Refactoring ResourceValidationTracker

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/instancevalidator/InstanceValidator.java

@@ -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;
@@ -150,12 +153,11 @@ import ca.uhn.fhir.util.ObjectUtil;
 /**
  * Thinking of using this in a java program? Don't!
  * You should use one of the wrappers instead. Either in HAPI, or use ValidationEngine
- * 
+ * <p>
  * Validation todo:
  * - support @default slices
  *
  * @author Grahame Grieve
- *
  */
 /*
  * todo:
@@ -165,40 +167,159 @@ import ca.uhn.fhir.util.ObjectUtil;
 
 public class InstanceValidator extends BaseValidator implements IResourceValidator {
 
-    /**
+    private class ValidatorHostServices implements IEvaluationContext {
-   * 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<String, List<ValidationMessage>> validations = new HashMap<>();
 
-    private void startValidating(StructureDefinition sd) {
+        @Override
-      validations.put(sd.getUrl(), new ArrayList<ValidationMessage>());
+        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;
         }
 
-    private List<ValidationMessage> getOutcomes(StructureDefinition sd) {
+        @Override
-      return validations.get(sd.getUrl());  
+        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;
         }
 
-    public void storeOutcomes(StructureDefinition sd, List<ValidationMessage> errors) {
+        @Override
-      validations.put(sd.getUrl(), errors);      
+        public boolean log(String argument, List<Base> 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<TypeDetails> parameters) throws PathEngineException {
+            throw new Error("Not done yet (ValidatorHostServices.checkFunction)");
+        }
+
+        @Override
+        public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> 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<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
+            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<ValidationMessage> 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 IWorkerContext context;
@@ -254,7 +375,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         this.context = theContext;
         this.externalHostServices = hostServices;
         fpe = new FHIRPathEngine(context);
-    validatorServices = new ValidatorHostServices(this);
+        validatorServices = new ValidatorHostServices();
         fpe.setHostServices(validatorServices);
         if (theContext.getVersion().startsWith("3.0") || theContext.getVersion().startsWith("1.0"))
             fpe.setLegacyMode(true);
@@ -673,8 +794,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                 }
                 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) {
-      catch (Exception e) {
                 return true;
             }
         }
@@ -1401,7 +1521,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         }
 
         for (StructureDefinitionContextComponent ctxt : fixContexts(extUrl, definition.getContext())) {
-      if (ok) { break; }
+            if (ok) {
+                break;
+            }
             if (ctxt.getType() == ExtensionContextType.ELEMENT) {
                 String en = ctxt.getExpression();
                 contexts.append("e:" + en);
@@ -1411,7 +1533,9 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                     ok = true;
                 }
                 for (String p : plist) {
-          if (ok) {break; }
+                    if (ok) {
+                        break;
+                    }
                     if (p.equals(en)) {
                         ok = true;
                     } else {
@@ -2946,15 +3070,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
 
