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org.hl7.fhir.core
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update for changes to representation of special elements

This commit is contained in:
Grahame Grieve 2019-08-23 14:57:05 +10:00
parent b80c6e6af6
commit 3d7f701b00
24 changed files with 236 additions and 166 deletions
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30
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/SpecDifferenceEvaluator.java
View File

@ -847,7 +847,7 @@ public class SpecDifferenceEvaluator {
removed.append(describeType(tr));
}
for (TypeRefComponent tr : rev.getType()) {
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getCode()))
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getWorkingCode()))
added.append(describeType(tr));
}
for (TypeRefComponent tr : rev.getType()) {
@ -882,9 +882,9 @@ public class SpecDifferenceEvaluator {
}
if (!added.isEmpty())
bp.append("Type " +tr.getCode()+": Added Target "+Utilities.pluralize("Type", added.size())+" "+csv(added));
bp.append("Type " +tr.getWorkingCode()+": Added Target "+Utilities.pluralize("Type", added.size())+" "+csv(added));
if (!removed.isEmpty())
bp.append("Type " +tr.getCode()+": Removed Target "+Utilities.pluralize("Type", removed.size())+" "+csv(removed));
bp.append("Type " +tr.getWorkingCode()+": Removed Target "+Utilities.pluralize("Type", removed.size())+" "+csv(removed));
}
private String trimNS(String v) {
@ -913,7 +913,7 @@ public class SpecDifferenceEvaluator {
private boolean hasType(List<TypeRefComponent> types, TypeRefComponent tr) {
for (TypeRefComponent t : types) {
if (t.getCode().equals(tr.getCode())) {
if (t.getWorkingCode().equals(tr.getWorkingCode())) {
if (((!t.hasProfile() && !tr.hasProfile()) || (t.getProfile().equals(tr.getProfile()))))
return true;
}
@ -923,7 +923,7 @@ public class SpecDifferenceEvaluator {
private TypeRefComponent getType(List<TypeRefComponent> types, TypeRefComponent tr) {
for (TypeRefComponent t : types) {
if (t.getCode().equals(tr.getCode())) {
if (t.getWorkingCode().equals(tr.getWorkingCode())) {
return t;
}
}
@ -932,9 +932,9 @@ public class SpecDifferenceEvaluator {
private String describeType(TypeRefComponent tr) {
if (!tr.hasProfile() && !tr.hasTargetProfile())
return tr.getCode();
else if (Utilities.existsInList(tr.getCode(), "Reference", "canonical")) {
StringBuilder b = new StringBuilder(tr.getCode());
return tr.getWorkingCode();
else if (Utilities.existsInList(tr.getWorkingCode(), "Reference", "canonical")) {
StringBuilder b = new StringBuilder(tr.getWorkingCode());
b.append("(");
boolean first = true;
for (UriType u : tr.getTargetProfile()) {
@ -950,7 +950,7 @@ public class SpecDifferenceEvaluator {
b.append(")");
return b.toString();
} else {
StringBuilder b = new StringBuilder(tr.getCode());
StringBuilder b = new StringBuilder(tr.getWorkingCode());
if (tr.getProfile().size() > 0) {
b.append("(");
boolean first = true;
@ -1255,7 +1255,7 @@ public class SpecDifferenceEvaluator {
oa.add(new JsonPrimitive(describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getCode()))
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getWorkingCode()))
ra.add(new JsonPrimitive(describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
@ -1289,9 +1289,9 @@ public class SpecDifferenceEvaluator {
}
if (added.size() > 0)
element.add(tr.getCode()+"-target-added", added);
element.add(tr.getWorkingCode()+"-target-added", added);
if (removed.size() > 0)
element.add(tr.getCode()+"-target-removed", removed);
element.add(tr.getWorkingCode()+"-target-removed", removed);
}
private void analyseTypes(Document doc, Element element, ElementDefinition rev, ElementDefinition orig) {
@ -1312,7 +1312,7 @@ public class SpecDifferenceEvaluator {
element.appendChild(makeElementWithAttribute(doc, "removed-type", "name", describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getCode()))
if (!hasType(orig.getType(), tr) && !isAbstractType(tr.getWorkingCode()))
element.appendChild(makeElementWithAttribute(doc, "added-type", "name", describeType(tr)));
}
for (TypeRefComponent tr : rev.getType()) {
@ -1328,13 +1328,13 @@ public class SpecDifferenceEvaluator {
for (CanonicalType p : tr.getTargetProfile()) {
if (!hasParam(tm, p.asStringValue())) {
element.appendChild(makeElementWithAttribute(doc, tr.getCode()+"-target-added", "name", p.asStringValue()));
element.appendChild(makeElementWithAttribute(doc, tr.getWorkingCode()+"-target-added", "name", p.asStringValue()));
}
}
for (CanonicalType p : tm.getTargetProfile()) {
if (!hasParam(tr, p.asStringValue())) {
element.appendChild(makeElementWithAttribute(doc, tr.getCode()+"-target-removed", "name", p.asStringValue()));
element.appendChild(makeElementWithAttribute(doc, tr.getWorkingCode()+"-target-removed", "name", p.asStringValue()));
}
}
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_40_50.java
View File

@ -20,7 +20,12 @@ package org.hl7.fhir.convertors;
* #L%
*/
/*
* public static final String EXT_JSON_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type";
public static final String EXT_RDF_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-rdf-type";
public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type";
*/
import org.hl7.fhir.convertors.conv40_50.*;
import org.hl7.fhir.exceptions.FHIRException;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileComparer.java
View File

