Example 11 with TS
use of org.hl7.v3.TS in project integration-adaptor-111 by nhsconnect.
the class ProcedureRequestMapperTest method setUp.
@BeforeEach
public void setUp() {
TS effectiveTime = TS.Factory.newInstance();
effectiveTime.setValue("20220304");
reasonReferenceList.add(reasonReference);
when(clinicalDocument1.isSetComponentOf()).thenReturn(true);
when(clinicalDocument1.getComponentOf()).thenReturn(component1);
when(clinicalDocument1.getEffectiveTime()).thenReturn(effectiveTime);
when(component1.getEncompassingEncounter()).thenReturn(encompassingEncounter);
when(encompassingEncounter.isSetDischargeDispositionCode()).thenReturn(true);
when(encompassingEncounter.getDischargeDispositionCode()).thenReturn(ce);
when(ce.isSetDisplayName()).thenReturn(true);
when(ce.getDisplayName()).thenReturn(DISPLAY_NAME);
when(ce.isSetCode()).thenReturn(true);
when(ce.getCode()).thenReturn(CODE);
when(ce.isSetCodeSystem()).thenReturn(true);
when(ce.getCodeSystem()).thenReturn(CODESYSTEM);
when(referralRequest.getReasonReference()).thenReturn(reasonReferenceList);
when(resourceUtil.newRandomUuid()).thenReturn(new IdType(RANDOM_UUID));
when(periodMapper.mapPeriod(effectiveTime)).thenReturn(occurrence);
}
Also used :
TS(uk.nhs.connect.iucds.cda.ucr.TS)
IdType(org.hl7.fhir.dstu3.model.IdType)
BeforeEach(org.junit.jupiter.api.BeforeEach)
Example 12 with TS
use of org.hl7.v3.TS in project integration-adaptor-111 by nhsconnect.
the class DataEntererMapperTest method shouldMapDataEntererToParticipantComponent.
@Test
public void shouldMapDataEntererToParticipantComponent() {
POCDMT000002UK01DataEnterer dataEnterer = mock(POCDMT000002UK01DataEnterer.class);
POCDMT000002UK01AssignedEntity assignedEntity = mock(POCDMT000002UK01AssignedEntity.class);
TS time = mock(TS.class);
when(dataEnterer.getAssignedEntity()).thenReturn(assignedEntity);
when(dataEnterer.isSetTime()).thenReturn(true);
when(dataEnterer.getTime()).thenReturn(time);
when(dataEnterer.getTypeCode()).thenReturn("CON");
when(practitionerMapper.mapPractitioner(isA(POCDMT000002UK01AssignedEntity.class))).thenReturn(practitioner);
when(periodMapper.mapPeriod(isA(TS.class))).thenReturn(period);
when(resourceUtil.createReference(practitioner)).thenReturn(new Reference(practitioner));
Encounter.EncounterParticipantComponent participantComponent = dataEntererMapper.mapDataEntererIntoParticipantComponent(dataEnterer);
assertThat(participantComponent.getIndividualTarget()).isEqualTo(practitioner);
assertThat(participantComponent.getPeriod()).isEqualTo(period);
assertThat(participantComponent.getType().get(0).getText()).isEqualTo("CON");
}
Also used :
POCDMT000002UK01DataEnterer(uk.nhs.connect.iucds.cda.ucr.POCDMT000002UK01DataEnterer)
Reference(org.hl7.fhir.dstu3.model.Reference)
Encounter(org.hl7.fhir.dstu3.model.Encounter)
POCDMT000002UK01AssignedEntity(uk.nhs.connect.iucds.cda.ucr.POCDMT000002UK01AssignedEntity)
TS(uk.nhs.connect.iucds.cda.ucr.TS)
Test(org.junit.jupiter.api.Test)
Example 13 with TS
use of org.hl7.v3.TS in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method updateFromDefinition.
private void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl) throws DefinitionException, FHIRException {
source.setUserData(GENERATED_IN_SNAPSHOT, true);
// we start with a clone of the base profile ('dest') and we copy from the profile ('source')
// over the top for anything the source has
ElementDefinition base = dest;
ElementDefinition derived = source;
derived.setUserData(DERIVATION_POINTER, base);
// Before applying changes, apply them to what's in the profile
// TODO: follow Chris's rules
StructureDefinition profile = source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, source.getTypeFirstRep().getProfile()) : null;
if (profile != null) {
ElementDefinition e = profile.getSnapshot().getElement().get(0);
base.setDefinition(e.getDefinition());
base.setShort(e.getShort());
if (e.hasCommentElement())
base.setCommentElement(e.getCommentElement());
if (e.hasRequirementsElement())
base.setRequirementsElement(e.getRequirementsElement());
base.getAlias().clear();
base.getAlias().addAll(e.getAlias());
base.getMapping().clear();
base.getMapping().addAll(e.getMapping());
}
if (derived != null) {
boolean isExtension = checkExtensionDoco(base);
if (derived.hasSliceName()) {
base.setSliceName(derived.getSliceName());
}
if (derived.hasShortElement()) {
if (!Base.compareDeep(derived.getShortElement(), base.getShortElement(), false))
base.setShortElement(derived.getShortElement().copy());
else if (trimDifferential)
derived.setShortElement(null);
else if (derived.hasShortElement())
derived.getShortElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasDefinitionElement()) {
if (derived.getDefinition().startsWith("..."))
