contain a type"); + } else if (qItem.getType() == QuestionnaireItemType.DISPLAY) { + List items = new ArrayList(); + element.getNamedChildren("item", items); + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), items.isEmpty(), "Items not of type DISPLAY should not have items - linkId {0}", qItem.getLinkId()); + } else { + validateQuestionannaireResponseItems(hostContext, qsrc, qItem.getItem(), errors, element, stack, inProgress, questionnaireResponseRoot, qstack); + } + } + + private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, List answers) { + return !answers.isEmpty() || !qItem.getRequired() || qItem.getType() == QuestionnaireItemType.GROUP; + } + + private void validateQuestionnaireResponseItem(ValidatorHostContext hostcontext, Questionnaire qsrc, QuestionnaireItemComponent qItem, List errors, List elements, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { + if (elements.size() > 1) + rule(errors, IssueType.INVALID, elements.get(1).line(), elements.get(1).col(), stack.getLiteralPath(), qItem.getRepeats(), "Only one response item with this linkId allowed - " + qItem.getLinkId()); + int i = 0; + for (Element element : elements) { + NodeStack ns = stack.push(element, i, null, null); + validateQuestionnaireResponseItem(hostcontext, qsrc, qItem, errors, element, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, element)); + i++; + } + } + + private int getLinkIdIndex(List qItems, String linkId) { + for (int i = 0; i < qItems.size(); i++) { + if (linkId.equals(qItems.get(i).getLinkId())) + return i; + } + return -1; + } + + private void validateQuestionannaireResponseItems(ValidatorHostContext hostContext, Questionnaire qsrc, List qItems, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QStack qstack) { + List items = new ArrayList(); + element.getNamedChildren("item", items); + // now, sort into stacks + Map> map = new HashMap>(); + int lastIndex = -1; + for (Element item : items) { + String linkId = item.getNamedChildValue("linkId"); + if (rule(errors, IssueType.REQUIRED, item.line(), item.col(), stack.getLiteralPath(), !Utilities.noString(linkId), "No LinkId, so can't be validated")) { + int index = getLinkIdIndex(qItems, linkId); + if (index == -1) { + QuestionnaireItemComponent qItem = findQuestionnaireItem(qsrc, linkId); + if (qItem != null) { + rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index > -1, misplacedItemError(qItem)); + NodeStack ns = stack.push(item, -1, null, null); + validateQuestionnaireResponseItem(hostContext, qsrc, qItem, errors, item, ns, inProgress, questionnaireResponseRoot, qstack.push(qItem, item)); + } else + rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, "LinkId \"" + linkId + "\" not found in questionnaire"); + } else { + rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index >= lastIndex, "Structural Error: items are out of order"); + lastIndex = index; + + // If an item has a child called "linkId" but no child called "answer", + // we'll treat it as not existing for the purposes of enableWhen validation + if (item.hasChildren("answer") || item.hasChildren("item")) { + List mapItem = map.computeIfAbsent(linkId, key -> new ArrayList<>()); + mapItem.add(item); + } + } + } + } + + // ok, now we have a list of known items, grouped by linkId. We've made an error for anything out of order + for (QuestionnaireItemComponent qItem : qItems) { + List mapItem = map.get(qItem.getLinkId()); + validateQuestionnaireResponseItem(hostContext, qsrc, errors, element, stack, inProgress, questionnaireResponseRoot, qItem, mapItem, qstack); + } + } + + public void validateQuestionnaireResponseItem(ValidatorHostContext hostContext, Questionnaire qsrc, List errors, Element element, NodeStack stack, boolean inProgress, Element questionnaireResponseRoot, QuestionnaireItemComponent qItem, List mapItem, QStack qstack) { + boolean enabled = myEnableWhenEvaluator.isQuestionEnabled(hostContext, qItem, qstack, fpe); + if (mapItem != null) { + if (!enabled) { + int i = 0; + for (Element e : mapItem) { + NodeStack ns = stack.push(e, i, e.getProperty().getDefinition(), e.getProperty().getDefinition()); + rule(errors, IssueType.INVALID, e.line(), e.col(), ns.getLiteralPath(), enabled, "Item has answer, even though it is not enabled (item id = '" + qItem.getLinkId() + "')"); + i++; + } + } + + // Recursively validate child items + validateQuestionnaireResponseItem(hostContext, qsrc, qItem, errors, mapItem, stack, inProgress, questionnaireResponseRoot, qstack); + + } else { + + // item is missing, is the question enabled? + if (enabled && qItem.getRequired()) { + String message = "No response found for required item with id = '" + qItem.getLinkId() + "'"; + if (inProgress) { + warning(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, message); + } else { + rule(errors, IssueType.REQUIRED, element.line(), element.col(), stack.getLiteralPath(), false, message); + } + } + + } + + } + + private String misplacedItemError(QuestionnaireItemComponent qItem) { + return qItem.hasLinkId() ? String.format("Structural Error: item with linkid %s is in the wrong place", qItem.getLinkId()) : "Structural Error: item is in the wrong place"; + } + + private void validateQuestionnaireResponseItemQuantity(List errors, Element answer, NodeStack stack) { + + } + + private String validateQuestionnaireResponseItemType(List errors, Element element, NodeStack stack, String... types) { + List values = new ArrayList(); + element.getNamedChildrenWithWildcard("value[x]", values); + for (int i = 0; i < types.length; i++) { + if (types[i].equals("text")) { + types[i] = "string"; + } + } + if (values.size() > 0) { + NodeStack ns = stack.push(values.get(0), -1, null, null); + CommaSeparatedStringBuilder l = new CommaSeparatedStringBuilder(); + for (String s : types) { + l.append(s); + if (values.get(0).getName().equals("value" + Utilities.capitalize(s))) + return (s); + } + if (types.length == 1) + rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be of type " + types[0]); + else + rule(errors, IssueType.STRUCTURE, values.get(0).line(), values.get(0).col(), ns.getLiteralPath(), false, "Answer value must be one of the types " + l.toString()); + } + return null; + } + + private QuestionnaireItemComponent findQuestionnaireItem(Questionnaire qSrc, String linkId) { + return findItem(qSrc.getItem(), linkId); + } + + private QuestionnaireItemComponent findItem(List list, String linkId) { + for (QuestionnaireItemComponent item : list) { + if (linkId.equals(item.getLinkId())) + return item; + QuestionnaireItemComponent result = findItem(item.getItem(), linkId); + if (result != null) + return result; + } + return null; + } + + private void validateAnswerCode(List errors, Element value, NodeStack stack, Questionnaire qSrc, String ref, boolean theOpenChoice) { + ValueSet vs = resolveBindingReference(qSrc, ref, qSrc.getUrl()); + if (warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), vs != null, "ValueSet " + describeReference(ref) + " not found by validator")) { + try { + Coding c = ObjectConverter.readAsCoding(value); + if (isBlank(c.getCode()) && isBlank(c.getSystem()) && isNotBlank(c.getDisplay())) { + if (theOpenChoice) { + return; + } + } + + long t = System.nanoTime(); + ValidationResult res = context.validateCode(new ValidationOptions(stack.workingLang), c, vs); + txTime = txTime + (System.nanoTime() - t); + if (!res.isOk()) { + txRule(errors, res.getTxLink(), IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "The value provided (" + c.getSystem() + "::" + c.getCode() + ") is not in the options value set in the questionnaire"); + } else if (res.getSeverity() != null) { + super.addValidationMessage(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), res.getMessage(), res.getSeverity(), Source.TerminologyEngine); + } + } catch (Exception e) { + warning(errors, IssueType.CODEINVALID, value.line(), value.col(), stack.getLiteralPath(), false, "Error " + e.getMessage() + " validating Coding against Questionnaire Options"); + } + } + } + + private void validateAnswerCode(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean theOpenChoice) { + Element v = answer.getNamedChild("valueCoding"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) + checkCodingOption(errors, answer, stack, qSrc, qItem, theOpenChoice); + // validateAnswerCode(errors, v, stack, qItem.getOption()); + else if (qItem.hasAnswerValueSet()) + validateAnswerCode(errors, v, stack, qSrc, qItem.getAnswerValueSet(), theOpenChoice); + else + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate options because no option or options are provided"); + } + + private void checkOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type) { + checkOption(errors, answer, stack, qSrc, qItem, type, false); + } + + private void checkOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, String type, boolean openChoice) { + if (type.equals("integer")) checkIntegerOption(errors, answer, stack, qSrc, qItem, openChoice); + else if (type.equals("date")) checkDateOption(errors, answer, stack, qSrc, qItem, openChoice); + else if (type.equals("time")) checkTimeOption(errors, answer, stack, qSrc, qItem, openChoice); + else if (type.equals("string")) checkStringOption(errors, answer, stack, qSrc, qItem, openChoice); + else if (type.equals("Coding")) checkCodingOption(errors, answer, stack, qSrc, qItem, openChoice); + } + + private void checkIntegerOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { + Element v = answer.getNamedChild("valueInteger"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) { + List list = new ArrayList(); + for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { + try { + list.add(components.getValueIntegerType()); + } catch (FHIRException e) { + // If it's the wrong type, just keep going + } + } + if (list.isEmpty() && !openChoice) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type integer"); + } else { + boolean found = false; + for (IntegerType item : list) { + if (item.getValue() == Integer.parseInt(v.primitiveValue())) { + found = true; + break; + } + } + if (!found) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The integer " + v.primitiveValue() + " is not a valid option"); + } + } + } else + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate integer answer option because no option list is provided"); + } + + private void checkDateOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { + Element v = answer.getNamedChild("valueDate"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) { + List list = new ArrayList(); + for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { + try { + list.add(components.getValueDateType()); + } catch (FHIRException e) { + // If it's the wrong type, just keep going + } + } + if (list.isEmpty() && !openChoice) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type date"); + } else { + boolean found = false; + for (DateType item : list) { + if (item.getValue().equals(v.primitiveValue())) { + found = true; + break; + } + } + if (!found) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The date " + v.primitiveValue() + " is not a valid option"); + } + } + } else + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate date answer option because no option list is provided"); + } + + private void checkTimeOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { + Element v = answer.getNamedChild("valueTime"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) { + List list = new ArrayList(); + for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { + try { + list.add(components.getValueTimeType()); + } catch (FHIRException e) { + // If it's the wrong type, just keep going + } + } + if (list.isEmpty() && !openChoice) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type time"); + } else { + boolean found = false; + for (TimeType item : list) { + if (item.getValue().equals(v.primitiveValue())) { + found = true; + break; + } + } + if (!found) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The time " + v.primitiveValue() + " is not a valid option"); + } + } + } else + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate time answer option because no option list is provided"); + } + + private void checkStringOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { + Element v = answer.getNamedChild("valueString"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) { + List list = new ArrayList(); + for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { + try { + if (components.getValue() != null) { + list.add(components.getValueStringType()); + } + } catch (FHIRException e) { + // If it's the wrong type, just keep going + } + } + if (!openChoice) { + if (list.isEmpty()) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type string"); + } else { + boolean found = false; + for (StringType item : list) { + if (item.getValue().equals((v.primitiveValue()))) { + found = true; + break; + } + } + if (!found) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The string " + v.primitiveValue() + " is not a valid option"); + } + } + } + } else { + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate string answer option because no option list is provided"); + } + } + + private void checkCodingOption(List errors, Element answer, NodeStack stack, Questionnaire qSrc, QuestionnaireItemComponent qItem, boolean openChoice) { + Element v = answer.getNamedChild("valueCoding"); + String system = v.getNamedChildValue("system"); + String code = v.getNamedChildValue("code"); + NodeStack ns = stack.push(v, -1, null, null); + if (qItem.getAnswerOption().size() > 0) { + List list = new ArrayList(); + for (QuestionnaireItemAnswerOptionComponent components : qItem.getAnswerOption()) { + try { + if (components.getValue() != null) { + list.add(components.getValueCoding()); + } + } catch (FHIRException e) { + // If it's the wrong type, just keep going + } + } + if (list.isEmpty() && !openChoice) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Option list has no option values of type coding"); + } else { + boolean found = false; + for (Coding item : list) { + if (ObjectUtil.equals(item.getSystem(), system) && ObjectUtil.equals(item.getCode(), code)) { + found = true; + break; + } + } + if (!found) { + rule(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), found, "The code " + system + "::" + code + " is not a valid option"); + } + } + } else + hint(errors, IssueType.STRUCTURE, v.line(), v.col(), stack.getLiteralPath(), false, "Cannot validate Coding option because no option list is provided"); + } + + private String tail(String path) { + return path.substring(path.lastIndexOf(".") + 1); + } + + private String tryParse(String ref) { + String[] parts = ref.split("\\/"); + switch (parts.length) { + case 1: + return null; + case 2: + return checkResourceType(parts[0]); + default: + if (parts[parts.length - 2].equals("_history")) + return checkResourceType(parts[parts.length - 4]); + else + return checkResourceType(parts[parts.length - 2]); + } + } + + private boolean typesAreAllReference(List theType) { + for (TypeRefComponent typeRefComponent : theType) { + if (typeRefComponent.getCode().equals("Reference") == false) { + return false; + } + } + return true; + } + + private void validateBundle(List errors, Element bundle, NodeStack stack, boolean checkSpecials) { + List entries = new ArrayList(); + bundle.getNamedChildren("entry", entries); + String type = bundle.getNamedChildValue("type"); + type = StringUtils.defaultString(type); + + if (entries.size() == 0) { + rule(errors, IssueType.INVALID, stack.getLiteralPath(), !(type.equals("document") || type.equals("message")), "Documents or Messages must contain at least one entry"); + } else { + // Get the first entry, the MessageHeader + Element firstEntry = entries.get(0); + // Get the stack of the first entry + NodeStack firstStack = stack.push(firstEntry, 1, null, null); + + String fullUrl = firstEntry.getNamedChildValue("fullUrl"); + + if (type.equals("document")) { + Element resource = firstEntry.getNamedChild("resource"); + String id = resource.getNamedChildValue("id"); + if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath("entry", ":0"), resource != null, "No resource on first entry")) { + validateDocument(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id); + } + checkAllInterlinked(errors, entries, stack, bundle, true); + } + if (type.equals("message")) { + Element resource = firstEntry.getNamedChild("resource"); + String id = resource.getNamedChildValue("id"); + if (rule(errors, IssueType.INVALID, firstEntry.line(), firstEntry.col(), stack.addToLiteralPath("entry", ":0"), resource != null, "No resource on first entry")) { + validateMessage(errors, entries, resource, firstStack.push(resource, -1, null, null), fullUrl, id); + } + checkAllInterlinked(errors, entries, stack, bundle, VersionUtilities.isR5Ver(context.getVersion())); + } + // We do not yet have rules requiring that the id and fullUrl match when dealing with messaging Bundles + // validateResourceIds(errors, entries, stack); + } + for (Element entry : entries) { + String fullUrl = entry.getNamedChildValue("fullUrl"); + String url = getCanonicalURLForEntry(entry); + String id = getIdForEntry(entry); + if (url != null) { + if (!