@ -891,7 +891,7 @@ public class ProfileComparer {
if (nw.hasAggregation())
throw new DefinitionException("Aggregation not supported: "+path);
for (TypeRefComponent ex : results) {
if (Utilities.equals(ex.getCode(), nw.getCode())) {
if (Utilities.equals(ex.getWorkingCode(), nw.getWorkingCode())) {
if (!ex.hasProfile() && !nw.hasProfile())
pfound = true;
else if (!ex.hasProfile()) {
@ -1070,7 +1070,7 @@ public class ProfileComparer {
private String typeCode(DefinitionNavigator defn) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent t : defn.current().getType())
b.append(t.getCode()+(t.hasProfile() ? "("+t.getProfile()+")" : "")+(t.hasTargetProfile() ? "("+t.getTargetProfile()+")" : "")); // todo: other properties
b.append(t.getWorkingCode()+(t.hasProfile() ? "("+t.getProfile()+")" : "")+(t.hasTargetProfile() ? "("+t.getTargetProfile()+")" : "")); // todo: other properties
return b.toString();
}

28
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ShExGenerator.java
View File

@ -34,6 +34,7 @@ import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.Enumerations;
@ -568,7 +569,7 @@ public class ShExGenerator {
private String genTypeRef(StructureDefinition sd, ElementDefinition ed, String id, ElementDefinition.TypeRefComponent typ) {
if(typ.hasProfile()) {
if(typ.getCode().equals("Reference"))
if(typ.getWorkingCode().equals("Reference"))
return genReference("", typ);
else if(ProfileUtilities.getChildList(sd, ed).size() > 0) {
// inline anonymous type - give it a name and factor it out
@ -581,13 +582,8 @@ public class ShExGenerator {
return simpleElement(sd, ed, ref);
}
} else if (typ.getCodeElement().getExtensionsByUrl(ToolingExtensions.EXT_RDF_TYPE).size() > 0) {
String xt = null;
try {
xt = typ.getCodeElement().getExtensionString(ToolingExtensions.EXT_RDF_TYPE);
} catch (FHIRException e) {
e.printStackTrace();
}
} else if (typ.getWorkingCode().startsWith(Constants.NS_SYSTEM_TYPE)) {
String xt = typ.getWorkingCode();
// TODO: Remove the next line when the type of token gets switched to string
// TODO: Add a rdf-type entry for valueInteger to xsd:integer (instead of int)
ST td_entry = tmplt(PRIMITIVE_ELEMENT_DEFN_TEMPLATE).add("typ",
@ -612,16 +608,16 @@ public class ShExGenerator {
td_entry.add("facets", facets.toString());
return td_entry.render();
} else if (typ.getCode() == null) {
} else if (typ.getWorkingCode() == null) {
ST primitive_entry = tmplt(PRIMITIVE_ELEMENT_DEFN_TEMPLATE);
primitive_entry.add("typ", "xsd:string");
return primitive_entry.render();
} else if(typ.getCode().equals("xhtml")) {
} else if(typ.getWorkingCode().equals("xhtml")) {
return tmplt(XHTML_TYPE_TEMPLATE).render();
} else {
datatypes.add(typ.getCode());
return simpleElement(sd, ed, typ.getCode());
datatypes.add(typ.getWorkingCode());
return simpleElement(sd, ed, typ.getWorkingCode());
}
}
@ -653,8 +649,8 @@ public class ShExGenerator {
* @return ShEx equivalent
*/
private String genAltEntry(String id, ElementDefinition.TypeRefComponent typ) {
if(!typ.getCode().equals("Reference"))
throw new AssertionError("We do not handle " + typ.getCode() + " alternatives");
if(!typ.getWorkingCode().equals("Reference"))
throw new AssertionError("We do not handle " + typ.getWorkingCode() + " alternatives");
return genReference(id, typ);
}
@ -685,7 +681,7 @@ public class ShExGenerator {
private String genChoiceEntry(StructureDefinition sd, ElementDefinition ed, String id, String base, ElementDefinition.TypeRefComponent typ) {
ST shex_choice_entry = tmplt(ELEMENT_TEMPLATE);
String ext = typ.getCode();
String ext = typ.getWorkingCode();
shex_choice_entry.add("id", "fhir:" + base+Character.toUpperCase(ext.charAt(0)) + ext.substring(1) + " ");
shex_choice_entry.add("card", "");
shex_choice_entry.add("defn", genTypeRef(sd, ed, id, typ));
@ -745,7 +741,7 @@ public class ShExGenerator {
String[] els = typ.getProfile().get(0).getValue().split("/");
return els[els.length - 1];
} else {
return typ.getCode();
return typ.getWorkingCode();
}
}

21
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/XmlSchemaGenerator.java
View File

@ -355,7 +355,7 @@ public class XmlSchemaGenerator {
throw new Error("Common ancester not found at "+edc.getPath());
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent t : edc.getType()) {
b.append(getQN(sd, edc, t.getCode(), true).toString());
b.append(getQN(sd, edc, t.getWorkingCode(), true).toString());
}
String name = tailDot(edc.getPath());
@ -376,8 +376,8 @@ public class XmlSchemaGenerator {
} else for (TypeRefComponent t : edc.getType()) {
String name = tailDot(edc.getPath());
if (edc.getType().size() > 1)
name = name + Utilities.capitalize(t.getCode());
QName qn = getQN(sd, edc, t.getCode(), true);
name = name + Utilities.capitalize(t.getWorkingCode());
QName qn = getQN(sd, edc, t.getWorkingCode(), true);
String min = String.valueOf(edc.getMin());
String max = edc.getMax();
if ("*".equals(max))
@ -436,13 +436,13 @@ public class XmlSchemaGenerator {
}
private StructureDefinition getCommonAncestor(List<TypeRefComponent> type) throws FHIRException {
StructureDefinition sd = library.get(type.get(0).getCode());
StructureDefinition sd = library.get(type.get(0).getWorkingCode());
if (sd == null)
throw new FHIRException("Unable to find definition for "+type.get(0).getCode());
throw new FHIRException("Unable to find definition for "+type.get(0).getWorkingCode());
for (int i = 1; i < type.size(); i++) {
StructureDefinition t = library.get(type.get(i).getCode());
StructureDefinition t = library.get(type.get(i).getWorkingCode());
if (t == null)
throw new FHIRException("Unable to find definition for "+type.get(i).getCode());
throw new FHIRException("Unable to find definition for "+type.get(i).getWorkingCode());
sd = getCommonAncestor(sd, t);
}
return sd;
@ -520,10 +520,11 @@ public class XmlSchemaGenerator {
// if (!max.equals("1"))
// throw new FHIRException("Illegal cardinality \""+max+"\" for attribute "+edc.getPath());
if (Utilities.isAbsoluteUrl(t.getCode()))
throw new FHIRException("Only FHIR primitive types are supported for attributes ("+t.getCode()+")");
String tc = t.getWorkingCode();
if (Utilities.isAbsoluteUrl(tc))
throw new FHIRException("Only FHIR primitive types are supported for attributes ("+tc+")");
String typeNs = namespaces.get("http://hl7.org/fhir");
String type = t.getCode();
String type = tc;
w(" <xs:attribute name=\""+name+"\" use=\""+(min.equals("0") || edc.hasFixed() || edc.hasDefaultValue() ? "optional" : "required")+"\" type=\""+typeNs+":"+type+(typeNs.equals("fhir") ? "-primitive" : "")+"\""+
(edc.hasFixed() ? " fixed=\""+edc.getFixed().primitiveValue()+"\"" : "")+(edc.hasDefaultValue() && !edc.hasFixed() ? " default=\""+edc.getDefaultValue().primitiveValue()+"\"" : "")+"");