base.setDefinition(base.getDefinition() + "\r\n" + derived.getDefinition().substring(3));
else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false))
base.setDefinitionElement(derived.getDefinitionElement().copy());
else if (trimDifferential)
derived.setDefinitionElement(null);
else if (derived.hasDefinitionElement())
derived.getDefinitionElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasCommentElement()) {
if (derived.getComment().startsWith("..."))
base.setComment(base.getComment() + "\r\n" + derived.getComment().substring(3));
else if (derived.hasCommentElement() != base.hasCommentElement() || !Base.compareDeep(derived.getCommentElement(), base.getCommentElement(), false))
base.setCommentElement(derived.getCommentElement().copy());
else if (trimDifferential)
base.setCommentElement(derived.getCommentElement().copy());
else if (derived.hasCommentElement())
derived.getCommentElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasLabelElement()) {
if (derived.getLabel().startsWith("..."))
base.setLabel(base.getLabel() + "\r\n" + derived.getLabel().substring(3));
else if (!base.hasLabelElement() || !Base.compareDeep(derived.getLabelElement(), base.getLabelElement(), false))
base.setLabelElement(derived.getLabelElement().copy());
else if (trimDifferential)
base.setLabelElement(derived.getLabelElement().copy());
else if (derived.hasLabelElement())
derived.getLabelElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasRequirementsElement()) {
if (derived.getRequirements().startsWith("..."))
base.setRequirements(base.getRequirements() + "\r\n" + derived.getRequirements().substring(3));
else if (!base.hasRequirementsElement() || !Base.compareDeep(derived.getRequirementsElement(), base.getRequirementsElement(), false))
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (trimDifferential)
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (derived.hasRequirementsElement())
derived.getRequirementsElement().setUserData(DERIVATION_EQUALS, true);
}
// sdf-9
if (derived.hasRequirements() && !base.getPath().contains("."))
derived.setRequirements(null);
if (base.hasRequirements() && !base.getPath().contains("."))
base.setRequirements(null);
if (derived.hasAlias()) {
if (!Base.compareDeep(derived.getAlias(), base.getAlias(), false))
for (StringType s : derived.getAlias()) {
if (!base.hasAlias(s.getValue()))
base.getAlias().add(s.copy());
}
else if (trimDifferential)
derived.getAlias().clear();
else
for (StringType t : derived.getAlias()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinElement()) {
if (!Base.compareDeep(derived.getMinElement(), base.getMinElement(), false)) {
if (derived.getMin() < base.getMin())
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + source.getPath(), "Derived min (" + Integer.toString(derived.getMin()) + ") cannot be less than base min (" + Integer.toString(base.getMin()) + ")", ValidationMessage.IssueSeverity.ERROR));
base.setMinElement(derived.getMinElement().copy());
} else if (trimDifferential)
derived.setMinElement(null);
else
derived.getMinElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxElement()) {
if (!Base.compareDeep(derived.getMaxElement(), base.getMaxElement(), false)) {
if (isLargerMax(derived.getMax(), base.getMax()))
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + source.getPath(), "Derived max (" + derived.getMax() + ") cannot be greater than base max (" + base.getMax() + ")", ValidationMessage.IssueSeverity.ERROR));
base.setMaxElement(derived.getMaxElement().copy());
} else if (trimDifferential)
derived.setMaxElement(null);
else
derived.getMaxElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasFixed()) {
if (!Base.compareDeep(derived.getFixed(), base.getFixed(), true)) {
base.setFixed(derived.getFixed().copy());
} else if (trimDifferential)
derived.setFixed(null);
else
derived.getFixed().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasPattern()) {
if (!Base.compareDeep(derived.getPattern(), base.getPattern(), false)) {
base.setPattern(derived.getPattern().copy());
} else if (trimDifferential)
derived.setPattern(null);
else
derived.getPattern().setUserData(DERIVATION_EQUALS, true);
}
for (ElementDefinitionExampleComponent ex : derived.getExample()) {
boolean found = false;
for (ElementDefinitionExampleComponent exS : base.getExample()) if (Base.compareDeep(ex, exS, false))
found = true;
if (!found)
base.addExample(ex.copy());
else if (trimDifferential)
derived.getExample().remove(ex);
else
ex.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxLengthElement()) {
if (!Base.compareDeep(derived.getMaxLengthElement(), base.getMaxLengthElement(), false))
base.setMaxLengthElement(derived.getMaxLengthElement().copy());
else if (trimDifferential)
derived.setMaxLengthElement(null);
else
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMustSupportElement()) {
if (!(base.hasMustSupportElement() && Base.compareDeep(derived.getMustSupportElement(), base.getMustSupportElement(), false)))
