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Validator incorrectly rejected references where only an identifier was 

populated
This commit is contained in:
James Agnew 2017-05-26 21:32:12 -04:00
parent ba40f44d27
commit 7d659c88e5
3 changed files with 68 additions and 59 deletions
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97
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/validation/InstanceValidator.java
View File

@ -14,7 +14,6 @@ import java.util.Set;
import java.util.regex.Matcher; import java.util.regex.Matcher;
import java.util.regex.Pattern; import java.util.regex.Pattern;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.dstu3.conformance.ProfileUtilities; import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
import org.hl7.fhir.dstu3.context.IWorkerContext; import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult; import org.hl7.fhir.dstu3.context.IWorkerContext.ValidationResult;
@ -28,20 +27,9 @@ import org.hl7.fhir.dstu3.elementmodel.ParserBase;
import org.hl7.fhir.dstu3.elementmodel.ParserBase.ValidationPolicy; import org.hl7.fhir.dstu3.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.dstu3.elementmodel.XmlParser; import org.hl7.fhir.dstu3.elementmodel.XmlParser;
import org.hl7.fhir.dstu3.formats.FormatUtilities; import org.hl7.fhir.dstu3.formats.FormatUtilities;
import org.hl7.fhir.dstu3.model.Address; import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Attachment;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent; import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent; import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.ContactPoint;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.DecimalType;
import org.hl7.fhir.dstu3.model.DomainResource;
import org.hl7.fhir.dstu3.model.ElementDefinition;
import org.hl7.fhir.dstu3.model.ElementDefinition.AggregationMode; import org.hl7.fhir.dstu3.model.ElementDefinition.AggregationMode;
import org.hl7.fhir.dstu3.model.ElementDefinition.ConstraintSeverity; import org.hl7.fhir.dstu3.model.ElementDefinition.ConstraintSeverity;
import org.hl7.fhir.dstu3.model.ElementDefinition.DiscriminatorType; import org.hl7.fhir.dstu3.model.ElementDefinition.DiscriminatorType;
@ -50,35 +38,14 @@ import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionConstraintCom
import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent; import org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionSlicingDiscriminatorComponent;
import org.hl7.fhir.dstu3.model.ElementDefinition.PropertyRepresentation; import org.hl7.fhir.dstu3.model.ElementDefinition.PropertyRepresentation;
import org.hl7.fhir.dstu3.model.ElementDefinition.TypeRefComponent; import org.hl7.fhir.dstu3.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.dstu3.model.Enumeration;
import org.hl7.fhir.dstu3.model.Enumerations.BindingStrength; import org.hl7.fhir.dstu3.model.Enumerations.BindingStrength;
import org.hl7.fhir.dstu3.model.ExpressionNode;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.HumanName;
import org.hl7.fhir.dstu3.model.Identifier;
import org.hl7.fhir.dstu3.model.IntegerType;
import org.hl7.fhir.dstu3.model.Period;
import org.hl7.fhir.dstu3.model.Quantity;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemComponent; import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemOptionComponent; import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemOptionComponent;
import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType; import org.hl7.fhir.dstu3.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.dstu3.model.Range;
import org.hl7.fhir.dstu3.model.Ratio;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.Resource;
import org.hl7.fhir.dstu3.model.SampledData;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.StructureDefinition.ExtensionContext; import org.hl7.fhir.dstu3.model.StructureDefinition.ExtensionContext;
import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionKind; import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionSnapshotComponent; import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionSnapshotComponent;
import org.hl7.fhir.dstu3.model.StructureDefinition.TypeDerivationRule; import org.hl7.fhir.dstu3.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.dstu3.model.TimeType;
import org.hl7.fhir.dstu3.model.Timing;
import org.hl7.fhir.dstu3.model.Type;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent; import org.hl7.fhir.dstu3.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.dstu3.utils.FHIRLexer.FHIRLexerException; import org.hl7.fhir.dstu3.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.dstu3.utils.FHIRPathEngine; import org.hl7.fhir.dstu3.utils.FHIRPathEngine;