36
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -159,22 +159,7 @@ public class JsonParser extends ParserBase {
// note that we do not trouble ourselves to maintain the wire format order here - we don't even know what it was anyway
// first pass: process the properties
for (Property property : properties) {
if (property.isChoice()) {
for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getCode());
if (!isPrimitive(type.getCode()) && object.has(eName)) {
parseChildComplex(path, object, context, processed, property, eName);
break;
} else if (isPrimitive(type.getCode()) && (object.has(eName) || object.has("_"+eName))) {
parseChildPrimitive(object, context, processed, property, path, eName);
break;
}
}
} else if (property.isPrimitive(property.getType(null))) {
parseChildPrimitive(object, context, processed, property, path, property.getName());
} else if (object.has(property.getName())) {
parseChildComplex(path, object, context, processed, property, property.getName());
}
parseChildItem(path, object, context, processed, property);
}
// second pass: check for things not processed
@ -187,6 +172,25 @@ public class JsonParser extends ParserBase {
}
}
public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) {
if (property.isChoice()) {
for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {
parseChildComplex(path, object, context, processed, property, eName);
break;
} else if (isPrimitive(type.getWorkingCode()) && (object.has(eName) || object.has("_"+eName))) {
parseChildPrimitive(object, context, processed, property, path, eName);
break;
}
}
} else if (property.isPrimitive(property.getType(null))) {
parseChildPrimitive(object, context, processed, property, path, property.getName());
} else if (object.has(property.getName())) {
parseChildComplex(path, object, context, processed, property, property.getName());
}
}
private void parseChildComplex(String path, JsonObject object, Element context, Set<String> processed, Property property, String name) throws FHIRException {
processed.add(name);
String npath = path+"/"+property.getName();

24
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java
View File

@ -64,14 +64,14 @@ public class Property {
if (definition.getType().size() == 0)
return null;
else if (definition.getType().size() > 1) {
String tn = definition.getType().get(0).getCode();
String tn = definition.getType().get(0).getWorkingCode();
for (int i = 1; i < definition.getType().size(); i++) {
if (!tn.equals(definition.getType().get(i).getCode()))
if (!tn.equals(definition.getType().get(i).getWorkingCode()))
throw new Error("logic error, gettype when types > 1");
}
return tn;
} else
return definition.getType().get(0).getCode();
return definition.getType().get(0).getWorkingCode();
}
public String getType(String elementName) {
@ -114,7 +114,7 @@ public class Property {
else
return structure.getId();
} else
return ed.getType().get(0).getCode();
return ed.getType().get(0).getWorkingCode();
}
public boolean hasType(String elementName) {
@ -251,14 +251,14 @@ public class Property {
// ok, find the right definitions
String t = null;
if (ed.getType().size() == 1)
t = ed.getType().get(0).getCode();
t = ed.getType().get(0).getWorkingCode();
else if (ed.getType().size() == 0)
throw new Error("types == 0, and no children found on "+getDefinition().getPath());
else {
t = ed.getType().get(0).getCode();
t = ed.getType().get(0).getWorkingCode();
boolean all = true;
for (TypeRefComponent tr : ed.getType()) {
if (!tr.getCode().equals(t)) {
if (!tr.getWorkingCode().equals(t)) {
all = false;
break;
}
@ -271,12 +271,12 @@ public class Property {
t = ToolingExtensions.readStringExtension(ed, "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype");
boolean ok = false;
for (TypeRefComponent tr : ed.getType()) {
if (tr.getCode().equals(t))
if (tr.getWorkingCode().equals(t))
ok = true;
if (Utilities.isAbsoluteUrl(tr.getCode())) {
StructureDefinition sdt = context.fetchResource(StructureDefinition.class, tr.getCode());
if (Utilities.isAbsoluteUrl(tr.getWorkingCode())) {
StructureDefinition sdt = context.fetchResource(StructureDefinition.class, tr.getWorkingCode());
if (sdt != null && sdt.getType().equals(t)) {
url = tr.getCode();
url = tr.getWorkingCode();
ok = true;
}
}
@ -295,7 +295,7 @@ public class Property {
}
if (!"xhtml".equals(t)) {
for (TypeRefComponent aType: ed.getType()) {
if (aType.getCode().equals(t)) {
if (aType.getWorkingCode().equals(t)) {
if (aType.hasProfile()) {
assert aType.getProfile().size() == 1;
url = aType.getProfile().get(0).getValue();