base.setMustSupportElement(derived.getMustSupportElement().copy());
else if (trimDifferential)
derived.setMustSupportElement(null);
else
derived.getMustSupportElement().setUserData(DERIVATION_EQUALS, true);
}
// but extensions can change isModifier
if (isExtension) {
if (derived.hasIsModifierElement() && !(base.hasIsModifierElement() && Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false)))
base.setIsModifierElement(derived.getIsModifierElement().copy());
else if (trimDifferential)
derived.setIsModifierElement(null);
else if (derived.hasIsModifierElement())
derived.getIsModifierElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasBinding()) {
if (!base.hasBinding() || !Base.compareDeep(derived.getBinding(), base.getBinding(), false)) {
if (base.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && derived.getBinding().getStrength() != BindingStrength.REQUIRED)
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "illegal attempt to change the binding on " + derived.getPath() + " from " + base.getBinding().getStrength().toCode() + " to " + derived.getBinding().getStrength().toCode(), ValidationMessage.IssueSeverity.ERROR));
else // throw new DefinitionException("StructureDefinition "+pn+" at "+derived.getPath()+": illegal attempt to change a binding from "+base.getBinding().getStrength().toCode()+" to "+derived.getBinding().getStrength().toCode());
if (base.hasBinding() && derived.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && base.getBinding().hasValueSetReference() && derived.getBinding().hasValueSetReference()) {
ValueSetExpansionOutcome expBase = context.expandVS(context.fetchResource(ValueSet.class, base.getBinding().getValueSetReference().getReference()), true, false);
ValueSetExpansionOutcome expDerived = context.expandVS(context.fetchResource(ValueSet.class, derived.getBinding().getValueSetReference().getReference()), true, false);
if (expBase.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + base.getPath(), "Binding " + base.getBinding().getValueSetReference().getReference() + " could not be expanded", ValidationMessage.IssueSeverity.WARNING));
else if (expDerived.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " could not be expanded", ValidationMessage.IssueSeverity.WARNING));
else if (!isSubset(expBase.getValueset(), expDerived.getValueset()))
messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " is not a subset of binding " + base.getBinding().getValueSetReference().getReference(), ValidationMessage.IssueSeverity.ERROR));
}
base.setBinding(derived.getBinding().copy());
} else if (trimDifferential)
derived.setBinding(null);
else
derived.getBinding().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasIsSummaryElement()) {
if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false)) {
if (base.hasIsSummary())
throw new Error("Error in profile " + pn + " at " + derived.getPath() + ": Base isSummary = " + base.getIsSummaryElement().asStringValue() + ", derived isSummary = " + derived.getIsSummaryElement().asStringValue());
base.setIsSummaryElement(derived.getIsSummaryElement().copy());
} else if (trimDifferential)
derived.setIsSummaryElement(null);
else
derived.getIsSummaryElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasType()) {
if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
if (base.hasType()) {
for (TypeRefComponent ts : derived.getType()) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent td : base.getType()) {
;
b.append(td.getCode());
if (td.hasCode() && (td.getCode().equals(ts.getCode()) || td.getCode().equals("Extension") || td.getCode().equals("Element") || td.getCode().equals("*") || ((td.getCode().equals("Resource") || (td.getCode().equals("DomainResource")) && pkp.isResource(ts.getCode())))))
ok = true;
}
if (!ok)
throw new DefinitionException("StructureDefinition " + pn + " at " + derived.getPath() + ": illegal constrained type " + ts.getCode() + " from " + b.toString());
}
}
base.getType().clear();
for (TypeRefComponent t : derived.getType()) {
TypeRefComponent tt = t.copy();
// tt.setUserData(DERIVATION_EQUALS, true);
base.getType().add(tt);
}
} else if (trimDifferential)
derived.getType().clear();
else
for (TypeRefComponent t : derived.getType()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMapping()) {
// todo: mappings are not cumulative - one replaces another
if (!Base.compareDeep(derived.getMapping(), base.getMapping(), false)) {
for (ElementDefinitionMappingComponent s : derived.getMapping()) {
boolean found = false;
for (ElementDefinitionMappingComponent d : base.getMapping()) {
found = found || (d.getIdentity().equals(s.getIdentity()) && d.getMap().equals(s.getMap()));
}
if (!found)
base.getMapping().add(s);
}
} else if (trimDifferential)
derived.getMapping().clear();
else
for (ElementDefinitionMappingComponent t : derived.getMapping()) t.setUserData(DERIVATION_EQUALS, true);
}