(!url.equals(fullUrl) || (url.matches(uriRegexForVersion()) && url.endsWith("/" + id))) && !isV3orV2Url(url)) + rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry", ":0"), false, "The canonical URL (" + url + ") cannot match the fullUrl (" + fullUrl + ") unless the resource id (" + id + ") also matches"); + rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry", ":0"), !url.equals(fullUrl) || serverBase == null || (url.equals(Utilities.pathURL(serverBase, entry.getNamedChild("resource").fhirType(), id))), "The canonical URL (" + url + ") cannot match the fullUrl (" + fullUrl + ") unless on the canonical server itself"); + } + // todo: check specials + } + } + + // hack for pre-UTG v2/v3 + private boolean isV3orV2Url(String url) { + return url.startsWith("http://hl7.org/fhir/v3/") || url.startsWith("http://hl7.org/fhir/v2/"); + } + + public final static String URI_REGEX3 = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AllergyIntolerance|AdverseEvent|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BodySite|Bundle|CapabilityStatement|CarePlan|CareTeam|ChargeItem|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition (aka Problem)|Consent|Contract|Coverage|DataElement|DetectedIssue|Device|DeviceComponent|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EligibilityRequest|EligibilityResponse|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|ExpansionProfile|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingManifest|ImagingStudy|Immunization|ImmunizationRecommendation|ImplementationGuide|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationRequest|MedicationStatement|MessageDefinition|MessageHeader|NamingSystem|NutritionOrder|Observation|OperationDefinition|OperationOutcome|Organization|Parameters|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|ProcedureRequest|ProcessRequest|ProcessResponse|Provenance|Questionnaire|QuestionnaireResponse|ReferralRequest|RelatedPerson|RequestGroup|ResearchStudy|ResearchSubject|RiskAssessment|Schedule|SearchParameter|Sequence|ServiceDefinition|Slot|Specimen|StructureDefinition|StructureMap|Subscription|Substance|SupplyDelivery|SupplyRequest|Task|TestScript|TestReport|ValueSet|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?"; + private static final String EXECUTED_CONSTRAINT_LIST = "validator.executed.invariant.list"; + private static final String EXECUTION_ID = "validator.execution.id"; + + private String uriRegexForVersion() { + if (VersionUtilities.isR3Ver(context.getVersion())) + return URI_REGEX3; + else + return Constants.URI_REGEX; + } + + private String getCanonicalURLForEntry(Element entry) { + Element e = entry.getNamedChild("resource"); + if (e == null) + return null; + return e.getNamedChildValue("url"); + } + + private String getIdForEntry(Element entry) { + Element e = entry.getNamedChild("resource"); + if (e == null) + return null; + return e.getNamedChildValue("id"); + } + + /** + * Check each resource entry to ensure that the entry's fullURL includes the resource's id + * value. Adds an ERROR ValidationMessge to errors List for a given entry if it references + * a resource and fullURL does not include the resource's id. + * + * @param errors List of ValidationMessage objects that new errors will be added to. + * @param entries List of entry Element objects to be checked. + * @param stack Current NodeStack used to create path names in error detail messages. + */ + private void validateResourceIds(List errors, List entries, NodeStack stack) { + // TODO: Need to handle _version + int i = 1; + for (Element entry : entries) { + String fullUrl = entry.getNamedChildValue("fullUrl"); + Element resource = entry.getNamedChild("resource"); + String id = resource != null ? resource.getNamedChildValue("id") : null; + if (id != null && fullUrl != null) { + String urlId = null; + if (fullUrl.startsWith("https://") || fullUrl.startsWith("http://")) { + urlId = fullUrl.substring(fullUrl.lastIndexOf('/') + 1); + } else if (fullUrl.startsWith("urn:uuid") || fullUrl.startsWith("urn:oid")) { + urlId = fullUrl.substring(fullUrl.lastIndexOf(':') + 1); + } + rule(errors, IssueType.INVALID, entry.line(), entry.col(), stack.addToLiteralPath("entry[" + i + "]"), urlId.equals(id), + "Resource ID does not match the ID in the entry full URL ('" + id + "' vs '" + fullUrl + "') "); + } + i++; + } + } private void checkAllInterlinked(List errors, List entries, NodeStack stack, Element bundle, boolean isError) { - List entryList = new ArrayList<>(); - for (Element entry: entries) { - Element r = entry.getNamedChild("resource"); - if (r != null) { - entryList.add(new EntrySummary(entry, r)); - } - } - for (EntrySummary e : entryList) { - Set references = findReferences(e.getEntry()); - for (String ref : references) { - Element tgt = resolveInBundle(entries, ref, e.getEntry().getChildValue("fullUrl"), e.getResource().fhirType(), e.getResource().getIdBase()); - if (tgt != null) { - EntrySummary t = entryForTarget(entryList, tgt); - if (t != null) { - e.getTargets().add(t); - } - } - } - } - - Set visited = new HashSet<>(); - visitLinked(visited, entryList.get(0)); - boolean foundRevLinks; - do { - foundRevLinks = false; - for (EntrySummary e : entryList) { - if (!visited.contains(e)) { - boolean add = false; - for (EntrySummary t : e.getTargets()) { - if (visited.contains(t)) { - add = true; + List entryList = new ArrayList<>(); + for (Element entry : entries) { + Element r = entry.getNamedChild("resource"); + if (r != null) { + entryList.add(new EntrySummary(entry, r)); } - } - if (add) { - foundRevLinks = true; - visitLinked(visited, e); - } } - } - } while (foundRevLinks); - - int i = 0; - for (EntrySummary e : entryList) { - Element entry = e.getEntry(); - if (isError) { - rule(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath("entry" + '[' + (i+1) + ']'), visited.contains(e), "Entry "+(entry.getChildValue("fullUrl") != null ? "'"+entry.getChildValue("fullUrl")+"'" : "")+" isn't reachable by traversing from first Bundle entry"); - } else { - warning(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath("entry" + '[' + (i+1) + ']'), visited.contains(e), "Entry "+(entry.getChildValue("fullUrl") != null ? "'"+entry.getChildValue("fullUrl")+"'" : "")+" isn't reachable by traversing from first Bundle entry"); - } - i++; - } - } - - private EntrySummary entryForTarget(List entryList, Element tgt) { - for (EntrySummary e : entryList) { - if (e.getEntry() == tgt) { - return e; - } - } - return null; - } - - private void visitLinked(Set visited, EntrySummary t) { - if (!visited.contains(t)) { - visited.add(t); - for (EntrySummary e : t.getTargets()) { - visitLinked(visited, e); - } - } - } - - private void followResourceLinks(Element entry, Map visitedResources, Map candidateEntries, List candidateResources, List errors, NodeStack stack) { - followResourceLinks(entry, visitedResources, candidateEntries, candidateResources, errors, stack, 0); - } - - private void followResourceLinks(Element entry, Map visitedResources, Map candidateEntries, List candidateResources, List errors, NodeStack stack, int depth) { - Element resource = entry.getNamedChild("resource"); - if (visitedResources.containsValue(resource)) - return; - - visitedResources.put(entry.getNamedChildValue("fullUrl"), resource); - - String type = null; - Set references = findReferences(resource); - for (String reference: references) { - // We don't want errors when just retrieving the element as they will be caught (with better path info) in subsequent processing - IndexedElement r = getFromBundle(stack.getElement(), reference, entry.getChildValue("fullUrl"), new ArrayList(), stack.addToLiteralPath("entry[" + candidateResources.indexOf(resource) + "]"), type, "transaction".equals(stack.getElement().getChildValue("type"))); - if (r!=null && !visitedResources.containsValue(r.getMatch())) { - followResourceLinks(candidateEntries.get(r.getMatch()), visitedResources, candidateEntries, candidateResources, errors, stack, depth+1); - } - } - } - - private Set findReferences(Element start) { - Set references = new HashSet(); - findReferences(start, references); - return references; - } - - private void findReferences(Element start, Set references) { - for (Element child : start.getChildren()) { - if (child.getType().equals("Reference")) { - String ref = child.getChildValue("reference"); - if (ref != null && !ref.startsWith("#")) - references.add(ref); - } - if (child.getType().equals("url") || child.getType().equals("uri") || child.getType().equals("canonical")) { - String ref = child.primitiveValue(); - if (ref != null && !ref.startsWith("#")) - references.add(ref); - } - findReferences(child, references); - } - } - - private void validateBundleReference(List errors, List entries, Element ref, String name, NodeStack stack, String fullUrl, String type, String id) { - String reference = null; - try { - reference = ref.getNamedChildValue("reference"); - } catch (Error e) { - - } - - if (ref != null && !Utilities.noString(reference)) { - Element target = resolveInBundle(entries, reference, fullUrl, type, id); - rule(errors, IssueType.INVALID, ref.line(), ref.col(), stack.addToLiteralPath("reference"), target != null, "Can't find '"+reference+"' in the bundle (" + name + ")"); - } - } - - private void validateContains(ValidatorHostContext hostContext, List errors, String path, ElementDefinition child, ElementDefinition context, Element resource, Element element, NodeStack stack, IdStatus idstatus) throws FHIRException { - String resourceName = element.getType(); - TypeRefComponent trr = null; - for (TypeRefComponent tr : child.getType()) { - if (tr.getCode().equals("Resource")) { - trr = tr; - break; - } - } - if (trr == null) { - rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+" is not valid - no resources allowed here"); - } else if (isValidResourceType(resourceName, trr)) { - long t = System.nanoTime(); - StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName); - sdTime = sdTime + (System.nanoTime() - t); - // special case: resource wrapper is reset if we're crossing a bundle boundary, but not otherwise - ValidatorHostContext hc = null; - if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY || element.getSpecial() == SpecialElement.BUNDLE_OUTCOME || element.getSpecial() == SpecialElement.PARAMETER ) { - resource = element; - hc = hostContext.forEntry(element); - } else { - hc = hostContext.forContained(element); - } - trackUsage(profile, hostContext, element); - if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), profile != null, "No profile found for contained resource of type '" + resourceName + "'")) { - validateResource(hc, errors, resource, element, profile, idstatus, stack); - } - } else { - List types = new ArrayList<>(); - for (UriType u : trr.getProfile()) { - StructureDefinition sd = this.context.fetchResource(StructureDefinition.class, u.getValue()); - if (sd != null && !types.contains(sd.getType())) { - types.add(sd.getType()); - } - } - if (types.size() == 1) { - rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+"' is not valid - must be "+types.get(0)); - } else { - rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '"+resourceName+"' is not valid - must be one of "+types); - } - } - } - - private boolean isValidResourceType(String type, TypeRefComponent def) { - if (!def.hasProfile()) { - return true; - } - List list = new ArrayList<>(); - for (UriType u : def.getProfile()) { - StructureDefinition sdt = context.fetchResource(StructureDefinition.class, u.getValue()); - if (sdt != null) { - list.add(sdt); - } - } - - StructureDefinition sdt = context.fetchTypeDefinition(type); - while (sdt != null) { - if (def.getWorkingCode().equals("Resource")) { - for (StructureDefinition sd : list) { - if (sd.getUrl().equals(sdt.getUrl())) { - return true; - } - if (sd.getType().equals(sdt.getType())) { - return true; - } - } - } - sdt = context.fetchResource(StructureDefinition.class, sdt.getBaseDefinition()); - } - return false; - } - - private void validateDocument(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id) { - // first entry must be a composition - if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"), - "The first entry in a document must be a composition")) { - - // the composition subject etc references must resolve in the bundle - validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "subject", "Composition"); - validateDocumentReference(errors, entries, composition, stack, fullUrl, id, true, "author", "Composition"); - validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "encounter", "Composition"); - validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "custodian", "Composition"); - validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "attester", false, "party"); - validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "event", true, "detail"); - - validateSections(errors, entries, composition, stack, fullUrl, id); - } - } - - public void validateDocumentSubReference(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id, String title, String parent, boolean repeats, String propName) { - List list = new ArrayList<>(); - composition.getNamedChildren(parent, list); - int i = 1; - for (Element elem : list) { - validateDocumentReference(errors, entries, elem, stack.push(elem, i, null, null), fullUrl, id, repeats, propName, title+"."+parent); - i++; - } - } - - public void validateDocumentReference(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id, boolean repeats, String propName, String title) { - if (repeats) { - List list = new ArrayList<>(); - composition.getNamedChildren(propName, list); - int i = 1; - for (Element elem : list) { - validateBundleReference(errors, entries, elem, title+"."+propName, stack.push(elem, i, null, null), fullUrl, "Composition", id); - i++; - } - - } else { - Element elem = composition.getNamedChild(propName); - if (elem != null) { - validateBundleReference(errors, entries, elem, title+"."+propName, stack.push(elem, -1, null, null), fullUrl, "Composition", id); - } - } - } - - private void validateElement(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context, - Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, String extensionUrl) throws FHIRException { - // element.markValidation(profile, definition); - - // time = System.nanoTime(); - // check type invariants - checkInvariants(hostContext, errors, profile, definition, resource, element, stack, false); - if (definition.getFixed() != null) - checkFixedValue(errors, stack.getLiteralPath(), element, definition.getFixed(), profile.getUrl(), definition.getSliceName(), null); - - - // get the list of direct defined children, including slices - List childDefinitions = ProfileUtilities.getChildMap(profile, definition); - if (childDefinitions.isEmpty()) { - if (actualType == null) - return; // there'll be an error elsewhere in this case, and we're going to stop. - childDefinitions = getActualTypeChildren(hostContext, element, actualType); - } else if (definition.getType().size() > 1) { - // this only happens when the profile constrains the abstract children but leaves th choice open. - if (actualType == null) - return; // there'll be an error elsewhere in this case, and we're going to stop. - List typeChildDefinitions = getActualTypeChildren(hostContext, element, actualType); - // what were going to do is merge them - the type is not allowed to constrain things that the child definitions already do (well, if it does, it'll be ignored) - mergeChildLists(childDefinitions, typeChildDefinitions, definition.getPath(), actualType); - } - - List children = listChildren(element, stack); - List problematicPaths = assignChildren(hostContext, errors, profile, resource, stack, childDefinitions, children); - - checkCardinalities(errors, profile, element, stack, childDefinitions, children, problematicPaths); - // 4. check order if any slices are ordered. (todo) - - // 5. inspect each child for validity - for (ElementInfo ei : children) { - checkChild(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei, extensionUrl); - } - } - - private void mergeChildLists(List master, List additional, String masterPath, String typePath) { - for (ElementDefinition ed : additional) { - boolean inMaster = false; - for (ElementDefinition t : master) { - String tp = masterPath + ed.getPath().substring(typePath.length()); - if (t.getPath().equals(tp)) { - inMaster = true; - } - } - if (!inMaster) { - master.add(ed); - } - } - - - } - - // todo: the element definition in context might assign a constrained profile for the type? - public List getActualTypeChildren(ValidatorHostContext hostContext, Element element, String actualType) { - List childDefinitions; - StructureDefinition dt = null; - if (isAbsolute(actualType)) - dt = this.context.fetchResource(StructureDefinition.class, actualType); - else - dt = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + actualType); - if (dt == null) - throw new DefinitionException("Unable to resolve actual type " + actualType); - trackUsage(dt, hostContext, element); - - childDefinitions = ProfileUtilities.getChildMap(dt, dt.getSnapshot().getElement().get(0)); - return childDefinitions; - } - - public void checkChild(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, - Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, ElementInfo ei, String extensionUrl) - throws FHIRException, DefinitionException { - - List profiles = new ArrayList(); - if (ei.definition != null) { - String type = null; - ElementDefinition typeDefn = null; - checkMustSupport(profile, ei); - - if (ei.definition.getType().size() == 1 && !"