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Constants.java
View File

@ -60,4 +60,6 @@ public class Constants {
public final static String DATE = "Thu Dec 13 14:07:26 AEDT 2018";
public final static String URI_REGEX = "((http|https)://([A-Za-z0-9\\\\\\.\\:\\%\\$]*\\/)*)?(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}(\\/_history\\/[A-Za-z0-9\\-\\.]{1,64})?";
public final static String LOCAL_REF_REGEX = "(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)\\/[A-Za-z0-9\\-\\.]{1,64}";
public final static String NS_SYSTEM_TYPE = "http://hl7.org/fhirpath/System.";
}

45
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java
View File

@ -58,6 +58,7 @@ import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
import org.hl7.fhir.instance.model.api.ICompositeType;
import org.hl7.fhir.r5.model.Enumerations.BindingStrength;
import org.hl7.fhir.r5.model.Enumerations.BindingStrengthEnumFactory;
import org.hl7.fhir.r5.utils.ToolingExtensions;
// added from java-adornments.txt:
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
@ -2256,6 +2257,50 @@ public class ElementDefinition extends BackboneType implements ICompositeType {
return Utilities.existsInList(getCode(), "Reference", "canonical");
}
/**
* This code checks for the system prefix and returns the FHIR type
*
* @return
*/
public String getWorkingCode() {
if (hasExtension(ToolingExtensions.EXT_FHIR_TYPE))
return getExtensionString(ToolingExtensions.EXT_FHIR_TYPE);
if (!hasCodeElement())
return null;
if (getCodeElement().hasExtension(ToolingExtensions.EXT_XML_TYPE)) {
String s = getCodeElement().getExtensionString(ToolingExtensions.EXT_XML_TYPE);
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date OR xsd:dateTime".equals(s))
return "dateTime";
if ("xsd:gYear OR xsd:gYearMonth OR xsd:date".equals(s))
return "date";
if ("xsd:dateTime".equals(s))
return "instant";
if ("xsd:token".equals(s))
return "code";
if ("xsd:boolean".equals(s))
return "boolean";
if ("xsd:string".equals(s))
return "string";
if ("xsd:time".equals(s))
return "time";
if ("xsd:int".equals(s))
return "integer";
if ("xsd:decimal OR xsd:double".equals(s))
return "decimal";
if ("xsd:base64Binary".equals(s))
return "base64Binary";
if ("xsd:positiveInteger".equals(s))
return "positiveInt";
if ("xsd:nonNegativeInteger".equals(s))
return "unsignedInt";
if ("xsd:anyURI".equals(s))
return "uri";
throw new Error("Unknown xml type '"+s+"'");
}
return getCode();
}
// end addition
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/DefinitionNavigator.java
View File

@ -166,12 +166,12 @@ public class DefinitionNavigator {
private void loadTypedChildren(TypeRefComponent type) throws DefinitionException {
typeOfChildren = null;
StructureDefinition sd = context.fetchResource(StructureDefinition.class, /* GF#13465 : this somehow needs to be revisited type.hasProfile() ? type.getProfile() : */ type.getCode());
StructureDefinition sd = context.fetchResource(StructureDefinition.class, /* GF#13465 : this somehow needs to be revisited type.hasProfile() ? type.getProfile() : */ type.getWorkingCode());
if (sd != null) {
DefinitionNavigator dn = new DefinitionNavigator(context, sd, 0, path, names, sd.getType());
typeChildren = dn.children();
} else
throw new DefinitionException("Unable to find definition for "+type.getCode()+(type.hasProfile() ? "("+type.getProfile()+")" : ""));
throw new DefinitionException("Unable to find definition for "+type.getWorkingCode()+(type.hasProfile() ? "("+type.getProfile()+")" : ""));
typeOfChildren = type;
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ElementDefinitionUtilities.java
View File

@ -31,7 +31,7 @@ public class ElementDefinitionUtilities {
return false;
for (TypeRefComponent tr : ed.getType()) {
if (name.equals(tr.getCode()))
if (name.equals(tr.getWorkingCode()))
return true;
}
return false;

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -3518,8 +3518,10 @@ public class FHIRPathEngine {
String st = convertToString(focus.get(0));
if (Utilities.noString(st))
result.add(new BooleanType(false).noExtensions());
else
result.add(new BooleanType(st.matches(sw)).noExtensions());
else {
boolean ok = st.matches(sw);
result.add(new BooleanType(ok).noExtensions());
}
} else
result.add(new BooleanType(false).noExtensions());
return result;
@ -3913,7 +3915,7 @@ public class FHIRPathEngine {
throw new PathEngineException("No type provided in BuildToolPathEvaluator.getChildTypesByName");
if (type.equals("http://hl7.org/fhir/StructureDefinition/xhtml"))
return;
if (type.startsWith("http://hl7.org/fhir/StructureDefinition/System."))
if (type.startsWith(Constants.NS_SYSTEM_TYPE))
return;
if (type.equals(TypeDetails.FP_SimpleTypeInfo)) {

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLSchemaGenerator.java
View File

@ -297,18 +297,18 @@ public class GraphQLSchemaGenerator {
private void generateProperty(List<StringBuilder> list, StringBuilder b, String typeName, StructureDefinition sd, ElementDefinition child, TypeRefComponent typeDetails, boolean suffix, ElementDefinition cr, String mode, String suffixS) throws IOException {
if (isPrimitive(typeDetails)) {
String n = getGqlname(typeDetails.getCode());
String n = getGqlname(typeDetails.getWorkingCode());
b.append(" ");
b.append(tail(child.getPath(), suffix));
if (suffix)
b.append(Utilities.capitalize(typeDetails.getCode()));
b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
b.append(": ");
b.append(n);
if (!child.getPath().endsWith(".id")) {
b.append(" _");
b.append(tail(child.getPath(), suffix));
if (suffix)
b.append(Utilities.capitalize(typeDetails.getCode()));
b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
if (!child.getMax().equals("1"))
b.append(": [ElementBase]\r\n");
else
@ -319,11 +319,11 @@ public class GraphQLSchemaGenerator {
b.append(" ");
b.append(tail(child.getPath(), suffix));
if (suffix)
b.append(Utilities.capitalize(typeDetails.getCode()));
b.append(Utilities.capitalize(typeDetails.getWorkingCode()));
b.append(": ");
if (!child.getMax().equals("1"))
b.append("[");
String type = typeDetails.getCode();
String type = typeDetails.getWorkingCode();
if (cr != null)
b.append(generateInnerType(list, sd, typeName, cr, mode, suffixS));
else if (Utilities.existsInList(type, "Element", "BackboneElement"))
@ -366,7 +366,7 @@ public class GraphQLSchemaGenerator {
}
private boolean isPrimitive(TypeRefComponent type) {
String typeName = type.getCode();
String typeName = type.getWorkingCode();
StructureDefinition sd = context.fetchTypeDefinition(typeName);
if (sd == null)
return false;