// todo: constraints are cumulative. there is no replacing
for (ElementDefinitionConstraintComponent s : base.getConstraint()) {
s.setUserData(IS_DERIVED, true);
if (!s.hasSource())
s.setSource(base.getId());
}
if (derived.hasConstraint()) {
for (ElementDefinitionConstraintComponent s : derived.getConstraint()) {
ElementDefinitionConstraintComponent inv = s.copy();
base.getConstraint().add(inv);
}
}
// now, check that we still have a bindable type; if not, delete the binding - see task 8477
if (dest.hasBinding() && !hasBindableType(dest))
dest.setBinding(null);
// finally, we copy any extensions from source to dest
for (Extension ex : base.getExtension()) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, ex.getUrl());
if (sd == null || sd.getSnapshot() == null || sd.getSnapshot().getElementFirstRep().getMax().equals("1"))
ToolingExtensions.removeExtension(dest, ex.getUrl());
dest.addExtension(ex);
}
}
}
Also used :
ElementDefinitionExampleComponent(org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionExampleComponent)
ValidationMessage(org.hl7.fhir.utilities.validation.ValidationMessage)
StringType(org.hl7.fhir.dstu3.model.StringType)
FHIRFormatError(org.hl7.fhir.exceptions.FHIRFormatError)
CommaSeparatedStringBuilder(org.hl7.fhir.utilities.CommaSeparatedStringBuilder)
ElementDefinitionConstraintComponent(org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionConstraintComponent)
Extension(org.hl7.fhir.dstu3.model.Extension)
StructureDefinition(org.hl7.fhir.dstu3.model.StructureDefinition)
TypeRefComponent(org.hl7.fhir.dstu3.model.ElementDefinition.TypeRefComponent)
ValueSetExpansionOutcome(org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome)
ElementDefinition(org.hl7.fhir.dstu3.model.ElementDefinition)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
ElementDefinitionMappingComponent(org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionMappingComponent)
Example 14 with TS
use of org.hl7.v3.TS in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method updateFromDefinition.
private void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl) throws DefinitionException, FHIRException {
// we start with a clone of the base profile ('dest') and we copy from the profile ('source')
// over the top for anything the source has
ElementDefinition base = dest;
ElementDefinition derived = source;
derived.setUserData(DERIVATION_POINTER, base);
if (derived != null) {
boolean isExtension = checkExtensionDoco(base);
if (derived.hasShortElement()) {
if (!Base.compareDeep(derived.getShortElement(), base.getShortElement(), false))
base.setShortElement(derived.getShortElement().copy());
else if (trimDifferential)
derived.setShortElement(null);
else if (derived.hasShortElement())
derived.getShortElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasDefinitionElement()) {
if (derived.getDefinition().startsWith("..."))
base.setDefinition(base.getDefinition() + "\r\n" + derived.getDefinition().substring(3));
else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false))
base.setDefinitionElement(derived.getDefinitionElement().copy());
else if (trimDifferential)
derived.setDefinitionElement(null);
else if (derived.hasDefinitionElement())
derived.getDefinitionElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasCommentsElement()) {
if (derived.getComments().startsWith("..."))
base.setComments(base.getComments() + "\r\n" + derived.getComments().substring(3));
else if (!Base.compareDeep(derived.getCommentsElement(), base.getCommentsElement(), false))
base.setCommentsElement(derived.getCommentsElement().copy());
else if (trimDifferential)
base.setCommentsElement(derived.getCommentsElement().copy());
else if (derived.hasCommentsElement())
derived.getCommentsElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasLabelElement()) {
if (derived.getLabel().startsWith("..."))
base.setLabel(base.getLabel() + "\r\n" + derived.getLabel().substring(3));
else if (!Base.compareDeep(derived.getLabelElement(), base.getLabelElement(), false))
base.setLabelElement(derived.getLabelElement().copy());
else if (trimDifferential)
base.setLabelElement(derived.getLabelElement().copy());
else if (derived.hasLabelElement())
derived.getLabelElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasRequirementsElement()) {
if (derived.getRequirements().startsWith("..."))
base.setRequirements(base.getRequirements() + "\r\n" + derived.getRequirements().substring(3));
else if (!Base.compareDeep(derived.getRequirementsElement(), base.getRequirementsElement(), false))
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (trimDifferential)
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (derived.hasRequirementsElement())
derived.getRequirementsElement().setUserData(DERIVATION_EQUALS, true);
}
// sdf-9
if (derived.hasRequirements() && !base.getPath().contains("."))
derived.setRequirements(null);
if (base.hasRequirements() && !base.getPath().contains("."))