*".equals(ei.definition.getType().get(0).getWorkingCode()) && !"Element".equals(ei.definition.getType().get(0).getWorkingCode()) - && !"BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode())) { - type = ei.definition.getType().get(0).getWorkingCode(); - // Excluding reference is a kludge to get around versioning issues - if (ei.definition.getType().get(0).hasProfile()) { - for (CanonicalType p : ei.definition.getType().get(0).getProfile()) { - profiles.add(p.getValue()); - } - } - } else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getWorkingCode())) { - String prefix = tail(ei.definition.getPath()); - assert prefix.endsWith("[x]"); - type = ei.getName().substring(prefix.length() - 3); - if (isPrimitiveType(type)) - type = Utilities.uncapitalize(type); - if (ei.definition.getType().get(0).hasProfile()) { - for (CanonicalType p : ei.definition.getType().get(0).getProfile()) { - profiles.add(p.getValue()); - } - } - } else if (ei.definition.getType().size() > 1) { - - String prefix = tail(ei.definition.getPath()); - assert typesAreAllReference(ei.definition.getType()) || ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix; - - if (ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR)) - type = ei.getElement().getType(); - else { - prefix = prefix.substring(0, prefix.length() - 3); - for (TypeRefComponent t : ei.definition.getType()) - if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) { - type = t.getWorkingCode(); - // Excluding reference is a kludge to get around versioning issues - if (t.hasProfile() && !type.equals("Reference")) - profiles.add(t.getProfile().get(0).getValue()); - } - } - if (type == null) { - TypeRefComponent trc = ei.definition.getType().get(0); - if (trc.getWorkingCode().equals("Reference")) - type = "Reference"; - else - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, - "The type of element " + ei.getName() + " is not known, which is illegal. Valid types at this point are " + describeTypes(ei.definition.getType())); - } - } else if (ei.definition.getContentReference() != null) { - typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference()); - } else if (ei.definition.getType().size() == 1 && ("Element".equals(ei.definition.getType().get(0).getWorkingCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode()))) { - if (ei.definition.getType().get(0).hasProfile()) { - CanonicalType pu = ei.definition.getType().get(0).getProfile().get(0); - if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) - profiles.add(pu.getValue()+"#"+pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT)); - else - profiles.add(pu.getValue()); - } - } - - if (type != null) { - if (type.startsWith("@")) { - ei.definition = findElement(profile, type.substring(1)); - type = null; - } - } - NodeStack localStack = stack.push(ei.getElement(), ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType())); - if (debug) { - System.out.println(" "+localStack.getLiteralPath()); - } - String localStackLiterapPath = localStack.getLiteralPath(); - String eiPath = ei.getPath(); - assert(eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath; - boolean thisIsCodeableConcept = false; - String thisExtension = null; - boolean checkDisplay = true; - - checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.getElement(), localStack, true); - - ei.getElement().markValidation(profile, ei.definition); - boolean elementValidated = false; - if (type != null) { - if (isPrimitiveType(type)) { - checkPrimitive(hostContext, errors, ei.getPath(), type, ei.definition, ei.getElement(), profile, stack); - } else { - if (ei.definition.hasFixed()) { - checkFixedValue(errors,ei.getPath(), ei.getElement(), ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null); - } - if (ei.definition.hasPattern()) { - checkFixedValue(errors,ei.getPath(), ei.getElement(), ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true); - } - } - if (type.equals("Identifier")) { - checkIdentifier(errors, ei.getPath(), ei.getElement(), ei.definition); - } else if (type.equals("Coding")) { - checkCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack); - } else if (type.equals("CodeableConcept")) { - checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack); - thisIsCodeableConcept = true; - } else if (type.equals("Reference")) { - checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, ei.definition, actualType, localStack); - // We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension - } else if (type.equals("Extension")) { - Element eurl = ei.getElement().getNamedChild("url"); - if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, "Extension.url is required")) { - String url = eurl.primitiveValue(); - thisExtension = url; - if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), "Extension.url is required")) { - if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), "Extension.url must be an absolute URL")) { - checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), ei.definition, profile, localStack, stack, extensionUrl); - } + for (EntrySummary e : entryList) { + Set references = findReferences(e.getEntry()); + for (String ref : references) { + Element tgt = resolveInBundle(entries, ref, e.getEntry().getChildValue("fullUrl"), e.getResource().fhirType(), e.getResource().getIdBase()); + if (tgt != null) { + EntrySummary t = entryForTarget(entryList, tgt); + if (t != null) { + e.getTargets().add(t); + } + } } - } - } else if (type.equals("Resource")) { - validateContains(hostContext, errors, ei.getPath(), ei.definition, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if - elementValidated = true; - // (str.matches(".*([.,/])work\\1$")) - } else if (Utilities.isAbsoluteUrl(type)) { - StructureDefinition defn = context.fetchTypeDefinition(type); - if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) { - List txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep()); - if (txtype.contains("CodeableConcept")) { - checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack, defn); - thisIsCodeableConcept = true; - } else if (txtype.contains("Coding")) { - checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn); + } + + Set visited = new HashSet<>(); + visitLinked(visited, entryList.get(0)); + boolean foundRevLinks; + do { + foundRevLinks = false; + for (EntrySummary e : entryList) { + if (!visited.contains(e)) { + boolean add = false; + for (EntrySummary t : e.getTargets()) { + if (visited.contains(t)) { + add = true; + } + } + if (add) { + foundRevLinks = true; + visitLinked(visited, e); + } + } } - } - } - } else { - if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.getName())) - validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, false, true, null); - } - StructureDefinition p = null; - String tail = null; - if (profiles.isEmpty()) { - if (type != null) { - p = getProfileForType(type, ei.definition.getType()); + } while (foundRevLinks); - // If dealing with a primitive type, then we need to check the current child against - // the invariants (constraints) on the current element, because otherwise it only gets - // checked against the primary type's invariants: LLoyd - //if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) { - // checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element); - //} - - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown type " + type); - } - } else if (profiles.size()==1) { - String url = profiles.get(0); - if (url.contains("#")) { - tail = url.substring(url.indexOf("#")+1); - url = url.substring(0, url.indexOf("#")); - } - p = this.context.fetchResource(StructureDefinition.class, url); - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + profiles.get(0)); - } else { - elementValidated = true; - HashMap> goodProfiles = new HashMap>(); - HashMap> badProfiles = new HashMap>(); - for (String typeProfile : profiles) { - String url = typeProfile; - tail = null; - if (url.contains("#")) { - tail = url.substring(url.indexOf("#")+1); - url = url.substring(0, url.indexOf("#")); - } - p = this.context.fetchResource(StructureDefinition.class, typeProfile); - if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + typeProfile)) { - List profileErrors = new ArrayList(); - validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); - if (hasErrors(profileErrors)) - badProfiles.put(typeProfile, profileErrors); - else - goodProfiles.put(typeProfile, profileErrors); - } - } - if (goodProfiles.size()==1) { - errors.addAll(goodProfiles.values().iterator().next()); - } else if (goodProfiles.size()==0) { - rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles)); - for (String m : badProfiles.keySet()) { - p = this.context.fetchResource(StructureDefinition.class, m); - for (ValidationMessage message : badProfiles.get(m)) { - message.setMessage(message.getMessage()+" (validating against "+p.getUrl()+(p.hasVersion() ?"|"+p.getVersion(): "")+" ["+p.getName()+"])"); - errors.add(message); + int i = 0; + for (EntrySummary e : entryList) { + Element entry = e.getEntry(); + if (isError) { + rule(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath("entry" + '[' + (i + 1) + ']'), visited.contains(e), "Entry " + (entry.getChildValue("fullUrl") != null ? "'" + entry.getChildValue("fullUrl") + "'" : "") + " isn't reachable by traversing from first Bundle entry"); + } else { + warning(errors, IssueType.INFORMATIONAL, entry.line(), entry.col(), stack.addToLiteralPath("entry" + '[' + (i + 1) + ']'), visited.contains(e), "Entry " + (entry.getChildValue("fullUrl") != null ? "'" + entry.getChildValue("fullUrl") + "'" : "") + " isn't reachable by traversing from first Bundle entry"); } - } - } else { - warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Found multiple matching profiles among choices: " + StringUtils.join("; ", goodProfiles.keySet())); - for (String m : goodProfiles.keySet()) { - p = this.context.fetchResource(StructureDefinition.class, m); - for (ValidationMessage message : goodProfiles.get(m)) { - message.setMessage(message.getMessage()+" (validating against "+p.getUrl()+(p.hasVersion() ?"|"+p.getVersion(): "")+" ["+p.getName()+"])"); - errors.add(message); + i++; + } + } + + private EntrySummary entryForTarget(List entryList, Element tgt) { + for (EntrySummary e : entryList) { + if (e.getEntry() == tgt) { + return e; } - } } - } - if (p!=null) { - trackUsage(p, hostContext, element); + return null; + } - if (!elementValidated) { - if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER ) - validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.getElement(), ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); - else - validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + private void visitLinked(Set visited, EntrySummary t) { + if (!visited.contains(t)) { + visited.add(t); + for (EntrySummary e : t.getTargets()) { + visitLinked(visited, e); + } } - int index = profile.getSnapshot().getElement().indexOf(ei.definition); - if (index < profile.getSnapshot().getElement().size() - 1) { - String nextPath = profile.getSnapshot().getElement().get(index+1).getPath(); - if (!nextPath.equals(ei.definition.getPath()) && nextPath.startsWith(ei.definition.getPath())) - validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); - } - } } - } - private void trackUsage(StructureDefinition profile, ValidatorHostContext hostContext, Element element) { - if (tracker != null) { - tracker.recordProfileUsage(profile, hostContext.getAppContext(), element); - } - } + private void followResourceLinks(Element entry, Map visitedResources, Map candidateEntries, List candidateResources, List errors, NodeStack stack) { + followResourceLinks(entry, visitedResources, candidateEntries, candidateResources, errors, stack, 0); + } - private boolean hasMapping(String url, StructureDefinition defn, ElementDefinition elem) { - String id = null; - for (StructureDefinitionMappingComponent m : defn.getMapping()) { - if (url.equals(m.getUri())) { - id = m.getIdentity(); - break; - } - } - if (id != null) { - for (ElementDefinitionMappingComponent m : elem.getMapping()) { - if (id.equals(m.getIdentity())) { - return true; - } - } - - } - return false; - } + private void followResourceLinks(Element entry, Map visitedResources, Map candidateEntries, List candidateResources, List errors, NodeStack stack, int depth) { + Element resource = entry.getNamedChild("resource"); + if (visitedResources.containsValue(resource)) + return; - private List getMapping(String url, StructureDefinition defn, ElementDefinition elem) { - List res = new ArrayList<>(); - String id = null; - for (StructureDefinitionMappingComponent m : defn.getMapping()) { - if (url.equals(m.getUri())) { - id = m.getIdentity(); - break; - } - } - if (id != null) { - for (ElementDefinitionMappingComponent m : elem.getMapping()) { - if (id.equals(m.getIdentity())) { - res.add(m.getMap()); - } - } - } - return res; - } + visitedResources.put(entry.getNamedChildValue("fullUrl"), resource); - public void checkMustSupport(StructureDefinition profile, ElementInfo ei) { - String usesMustSupport = profile.getUserString("usesMustSupport"); - if (usesMustSupport == null) { - usesMustSupport = "N"; - for (ElementDefinition pe: profile.getSnapshot().getElement()) { - if (pe.getMustSupport()) { - usesMustSupport = "Y"; - break; - } - } - profile.setUserData("usesMustSupport", usesMustSupport); - } - if (usesMustSupport.equals("Y")) { - String elementSupported = ei.getElement().getUserString("elementSupported"); - if (elementSupported==null || ei.definition.getMustSupport()) - if (ei.definition.getMustSupport()) { - ei.getElement().setUserData("elementSupported", "Y"); + String type = null; + Set references = findReferences(resource); + for (String reference : references) { + // We don't want errors when just retrieving the element as they will be caught (with better path info) in subsequent processing + IndexedElement r = getFromBundle(stack.getElement(), reference, entry.getChildValue("fullUrl"), new ArrayList(), stack.addToLiteralPath("entry[" + candidateResources.indexOf(resource) + "]"), type, "transaction".equals(stack.getElement().getChildValue("type"))); + if (r != null && !visitedResources.containsValue(r.getMatch())) { + followResourceLinks(candidateEntries.get(r.getMatch()), visitedResources, candidateEntries, candidateResources, errors, stack, depth + 1); + } } } - } - public void checkCardinalities(List errors, StructureDefinition profile, Element element, NodeStack stack, - List childDefinitions, List children, List problematicPaths) throws DefinitionException { - // 3. report any definitions that have a cardinality problem - for (ElementDefinition ed : childDefinitions) { - if (ed.getRepresentation().isEmpty()) { // ignore xml attributes - int count = 0; - List slices = null; - if (ed.hasSlicing()) - slices = ProfileUtilities.getSliceList(profile, ed); - for (ElementInfo ei : children) - if (ei.definition == ed) - count++; - else if (slices!