@ -105,6 +72,7 @@ import org.w3c.dom.Node;
import com.google.gson.Gson; import com.google.gson.Gson;
import com.google.gson.JsonObject; import com.google.gson.JsonObject;
import com.google.gson.stream.JsonWriter;
import ca.uhn.fhir.util.ObjectUtil; import ca.uhn.fhir.util.ObjectUtil;
@ -292,13 +260,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
source = Source.InstanceValidator; source = Source.InstanceValidator;
} }
public InstanceValidator(ValidationEngine engine) { public InstanceValidator(ValidationEngine engine) {
super(); super();
this.context = engine.getContext(); this.context = engine.getContext();
fpe = engine.getFpe(); fpe = engine.getFpe();
source = Source.InstanceValidator; source = Source.InstanceValidator;
} }
@Override @Override
public boolean isNoInvariantChecks() { public boolean isNoInvariantChecks() {
@ -788,6 +755,24 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return c; return c;
} }
private Reference readAsReference(Element item) {
Reference r = new Reference();
r.setDisplay(item.getNamedChildValue("display"));
r.setReference(item.getNamedChildValue("reference"));
List<Element> identifier = item.getChildrenByName("identifier");
if (identifier.isEmpty() == false) {
r.setIdentifier(readAsIdentifier(identifier.get(0)));
}
return r;
}
private Identifier readAsIdentifier(Element item) {
Identifier r = new Identifier();
r.setSystem(item.getNamedChildValue("system"));
r.setValue(item.getNamedChildValue("value"));
return r;
}
private void checkCoding(List<ValidationMessage> errors, String path, Element focus, Coding fixed) { private void checkCoding(List<ValidationMessage> errors, String path, Element focus, Coding fixed) {
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system", focus); checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system", focus);
checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), "code", focus); checkFixedValue(errors, path + ".code", focus.getNamedChild("code"), fixed.getCodeElement(), "code", focus);
@ -1365,16 +1350,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} }
private void checkReference(Object appContext, List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException, IOException { private void checkReference(Object appContext, List<ValidationMessage> errors, String path, Element element, StructureDefinition profile, ElementDefinition container, String parentType, NodeStack stack) throws FHIRException, IOException {
String ref = null; Reference reference = readAsReference(element);
try {
// Do this inside a try because invalid instances might provide more than one reference. String ref = reference.getReference();
ref = element.getNamedChildValue("reference");
} catch (Error e) {
}
if (Utilities.noString(ref)) { if (Utilities.noString(ref)) {
// todo - what should we do in this case? 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 should have a display"); 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; return;
} }
@ -1627,12 +1609,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return element; return element;
List<String> nodes = new ArrayList<String>(); List<String> nodes = new ArrayList<String>();
Matcher matcher = Pattern.compile("([a-zA-Z0-0]+(\\([^\\(^\\)]*\\))?)(\\.([a-zA-Z0-0]+(\\([^\\(^\\)]*\\))?))*").matcher(discriminator); Matcher matcher = Pattern.compile("\\.([a-zA-Z0-0]+(\\([^\\(^\\)]*\\))?)").matcher("."+discriminator);
while (matcher.find()) { while (matcher.find()) {
if (!matcher.group(1).startsWith("@")) if (!matcher.group(1).startsWith("@"))
nodes.add(matcher.group(1)); nodes.add(matcher.group(1));
if (matcher.groupCount()>4 && matcher.group(4)!= null && !matcher.group(4).startsWith("@"))
nodes.add(matcher.group(4));
} }
for (String fullnode : nodes) { for (String fullnode : nodes) {
@ -2269,8 +2249,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
type = criteriaElement.getType().get(0).getCode(); type = criteriaElement.getType().get(0).getCode();
} }
if (type==null) if (type==null)
// Slicer won't ever have a slice name, so this error needs to be reworked throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " does not declare a type");
throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + slicer.getSliceName() + " does not declare a type");
if (discriminator.isEmpty()) if (discriminator.isEmpty())
expression = expression + " and this is " + type; expression = expression + " and this is " + type;
else else
@ -2293,7 +2272,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (fixed instanceof BooleanType) { } else if (fixed instanceof BooleanType) {
expression = expression + ((BooleanType)fixed).asStringValue(); expression = expression + ((BooleanType)fixed).asStringValue();