base.setRequirements(null);
if (derived.hasAlias()) {
if (!Base.compareDeep(derived.getAlias(), base.getAlias(), false))
for (StringType s : derived.getAlias()) {
if (!base.hasAlias(s.getValue()))
base.getAlias().add(s.copy());
}
else if (trimDifferential)
derived.getAlias().clear();
else
for (StringType t : derived.getAlias()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinElement()) {
if (!Base.compareDeep(derived.getMinElement(), base.getMinElement(), false)) {
if (derived.getMin() < base.getMin())
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived min (" + Integer.toString(derived.getMin()) + ") cannot be less than base min (" + Integer.toString(base.getMin()) + ")", IssueSeverity.ERROR));
base.setMinElement(derived.getMinElement().copy());
} else if (trimDifferential)
derived.setMinElement(null);
else
derived.getMinElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxElement()) {
if (!Base.compareDeep(derived.getMaxElement(), base.getMaxElement(), false)) {
if (isLargerMax(derived.getMax(), base.getMax()))
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived max (" + derived.getMax() + ") cannot be greater than base max (" + base.getMax() + ")", IssueSeverity.ERROR));
base.setMaxElement(derived.getMaxElement().copy());
} else if (trimDifferential)
derived.setMaxElement(null);
else
derived.getMaxElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasFixed()) {
if (!Base.compareDeep(derived.getFixed(), base.getFixed(), true)) {
base.setFixed(derived.getFixed().copy());
} else if (trimDifferential)
derived.setFixed(null);
else
derived.getFixed().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasPattern()) {
if (!Base.compareDeep(derived.getPattern(), base.getPattern(), false)) {
base.setPattern(derived.getPattern().copy());
} else if (trimDifferential)
derived.setPattern(null);
else
derived.getPattern().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasExample()) {
if (!Base.compareDeep(derived.getExample(), base.getExample(), false))
base.setExample(derived.getExample().copy());
else if (trimDifferential)
derived.setExample(null);
else
derived.getExample().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxLengthElement()) {
if (!Base.compareDeep(derived.getMaxLengthElement(), base.getMaxLengthElement(), false))
base.setMaxLengthElement(derived.getMaxLengthElement().copy());
else if (trimDifferential)
derived.setMaxLengthElement(null);
else
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMustSupportElement()) {
if (!Base.compareDeep(derived.getMustSupportElement(), base.getMustSupportElement(), false))
base.setMustSupportElement(derived.getMustSupportElement().copy());
else if (trimDifferential)
derived.setMustSupportElement(null);
else
derived.getMustSupportElement().setUserData(DERIVATION_EQUALS, true);
}
// but extensions can change isModifier
if (isExtension) {
if (!Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false))
base.setIsModifierElement(derived.getIsModifierElement().copy());
else if (trimDifferential)
derived.setIsModifierElement(null);
else
derived.getIsModifierElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasBinding()) {
if (!Base.compareDeep(derived.getBinding(), base.getBinding(), false)) {
if (base.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && derived.getBinding().getStrength() != BindingStrength.REQUIRED)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "illegal attempt to change a binding from " + base.getBinding().getStrength().toCode() + " to " + derived.getBinding().getStrength().toCode(), IssueSeverity.ERROR));
else // throw new DefinitionException("StructureDefinition "+pn+" at "+derived.getPath()+": illegal attempt to change a binding from "+base.getBinding().getStrength().toCode()+" to "+derived.getBinding().getStrength().toCode());
if (base.hasBinding() && derived.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED) {
ValueSetExpansionOutcome expBase = context.expandVS(context.fetchResource(ValueSet.class, base.getBinding().getValueSetReference().getReference()), true);
ValueSetExpansionOutcome expDerived = context.expandVS(context.fetchResource(ValueSet.class, derived.getBinding().getValueSetReference().getReference()), true);
if (expBase.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + base.getPath(), "Binding " + base.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
else if (expDerived.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
else if (!isSubset(expBase.getValueset(), expDerived.getValueset()))
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " is not a subset of binding " + base.getBinding().getValueSetReference().getReference(), IssueSeverity.ERROR));
}
base.setBinding(derived.getBinding().copy());
} else if (trimDifferential)
derived.setBinding(null);
else
derived.getBinding().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasIsSummaryElement()) {
if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false))
base.setIsSummaryElement(derived.getIsSummaryElement().copy());
else if (trimDifferential)
derived.setIsSummaryElement(null);
else
derived.getIsSummaryElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasType()) {
if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
if (base.hasType()) {
for (TypeRefComponent ts : derived.getType()) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent td : base.getType()) {
b.append(td.getCode());