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/NarrativeGenerator.java
View File

@ -500,9 +500,9 @@ public class NarrativeGenerator implements INarrativeGenerator {
if (definition.getType().isEmpty())
return null;
if (definition.getType().size() == 1) {
if (definition.getType().get(0).getCode().equals("Element") || definition.getType().get(0).getCode().equals("BackboneElement"))
if (definition.getType().get(0).getWorkingCode().equals("Element") || definition.getType().get(0).getWorkingCode().equals("BackboneElement"))
return null;
return definition.getType().get(0).getCode();
return definition.getType().get(0).getWorkingCode();
}
String t = e.getNodeName().substring(tail(definition.getPath()).length()-3);
@ -521,7 +521,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
public String getTypeCode() {
if (definition == null || definition.getType().size() != 1)
throw new Error("not handled");
return definition.getType().get(0).getCode();
return definition.getType().get(0).getWorkingCode();
}
@Override
@ -1303,7 +1303,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
private boolean renderAsList(ElementDefinition child) {
if (child.getType().size() == 1) {
String t = child.getType().get(0).getCode();
String t = child.getType().get(0).getWorkingCode();
if (t.equals("Address") || t.equals("Reference"))
return true;
}
@ -1358,7 +1358,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
//we can tell if e is a primitive because it has types
if (e.getType().isEmpty())
return false;
if (e.getType().size() == 1 && isBase(e.getType().get(0).getCode()))
if (e.getType().size() == 1 && isBase(e.getType().get(0).getWorkingCode()))
return false;
return true;
// return !e.getType().isEmpty()
@ -1683,7 +1683,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
if (child.getMustSupport())
return true;
if (child.getType().size() == 1) {
String t = child.getType().get(0).getCode();
String t = child.getType().get(0).getWorkingCode();
if (t.equals("Address") || t.equals("Contact") || t.equals("Reference") || t.equals("Uri") || t.equals("Url") || t.equals("Canonical"))
return false;
}
@ -3043,7 +3043,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
String l = ToolingExtensions.readStringExtension(ext, "lang");
if (lang.equals(l))
d = ToolingExtensions.readStringExtension(ext, "content");;
d = ToolingExtensions.readStringExtension(ext, "content");
}
}
tr.td().addText(d == null ? "" : d);
@ -3127,9 +3127,7 @@ public class NarrativeGenerator implements INarrativeGenerator {
private boolean checkDoSystem(ValueSet vs, ValueSet src) {
if (src != null)
vs = src;
if (vs.hasCompose())
return true;
return false;
return vs.hasCompose();
}
private boolean IsNotFixedExpansion(ValueSet vs) {

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ProtoBufGenerator.java
View File

@ -114,18 +114,18 @@ public class ProtoBufGenerator {
if (ed.getType().size() != 1)
fld.type = "Unknown";
else {
StructureDefinition td = context.fetchTypeDefinition(ed.getTypeFirstRep().getCode());
StructureDefinition td = context.fetchTypeDefinition(ed.getTypeFirstRep().getWorkingCode());
if (td == null)
fld.type = "Unresolved";
else if (td.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
fld.type = protoTypeForFhirType(ed.getTypeFirstRep().getCode());
fld.type = protoTypeForFhirType(ed.getTypeFirstRep().getWorkingCode());
fld = new Field();
fld.name = tail(ed.getPath())+"Extra";
fld.repeating = (!ed.getMax().equals("1"));
fld.type = "Primitive";
message.fields.add(fld);
} else
fld.type = ed.getTypeFirstRep().getCode();
fld.type = ed.getTypeFirstRep().getWorkingCode();
}
}
}

89
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/QuestionnaireBuilder.java
View File