} else } else
throw new DefinitionException("Unsupported fixed value type for discriminator(" + discriminator + ") for slice " + slicer.getSliceName() + ": " + fixed.getClass().getName()); throw new DefinitionException("Unsupported fixed value type for discriminator(" + discriminator + ") for slice " + ed.getId() + ": " + fixed.getClass().getName());
} else if (criteriaElement.hasBinding() && criteriaElement.getBinding().hasStrength() && criteriaElement.getBinding().getStrength().equals(BindingStrength.REQUIRED) && criteriaElement.getBinding().getValueSetReference()!=null) { } else if (criteriaElement.hasBinding() && criteriaElement.getBinding().hasStrength() && criteriaElement.getBinding().getStrength().equals(BindingStrength.REQUIRED) && criteriaElement.getBinding().getValueSetReference()!=null) {
expression = expression + " and " + discriminator + " in '" + criteriaElement.getBinding().getValueSetReference().getReference() + "'"; expression = expression + " and " + discriminator + " in '" + criteriaElement.getBinding().getValueSetReference().getReference() + "'";
} else if (criteriaElement.hasMin() && criteriaElement.getMin()>0) { } else if (criteriaElement.hasMin() && criteriaElement.getMin()>0) {
@ -2301,7 +2280,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (criteriaElement.hasMax() && criteriaElement.getMax().equals("0")) { } else if (criteriaElement.hasMax() && criteriaElement.getMax().equals("0")) {
expression = expression + " and " + discriminator + ".exists().not()"; expression = expression + " and " + discriminator + ".exists().not()";
} else { } else {
throw new DefinitionException("Could not match discriminator (" + discriminator + ") for slice " + slicer.getSliceName() + " - does not have fixed value, binding or existence assertions"); throw new DefinitionException("Could not match discriminator (" + discriminator + ") for slice " + ed.getId() + " - does not have fixed value, binding or existence assertions");
} }
} }
@ -3225,12 +3204,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (goodProfiles.size()==1) { if (goodProfiles.size()==1) {
errors.addAll(goodProfiles.get(0)); errors.addAll(goodProfiles.get(0));
} else if (goodProfiles.size()==0) { } 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.path, false, "Unable to find matching profile among choices: " + String.join("; ", profiles));
for (List<ValidationMessage> messages : badProfiles) { for (List<ValidationMessage> messages : badProfiles) {
errors.addAll(messages); errors.addAll(messages);
} }
} else { } 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.path, false, "Found multiple matching profiles among choices: " + String.join("; ", goodProfiles.keySet()));
for (List<ValidationMessage> messages : goodProfiles.values()) { for (List<ValidationMessage> messages : goodProfiles.values()) {
errors.addAll(messages); errors.addAll(messages);
} }

27
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorDstu3Test.java
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@ -234,6 +234,33 @@ public class FhirInstanceValidatorDstu3Test {
assertTrue(output.isSuccessful()); assertTrue(output.isSuccessful());
} }
/**
* A reference with only an identifier should be valid
*/
@Test
public void testValidateReferenceWithIdentifierValid() throws Exception {
Patient p = new Patient();
p.getManagingOrganization().getIdentifier().setSystem("http://acme.org");
p.getManagingOrganization().getIdentifier().setValue("foo");
ValidationResult output = myVal.validateWithResult(p);
List<SingleValidationMessage> nonInfo = logResultsAndReturnNonInformationalOnes(output);
assertThat(nonInfo, empty());
}
/**
* A reference with only an identifier should be valid
*/
@Test
public void testValidateReferenceWithDisplayValid() throws Exception {
Patient p = new Patient();
p.getManagingOrganization().setDisplay("HELLO");
ValidationResult output = myVal.validateWithResult(p);
List<SingleValidationMessage> nonInfo = logResultsAndReturnNonInformationalOnes(output);
assertThat(nonInfo, empty());
}
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
@Before @Before
public void before() { public void before() {

3
src/changes/changes.xml
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@ -146,6 +146,9 @@
JPA server failed to index search parameters on paths containing a decimal JPA server failed to index search parameters on paths containing a decimal
data type data type
</action> </action>
<action type="fix">
Validator incorrectly rejected references where only an identifier was populated
</action>
</release> </release>
<release version="2.4" date="2017-04-19"> <release version="2.4" date="2017-04-19">
<action type="add"> <action type="add">