if (td.hasCode() && (td.getCode().equals(ts.getCode()) || td.getCode().equals("Extension") || td.getCode().equals("Element") || td.getCode().equals("*") || ((td.getCode().equals("Resource") || (td.getCode().equals("DomainResource")) && pkp.isResource(ts.getCode())))))
ok = true;
}
if (!ok)
throw new DefinitionException("StructureDefinition " + pn + " at " + derived.getPath() + ": illegal constrained type " + ts.getCode() + " from " + b.toString());
}
}
base.getType().clear();
for (TypeRefComponent t : derived.getType()) {
TypeRefComponent tt = t.copy();
// tt.setUserData(DERIVATION_EQUALS, true);
base.getType().add(tt);
}
} else if (trimDifferential)
derived.getType().clear();
else
for (TypeRefComponent t : derived.getType()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMapping()) {
// todo: mappings are not cumulative - one replaces another
if (!Base.compareDeep(derived.getMapping(), base.getMapping(), false)) {
for (ElementDefinitionMappingComponent s : derived.getMapping()) {
boolean found = false;
for (ElementDefinitionMappingComponent d : base.getMapping()) {
found = found || (d.getIdentity().equals(s.getIdentity()) && d.getMap().equals(s.getMap()));
}
if (!found)
base.getMapping().add(s);
}
} else if (trimDifferential)
derived.getMapping().clear();
else
for (ElementDefinitionMappingComponent t : derived.getMapping()) t.setUserData(DERIVATION_EQUALS, true);
}
// todo: constraints are cumulative. there is no replacing
for (ElementDefinitionConstraintComponent s : base.getConstraint()) s.setUserData(IS_DERIVED, true);
if (derived.hasConstraint()) {
for (ElementDefinitionConstraintComponent s : derived.getConstraint()) {
base.getConstraint().add(s.copy());
}
}
}
}
Also used :
ValidationMessage(org.hl7.fhir.utilities.validation.ValidationMessage)
StringType(org.hl7.fhir.dstu2.model.StringType)
TypeRefComponent(org.hl7.fhir.dstu2.model.ElementDefinition.TypeRefComponent)
ValueSetExpansionOutcome(org.hl7.fhir.dstu2.terminologies.ValueSetExpander.ValueSetExpansionOutcome)
CommaSeparatedStringBuilder(org.hl7.fhir.utilities.CommaSeparatedStringBuilder)
ElementDefinition(org.hl7.fhir.dstu2.model.ElementDefinition)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
ElementDefinitionMappingComponent(org.hl7.fhir.dstu2.model.ElementDefinition.ElementDefinitionMappingComponent)
ElementDefinitionConstraintComponent(org.hl7.fhir.dstu2.model.ElementDefinition.ElementDefinitionConstraintComponent)
Example 15 with TS
use of org.hl7.v3.TS in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilities method updateFromDefinition.
private void updateFromDefinition(ElementDefinition dest, ElementDefinition source, String pn, boolean trimDifferential, String purl) throws DefinitionException, FHIRException {
// we start with a clone of the base profile ('dest') and we copy from the profile ('source')
// over the top for anything the source has
ElementDefinition base = dest;
ElementDefinition derived = source;
derived.setUserData(DERIVATION_POINTER, base);
if (derived != null) {
boolean isExtension = checkExtensionDoco(base);
if (derived.hasShortElement()) {
if (!Base.compareDeep(derived.getShortElement(), base.getShortElement(), false))
base.setShortElement(derived.getShortElement().copy());
else if (trimDifferential)
derived.setShortElement(null);
else if (derived.hasShortElement())
derived.getShortElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasDefinitionElement()) {
if (derived.getDefinition().startsWith("..."))
base.setDefinition(base.getDefinition() + "\r\n" + derived.getDefinition().substring(3));
else if (!Base.compareDeep(derived.getDefinitionElement(), base.getDefinitionElement(), false))
base.setDefinitionElement(derived.getDefinitionElement().copy());
else if (trimDifferential)
derived.setDefinitionElement(null);
else if (derived.hasDefinitionElement())
derived.getDefinitionElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasCommentsElement()) {
if (derived.getComments().startsWith("..."))
base.setComments(base.getComments() + "\r\n" + derived.getComments().substring(3));
else if (!Base.compareDeep(derived.getCommentsElement(), base.getCommentsElement(), false))
base.setCommentsElement(derived.getCommentsElement().copy());
else if (trimDifferential)
base.setCommentsElement(derived.getCommentsElement().copy());
else if (derived.hasCommentsElement())
derived.getCommentsElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasLabelElement()) {
if (derived.getLabel().startsWith("..."))
base.setLabel(base.getLabel() + "\r\n" + derived.getLabel().substring(3));
else if (!Base.compareDeep(derived.getLabelElement(), base.getLabelElement(), false))
base.setLabelElement(derived.getLabelElement().copy());
else if (trimDifferential)
base.setLabelElement(derived.getLabelElement().copy());
else if (derived.hasLabelElement())
derived.getLabelElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasRequirementsElement()) {
if (derived.getRequirements().startsWith("..."))
base.setRequirements(base.getRequirements() + "\r\n" + derived.getRequirements().substring(3));
else if (!Base.compareDeep(derived.getRequirementsElement(), base.getRequirementsElement(), false))
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (trimDifferential)
base.setRequirementsElement(derived.getRequirementsElement().copy());
else if (derived.hasRequirementsElement())
derived.getRequirementsElement().setUserData(DERIVATION_EQUALS, true);
}
// sdf-9
if (derived.hasRequirements() && !base.getPath().contains("."))