@ -316,11 +316,11 @@ public class QuestionnaireBuilder {
}
private boolean isAbstractType(List<TypeRefComponent> type) {
return type.size() == 1 && (type.get(0).getCode().equals("Element") || type.get(0).getCode().equals("BackboneElement"));
return type.size() == 1 && (type.get(0).getWorkingCode().equals("Element") || type.get(0).getWorkingCode().equals("BackboneElement"));
}
private boolean isInlineDataType(List<TypeRefComponent> type) {
return type.size() == 1 && !Utilities.existsInList(type.get(0).getCode(), "code", "string", "id", "oid", "markdown", "uri", "boolean", "decimal", "dateTime", "date", "instant", "time", "CodeableConcept", "Period", "Ratio",
return type.size() == 1 && !Utilities.existsInList(type.get(0).getWorkingCode(), "code", "string", "id", "oid", "markdown", "uri", "boolean", "decimal", "dateTime", "date", "instant", "time", "CodeableConcept", "Period", "Ratio",
"HumanName", "Address", "ContactPoint", "Identifier", "integer", "positiveInt", "unsignedInt", "Coding", "Quantity", "Count", "Age", "Duration",
"Distance", "Money", "Money", "Reference", "Duration", "base64Binary", "Attachment", "Age", "Range", "Timing", "Annotation", "SampledData", "Extension",
"SampledData", "Narrative", "Resource", "Meta", "url", "canonical");
@ -330,7 +330,7 @@ public class QuestionnaireBuilder {
String n = tail(child.getPath());
String t = "";
if (!element.getType().isEmpty())
t = element.getType().get(0).getCode();
t = element.getType().get(0).getWorkingCode();
// we don't generate questions for the base stuff in every element
if (t.equals("Resource") && (n.equals("text") || n.equals("language") || n.equals("contained")))
@ -385,7 +385,7 @@ public class QuestionnaireBuilder {
else
ToolingExtensions.addFlyOver(group, element.getDefinition());
if (element.getType().size() > 1 || element.getType().get(0).getCode().equals("*")) {
if (element.getType().size() > 1 || element.getType().get(0).getWorkingCode().equals("*")) {
List<TypeRefComponent> types = expandTypeList(element.getType());
Questionnaire.QuestionnaireItemComponent q = addQuestion(group, QuestionnaireItemType.CHOICE, element.getPath(), "_type", "type", null, makeTypeList(profile, types, element.getPath()));
for (TypeRefComponent t : types) {
@ -410,7 +410,7 @@ public class QuestionnaireBuilder {
for (TypeRefComponent t : types) {
if (t.hasProfile())
result.add(t);
else if (t.getCode().equals("*")) {
else if (t.getWorkingCode().equals("*")) {
result.add(new TypeRefComponent().setCode("integer"));
result.add(new TypeRefComponent().setCode("decimal"));
result.add(new TypeRefComponent().setCode("dateTime"));
@ -459,8 +459,8 @@ public class QuestionnaireBuilder {
}
} else if (!t.hasProfile()) {
ValueSetExpansionContainsComponent cc = vs.getExpansion().addContains();
cc.setCode(t.getCode());
cc.setDisplay(t.getCode());
cc.setCode(t.getWorkingCode());
cc.setDisplay(t.getWorkingCode());
cc.setSystem("http://hl7.org/fhir/data-types");
} else for (UriType u : t.getProfile()) {
ProfileUtilities pu = new ProfileUtilities(context, null, null);
@ -514,7 +514,7 @@ public class QuestionnaireBuilder {
cc.setCode(t.getProfile().get(0).getValue());
cc.setSystem("http://hl7.org/fhir/resource-types");
} else {
cc.setCode(t.getCode());
cc.setCode(t.getWorkingCode());
cc.setSystem("http://hl7.org/fhir/data-types");
}
}
@ -529,7 +529,7 @@ public class QuestionnaireBuilder {
}
private boolean instanceOf(TypeRefComponent t, Element obj) {
if (t.getCode().equals("Reference")) {
if (t.getWorkingCode().equals("Reference")) {
if (!(obj instanceof Reference)) {
return false;
} else {
@ -542,7 +542,7 @@ public class QuestionnaireBuilder {
else
return true;
}
} else if (t.getCode().equals("Quantity")) {
} else if (t.getWorkingCode().equals("Quantity")) {
return obj instanceof Quantity;
} else
throw new NotImplementedException("Not Done Yet");
@ -703,77 +703,78 @@ public class QuestionnaireBuilder {
}
private boolean isPrimitive(TypeRefComponent t) {
String code = t.getCode();
String code = t.getWorkingCode();
StructureDefinition sd = context.fetchTypeDefinition(code);
return sd != null && sd.getKind() == StructureDefinitionKind.PRIMITIVETYPE;
}
private void processDataType(StructureDefinition profile, QuestionnaireItemComponent group, ElementDefinition element, String path, TypeRefComponent t, List<QuestionnaireResponse.QuestionnaireResponseItemComponent> answerGroups, List<ElementDefinition> parents) throws FHIRException {
if (t.getCode().equals("code"))
String tc = t.getWorkingCode();
if (tc.equals("code"))
addCodeQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(t.getCode(), "string", "id", "oid", "uuid", "markdown"))
else if (Utilities.existsInList(tc, "string", "id", "oid", "uuid", "markdown"))
addStringQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(t.getCode(), "uri", "url", "canonical"))
else if (Utilities.existsInList(tc, "uri", "url", "canonical"))
addUriQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("boolean"))
else if (tc.equals("boolean"))
addBooleanQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("decimal"))
else if (tc.equals("decimal"))
addDecimalQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("dateTime") || t.getCode().equals("date"))
else if (tc.equals("dateTime") || tc.equals("date"))
addDateTimeQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("instant"))
else if (tc.equals("instant"))
addInstantQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("time"))
else if (tc.equals("time"))
addTimeQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("CodeableConcept"))
else if (tc.equals("CodeableConcept"))
addCodeableConceptQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Period"))
else if (tc.equals("Period"))
addPeriodQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Ratio"))
else if (tc.equals("Ratio"))
addRatioQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("HumanName"))
else if (tc.equals("HumanName"))
addHumanNameQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Address"))
else if (tc.equals("Address"))
addAddressQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("ContactPoint"))
else if (tc.equals("ContactPoint"))
addContactPointQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Identifier"))
else if (tc.equals("Identifier"))
addIdentifierQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("integer") || t.getCode().equals("positiveInt") || t.getCode().equals("unsignedInt") )
else if (tc.equals("integer") || tc.equals("positiveInt") || tc.equals("unsignedInt") )
addIntegerQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Coding"))
else if (tc.equals("Coding"))
addCodingQuestions(group, element, path, answerGroups);
else if (Utilities.existsInList(t.getCode(), "Quantity", "Count", "Age", "Duration", "Distance", "Money"))
else if (Utilities.existsInList(tc, "Quantity", "Count", "Age", "Duration", "Distance", "Money"))
addQuantityQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Money"))
else if (tc.equals("Money"))
addMoneyQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Reference"))
else if (tc.equals("Reference"))
addReferenceQuestions(group, element, path, t.getTargetProfile(), answerGroups);
else if (t.getCode().equals("Duration"))
else if (tc.equals("Duration"))
addDurationQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("base64Binary"))
else if (tc.equals("base64Binary"))
addBinaryQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Attachment"))
else if (tc.equals("Attachment"))
addAttachmentQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Age"))
else if (tc.equals("Age"))
addAgeQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Range"))
else if (tc.equals("Range"))
addRangeQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Timing"))
else if (tc.equals("Timing"))
addTimingQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Annotation"))
else if (tc.equals("Annotation"))
addAnnotationQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("SampledData"))
else if (tc.equals("SampledData"))
addSampledDataQuestions(group, element, path, answerGroups);
else if (t.getCode().equals("Extension")) {
else if (tc.equals("Extension")) {
if (t.hasProfile())
addExtensionQuestions(profile, group, element, path, t.getProfile().get(0).getValue(), answerGroups, parents);
} else if (t.getCode().equals("SampledData"))
} else if (tc.equals("SampledData"))
addSampledDataQuestions(group, element, path, answerGroups);
else if (!t.getCode().equals("Narrative") && !t.getCode().equals("Resource") && !t.getCode().equals("Meta") && !t.getCode().equals("Signature")) {
StructureDefinition sd = context.fetchTypeDefinition(t.getCode());
else if (!tc.equals("Narrative") && !tc.equals("Resource") && !tc.equals("Meta") && !tc.equals("Signature")) {
StructureDefinition sd = context.fetchTypeDefinition(tc);
if (sd == null)
throw new NotImplementedException("Unhandled Data Type: "+t.getCode()+" on element "+element.getPath());
throw new NotImplementedException("Unhandled Data Type: "+tc+" on element "+element.getPath());
buildGroup(group, sd, sd.getSnapshot().getElementFirstRep(), parents, answerGroups);
}
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ResourceUtilities.java
View File

