Validator incorrectly rejected references where only an identifier was
populated
This commit is contained in:
parent
ba40f44d27
commit
7d659c88e5
|
@ -14,7 +14,6 @@ import java.util.Set;
|
|||
import java.util.regex.Matcher;
|
||||
import java.util.regex.Pattern;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.dstu3.conformance.ProfileUtilities;
|
||||
import org.hl7.fhir.dstu3.context.IWorkerContext;
|
||||
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.XmlParser;
|
||||
import org.hl7.fhir.dstu3.formats.FormatUtilities;
|
||||
import org.hl7.fhir.dstu3.model.Address;
|
||||
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.*;
|
||||
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.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.ConstraintSeverity;
|
||||
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.PropertyRepresentation;
|
||||
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.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.QuestionnaireItemOptionComponent;
|
||||
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.StructureDefinitionKind;
|
||||
import org.hl7.fhir.dstu3.model.StructureDefinition.StructureDefinitionSnapshotComponent;
|
||||
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.utils.FHIRLexer.FHIRLexerException;
|
||||
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.JsonObject;
|
||||
import com.google.gson.stream.JsonWriter;
|
||||
|
||||
import ca.uhn.fhir.util.ObjectUtil;
|
||||
|
||||
|
@ -292,13 +260,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
source = Source.InstanceValidator;
|
||||
}
|
||||
|
||||
public InstanceValidator(ValidationEngine engine) {
|
||||
super();
|
||||
this.context = engine.getContext();
|
||||
fpe = engine.getFpe();
|
||||
source = Source.InstanceValidator;
|
||||
}
|
||||
|
||||
public InstanceValidator(ValidationEngine engine) {
|
||||
super();
|
||||
this.context = engine.getContext();
|
||||
fpe = engine.getFpe();
|
||||
source = Source.InstanceValidator;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean isNoInvariantChecks() {
|
||||
|
@ -788,6 +755,24 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
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) {
|
||||
checkFixedValue(errors, path + ".system", focus.getNamedChild("system"), fixed.getSystemElement(), "system", 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 {
|
||||
String ref = null;
|
||||
try {
|
||||
// Do this inside a try because invalid instances might provide more than one reference.
|
||||
ref = element.getNamedChildValue("reference");
|
||||
} catch (Error e) {
|
||||
|
||||
}
|
||||
Reference reference = readAsReference(element);
|
||||
|
||||
String ref = reference.getReference();
|
||||
if (Utilities.noString(ref)) {
|
||||
// todo - what should we do in this case?
|
||||
warning(errors, IssueType.STRUCTURE, element.line(), element.col(), path, !Utilities.noString(element.getNamedChildValue("display")), "A Reference without an actual reference should have a display");
|
||||
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;
|
||||
}
|
||||
|
||||
|
@ -1627,12 +1609,10 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
return element;
|
||||
|
||||
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()) {
|
||||
if (!matcher.group(1).startsWith("@"))
|
||||
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) {
|
||||
|
@ -2269,8 +2249,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
type = criteriaElement.getType().get(0).getCode();
|
||||
}
|
||||
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 " + slicer.getSliceName() + " does not declare a type");
|
||||
throw new DefinitionException("Discriminator (" + discriminator + ") is based on type, but slice " + ed.getId() + " does not declare a type");
|
||||
if (discriminator.isEmpty())
|
||||
expression = expression + " and this is " + type;
|
||||
else
|
||||
|
@ -2293,7 +2272,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
|
|||
} else if (fixed instanceof BooleanType) {
|
||||
expression = expression + ((BooleanType)fixed).asStringValue();
|
||||
} 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) {
|
||||
expression = expression + " and " + discriminator + " in '" + criteriaElement.getBinding().getValueSetReference().getReference() + "'";
|
||||
} 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")) {
|
||||
expression = expression + " and " + discriminator + ".exists().not()";
|
||||
} 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) {
|
||||
errors.addAll(goodProfiles.get(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) {
|
||||
errors.addAll(messages);
|
||||
}
|
||||
} 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()) {
|
||||
errors.addAll(messages);
|
||||
}
|
||||
|
|
|
@ -234,6 +234,33 @@ public class FhirInstanceValidatorDstu3Test {
|
|||
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")
|
||||
@Before
|
||||
public void before() {
|
||||
|
|
|
@ -146,6 +146,9 @@
|
|||
JPA server failed to index search parameters on paths containing a decimal
|
||||
data type
|
||||
</action>
|
||||
<action type="fix">
|
||||
Validator incorrectly rejected references where only an identifier was populated
|
||||
</action>
|
||||
</release>
|
||||
<release version="2.4" date="2017-04-19">
|
||||
<action type="add">
|
||||
|
|
Loading…
Reference in New Issue