derived.setRequirements(null);
if (base.hasRequirements() && !base.getPath().contains("."))
base.setRequirements(null);
if (derived.hasAlias()) {
if (!Base.compareDeep(derived.getAlias(), base.getAlias(), false))
for (StringType s : derived.getAlias()) {
if (!base.hasAlias(s.getValue()))
base.getAlias().add(s.copy());
}
else if (trimDifferential)
derived.getAlias().clear();
else
for (StringType t : derived.getAlias()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinElement()) {
if (!Base.compareDeep(derived.getMinElement(), base.getMinElement(), false)) {
if (derived.getMin() < base.getMin())
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived min (" + Integer.toString(derived.getMin()) + ") cannot be less than base min (" + Integer.toString(base.getMin()) + ")", IssueSeverity.ERROR));
base.setMinElement(derived.getMinElement().copy());
} else if (trimDifferential)
derived.setMinElement(null);
else
derived.getMinElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxElement()) {
if (!Base.compareDeep(derived.getMaxElement(), base.getMaxElement(), false)) {
if (isLargerMax(derived.getMax(), base.getMax()))
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Derived max (" + derived.getMax() + ") cannot be greater than base max (" + base.getMax() + ")", IssueSeverity.ERROR));
base.setMaxElement(derived.getMaxElement().copy());
} else if (trimDifferential)
derived.setMaxElement(null);
else
derived.getMaxElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasFixed()) {
if (!Base.compareDeep(derived.getFixed(), base.getFixed(), true)) {
base.setFixed(derived.getFixed().copy());
} else if (trimDifferential)
derived.setFixed(null);
else
derived.getFixed().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasPattern()) {
if (!Base.compareDeep(derived.getPattern(), base.getPattern(), false)) {
base.setPattern(derived.getPattern().copy());
} else if (trimDifferential)
derived.setPattern(null);
else
derived.getPattern().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasExample()) {
if (!Base.compareDeep(derived.getExample(), base.getExample(), false))
base.setExample(derived.getExample().copy());
else if (trimDifferential)
derived.setExample(null);
else
derived.getExample().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxLengthElement()) {
if (!Base.compareDeep(derived.getMaxLengthElement(), base.getMaxLengthElement(), false))
base.setMaxLengthElement(derived.getMaxLengthElement().copy());
else if (trimDifferential)
derived.setMaxLengthElement(null);
else
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMustSupportElement()) {
if (!Base.compareDeep(derived.getMustSupportElement(), base.getMustSupportElement(), false))
base.setMustSupportElement(derived.getMustSupportElement().copy());
else if (trimDifferential)
derived.setMustSupportElement(null);
else
derived.getMustSupportElement().setUserData(DERIVATION_EQUALS, true);
}
// but extensions can change isModifier
if (isExtension) {
if (!Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false))
base.setIsModifierElement(derived.getIsModifierElement().copy());
else if (trimDifferential)
derived.setIsModifierElement(null);
else
derived.getIsModifierElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasBinding()) {
if (!Base.compareDeep(derived.getBinding(), base.getBinding(), false)) {
if (base.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && derived.getBinding().getStrength() != BindingStrength.REQUIRED)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "illegal attempt to change a binding from " + base.getBinding().getStrength().toCode() + " to " + derived.getBinding().getStrength().toCode(), IssueSeverity.ERROR));
else // throw new DefinitionException("StructureDefinition "+pn+" at "+derived.getPath()+": illegal attempt to change a binding from "+base.getBinding().getStrength().toCode()+" to "+derived.getBinding().getStrength().toCode());
if (base.hasBinding() && derived.hasBinding() && base.getBinding().getStrength() == BindingStrength.REQUIRED && base.getBinding().hasValueSetReference() && derived.getBinding().hasValueSetReference()) {
ValueSetExpansionOutcome expBase = context.expandVS(context.fetchResource(ValueSet.class, base.getBinding().getValueSetReference().getReference()), true);
ValueSetExpansionOutcome expDerived = context.expandVS(context.fetchResource(ValueSet.class, derived.getBinding().getValueSetReference().getReference()), true);
if (expBase.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + base.getPath(), "Binding " + base.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
else if (expDerived.getValueset() == null)