@ -363,7 +363,7 @@ public class ResourceUtilities {
private static String renderType(TypeRefComponent type) {
if (type == null || type.isEmpty())
return "";
return type.getCode();
return type.getWorkingCode();
}
public static void renderContactPoint(StringBuilder b, ContactPoint cp) {

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/StructureMapUtilities.java
View File

@ -2452,7 +2452,7 @@ public class StructureMapUtilities {
for (TypeRefComponent tr : element.getDefinition().getType()) {
if (!tr.hasCode())
throw new Error("Rule \""+ruleId+"\": Element has no type");
ProfiledType pt = new ProfiledType(tr.getCode());
ProfiledType pt = new ProfiledType(tr.getWorkingCode());
if (tr.hasProfile())
pt.addProfiles(tr.getProfile());
if (element.getDefinition().hasBinding())
@ -2710,11 +2710,11 @@ public class StructureMapUtilities {
private String checkType(String t, Property pvb, List<String> profiles) throws FHIRException {
if (pvb.getDefinition().getType().size() == 1 && isCompatibleType(t, pvb.getDefinition().getType().get(0).getCode()) && profilesMatch(profiles, pvb.getDefinition().getType().get(0).getProfile()))
if (pvb.getDefinition().getType().size() == 1 && isCompatibleType(t, pvb.getDefinition().getType().get(0).getWorkingCode()) && profilesMatch(profiles, pvb.getDefinition().getType().get(0).getProfile()))
return null;
for (TypeRefComponent tr : pvb.getDefinition().getType()) {
if (isCompatibleType(t, tr.getCode()))
return tr.getCode(); // note what is returned - the base type, not the inferred mapping type
if (isCompatibleType(t, tr.getWorkingCode()))
return tr.getWorkingCode(); // note what is returned - the base type, not the inferred mapping type
}
throw new FHIRException("The type "+t+" is not compatible with the allowed types for "+pvb.getDefinition().getPath());
}

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -105,9 +105,6 @@ public class ToolingExtensions {
public static final String EXT_ISSUE_COL = "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col";
public static final String EXT_DISPLAY_HINT = "http://hl7.org/fhir/StructureDefinition/structuredefinition-display-hint";
public static final String EXT_REPLACED_BY = "http://hl7.org/fhir/StructureDefinition/valueset-replacedby";
public static final String EXT_JSON_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type";
public static final String EXT_RDF_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-rdf-type";
public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type";
public static final String EXT_REGEX = "http://hl7.org/fhir/StructureDefinition/regex";
public static final String EXT_CONTROL = "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl";
public static final String EXT_MINOCCURS = "http://hl7.org/fhir/StructureDefinition/questionnaire-minOccurs";
@ -163,6 +160,8 @@ public class ToolingExtensions {
public static final String EXT_MAPPING_TGTCARD = "http://hl7.org/fhir/tools/StructureDefinition/conceptmap-target-cardinality";
public static final String EXT_PRIVATE_BASE = "http://hl7.org/fhir/tools/";
public static final String EXT_ALLOWED_TYPE = "http://hl7.org/fhir/StructureDefinition/operationdefinition-allowed-type";
public static final String EXT_FHIR_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type";
public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type";
// specific extension helpers
@ -214,6 +213,16 @@ public class ToolingExtensions {
}
}
public static void addCodeExtension(Element e, String url, String content) {
if (!StringUtils.isBlank(content)) {
Extension ex = getExtension(e, url);
if (ex != null)
ex.setValue(new CodeType(content));
else
e.getExtension().add(Factory.newExtension(url, new CodeType(content), true));
}
}
public static void addStringExtension(DomainResource e, String url, String content) {
if (!StringUtils.isBlank(content)) {
Extension ex = getExtension(e, url);
@ -224,6 +233,7 @@ public class ToolingExtensions {
}
}
public static void addBooleanExtension(Element e, String url, boolean content) {
Extension ex = getExtension(e, url);
if (ex != null)

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/formats/CSVWriter.java
View File