=null) { - for (ElementDefinition sed : slices) { - if (ei.definition == sed) { - count++; + private Set findReferences(Element start) { + Set references = new HashSet(); + findReferences(start, references); + return references; + } + + private void findReferences(Element start, Set references) { + for (Element child : start.getChildren()) { + if (child.getType().equals("Reference")) { + String ref = child.getChildValue("reference"); + if (ref != null && !ref.startsWith("#")) + references.add(ref); + } + if (child.getType().equals("url") || child.getType().equals("uri") || child.getType().equals("canonical")) { + String ref = child.primitiveValue(); + if (ref != null && !ref.startsWith("#")) + references.add(ref); + } + findReferences(child, references); + } + } + + private void validateBundleReference(List errors, List entries, Element ref, String name, NodeStack stack, String fullUrl, String type, String id) { + String reference = null; + try { + reference = ref.getNamedChildValue("reference"); + } catch (Error e) { + + } + + if (ref != null && !Utilities.noString(reference)) { + Element target = resolveInBundle(entries, reference, fullUrl, type, id); + rule(errors, IssueType.INVALID, ref.line(), ref.col(), stack.addToLiteralPath("reference"), target != null, "Can't find '" + reference + "' in the bundle (" + name + ")"); + } + } + + private void validateContains(ValidatorHostContext hostContext, List errors, String path, ElementDefinition child, ElementDefinition context, Element resource, Element element, NodeStack stack, IdStatus idstatus) throws FHIRException { + String resourceName = element.getType(); + TypeRefComponent trr = null; + for (TypeRefComponent tr : child.getType()) { + if (tr.getCode().equals("Resource")) { + trr = tr; break; - } } - } - String location = "Profile " + profile.getUrl() + ", Element '" + stack.getLiteralPath() + "." + tail(ed.getPath()) + (ed.hasSliceName()? "[" + ed.getSliceName() + (ed.hasLabel() ? " ("+ed.getLabel()+")" : "")+"]": "") + "'"; - if (ed.getMin() > 0) { - if (problematicPaths.contains(ed.getPath())) - hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), location + "': Unable to check minimum required (" + Integer.toString(ed.getMin()) + ") due to lack of slicing validation"); - else - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), location + ": minimum required = " + Integer.toString(ed.getMin()) + ", but only found " + Integer.toString(count)); } - if (ed.hasMax() && !ed.getMax().equals("*")) { - if (problematicPaths.contains(ed.getPath())) - hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), location + ": Unable to check max allowed (" + ed.getMax() + ") due to lack of slicing validation"); - else - rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), location + ": max allowed = " + ed.getMax() + ", but found " + Integer.toString(count)); + if (trr == null) { + rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '" + resourceName + " is not valid - no resources allowed here"); + } else if (isValidResourceType(resourceName, trr)) { + long t = System.nanoTime(); + StructureDefinition profile = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName); + sdTime = sdTime + (System.nanoTime() - t); + // special case: resource wrapper is reset if we're crossing a bundle boundary, but not otherwise + ValidatorHostContext hc = null; + if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY || element.getSpecial() == SpecialElement.BUNDLE_OUTCOME || element.getSpecial() == SpecialElement.PARAMETER) { + resource = element; + hc = hostContext.forEntry(element); + } else { + hc = hostContext.forContained(element); + } + trackUsage(profile, hostContext, element); + if (rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), profile != null, "No profile found for contained resource of type '" + resourceName + "'")) { + validateResource(hc, errors, resource, element, profile, idstatus, stack); + } + } else { + List types = new ArrayList<>(); + for (UriType u : trr.getProfile()) { + StructureDefinition sd = this.context.fetchResource(StructureDefinition.class, u.getValue()); + if (sd != null && !types.contains(sd.getType())) { + types.add(sd.getType()); + } + } + if (types.size() == 1) { + rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '" + resourceName + "' is not valid - must be " + types.get(0)); + } else { + rule(errors, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), false, "The type '" + resourceName + "' is not valid - must be one of " + types); + } } - } } - } - public List assignChildren(ValidatorHostContext hostContext, List errors, StructureDefinition profile, Element resource, - NodeStack stack, List childDefinitions, List children) throws DefinitionException { - // 2. assign children to a definition - // for each definition, for each child, check whether it belongs in the slice - ElementDefinition slicer = null; - boolean unsupportedSlicing = false; - List problematicPaths = new ArrayList(); - String slicingPath = null; - int sliceOffset = 0; - for (int i = 0; i < childDefinitions.size(); i++) { - ElementDefinition ed = childDefinitions.get(i); - boolean childUnsupportedSlicing = false; - boolean process = true; - if (ed.hasSlicing() && !ed.getSlicing().getOrdered()) - slicingPath = ed.getPath(); - else if (slicingPath!=null && ed.getPath().equals(slicingPath)) - ; // nothing - else if (slicingPath != null && !ed.getPath().startsWith(slicingPath)) - slicingPath = null; - // where are we with slicing - if (ed.hasSlicing()) { - if (slicer != null && slicer.getPath().equals(ed.getPath())) { - String errorContext = "profile " + profile.getUrl(); - if (!resource.getChildValue("id").isEmpty()) - errorContext += "; instance " + resource.getChildValue("id"); - throw new DefinitionException("Slice encountered midway through set (path = " + slicer.getPath() + ", id = "+slicer.getId()+"); " + errorContext); + private boolean isValidResourceType(String type, TypeRefComponent def) { + if (!def.hasProfile()) { + return true; } - slicer = ed; - process = false; - sliceOffset = i; - } else if (slicer != null && !slicer.getPath().equals(ed.getPath())) - slicer = null; + List list = new ArrayList<>(); + for (UriType u : def.getProfile()) { + StructureDefinition sdt = context.fetchResource(StructureDefinition.class, u.getValue()); + if (sdt != null) { + list.add(sdt); + } + } + + StructureDefinition sdt = context.fetchTypeDefinition(type); + while (sdt != null) { + if (def.getWorkingCode().equals("Resource")) { + for (StructureDefinition sd : list) { + if (sd.getUrl().equals(sdt.getUrl())) { + return true; + } + if (sd.getType().equals(sdt.getType())) { + return true; + } + } + } + sdt = context.fetchResource(StructureDefinition.class, sdt.getBaseDefinition()); + } + return false; + } + + private void validateDocument(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id) { + // first entry must be a composition + if (rule(errors, IssueType.INVALID, composition.line(), composition.col(), stack.getLiteralPath(), composition.getType().equals("Composition"), + "The first entry in a document must be a composition")) { + + // the composition subject etc references must resolve in the bundle + validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "subject", "Composition"); + validateDocumentReference(errors, entries, composition, stack, fullUrl, id, true, "author", "Composition"); + validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "encounter", "Composition"); + validateDocumentReference(errors, entries, composition, stack, fullUrl, id, false, "custodian", "Composition"); + validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "attester", false, "party"); + validateDocumentSubReference(errors, entries, composition, stack, fullUrl, id, "Composition", "event", true, "detail"); + + validateSections(errors, entries, composition, stack, fullUrl, id); + } + } + + public void validateDocumentSubReference(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id, String title, String parent, boolean repeats, String propName) { + List list = new ArrayList<>(); + composition.getNamedChildren(parent, list); + int i = 1; + for (Element elem : list) { + validateDocumentReference(errors, entries, elem, stack.push(elem, i, null, null), fullUrl, id, repeats, propName, title + "." + parent); + i++; + } + } + + public void validateDocumentReference(List errors, List entries, Element composition, NodeStack stack, String fullUrl, String id, boolean repeats, String propName, String title) { + if (repeats) { + List list = new ArrayList<>(); + composition.getNamedChildren(propName, list); + int i = 1; + for (Element elem : list) { + validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, i, null, null), fullUrl, "Composition", id); + i++; + } + + } else { + Element elem = composition.getNamedChild(propName); + if (elem != null) { + validateBundleReference(errors, entries, elem, title + "." + propName, stack.push(elem, -1, null, null), fullUrl, "Composition", id); + } + } + } + + private void validateElement(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context, + Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, String extensionUrl) throws FHIRException { + // element.markValidation(profile, definition); + + // time = System.nanoTime(); + // check type invariants + checkInvariants(hostContext, errors, profile, definition, resource, element, stack, false); + if (definition.getFixed() != null) + checkFixedValue(errors, stack.getLiteralPath(), element, definition.getFixed(), profile.getUrl(), definition.getSliceName(), null); + + + // get the list of direct defined children, including slices + List childDefinitions = ProfileUtilities.getChildMap(profile, definition); + if (childDefinitions.isEmpty()) { + if (actualType == null) + return; // there'll be an error elsewhere in this case, and we're going to stop. + childDefinitions = getActualTypeChildren(hostContext, element, actualType); + } else if (definition.getType().size() > 1) { + // this only happens when the profile constrains the abstract children but leaves th choice open. + if (actualType == null) + return; // there'll be an error elsewhere in this case, and we're going to stop. + List typeChildDefinitions = getActualTypeChildren(hostContext, element, actualType); + // what were going to do is merge them - the type is not allowed to constrain things that the child definitions already do (well, if it does, it'll be ignored) + mergeChildLists(childDefinitions, typeChildDefinitions, definition.getPath(), actualType); + } + + List children = listChildren(element, stack); + List problematicPaths = assignChildren(hostContext, errors, profile, resource, stack, childDefinitions, children); + + checkCardinalities(errors, profile, element, stack, childDefinitions, children, problematicPaths); + // 4. check order if any slices are ordered. (todo) + + // 5. inspect each child for validity + for (ElementInfo ei : children) { + checkChild(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei, extensionUrl); + } + } + + private void mergeChildLists(List master, List additional, String masterPath, String typePath) { + for (ElementDefinition ed : additional) { + boolean inMaster = false; + for (ElementDefinition t : master) { + String tp = masterPath + ed.getPath().substring(typePath.length()); + if (t.getPath().equals(tp)) { + inMaster = true; + } + } + if (!inMaster) { + master.add(ed); + } + } + + + } + + // todo: the element definition in context might assign a constrained profile for the type? + public List getActualTypeChildren(ValidatorHostContext hostContext, Element element, String actualType) { + List childDefinitions; + StructureDefinition dt = null; + if (isAbsolute(actualType)) + dt = this.context.fetchResource(StructureDefinition.class, actualType); + else + dt = this.context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + actualType); + if (dt == null) + throw new DefinitionException("Unable to resolve actual type " + actualType); + trackUsage(dt, hostContext, element); + + childDefinitions = ProfileUtilities.getChildMap(dt, dt.getSnapshot().getElement().get(0)); + return childDefinitions; + } + + public void checkChild(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, + Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, ElementInfo ei, String extensionUrl) + throws FHIRException, DefinitionException { + + List profiles = new ArrayList(); + if (ei.definition != null) { + String type = null; + ElementDefinition typeDefn = null; + checkMustSupport(profile, ei); + + if (ei.definition.getType().size() == 1 && !"*".equals(ei.definition.getType().get(0).getWorkingCode()) && !"Element".equals(ei.definition.getType().get(0).getWorkingCode()) + && !"BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode())) { + type = ei.definition.getType().get(0).getWorkingCode(); + // Excluding reference is a kludge to get around versioning issues + if (ei.definition.getType().get(0).hasProfile()) { + for (CanonicalType p : ei.definition.getType().get(0).getProfile()) { + profiles.add(p.getValue()); + } + } + } else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getWorkingCode())) { + String prefix = tail(ei.definition.getPath()); + assert prefix.endsWith("[x]"); + type = ei.getName().substring(prefix.length() - 3); + if (isPrimitiveType(type)) + type = Utilities.uncapitalize(type); + if (ei.definition.getType().get(0).hasProfile()) { + for (CanonicalType p : ei.definition.getType().get(0).getProfile()) { + profiles.add(p.getValue()); + } + } + } else if (ei.definition.getType().size() > 1) { + + String prefix = tail(ei.definition.getPath()); + assert typesAreAllReference(ei.definition.getType()) || ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix; + + if (ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR)) + type = ei.getElement().getType(); + else { + prefix = prefix.substring(0, prefix.length() - 3); + for (TypeRefComponent t : ei.definition.getType()) + if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) { + type = t.getWorkingCode(); + // Excluding reference is a kludge to get around versioning issues + if (t.hasProfile() && !type.equals("Reference")) + profiles.add(t.getProfile().get(0).getValue()); + } + } + if (type == null) { + TypeRefComponent trc = ei.definition.getType().get(0); + if (trc.getWorkingCode().equals("Reference")) + type = "Reference"; + else + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, + "The type of element " + ei.getName() + " is not known, which is illegal. Valid types at this point are " + describeTypes(ei.definition.getType())); + } + } else if (ei.definition.getContentReference() != null) { + typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference()); + } else if (ei.definition.getType().size() == 1 && ("Element".equals(ei.definition.getType().get(0).getWorkingCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode()))) { + if (ei.definition.getType().get(0).hasProfile()) { + CanonicalType pu = ei.definition.getType().get(0).getProfile().get(0); + if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT)) + profiles.add(pu.getValue() + "#" + pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT)); + else + profiles.add(pu.getValue()); + } + } + + if (type != null) { + if (type.startsWith("@")) { + ei.definition = findElement(profile, type.substring(1)); + type = null; + } + } + NodeStack localStack = stack.push(ei.getElement(), ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType())); + if (debug) { + System.out.println(" " + localStack.getLiteralPath()); + } + String localStackLiterapPath = localStack.getLiteralPath(); + String eiPath = ei.getPath(); + assert (eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath; + boolean thisIsCodeableConcept = false; + String thisExtension = null; + boolean checkDisplay = true; + + checkInvariants(hostContext, errors, profile, ei.definition, resource, ei.getElement(), localStack, true); + + ei.getElement().markValidation(profile, ei.definition); + boolean elementValidated = false; + if (type != null) { + if (isPrimitiveType(type)) { + checkPrimitive(hostContext, errors, ei.getPath(), type, ei.definition, ei.getElement(), profile, stack); + } else { + if (ei.definition.hasFixed()) { + checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null); + } + if (ei.definition.hasPattern()) { + checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true); + } + } + if (type.equals("Identifier")) { + checkIdentifier(errors, ei.getPath(), ei.getElement(), ei.definition); + } else if (type.equals("Coding")) { + checkCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack); + } else if (type.equals("CodeableConcept")) { + checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack); + thisIsCodeableConcept = true; + } else if (type.equals("Reference")) { + checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, ei.definition, actualType, localStack); + // We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension + } else if (type.equals("Extension")) { + Element eurl = ei.getElement().getNamedChild("url"); + if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, "Extension.url is required")) { + String url = eurl.primitiveValue(); + thisExtension = url; + if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), "Extension.url is required")) { + if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), "Extension.url must be an absolute URL")) { + checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), ei.definition, profile, localStack, stack, extensionUrl); + } + } + } + } else if (type.equals("Resource")) { + validateContains(hostContext, errors, ei.getPath(), ei.definition, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if + elementValidated = true; + // (str.matches(".