     /**
-   *
+     * @param element - the candidate that might be in the slice
-   * @param element
+     * @param path    - for reporting any errors. the XPath for the element
-   *          - the candidate that might be in the slice
+     * @param slicer  - the definition of how slicing is determined
-   * @param path
+     * @param ed      - the slice for which to test membership
-   *          - 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
@@ -3145,7 +3264,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         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 ");
+            if (firstCoding) firstCoding = false;
+            else expression.append(" and ");
             expression.append(discriminator + ".coding.where(");
             boolean first = true;
             if (c.hasSystem()) {
@@ -3153,15 +3273,18 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                 expression.append("system = '" + c.getSystem() + "'");
             }
             if (c.hasVersion()) {
-        if (first) first = false; else expression.append(" and ");
+                if (first) first = false;
+                else expression.append(" and ");
                 expression.append("version = '" + c.getVersion() + "'");
             }
             if (c.hasCode()) {
-        if (first) first = false; else expression.append(" and ");
+                if (first) first = false;
+                else expression.append(" and ");
                 expression.append("code = '" + c.getCode() + "'");
             }
             if (c.hasDisplay()) {
-        if (first) first = false; else expression.append(" and ");
+                if (first) first = false;
+                else expression.append(" and ");
                 expression.append("display = '" + c.getDisplay() + "'");
             }
             expression.append(").exists()");
@@ -3501,6 +3624,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
             iRest++;
         }
     }
+
     private void validateCodeSystem(List<ValidationMessage> errors, Element cs, NodeStack stack) {
         String url = cs.getNamedChildValue("url");
         String vsu = cs.getNamedChildValue("valueSet");
@@ -3558,7 +3682,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                     new JsonParser(context).compose(contained, bs, OutputStyle.NORMAL, id);
                     byte[] json = bs.toByteArray();
                     switch (v) {
-          case DSTU1: throw new FHIRException("Unsupported version R1");
+                        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);
@@ -3674,7 +3799,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                             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("integer"))
+                                checkOption(errors, answer, ns, qsrc, qItem, "integer");
                             else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string");
                         }
                         break;
@@ -3684,8 +3810,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
                             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("integer"))
-              else if (itemType.equals("string")) checkOption(errors, answer, ns, qsrc, qItem, "string", true);
+                                checkOption(errors, answer, ns, qsrc, qItem, "integer");
+                            else if (itemType.equals("string"))
+                                checkOption(errors, answer, ns, qsrc, qItem, "string", true);
                         }
                         break;
 //          case QUESTION:
@@ -3746,12 +3874,9 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
                         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
-          else
                         rule(errors, IssueType.NOTFOUND, item.line(), item.col(), stack.getLiteralPath(), index > -1, "LinkId \"" + linkId + "\" not found in questionnaire");
-        }
+                } else {
-        else
-        {
                     rule(errors, IssueType.STRUCTURE, item.line(), item.col(), stack.getLiteralPath(), index >= lastIndex, "Structural Error: items are out of order");
                     lastIndex = index;
 
@@ -4168,6 +4293,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
      * 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.
@@ -5006,7 +5132,8 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
             }
             if (resp != null) {
                 return IdStatus.OPTIONAL;
-      } if (method == null) {
+            }
+            if (method == null) {
                 if (fullUrl == null)
                     return IdStatus.REQUIRED;
                 else if (fullUrl.primitiveValue().startsWith("urn:uuid:") || fullUrl.primitiveValue().startsWith("urn:oid:"))
@@ -5121,7 +5248,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
     /*
      * The actual base entry point for internal use (re-entrant)
      */
-  public void validateResource(ValidatorHostContext hostContext, List<ValidationMessage> errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException {
+    private void validateResource(ValidatorHostContext hostContext, List<ValidationMessage> errors, Element resource, Element element, StructureDefinition defn, IdStatus idstatus, NodeStack stack) throws FHIRException {
         assert stack != null;
         assert resource != null;
         boolean ok = true;
@@ -5224,7 +5351,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
         return Calendar.getInstance().get(Calendar.YEAR);
     }
 
-    public static class NodeStack {
+    public class NodeStack {
         private ElementDefinition definition;
         private Element element;
         private ElementDefinition extension;
@@ -5293,9 +5420,11 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
         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;

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)
+ * <p>
+ * 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.
+ * <p>
+ * We don't want to keep doing the same validation, so we remember the outcomes for each combination
+ * of resource + profile
+ * <p>
+ * 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.
+ * <p>
+ * 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<String, List<ValidationMessage>> validations = new HashMap<>();
+
+    public void startValidating(StructureDefinition sd) {
+        validations.put(sd.getUrl(), new ArrayList<ValidationMessage>());
+    }
+
+    public List<ValidationMessage> getOutcomes(StructureDefinition sd) {
+        return validations.get(sd.getUrl());
+    }
+
+    public void storeOutcomes(StructureDefinition sd, List<ValidationMessage> errors) {
+        validations.put(sd.getUrl(), errors);
+    }
+}