@ -230,7 +230,7 @@ public class CSVWriter extends TextStreamWriter {
val = o.toString();
} else if (o instanceof TypeRefComponent) {
TypeRefComponent t = (TypeRefComponent)o;
val = t.getCode() + (t.getProfile() == null ? "" : " {" + t.getProfile() + "}") +(t.getTargetProfile() == null ? "" : " {" + t.getTargetProfile() + "}") + (t.getAggregation() == null || t.getAggregation().isEmpty() ? "" : " (" + itemList(t.getAggregation()) + ")");
val = t.getWorkingCode() + (t.getProfile() == null ? "" : " {" + t.getProfile() + "}") +(t.getTargetProfile() == null ? "" : " {" + t.getTargetProfile() + "}") + (t.getAggregation() == null || t.getAggregation().isEmpty() ? "" : " (" + itemList(t.getAggregation()) + ")");
} else if (o instanceof Coding) {
Coding t = (Coding)o;
val = (t.getSystem()==null ? "" : t.getSystem()) + (t.getCode()==null ? "" : "#" + t.getCode()) + (t.getDisplay()==null ? "" : " (" + t.getDisplay() + ")");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/formats/XLSXWriter.java
View File

@ -267,7 +267,7 @@ public class XLSXWriter extends TextStreamWriter {
val = o.toString();
} else if (o instanceof TypeRefComponent) {
TypeRefComponent t = (TypeRefComponent)o;
val = t.getCode();
val = t.getWorkingCode();
if (val == null)
val = "";
if (val.startsWith("http://hl7.org/fhir/StructureDefinition/"))

6
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -231,6 +231,12 @@ public class SnapShotGenerationTests {
return false;
}
@Override
public String getLinkForUrl(String corePath, String s) {
// TODO Auto-generated method stub
return null;
}
}
private static class SnapShotGenerationTestsContext implements IEvaluationContext {

28
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java
View File

@ -1348,7 +1348,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
Set<String> res = new HashSet<String>();
if (vd != null && !"0".equals(vd.getMax())) {
for (TypeRefComponent tr : vd.getType()) {
res.add(tr.getCode());
res.add(tr.getWorkingCode());
}
}
return res;
@ -1928,7 +1928,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent type : container.getType()) {
if (!ok && type.getCode().equals("Reference")) {
if (!ok && type.getWorkingCode().equals("Reference")) {
// we validate as much as we can. First, can we infer a type from the profile?
if (!type.hasTargetProfile() || type.hasTargetProfile("http://hl7.org/fhir/StructureDefinition/Resource"))
ok = true;
@ -2105,7 +2105,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private String describeTypes(List<TypeRefComponent> types) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent t : types) {
b.append(t.getCode());
b.append(t.getWorkingCode());
}
return b.toString();
}
@ -2332,7 +2332,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private StructureDefinition getProfileForType(String type, List<TypeRefComponent> list) {
for (TypeRefComponent tr : list) {
String url = tr.getCode();
String url = tr.getWorkingCode();
if (!Utilities.isAbsoluteUrl(url))
url = "http://hl7.org/fhir/StructureDefinition/" + url;
long t = System.nanoTime();
@ -2640,7 +2640,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private ElementDefinition resolveType(String type, List<TypeRefComponent> list) {
for (TypeRefComponent tr : list) {
String url = tr.getCode();
String url = tr.getWorkingCode();
if (!Utilities.isAbsoluteUrl(url))
url = "http://hl7.org/fhir/StructureDefinition/" + url;
long t = System.nanoTime();
@ -2734,7 +2734,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (!criteriaElement.hasType() || criteriaElement.getType().size()==1) {
if (discriminator.contains("["))
discriminator = discriminator.substring(0, discriminator.indexOf('['));
type = criteriaElement.getType().get(0).getCode();
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
@ -3978,14 +3978,14 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
ei.element.setUserData("elementSupported", "N");
}
if (ei.definition.getType().size() == 1 && !"*".equals(ei.definition.getType().get(0).getCode()) && !"Element".equals(ei.definition.getType().get(0).getCode())
&& !"BackboneElement".equals(ei.definition.getType().get(0).getCode())) {
type = ei.definition.getType().get(0).getCode();
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())
profiles.add(ei.definition.getType().get(0).getProfile().get(0).getValue());
} else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getCode())) {
} 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);
@ -4004,8 +4004,8 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
else {
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : ei.definition.getType())
if ((prefix + Utilities.capitalize(t.getCode())).equals(ei.name)) {
type = t.getCode();
if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.name)) {
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());
@ -4013,7 +4013,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
}
if (type == null) {
TypeRefComponent trc = ei.definition.getType().get(0);
if (trc.getCode().equals("Reference"))
if (trc.getWorkingCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false,
@ -4021,7 +4021,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
}
} 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).getCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getCode()))) {
} 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))

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ProfileValidator.java
View File

@ -108,7 +108,7 @@ public class ProfileValidator extends BaseValidator {
warning(errors, IssueType.BUSINESSRULE, diffElement.getId(), !checkMustSupport || snapElement.hasMustSupport(), "Elements included in the differential should declare mustSupport");
if (checkAggregation) {
for (TypeRefComponent type : snapElement.getType()) {
if ("http://hl7.org/fhir/Reference".equals(type.getCode()) || "http://hl7.org/fhir/canonical".equals(type.getCode())) {
if ("http://hl7.org/fhir/Reference".equals(type.getWorkingCode()) || "http://hl7.org/fhir/canonical".equals(type.getWorkingCode())) {
warning(errors, IssueType.BUSINESSRULE, diffElement.getId(), type.hasAggregation(), "Elements with type Reference or canonical should declare aggregation");
}
}
@ -126,7 +126,7 @@ public class ProfileValidator extends BaseValidator {
}
private void checkExtensions(StructureDefinition profile, List<ValidationMessage> errors, String kind, ElementDefinition ec) {
if (!ec.getType().isEmpty() && "Extension".equals(ec.getType().get(0).getCode()) && ec.getType().get(0).hasProfile()) {
if (!ec.getType().isEmpty() && "Extension".equals(ec.getType().get(0).getWorkingCode()) && ec.getType().get(0).hasProfile()) {
String url = ec.getType().get(0).getProfile().get(0).getValue();
StructureDefinition defn = context.fetchResource(StructureDefinition.class, url);
rule(errors, IssueType.BUSINESSRULE, profile.getId(), defn != null, "Unable to find Extension '"+url+"' referenced at "+profile.getUrl()+" "+kind+" "+ec.getPath()+" ("+ec.getSliceName()+")");