*([.,/])work\\1$")) + } else if (Utilities.isAbsoluteUrl(type)) { + StructureDefinition defn = context.fetchTypeDefinition(type); + if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) { + List txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep()); + if (txtype.contains("CodeableConcept")) { + checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack, defn); + thisIsCodeableConcept = true; + } else if (txtype.contains("Coding")) { + checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn); + } + } + } + } else { + if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, "Unrecognised Content " + ei.getName())) + validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, false, true, null); + } + StructureDefinition p = null; + String tail = null; + if (profiles.isEmpty()) { + if (type != null) { + p = getProfileForType(type, ei.definition.getType()); + + // If dealing with a primitive type, then we need to check the current child against + // the invariants (constraints) on the current element, because otherwise it only gets + // checked against the primary type's invariants: LLoyd + //if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) { + // checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element); + //} + + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown type " + type); + } + } else if (profiles.size() == 1) { + String url = profiles.get(0); + if (url.contains("#")) { + tail = url.substring(url.indexOf("#") + 1); + url = url.substring(0, url.indexOf("#")); + } + p = this.context.fetchResource(StructureDefinition.class, url); + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + profiles.get(0)); + } else { + elementValidated = true; + HashMap> goodProfiles = new HashMap>(); + HashMap> badProfiles = new HashMap>(); + for (String typeProfile : profiles) { + String url = typeProfile; + tail = null; + if (url.contains("#")) { + tail = url.substring(url.indexOf("#") + 1); + url = url.substring(0, url.indexOf("#")); + } + p = this.context.fetchResource(StructureDefinition.class, typeProfile); + if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, "Unknown profile " + typeProfile)) { + List profileErrors = new ArrayList(); + validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + if (hasErrors(profileErrors)) + badProfiles.put(typeProfile, profileErrors); + else + goodProfiles.put(typeProfile, profileErrors); + } + } + if (goodProfiles.size() == 1) { + errors.addAll(goodProfiles.values().iterator().next()); + } else if (goodProfiles.size() == 0) { + rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Unable to find matching profile among choices: " + StringUtils.join("; ", profiles)); + for (String m : badProfiles.keySet()) { + p = this.context.fetchResource(StructureDefinition.class, m); + for (ValidationMessage message : badProfiles.get(m)) { + message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])"); + errors.add(message); + } + } + } else { + warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, "Found multiple matching profiles among choices: " + StringUtils.join("; ", goodProfiles.keySet())); + for (String m : goodProfiles.keySet()) { + p = this.context.fetchResource(StructureDefinition.class, m); + for (ValidationMessage message : goodProfiles.get(m)) { + message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])"); + errors.add(message); + } + } + } + } + if (p != null) { + trackUsage(p, hostContext, element); + + if (!elementValidated) { + if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER) + validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.getElement(), ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + else + validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + } + int index = profile.getSnapshot().getElement().indexOf(ei.definition); + if (index < profile.getSnapshot().getElement().size() - 1) { + String nextPath = profile.getSnapshot().getElement().get(index + 1).getPath(); + if (!nextPath.equals(ei.definition.getPath()) && nextPath.startsWith(ei.definition.getPath())) + validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension); + } + } + } + } + + private void trackUsage(StructureDefinition profile, ValidatorHostContext hostContext, Element element) { + if (tracker != null) { + tracker.recordProfileUsage(profile, hostContext.getAppContext(), element); + } + } + + private boolean hasMapping(String url, StructureDefinition defn, ElementDefinition elem) { + String id = null; + for (StructureDefinitionMappingComponent m : defn.getMapping()) { + if (url.equals(m.getUri())) { + id = m.getIdentity(); + break; + } + } + if (id != null) { + for (ElementDefinitionMappingComponent m : elem.getMapping()) { + if (id.equals(m.getIdentity())) { + return true; + } + } + + } + return false; + } + + private List getMapping(String url, StructureDefinition defn, ElementDefinition elem) { + List res = new ArrayList<>(); + String id = null; + for (StructureDefinitionMappingComponent m : defn.getMapping()) { + if (url.equals(m.getUri())) { + id = m.getIdentity(); + break; + } + } + if (id != null) { + for (ElementDefinitionMappingComponent m : elem.getMapping()) { + if (id.equals(m.getIdentity())) { + res.add(m.getMap()); + } + } + } + return res; + } + + public void checkMustSupport(StructureDefinition profile, ElementInfo ei) { + String usesMustSupport = profile.getUserString("usesMustSupport"); + if (usesMustSupport == null) { + usesMustSupport = "N"; + for (ElementDefinition pe : profile.getSnapshot().getElement()) { + if (pe.getMustSupport()) { + usesMustSupport = "Y"; + break; + } + } + profile.setUserData("usesMustSupport", usesMustSupport); + } + if (usesMustSupport.equals("Y")) { + String elementSupported = ei.getElement().getUserString("elementSupported"); + if (elementSupported == null || ei.definition.getMustSupport()) + if (ei.definition.getMustSupport()) { + ei.getElement().setUserData("elementSupported", "Y"); + } + } + } + + public void checkCardinalities(List errors, StructureDefinition profile, Element element, NodeStack stack, + List childDefinitions, List children, List problematicPaths) throws DefinitionException { + // 3. report any definitions that have a cardinality problem + for (ElementDefinition ed : childDefinitions) { + if (ed.getRepresentation().isEmpty()) { // ignore xml attributes + int count = 0; + List slices = null; + if (ed.hasSlicing()) + slices = ProfileUtilities.getSliceList(profile, ed); + for (ElementInfo ei : children) + if (ei.definition == ed) + count++; + else if (slices != null) { + for (ElementDefinition sed : slices) { + if (ei.definition == sed) { + count++; + break; + } + } + } + String location = "Profile " + profile.getUrl() + ", Element '" + stack.getLiteralPath() + "." + tail(ed.getPath()) + (ed.hasSliceName() ? "[" + ed.getSliceName() + (ed.hasLabel() ? " (" + ed.getLabel() + ")" : "") + "]" : "") + "'"; + if (ed.getMin() > 0) { + if (problematicPaths.contains(ed.getPath())) + hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), location + "': Unable to check minimum required (" + Integer.toString(ed.getMin()) + ") due to lack of slicing validation"); + else + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count >= ed.getMin(), location + ": minimum required = " + Integer.toString(ed.getMin()) + ", but only found " + Integer.toString(count)); + } + if (ed.hasMax() && !ed.getMax().equals("*")) { + if (problematicPaths.contains(ed.getPath())) + hint(errors, IssueType.NOTSUPPORTED, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), location + ": Unable to check max allowed (" + ed.getMax() + ") due to lack of slicing validation"); + else + rule(errors, IssueType.STRUCTURE, element.line(), element.col(), stack.getLiteralPath(), count <= Integer.parseInt(ed.getMax()), location + ": max allowed = " + ed.getMax() + ", but found " + Integer.toString(count)); + } + } + } + } + + public List assignChildren(ValidatorHostContext hostContext, List errors, StructureDefinition profile, Element resource, + NodeStack stack, List childDefinitions, List children) throws DefinitionException { + // 2. assign children to a definition + // for each definition, for each child, check whether it belongs in the slice + ElementDefinition slicer = null; + boolean unsupportedSlicing = false; + List problematicPaths = new ArrayList(); + String slicingPath = null; + int sliceOffset = 0; + for (int i = 0; i < childDefinitions.size(); i++) { + ElementDefinition ed = childDefinitions.get(i); + boolean childUnsupportedSlicing = false; + boolean process = true; + if (ed.hasSlicing() && !ed.getSlicing().getOrdered()) + slicingPath = ed.getPath(); + else if (slicingPath != null && ed.getPath().equals(slicingPath)) + ; // nothing + else if (slicingPath != null && !ed.getPath().startsWith(slicingPath)) + slicingPath = null; + // where are we with slicing + if (ed.hasSlicing()) { + if (slicer != null && slicer.getPath().equals(ed.getPath())) { + String errorContext = "profile " + profile.getUrl(); + if (!resource.getChildValue("id").isEmpty()) + errorContext += "; instance " + resource.getChildValue("id"); + throw new DefinitionException("Slice encountered midway through set (path = " + slicer.getPath() + ", id = " + slicer.getId() + "); " + errorContext); + } + slicer = ed; + process = false; + sliceOffset = i; + } else if (slicer != null && !slicer.getPath().equals(ed.getPath())) + slicer = null; // if (process) { - for (ElementInfo ei : children) { - if (ei.sliceInfo == null) { - ei.sliceInfo = new ArrayList<>(); - } - unsupportedSlicing = matchSlice(hostContext, errors, ei.sliceInfo, profile, stack, slicer, unsupportedSlicing, problematicPaths, sliceOffset, i, ed, childUnsupportedSlicing, ei); - } + for (ElementInfo ei : children) { + if (ei.sliceInfo == null) { + ei.sliceInfo = new ArrayList<>(); + } + unsupportedSlicing = matchSlice(hostContext, errors, ei.sliceInfo, profile, stack, slicer, unsupportedSlicing, problematicPaths, sliceOffset, i, ed, childUnsupportedSlicing, ei); + } // } + } + int last = -1; + int lastSlice = -1; + for (ElementInfo ei : children) { + String sliceInfo = ""; + if (slicer != null) + sliceInfo = " (slice: " + slicer.getPath() + ")"; + if (!unsupportedSlicing) + if (ei.additionalSlice && ei.definition != null) { + if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || + ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPENATEND) && true /* TODO: replace "true" with condition to check that this element is at "end" */) { + slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()), + "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl() + ": " + errorSummaryForSlicingAsHtml(ei.sliceInfo))); + } else if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.CLOSED)) { + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: " + errorSummaryForSlicing(ei.sliceInfo)), + "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: " + errorSummaryForSlicingAsHtml(ei.sliceInfo))); + } + } else { + // Don't raise this if we're in an abstract profile, like Resource + if (!profile.getAbstract()) + rule(errors, IssueType.NOTSUPPORTED, ei.line(), ei.col(), ei.getPath(), (ei.definition != null), "This element is not allowed by the profile " + profile.getUrl()); + } + // TODO: Should get the order of elements correct when parsing elements that are XML attributes vs. elements + boolean isXmlAttr = false; + if (ei.definition != null) { + for (Enumeration r : ei.definition.getRepresentation()) { + if (r.getValue() == PropertyRepresentation.XMLATTR) { + isXmlAttr = true; + break; + } + } + } + + if (!ToolingExtensions.readBoolExtension(profile, "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order")) { + boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr; + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, "As specified by profile " + profile.getUrl() + ", Element '" + ei.getName() + "' is out of order"); + } + if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) + rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), (ei.definition == null) || (ei.sliceindex >= lastSlice) || isXmlAttr, "As specified by profile " + profile.getUrl() + ", Element '" + ei.getName() + "' is out of order in ordered slice"); + if (ei.definition == null || !isXmlAttr) + last = ei.index; + if (ei.slice != null) + lastSlice = ei.sliceindex; + else + lastSlice = -1; + } + return problematicPaths; } - int last = -1; - int lastSlice = -1; - for (ElementInfo ei : children) { - String sliceInfo = ""; - if (slicer != null) - sliceInfo = " (slice: " + slicer.getPath()+")"; - if (!unsupportedSlicing) - if (ei.additionalSlice && ei.definition != null) { - if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPEN) || - ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.OPENATEND) && true /* TODO: replace "true" with condition to check that this element is at "end" */) { - slicingHint(errors, IssueType.INFORMATIONAL, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()), - "This element does not match any known slice" + (profile == null ? "" : " defined in the profile " + profile.getUrl()+": "+errorSummaryForSlicingAsHtml(ei.sliceInfo))); - } else if (ei.definition.getSlicing().getRules().equals(ElementDefinition.SlicingRules.CLOSED)) { - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), false, "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: "+errorSummaryForSlicing(ei.sliceInfo)), - "This element does not match any known slice " + (profile == null ? "" : " defined in the profile " + profile.getUrl() + " and slicing is CLOSED: "+errorSummaryForSlicingAsHtml(ei.sliceInfo))); - } + + public List listChildren(Element element, NodeStack stack) { + // 1. List the children, and remember their exact path (convenience) + List children = new ArrayList(); + ChildIterator iter = new ChildIterator(this, stack.getLiteralPath(), element); + while (iter.next()) + children.add(new ElementInfo(iter.name(), iter.element(), iter.path(), iter.count())); + return children; + } + + public void checkInvariants(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, Element resource, Element element, NodeStack stack, boolean onlyNonInherited) throws FHIRException { + checkInvariants(hostContext, errors, stack.getLiteralPath(), profile, definition, null, null, resource, element, onlyNonInherited); + } + + public boolean matchSlice(ValidatorHostContext hostContext, List errors, List sliceInfo, StructureDefinition profile, NodeStack stack, + ElementDefinition slicer, boolean unsupportedSlicing, List problematicPaths, int sliceOffset, int i, ElementDefinition ed, + boolean childUnsupportedSlicing, ElementInfo ei) { + boolean match = false; + if (slicer == null || slicer == ed) { + match = nameMatches(ei.getName(), tail(ed.getPath())); } else { - // Don't raise this if we're in an abstract profile, like Resource - if (!profile.getAbstract()) - rule(errors, IssueType.NOTSUPPORTED, ei.line(), ei.col(), ei.getPath(), (ei.definition != null), "This element is not allowed by the profile "+profile.getUrl()); + if (nameMatches(ei.getName(), tail(ed.getPath()))) + try { + match = sliceMatches(hostContext, ei.getElement(), ei.getPath(), slicer, ed, profile, errors, sliceInfo, stack); + if (match) { + ei.slice = slicer; + + // Since a defined slice was found, this is not an additional (undefined) slice. + ei.additionalSlice = false; + } else if (ei.slice == null) { + // if the specified slice is undefined, keep track of the fact this is an additional (undefined) slice, but only if a slice wasn't found previously + ei.additionalSlice = true; + } + } catch (FHIRException e) { + rule(errors, IssueType.PROCESSING, ei.line(), ei.col(), ei.getPath(), false, e.getMessage()); + unsupportedSlicing = true; + childUnsupportedSlicing = true; + } } - // TODO: Should get the order of elements correct when parsing elements that are XML attributes vs. elements - boolean isXmlAttr = false; - if (ei.definition != null) { - for (Enumeration r : ei.definition.getRepresentation()) { - if (r.getValue() == PropertyRepresentation.XMLATTR) { - isXmlAttr = true; - break; - } + if (match) { + boolean isOk = ei.definition == null || ei.definition == slicer || (ei.definition.getPath().endsWith("[x]") && ed.getPath().startsWith(ei.definition.getPath().replace("[x]", ""))); + if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), isOk, "Profile " + profile.getUrl() + ", Element matches more than one slice - " + (ei.definition == null || !ei.definition.hasSliceName() ? "" : ei.definition.getSliceName()) + ", " + (ed.hasSliceName() ? ed.getSliceName() : ""))) { + ei.definition = ed; + if (ei.slice == null) { + ei.index = i; + } else { + ei.index = sliceOffset; + ei.sliceindex = i - (sliceOffset + 1); + } + } + } else if (childUnsupportedSlicing) { + problematicPaths.add(ed.getPath()); } - } - - if (!ToolingExtensions.readBoolExtension(profile, "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order")) { - boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr; - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, "As specified by profile " + profile.getUrl() + ", Element '"+ei.getName()+"' is out of order"); - } - if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) - rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), (ei.definition == null) || (ei.sliceindex >= lastSlice) || isXmlAttr, "As specified by profile " + profile.getUrl() + ", Element '"+ei.getName()+"' is out of order in ordered slice"); - if (ei.definition == null || !isXmlAttr) - last = ei.index; - if (ei.slice != null) - lastSlice = ei.sliceindex; - else - lastSlice = -1; + return unsupportedSlicing; } - return problematicPaths; - } - public List listChildren(Element element, NodeStack stack) { - // 1. List the children, and remember their exact path (convenience) - List children = new ArrayList(); - ChildIterator iter = new ChildIterator(this, stack.getLiteralPath(), element); - while (iter.next()) - children.add(new ElementInfo(iter.name(), iter.element(), iter.path(), iter.count())); - return children; - } - - public void checkInvariants(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, Element resource, Element element, NodeStack stack, boolean onlyNonInherited) throws FHIRException { - checkInvariants(hostContext, errors, stack.getLiteralPath(), profile, definition, null, null, resource, element, onlyNonInherited); - } - - public boolean matchSlice(ValidatorHostContext hostContext, List errors, List sliceInfo, StructureDefinition profile, NodeStack stack, - ElementDefinition slicer, boolean unsupportedSlicing, List problematicPaths, int sliceOffset, int i, ElementDefinition ed, - boolean childUnsupportedSlicing, ElementInfo ei) { - boolean match = false; - if (slicer == null || slicer == ed) { - match = nameMatches(ei.getName(), tail(ed.getPath())); - } else { - if (nameMatches(ei.getName(), tail(ed.getPath()))) - try { - match = sliceMatches(hostContext, ei.getElement(), ei.getPath(), slicer, ed, profile, errors, sliceInfo, stack); - if (match) { - ei.slice = slicer; - - // Since a defined slice was found, this is not an additional (undefined) slice. - ei.additionalSlice = false; - } else if (ei.slice == null) { - // if the specified slice is undefined, keep track of the fact this is an additional (undefined) slice, but only if a slice wasn't found previously - ei.additionalSlice = true; - } - } catch (FHIRException e) { - rule(errors, IssueType.PROCESSING, ei.line(), ei.col(), ei.getPath(), false, e.getMessage()); - unsupportedSlicing = true; - childUnsupportedSlicing = true; + private ElementDefinition getElementByTail(StructureDefinition p, String tail) throws DefinitionException { + if (tail == null) + return p.getSnapshot().getElement().get(0); + for (ElementDefinition t : p.getSnapshot().getElement()) { + if (tail.equals(t.getId())) + return t; } + throw new DefinitionException("Unable to find element with id '" + tail + "'"); } - if (match) { - boolean isOk = ei.definition == null || ei.definition == slicer || (ei.definition.getPath().endsWith("[x]") && ed.getPath().startsWith(ei.definition.getPath().replace("[x]", ""))); - if (rule(errors, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), isOk, "Profile " + profile.getUrl() + ", Element matches more than one slice - " + (ei.definition==null || !ei.definition.hasSliceName() ? "" : ei.definition.getSliceName()) + ", " + (ed.hasSliceName() ? ed.getSliceName() : ""))) { - ei.definition = ed; - if (ei.slice == null) { - ei.index = i; - } else { - ei.index = sliceOffset; - ei.sliceindex = i - (sliceOffset + 1); - } - } - } else if (childUnsupportedSlicing) { - problematicPaths.add(ed.getPath()); - } - return unsupportedSlicing; - } - private ElementDefinition getElementByTail(StructureDefinition p, String tail) throws DefinitionException { - if (tail == null) - return p.getSnapshot().getElement().get(0); - for (ElementDefinition t : p.getSnapshot().getElement()) { - if (tail.equals(t.getId())) - return t; - } - throw new DefinitionException("Unable to find element with id '"+tail+"'"); - } - - private IdStatus idStatusForEntry(Element ep, ElementInfo ei) { - if (isBundleEntry(ei.getPath())) { - Element req = ep.getNamedChild("request"); - Element resp = ep.getNamedChild("response"); - Element fullUrl = ep.getNamedChild("fullUrl"); - Element method = null; - Element url = null; - if (req != null) { - method = req.getNamedChild("method"); - url = req.getNamedChild("url"); - } - if (resp != null) { - return IdStatus.OPTIONAL; - } if (method == null) { - if (fullUrl == null) - return IdStatus.REQUIRED; - else if (fullUrl.primitiveValue().startsWith("urn:uuid:") || fullUrl.primitiveValue().startsWith("urn:oid:")) - return IdStatus.OPTIONAL; + private IdStatus idStatusForEntry(Element ep, ElementInfo ei) { + if (isBundleEntry(ei.getPath())) { + Element req = ep.getNamedChild("request"); + Element resp = ep.getNamedChild("response"); + Element fullUrl = ep.getNamedChild("fullUrl"); + Element method = null; + Element url = null; + if (req != null) { + method = req.getNamedChild("method"); + url = req.getNamedChild("url"); + } + if (resp != null) { + return IdStatus.OPTIONAL; + } + if (method == null) { + if (fullUrl == null) + return IdStatus.REQUIRED; + else if (fullUrl.primitiveValue().startsWith("urn:uuid:") || fullUrl.primitiveValue().startsWith("urn:oid:")) + return IdStatus.OPTIONAL; + else + return IdStatus.REQUIRED; + } else { + String s = method.primitiveValue(); + if (s.equals("PUT")) { + if (url == null) + return IdStatus.REQUIRED; + else + return IdStatus.OPTIONAL; // or maybe prohibited? not clear + } else if (s.equals("POST")) + return IdStatus.OPTIONAL; // this should be prohibited, but see task 9102 + else // actually, we should never get to here; a bundle entry with method get/delete should not have a resource + return IdStatus.OPTIONAL; + } + } else if (isParametersEntry(ei.getPath()) || isBundleOutcome(ei.getPath())) + return IdStatus.OPTIONAL; else - return IdStatus.REQUIRED; - } else { - String s = method.primitiveValue(); - if (s.equals("PUT")) { - if (url == null) return IdStatus.REQUIRED; - else - return IdStatus.OPTIONAL; // or maybe prohibited? not clear - } else if (s.equals("POST")) - return IdStatus.OPTIONAL; // this should be prohibited, but see task 9102 - else // actually, we should never get to here; a bundle entry with method get/delete should not have a resource - return IdStatus.OPTIONAL; - } - } else if (isParametersEntry(ei.getPath()) || isBundleOutcome(ei.getPath())) - return IdStatus.OPTIONAL; - else - return IdStatus.REQUIRED; - } + } - private void checkInvariants(ValidatorHostContext hostContext, List errors, String path, StructureDefinition profile, ElementDefinition ed, String typename, String typeProfile, Element resource, Element element, boolean onlyNonInherited) throws FHIRException, FHIRException { - if (noInvariantChecks) - return; + private void checkInvariants(ValidatorHostContext hostContext, List errors, String path, StructureDefinition profile, ElementDefinition ed, String typename, String typeProfile, Element resource, Element element, boolean onlyNonInherited) throws FHIRException, FHIRException { + if (noInvariantChecks) + return; - for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) { - if (inv.hasExpression() && (!onlyNonInherited || !inv.hasSource() || profile.getUrl().equals(inv.getSource()))) { - @SuppressWarnings("unchecked") - Set invList = executionId.equals(element.getUserString(EXECUTION_ID)) ? (Set) element.getUserData(EXECUTED_CONSTRAINT_LIST) : null; - if (invList == null) { - invList = new HashSet<>(); - element.setUserData(EXECUTED_CONSTRAINT_LIST, invList); - element.setUserData(EXECUTION_ID, executionId); - } - if (!invList.contains(inv.getKey())) { - invList.add(inv.getKey()); - checkInvariant(hostContext, errors, path, profile, resource, element, inv); + for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) { + if (inv.hasExpression() && (!onlyNonInherited || !inv.hasSource() || profile.getUrl().equals(inv.getSource()))) { + @SuppressWarnings("unchecked") + Set invList = executionId.equals(element.getUserString(EXECUTION_ID)) ? (Set) element.getUserData(EXECUTED_CONSTRAINT_LIST) : null; + if (invList == null) { + invList = new HashSet<>(); + element.setUserData(EXECUTED_CONSTRAINT_LIST, invList); + element.setUserData(EXECUTION_ID, executionId); + } + if (!invList.contains(inv.getKey())) { + invList.add(inv.getKey()); + checkInvariant(hostContext, errors, path, profile, resource, element, inv); + } else { + //System.out.println("Skip "+inv.getKey()+" on "+path); + } + } + } + } + + public void checkInvariant(ValidatorHostContext hostContext, List errors, String path, StructureDefinition profile, Element resource, Element element, ElementDefinitionConstraintComponent inv) throws FHIRException { + ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache"); + if (n == null) { + long t = System.nanoTime(); + try { + n = fpe.parse(fixExpr(inv.getExpression())); + } catch (FHIRLexerException e) { + throw new FHIRException("Problem processing expression " + inv.getExpression() + " in profile " + profile.getUrl() + " path " + path + ": " + e.getMessage()); + } + fpeTime = fpeTime + (System.nanoTime() - t); + inv.setUserData("validator.expression.cache", n); + } + + String msg; + boolean ok; + try { + long t = System.nanoTime(); + ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n); + fpeTime = fpeTime + (System.nanoTime() - t); + msg = fpe.forLog(); + } catch (Exception ex) { + ok = false; + msg = ex.getMessage(); + } + if (!ok) { + if (!Utilities.noString(msg)) + msg = " (" + msg + ")"; + if (inv.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice") && + ToolingExtensions.readBooleanExtension(inv, "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice")) { + if (bpWarnings == BestPracticeWarningLevel.Hint) + hint(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey() + ": " + inv.getHuman() + msg + " [" + n.toString() + "]"); + else if (bpWarnings == BestPracticeWarningLevel.Warning) + warning(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey() + ": " + inv.getHuman() + msg + " [" + n.toString() + "]"); + else if (bpWarnings == BestPracticeWarningLevel.Error) + rule(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey() + ": " + inv.getHuman() + msg + " [" + n.toString() + "]"); + } else if (inv.getSeverity() == ConstraintSeverity.ERROR) { + rule(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey() + ": " + inv.getHuman() + msg + " [" + n.toString() + "]"); + } else if (inv.getSeverity() == ConstraintSeverity.WARNING) { + warning(errors, IssueType.INVARIANT, element.line(), element.line(), path, ok, inv.getKey() + ": " + inv.getHuman() + msg + " [" + n.toString() + "]"); + } + } + } + + private void validateMessage(List errors, List entries, Element messageHeader, NodeStack stack, String fullUrl, String id) { + // first entry must be a messageheader + if (rule(errors, IssueType.INVALID, messageHeader.line(), messageHeader.col(), stack.getLiteralPath(), messageHeader.getType().equals("MessageHeader"), + "The first entry in a message must be a MessageHeader")) { + List elements = messageHeader.getChildren("focus"); + for (Element elem : elements) + validateBundleReference(errors, entries, elem, "MessageHeader Data", stack.push(elem, -1, null, null), fullUrl, "MessageHeader", id); + } + } + + private void validateObservation(List errors, Element element, NodeStack stack) { + // all observations should have a subject, a performer, and a time + + bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("subject") != null, "All observations should have a subject"); + List performers = new ArrayList<>(); + element.getNamedChildren("performer", performers); + bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), performers.size() > 0, "All observations should have a performer"); + bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("effectiveDateTime") != null || element.getNamedChild("effectivePeriod") != null, + "All observations should have an effectiveDateTime or an effectivePeriod"); + } + + /* + * The actual base entry point for internal use (re-entrant) + */ + private void validateResource(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException { + assert stack != null; + assert resource != null; + boolean ok = true; + String resourceName = element.getType(); // todo: consider namespace...? + if (defn == null) { + long t = System.nanoTime(); + defn = element.getProperty().getStructure(); + if (defn == null) + defn = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName); + sdTime = sdTime + (System.nanoTime() - t); + ok = rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), defn != null, "No definition found for resource type '" + resourceName + "'"); + } + + String type = defn.getKind() == StructureDefinitionKind.LOGICAL ? defn.getId() : defn.getType(); + // special case: we have a bundle, and the profile is not for a bundle. We'll try the first entry instead + if (!type.equals(resourceName) && resourceName.equals("Bundle")) { + NodeStack first = getFirstEntry(stack); + if (first != null && first.getElement().getType().equals(type)) { + element = first.element; + stack = first; + resourceName = element.getType(); + idstatus = IdStatus.OPTIONAL; // why? + } + // todo: validate everything in this bundle. + } + ok = rule(errors, IssueType.INVALID, -1, -1, stack.getLiteralPath(), type.equals(resourceName), "Specified profile type was '" + type + "', but found type '" + resourceName + "'"); + + if (ok) { + if (idstatus == IdStatus.REQUIRED && (element.getNamedChild("id") == null)) + rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource requires an id, but none is present"); + else if (idstatus == IdStatus.PROHIBITED && (element.getNamedChild("id") != null)) + rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource has an id, but none is allowed"); + start(hostContext, errors, element, element, defn, stack); // root is both definition and type + } + } + + private NodeStack getFirstEntry(NodeStack bundle) { + List list = new ArrayList(); + bundle.getElement().getNamedChildren("entry", list); + if (list.isEmpty()) + return null; + Element resource = list.get(0).getNamedChild("resource"); + if (resource == null) + return null; + else { + NodeStack entry = bundle.push(list.get(0), 0, list.get(0).getProperty().getDefinition(), list.get(0).getProperty().getDefinition()); + return entry.push(resource, -1, resource.getProperty().getDefinition(), context.fetchTypeDefinition(resource.fhirType()).getSnapshot().getElementFirstRep()); + } + } + + private void validateSections(List errors, List entries, Element focus, NodeStack stack, String fullUrl, String id) { + List sections = new ArrayList(); + focus.getNamedChildren("section", sections); + int i = 1; + for (Element section : sections) { + NodeStack localStack = stack.push(section, i, null, null); + + // technically R4+, but there won't be matches from before that + validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "author", "Section"); + validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "focus", "Section"); + + List sectionEntries = new ArrayList(); + section.getNamedChildren("entry", sectionEntries); + int j = 1; + for (Element sectionEntry : sectionEntries) { + NodeStack localStack2 = localStack.push(sectionEntry, j, null, null); + validateBundleReference(errors, entries, sectionEntry, "Section Entry", localStack2, fullUrl, "Composition", id); + j++; + } + validateSections(errors, entries, section, localStack, fullUrl, id); + i++; + } + } + + private boolean valueMatchesCriteria(Element value, ElementDefinition criteria, StructureDefinition profile) throws FHIRException { + if (criteria.hasFixed()) { + List msgs = new ArrayList(); + checkFixedValue(msgs, "{virtual}", value, criteria.getFixed(), profile.getUrl(), "value", null); + return msgs.size() == 0; + } else if (criteria.hasBinding() && criteria.getBinding().getStrength() == BindingStrength.REQUIRED && criteria.getBinding().hasValueSet()) { + throw new FHIRException("Unable to resolve slice matching - slice matching by value set not done"); } else { - //System.out.println("Skip "+inv.getKey()+" on "+path); + throw new FHIRException("Unable to resolve slice matching - no fixed value or required value set"); } - } - } - } - - public void checkInvariant(ValidatorHostContext hostContext, List errors, String path, StructureDefinition profile, Element resource, Element element, ElementDefinitionConstraintComponent inv) throws FHIRException { - ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache"); - if (n == null) { - long t = System.nanoTime(); - try { - n = fpe.parse(fixExpr(inv.getExpression())); - } catch (FHIRLexerException e) { - throw new FHIRException("Problem processing expression "+inv.getExpression() +" in profile " + profile.getUrl() + " path " + path + ": " + e.getMessage()); - } - fpeTime = fpeTime + (System.nanoTime() - t); - inv.setUserData("validator.expression.cache", n); } - String msg; - boolean ok; - try { - long t = System.nanoTime(); - ok = fpe.evaluateToBoolean(hostContext, resource, hostContext.getRootResource(), element, n); - fpeTime = fpeTime + (System.nanoTime() - t); - msg = fpe.forLog(); - } catch (Exception ex) { - ok = false; - msg = ex.getMessage(); - } - if (!ok) { - if (!Utilities.noString(msg)) - msg = " ("+msg+")"; - if (inv.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice") && - ToolingExtensions.readBooleanExtension(inv, "http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice")) { - if (bpWarnings == BestPracticeWarningLevel.Hint) - hint(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey()+": "+inv.getHuman()+msg+" ["+n.toString()+"]"); - else if (bpWarnings == BestPracticeWarningLevel.Warning) - warning(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey()+": "+inv.getHuman()+msg+" ["+n.toString()+"]"); - else if (bpWarnings == BestPracticeWarningLevel.Error) - rule(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey()+": "+inv.getHuman()+msg+" ["+n.toString()+"]"); - } else if (inv.getSeverity() == ConstraintSeverity.ERROR) { - rule(errors, IssueType.INVARIANT, element.line(), element.col(), path, ok, inv.getKey()+": "+inv.getHuman() + msg + " [" + n.toString() + "]"); - } else if (inv.getSeverity() == ConstraintSeverity.WARNING) { - warning(errors, IssueType.INVARIANT, element.line(), element.line(), path, ok, inv.getKey()+": "+inv.getHuman() + msg + " [" + n.toString() + "]"); - } - } - } - - private void validateMessage(List errors, List entries, Element messageHeader, NodeStack stack, String fullUrl, String id) { - // first entry must be a messageheader - if (rule(errors, IssueType.INVALID, messageHeader.line(), messageHeader.col(), stack.getLiteralPath(), messageHeader.getType().equals("MessageHeader"), - "The first entry in a message must be a MessageHeader")) { - List elements = messageHeader.getChildren("focus"); - for (Element elem: elements) - validateBundleReference(errors, entries, elem, "MessageHeader Data", stack.push(elem, -1, null, null), fullUrl, "MessageHeader", id); - } - } - - private void validateObservation(List errors, Element element, NodeStack stack) { - // all observations should have a subject, a performer, and a time - - bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("subject") != null, "All observations should have a subject"); - List performers = new ArrayList<>(); - element.getNamedChildren("performer", performers); - bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), performers.size() > 0, "All observations should have a performer"); - bpCheck(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), element.getNamedChild("effectiveDateTime") != null || element.getNamedChild("effectivePeriod") != null, - "All observations should have an effectiveDateTime or an effectivePeriod"); - } - - /* - * The actual base entry point for internal use (re-entrant) - */ - public void validateResource(ValidatorHostContext hostContext, List errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException { - assert stack != null; - assert resource != null; - boolean ok = true; - String resourceName = element.getType(); // todo: consider namespace...? - if (defn == null) { - long t = System.nanoTime(); - defn = element.getProperty().getStructure(); - if (defn == null) - defn = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/" + resourceName); - sdTime = sdTime + (System.nanoTime() - t); - ok = rule(errors, IssueType.INVALID, element.line(), element.col(), stack.addToLiteralPath(resourceName), defn != null, "No definition found for resource type '" + resourceName + "'"); - } - - String type = defn.getKind() == StructureDefinitionKind.LOGICAL ? defn.getId() : defn.getType(); - // special case: we have a bundle, and the profile is not for a bundle. We'll try the first entry instead - if (!type.equals(resourceName) && resourceName.equals("Bundle")) { - NodeStack first = getFirstEntry(stack); - if (first != null && first.getElement().getType().equals(type)) { - element = first.element; - stack = first; - resourceName = element.getType(); - idstatus = IdStatus.OPTIONAL; // why? - } - // todo: validate everything in this bundle. - } - ok = rule(errors, IssueType.INVALID, -1, -1, stack.getLiteralPath(), type.equals(resourceName), "Specified profile type was '" + type + "', but found type '" + resourceName + "'"); - - if (ok) { - if (idstatus == IdStatus.REQUIRED && (element.getNamedChild("id") == null)) - rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource requires an id, but none is present"); - else if (idstatus == IdStatus.PROHIBITED && (element.getNamedChild("id") != null)) - rule(errors, IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, "Resource has an id, but none is allowed"); - start(hostContext, errors, element, element, defn, stack); // root is both definition and type - } - } - - private NodeStack getFirstEntry(NodeStack bundle) { - List list = new ArrayList(); - bundle.getElement().getNamedChildren("entry", list); - if (list.isEmpty()) - return null; - Element resource = list.get(0).getNamedChild("resource"); - if (resource == null) - return null; - else { - NodeStack entry = bundle.push(list.get(0), 0, list.get(0).getProperty().getDefinition(), list.get(0).getProperty().getDefinition()); - return entry.push(resource, -1, resource.getProperty().getDefinition(), context.fetchTypeDefinition(resource.fhirType()).getSnapshot().getElementFirstRep()); - } - } - - private void validateSections(List errors, List entries, Element focus, NodeStack stack, String fullUrl, String id) { - List sections = new ArrayList(); - focus.getNamedChildren("section", sections); - int i = 1; - for (Element section : sections) { - NodeStack localStack = stack.push(section, i, null, null); - - // technically R4+, but there won't be matches from before that - validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "author", "Section"); - validateDocumentReference(errors, entries, section, stack, fullUrl, id, false, "focus", "Section"); - - List sectionEntries = new ArrayList(); - section.getNamedChildren("entry", sectionEntries); - int j = 1; - for (Element sectionEntry : sectionEntries) { - NodeStack localStack2 = localStack.push(sectionEntry, j, null, null); - validateBundleReference(errors, entries, sectionEntry, "Section Entry", localStack2, fullUrl, "Composition", id); - j++; - } - validateSections(errors, entries, section, localStack, fullUrl, id); - i++; - } - } - - private boolean valueMatchesCriteria(Element value, ElementDefinition criteria, StructureDefinition profile) throws FHIRException { - if (criteria.hasFixed()) { - List msgs = new ArrayList(); - checkFixedValue(msgs, "{virtual}", value, criteria.getFixed(), profile.getUrl(), "value", null); - return msgs.size() == 0; - } else if (criteria.hasBinding() && criteria.getBinding().getStrength() == BindingStrength.REQUIRED && criteria.getBinding().hasValueSet()) { - throw new FHIRException("Unable to resolve slice matching - slice matching by value set not done"); - } else { - throw new FHIRException("Unable to resolve slice matching - no fixed value or required value set"); - } - } - - private boolean yearIsValid(String v) { - if (v == null) { - return false; - } - try { - int i = Integer.parseInt(v.substring(0, Math.min(4, v.length()))); - return i >= 1800 && i <= thisYear() + 80; - } catch (NumberFormatException e) { - return false; - } - } - - private int thisYear() { - return Calendar.getInstance().get(Calendar.YEAR); - } - - public static class NodeStack { - private ElementDefinition definition; - private Element element; - private ElementDefinition extension; - private String literalPath; // xpath format - private List logicalPaths; // dotted format, various entry points - private NodeStack parent; - private ElementDefinition type; - private String workingLang; - - public NodeStack() { - workingLang = validationLanguage; - } - - public NodeStack(Element element) { - this.element = element; - literalPath = element.getName(); - workingLang = validationLanguage; - if (!element.getName().equals(element.fhirType())) { - logicalPaths = new ArrayList<>(); - logicalPaths.add(element.fhirType()); - } - } - - public NodeStack(Element element, String refPath) { - this.element = element; - literalPath = refPath+"->"+element.getName(); - workingLang = validationLanguage; - } - - public String addToLiteralPath(String... path) { - StringBuilder b = new StringBuilder(); - b.append(getLiteralPath()); - for (String p : path) { - if (p.startsWith(":")) { - b.append("["); - b.append(p.substring(1)); - b.append("]"); - } else { - b.append("."); - b.append(p); - } - } - return b.toString(); - } - - private ElementDefinition getDefinition() { - return definition; - } - - private Element getElement() { - return element; - } - - protected String getLiteralPath() { - return literalPath == null ? "" : literalPath; - } - - private List getLogicalPaths() { - return logicalPaths == null ? new ArrayList() : logicalPaths; - } - - private ElementDefinition getType() { - return type; - } - - private NodeStack pushTarget(Element element, int count, ElementDefinition definition, ElementDefinition type) { - return pushInternal(element, count, definition, type, "->"); - } - private NodeStack push(Element element, int count, ElementDefinition definition, ElementDefinition type) { - return pushInternal(element, count, definition, type, "."); - } - private NodeStack pushInternal(Element element, int count, ElementDefinition definition, ElementDefinition type, String sep) { - NodeStack res = new NodeStack(); - res.parent = this; - res.workingLang = this.workingLang; - res.element = element; - res.definition = definition; - res.literalPath = getLiteralPath() + sep + element.getName(); - if (count > -1) - res.literalPath = res.literalPath + "[" + Integer.toString(count) + "]"; - else if (element.getSpecial() == null && element.getProperty().isList()) - res.literalPath = res.literalPath + "[0]"; - else if (element.getProperty().isChoice()) { - String n = res.literalPath.substring(res.literalPath.lastIndexOf(".")+1); - String en = element.getProperty().getName(); - en = en.substring(0, en.length()-3); - String t = n.substring(en.length()); - if (isPrimitiveType(Utilities.uncapitalize(t))) - t = Utilities.uncapitalize(t); - res.literalPath = res.literalPath.substring(0, res.literalPath.lastIndexOf("."))+"."+en+".ofType("+t+")"; - } - res.logicalPaths = new ArrayList(); - if (type != null) { - // type will be bull if we on a stitching point of a contained resource, or if.... - res.type = type; - String tn = res.type.getPath(); - String t = tail(definition.getPath()); - if ("Resource".equals(tn)) { - tn = element.fhirType(); + private boolean yearIsValid(String v) { + if (v == null) { + return false; } - for (String lp : getLogicalPaths()) { - res.logicalPaths.add(lp + "." + t); - if (t.endsWith("[x]")) - res.logicalPaths.add(lp + "." + t.substring(0, t.length() - 3) + type.getPath()); + try { + int i = Integer.parseInt(v.substring(0, Math.min(4, v.length()))); + return i >= 1800 && i <= thisYear() + 80; + } catch (NumberFormatException e) { + return false; } - res.logicalPaths.add(tn); - } else if (definition != null) { - for (String lp : getLogicalPaths()) { - res.logicalPaths.add(lp + "." + element.getName()); - } - res.logicalPaths.add(definition.typeSummary()); - } else - res.logicalPaths.addAll(getLogicalPaths()); - // CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - // for (String lp : res.logicalPaths) - // b.append(lp); - // System.out.println(res.literalPath+" : "+b.toString()); - return res; } - private void setType(ElementDefinition type) { - this.type = type; + private int thisYear() { + return Calendar.getInstance().get(Calendar.YEAR); + } + + public class NodeStack { + private ElementDefinition definition; + private Element element; + private ElementDefinition extension; + private String literalPath; // xpath format + private List logicalPaths; // dotted format, various entry points + private NodeStack parent; + private ElementDefinition type; + private String workingLang; + + public NodeStack() { + workingLang = validationLanguage; + } + + public NodeStack(Element element) { + this.element = element; + literalPath = element.getName(); + workingLang = validationLanguage; + if (!element.getName().equals(element.fhirType())) { + logicalPaths = new ArrayList<>(); + logicalPaths.add(element.fhirType()); + } + } + + public NodeStack(Element element, String refPath) { + this.element = element; + literalPath = refPath + "->" + element.getName(); + workingLang = validationLanguage; + } + + public String addToLiteralPath(String... path) { + StringBuilder b = new StringBuilder(); + b.append(getLiteralPath()); + for (String p : path) { + if (p.startsWith(":")) { + b.append("["); + b.append(p.substring(1)); + b.append("]"); + } else { + b.append("."); + b.append(p); + } + } + return b.toString(); + } + + private ElementDefinition getDefinition() { + return definition; + } + + private Element getElement() { + return element; + } + + protected String getLiteralPath() { + return literalPath == null ? "" : literalPath; + } + + private List getLogicalPaths() { + return logicalPaths == null ? new ArrayList() : logicalPaths; + } + + private ElementDefinition getType() { + return type; + } + + private NodeStack pushTarget(Element element, int count, ElementDefinition definition, ElementDefinition type) { + return pushInternal(element, count, definition, type, "->"); + } + + private NodeStack push(Element element, int count, ElementDefinition definition, ElementDefinition type) { + return pushInternal(element, count, definition, type, "."); + } + + private NodeStack pushInternal(Element element, int count, ElementDefinition definition, ElementDefinition type, String sep) { + NodeStack res = new NodeStack(); + res.parent = this; + res.workingLang = this.workingLang; + res.element = element; + res.definition = definition; + res.literalPath = getLiteralPath() + sep + element.getName(); + if (count > -1) + res.literalPath = res.literalPath + "[" + Integer.toString(count) + "]"; + else if (element.getSpecial() == null && element.getProperty().isList()) + res.literalPath = res.literalPath + "[0]"; + else if (element.getProperty().isChoice()) { + String n = res.literalPath.substring(res.literalPath.lastIndexOf(".") + 1); + String en = element.getProperty().getName(); + en = en.substring(0, en.length() - 3); + String t = n.substring(en.length()); + if (isPrimitiveType(Utilities.uncapitalize(t))) + t = Utilities.uncapitalize(t); + res.literalPath = res.literalPath.substring(0, res.literalPath.lastIndexOf(".")) + "." + en + ".ofType(" + t + ")"; + } + res.logicalPaths = new ArrayList(); + if (type != null) { + // type will be bull if we on a stitching point of a contained resource, or if.... + res.type = type; + String tn = res.type.getPath(); + String t = tail(definition.getPath()); + if ("Resource".equals(tn)) { + tn = element.fhirType(); + } + for (String lp : getLogicalPaths()) { + res.logicalPaths.add(lp + "." + t); + if (t.endsWith("[x]")) + res.logicalPaths.add(lp + "." + t.substring(0, t.length() - 3) + type.getPath()); + } + res.logicalPaths.add(tn); + } else if (definition != null) { + for (String lp : getLogicalPaths()) { + res.logicalPaths.add(lp + "." + element.getName()); + } + res.logicalPaths.add(definition.typeSummary()); + } else + res.logicalPaths.addAll(getLogicalPaths()); + // CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); + // for (String lp : res.logicalPaths) + // b.append(lp); + // System.out.println(res.literalPath+" : "+b.toString()); + return res; + } + + private void setType(ElementDefinition type) { + this.type = type; + } } - } public String reportTimes() { - String s = String.format("Times (ms): overall = %d, tx = %d, sd = %d, load = %d, fpe = %d", overall / 1000000, txTime / 1000000, sdTime / 1000000, loadTime / 1000000, fpeTime / 1000000); - overall = 0; - txTime = 0; - sdTime = 0; - loadTime = 0; - fpeTime = 0; - return s; - } + String s = String.format("Times (ms): overall = %d, tx = %d, sd = %d, load = %d, fpe = %d", overall / 1000000, txTime / 1000000, sdTime / 1000000, loadTime / 1000000, fpeTime / 1000000); + overall = 0; + txTime = 0; + sdTime = 0; + loadTime = 0; + fpeTime = 0; + return s; + } - public boolean isNoBindingMsgSuppressed() { - return noBindingMsgSuppressed; - } + public boolean isNoBindingMsgSuppressed() { + return noBindingMsgSuppressed; + } - public IResourceValidator setNoBindingMsgSuppressed(boolean noBindingMsgSuppressed) { - this.noBindingMsgSuppressed = noBindingMsgSuppressed; - return this; - } + public IResourceValidator setNoBindingMsgSuppressed(boolean noBindingMsgSuppressed) { + this.noBindingMsgSuppressed = noBindingMsgSuppressed; + return this; + } - - public boolean isNoTerminologyChecks() { - return noTerminologyChecks; - } - public IResourceValidator setNoTerminologyChecks(boolean noTerminologyChecks) { - this.noTerminologyChecks = noTerminologyChecks; - return this; - } + public boolean isNoTerminologyChecks() { + return noTerminologyChecks; + } - public void checkAllInvariants(){ - for (StructureDefinition sd : context.allStructures()) { - if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) { - for (ElementDefinition ed : sd.getSnapshot().getElement()) { - for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) { - if (inv.hasExpression()) { - try { - ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache"); - if (n == null) { - n = fpe.parse(fixExpr(inv.getExpression())); - inv.setUserData("validator.expression.cache", n); + public IResourceValidator setNoTerminologyChecks(boolean noTerminologyChecks) { + this.noTerminologyChecks = noTerminologyChecks; + return this; + } + + public void checkAllInvariants() { + for (StructureDefinition sd : context.allStructures()) { + if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION) { + for (ElementDefinition ed : sd.getSnapshot().getElement()) { + for (ElementDefinitionConstraintComponent inv : ed.getConstraint()) { + if (inv.hasExpression()) { + try { + ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache"); + if (n == null) { + n = fpe.parse(fixExpr(inv.getExpression())); + inv.setUserData("validator.expression.cache", n); + } + fpe.check(null, sd.getKind() == StructureDefinitionKind.RESOURCE ? sd.getType() : "DomainResource", ed.getPath(), n); + } catch (Exception e) { + System.out.println("Error processing structure [" + sd.getId() + "] path " + ed.getPath() + ":" + inv.getKey() + " (\"" + inv.getExpression() + "\"): " + e.getMessage()); + } + } + } } - fpe.check(null, sd.getKind() == StructureDefinitionKind.RESOURCE ? sd.getType() : "DomainResource", ed.getPath(), n); - } catch (Exception e) { - System.out.println("Error processing structure ["+sd.getId()+"] path "+ed.getPath()+":"+inv.getKey()+" (\""+inv.getExpression()+"\"): "+e.getMessage()); - } } - } } - } - } - } - - private String fixExpr(String expr) { - // this is a hack work around for past publication of wrong FHIRPath expressions - // R4 - // waiting for 4.0.2 - if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) { - return "probablility.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))"; } - // handled in 4.0.1 - if ("(component.empty() and hasMember.empty()) implies (dataAbsentReason or value)".equals(expr)) - return "(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())"; - if ("isModifier implies isModifierReason.exists()".equals(expr)) - return "(isModifier.exists() and isModifier) implies isModifierReason.exists()"; - if ("(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().not() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))".equals(expr)) - return "(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().empty() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))"; - if ("differential.element.all(id) and differential.element.id.trace('ids').isDistinct()".equals(expr)) - return "differential.element.all(id.exists()) and differential.element.id.trace('ids').isDistinct()"; - if ("snapshot.element.all(id) and snapshot.element.id.trace('ids').isDistinct()".equals(expr)) - return "snapshot.element.all(id.exists()) and snapshot.element.id.trace('ids').isDistinct()"; - - // R3 - if ("(code or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')".equals(expr)) - return "(code.exists() or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')"; - if ("value.empty() or code!=component.code".equals(expr)) - return "value.empty() or (code in component.code).not()"; - if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) - return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)"; - if ("element.all(definition and min and max)".equals(expr)) - return "element.all(definition.exists() and min.exists() and max.exists())"; - if ("telecom or endpoint".equals(expr)) - return "telecom.exists() or endpoint.exists()"; - if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) - return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)"; - if ("searchType implies type = 'string'".equals(expr)) - return "searchType.exists() implies type = 'string'"; - if ("abatement.empty() or (abatement as boolean).not() or clinicalStatus='resolved' or clinicalStatus='remission' or clinicalStatus='inactive'".equals(expr)) - return "abatement.empty() or (abatement is boolean).not() or (abatement as boolean).not() or (clinicalStatus = 'resolved') or (clinicalStatus = 'remission') or (clinicalStatus = 'inactive')"; - if ("(component.empty() and related.empty()) implies (dataAbsentReason or value)".equals(expr)) - return "(component.empty() and related.empty()) implies (dataAbsentReason.exists() or value.exists())"; - - if ("".equals(expr)) - return ""; - return expr; - } + private String fixExpr(String expr) { + // this is a hack work around for past publication of wrong FHIRPath expressions + // R4 + // waiting for 4.0.2 + if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) { + return "probablility.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))"; + } - public IEvaluationContext getExternalHostServices() { - return externalHostServices; - } + // handled in 4.0.1 + if ("(component.empty() and hasMember.empty()) implies (dataAbsentReason or value)".equals(expr)) + return "(component.empty() and hasMember.empty()) implies (dataAbsentReason.exists() or value.exists())"; + if ("isModifier implies isModifierReason.exists()".equals(expr)) + return "(isModifier.exists() and isModifier) implies isModifierReason.exists()"; + if ("(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().not() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))".equals(expr)) + return "(%resource.kind = 'logical' or element.first().path.startsWith(%resource.type)) and (element.tail().empty() or element.tail().all(path.startsWith(%resource.differential.element.first().path.replaceMatches('\\\\..*','')&'.')))"; + if ("differential.element.all(id) and differential.element.id.trace('ids').isDistinct()".equals(expr)) + return "differential.element.all(id.exists()) and differential.element.id.trace('ids').isDistinct()"; + if ("snapshot.element.all(id) and snapshot.element.id.trace('ids').isDistinct()".equals(expr)) + return "snapshot.element.all(id.exists()) and snapshot.element.id.trace('ids').isDistinct()"; - public String getValidationLanguage() { - return validationLanguage; - } + // R3 + if ("(code or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')".equals(expr)) + return "(code.exists() or value.empty()) and (system.empty() or system = 'urn:iso:std:iso:4217')"; + if ("value.empty() or code!=component.code".equals(expr)) + return "value.empty() or (code in component.code).not()"; + if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) + return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)"; + if ("element.all(definition and min and max)".equals(expr)) + return "element.all(definition.exists() and min.exists() and max.exists())"; + if ("telecom or endpoint".equals(expr)) + return "telecom.exists() or endpoint.exists()"; + if ("(code or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)".equals(expr)) + return "(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (value.empty() or value > 0)"; + if ("searchType implies type = 'string'".equals(expr)) + return "searchType.exists() implies type = 'string'"; + if ("abatement.empty() or (abatement as boolean).not() or clinicalStatus='resolved' or clinicalStatus='remission' or clinicalStatus='inactive'".equals(expr)) + return "abatement.empty() or (abatement is boolean).not() or (abatement as boolean).not() or (clinicalStatus = 'resolved') or (clinicalStatus = 'remission') or (clinicalStatus = 'inactive')"; + if ("(component.empty() and related.empty()) implies (dataAbsentReason or value)".equals(expr)) + return "(component.empty() and related.empty()) implies (dataAbsentReason.exists() or value.exists())"; - public void setValidationLanguage(String validationLanguage) { - this.validationLanguage = validationLanguage; - } + if ("".equals(expr)) + return ""; + return expr; + } - public boolean isDebug() { - return debug; - } + public IEvaluationContext getExternalHostServices() { + return externalHostServices; + } - public void setDebug(boolean debug) { - this.debug = debug; - } + public String getValidationLanguage() { + return validationLanguage; + } + + public void setValidationLanguage(String validationLanguage) { + this.validationLanguage = validationLanguage; + } + + public boolean isDebug() { + return debug; + } + + public void setDebug(boolean debug) { + this.debug = debug; + } } diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResourceValidationTracker.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResourceValidationTracker.java new file mode 100644 index 000000000..92962c578 --- /dev/null +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/utils/ResourceValidationTracker.java @@ -0,0 +1,44 @@ +package org.hl7.fhir.r5.validation.instancevalidator.utils; + +import org.hl7.fhir.r5.model.StructureDefinition; +import org.hl7.fhir.utilities.validation.ValidationMessage; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +/** + * The validator keeps one of these classes for each resource it validates (e.g. when chasing references) + *

    + * It keeps track of the state of resource validation - a given resrouce may be validated agaisnt multiple + * profiles during a single validation, and it may be valid against some, and invalid against others. + *

    + * We don't want to keep doing the same validation, so we remember the outcomes for each combination + * of resource + profile + *

    + * Additionally, profile validation may be circular - e.g. a Patient profile that applies the same profile + * to linked patients, and 2 patient resources that link to each other. So this class also tracks validation + * in process. + *

    + * If the validator comes back to the same point, and validates the same instance against the same profile + * while it's already validating, it assumes it's valid - it cannot have new errors that wouldn't already + * be found in the first iteration - in other words, there's no errors + * + * @author graha + */ +public class ResourceValidationTracker { + private Map> validations = new HashMap<>(); + + public void startValidating(StructureDefinition sd) { + validations.put(sd.getUrl(), new ArrayList()); + } + + public List getOutcomes(StructureDefinition sd) { + return validations.get(sd.getUrl()); + } + + public void storeOutcomes(StructureDefinition sd, List errors) { + validations.put(sd.getUrl(), errors); + } +} From a91b9886ce2f545adea66617e1ffa41f16f8db50 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 16:32:20 -0500 Subject: [PATCH 10/11] Trying to refactor the NodeStack class a little so I can pull it out --- .../fhir/r5/validation/instancevalidator/InstanceValidator.java | 1 - 1 file changed, 1 deletion(-) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 412210f65..7366f76a0 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -5362,7 +5362,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat private String workingLang; public NodeStack() { - workingLang = validationLanguage; } public NodeStack(Element element) { From dc40256af46cbc501ded120058e04d11afb85a83 Mon Sep 17 00:00:00 2001 From: markiantorno Date: Fri, 21 Feb 2020 17:05:49 -0500 Subject: [PATCH 11/11] Cleanup --- .../instancevalidator/InstanceValidator.java | 36 +++++++------------ 1 file changed, 12 insertions(+), 24 deletions(-) diff --git a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java index 7366f76a0..fa8e4c459 100644 --- a/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java +++ b/org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java @@ -3475,21 +3475,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat private void validateQuestionnaireElement(List errors, NodeStack ns, Element questionnaire, Element item, List parents) { // R4+ - if (FHIRVersion.isR4Plus(context.getVersion())) { - if (item.hasChildren("enableWhen")) { - List ewl = item.getChildren("enableWhen"); - for (Element ew : ewl) { -// Element ew = item.getNamedChild("enableWhen"); - String ql = ew.getNamedChildValue("question"); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, ql != null, "Questions with an enableWhen must have a value for the question link")) { - Element tgt = getQuestionById(item, ql); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt == null, "Questions with an enableWhen cannot refer to an inner question for it's enableWhen condition")) { - tgt = getQuestionById(questionnaire, ql); - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != null, "Unable to find target '" + ql + "' for this question enableWhen")) { - if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != item, "Target for this question enableWhen can't reference itself")) { - if (!isBefore(item, tgt, parents)) { - warning(errors, IssueType.BUSINESSRULE, ns.literalPath, false, "The target of this enableWhen rule (" + ql + ") comes after the question itself"); - } + if ((FHIRVersion.isR4Plus(context.getVersion())) && (item.hasChildren("enableWhen"))) { + List ewl = item.getChildren("enableWhen"); + for (Element ew : ewl) { + String ql = ew.getNamedChildValue("question"); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, ql != null, "Questions with an enableWhen must have a value for the question link")) { + Element tgt = getQuestionById(item, ql); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt == null, "Questions with an enableWhen cannot refer to an inner question for it's enableWhen condition")) { + tgt = getQuestionById(questionnaire, ql); + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != null, "Unable to find target '" + ql + "' for this question enableWhen")) { + if (rule(errors, IssueType.BUSINESSRULE, ns.literalPath, tgt != item, "Target for this question enableWhen can't reference itself")) { + if (!isBefore(item, tgt, parents)) { + warning(errors, IssueType.BUSINESSRULE, ns.literalPath, false, "The target of this enableWhen rule (" + ql + ") comes after the question itself"); } } } @@ -4568,15 +4565,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat private void validateElement(ValidatorHostContext hostContext, List errors, StructureDefinition profile, ElementDefinition definition, StructureDefinition cprofile, ElementDefinition context, Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, String extensionUrl) throws FHIRException { - // element.markValidation(profile, definition); - // time = System.nanoTime(); // check type invariants checkInvariants(hostContext, errors, profile, definition, resource, element, stack, false); if (definition.getFixed() != null) checkFixedValue(errors, stack.getLiteralPath(), element, definition.getFixed(), profile.getUrl(), definition.getSliceName(), null); - // get the list of direct defined children, including slices List childDefinitions = ProfileUtilities.getChildMap(profile, definition); if (childDefinitions.isEmpty()) { @@ -4997,14 +4991,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat } else if (slicer != null && !slicer.getPath().equals(ed.getPath())) slicer = null; -// if (process) { for (ElementInfo ei : children) { if (ei.sliceInfo == null) { ei.sliceInfo = new ArrayList<>(); } unsupportedSlicing = matchSlice(hostContext, errors, ei.sliceInfo, profile, stack, slicer, unsupportedSlicing, problematicPaths, sliceOffset, i, ed, childUnsupportedSlicing, ei); } -// } } int last = -1; int lastSlice = -1; @@ -5466,10 +5458,6 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat res.logicalPaths.add(definition.typeSummary()); } else res.logicalPaths.addAll(getLogicalPaths()); - // CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(); - // for (String lp : res.logicalPaths) - // b.append(lp); - // System.out.println(res.literalPath+" : "+b.toString()); return res; }