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " could not be expanded", IssueSeverity.WARNING));
else if (!isSubset(expBase.getValueset(), expDerived.getValueset()))
messages.add(new ValidationMessage(Source.ProfileValidator, IssueType.BUSINESSRULE, pn + "." + derived.getPath(), "Binding " + derived.getBinding().getValueSetReference().getReference() + " is not a subset of binding " + base.getBinding().getValueSetReference().getReference(), IssueSeverity.ERROR));
}
base.setBinding(derived.getBinding().copy());
} else if (trimDifferential)
derived.setBinding(null);
else
derived.getBinding().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasIsSummaryElement()) {
if (!Base.compareDeep(derived.getIsSummaryElement(), base.getIsSummaryElement(), false))
base.setIsSummaryElement(derived.getIsSummaryElement().copy());
else if (trimDifferential)
derived.setIsSummaryElement(null);
else
derived.getIsSummaryElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasType()) {
if (!Base.compareDeep(derived.getType(), base.getType(), false)) {
if (base.hasType()) {
for (TypeRefComponent ts : derived.getType()) {
boolean ok = false;
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (TypeRefComponent td : base.getType()) {
b.append(td.getCode());
if (td.hasCode() && (td.getCode().equals(ts.getCode()) || td.getCode().equals("Extension") || td.getCode().equals("Element") || td.getCode().equals("*") || ((td.getCode().equals("Resource") || (td.getCode().equals("DomainResource")) && pkp.isResource(ts.getCode())))))
ok = true;
}
if (!ok)
throw new DefinitionException("StructureDefinition " + pn + " at " + derived.getPath() + ": illegal constrained type " + ts.getCode() + " from " + b.toString());
}
}
base.getType().clear();
for (TypeRefComponent t : derived.getType()) {
TypeRefComponent tt = t.copy();
// tt.setUserData(DERIVATION_EQUALS, true);
base.getType().add(tt);
}
} else if (trimDifferential)
derived.getType().clear();
else
for (TypeRefComponent t : derived.getType()) t.setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMapping()) {
// todo: mappings are not cumulative - one replaces another
if (!Base.compareDeep(derived.getMapping(), base.getMapping(), false)) {
for (ElementDefinitionMappingComponent s : derived.getMapping()) {
boolean found = false;
for (ElementDefinitionMappingComponent d : base.getMapping()) {
found = found || (d.getIdentity().equals(s.getIdentity()) && d.getMap().equals(s.getMap()));
}
if (!found)
base.getMapping().add(s);
}
} else if (trimDifferential)
derived.getMapping().clear();
else
for (ElementDefinitionMappingComponent t : derived.getMapping()) t.setUserData(DERIVATION_EQUALS, true);
}
// todo: constraints are cumulative. there is no replacing
for (ElementDefinitionConstraintComponent s : base.getConstraint()) s.setUserData(IS_DERIVED, true);
if (derived.hasConstraint()) {
for (ElementDefinitionConstraintComponent s : derived.getConstraint()) {
base.getConstraint().add(s.copy());
}
}
}
}
Also used :
ValidationMessage(org.hl7.fhir.utilities.validation.ValidationMessage)
StringType(org.hl7.fhir.dstu2016may.model.StringType)
TypeRefComponent(org.hl7.fhir.dstu2016may.model.ElementDefinition.TypeRefComponent)
ValueSetExpansionOutcome(org.hl7.fhir.dstu2016may.terminologies.ValueSetExpander.ValueSetExpansionOutcome)
CommaSeparatedStringBuilder(org.hl7.fhir.utilities.CommaSeparatedStringBuilder)
ElementDefinition(org.hl7.fhir.dstu2016may.model.ElementDefinition)
DefinitionException(org.hl7.fhir.exceptions.DefinitionException)
ElementDefinitionMappingComponent(org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionMappingComponent)
ElementDefinitionConstraintComponent(org.hl7.fhir.dstu2016may.model.ElementDefinition.ElementDefinitionConstraintComponent)
Aggregations
ArrayList (java.util.ArrayList)15
DefinitionException (org.hl7.fhir.exceptions.DefinitionException)9
CS (net.ihe.gazelle.hl7v3.datatypes.CS)8
II (net.ihe.gazelle.hl7v3.datatypes.II)8
TS (net.ihe.gazelle.hl7v3.datatypes.TS)8
FHIRFormatError (org.hl7.fhir.exceptions.FHIRFormatError)8
BundleEntryComponent (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent)8
ByteArrayOutputStream (java.io.ByteArrayOutputStream)7
BL (net.ihe.gazelle.hl7v3.datatypes.BL)7
CD (net.ihe.gazelle.hl7v3.datatypes.CD)7
CE (net.ihe.gazelle.hl7v3.datatypes.CE)7
INT (net.ihe.gazelle.hl7v3.datatypes.INT)7
MCCIMT000100UV01Device (net.ihe.gazelle.hl7v3.mccimt000100UV01.MCCIMT000100UV01Device)7
MCCIMT000100UV01Receiver (net.ihe.gazelle.hl7v3.mccimt000100UV01.MCCIMT000100UV01Receiver)7
MCCIMT000100UV01Sender (net.ihe.gazelle.hl7v3.mccimt000100UV01.MCCIMT000100UV01Sender)7
FHIRException (org.hl7.fhir.exceptions.FHIRException)7
Identifier (org.hl7.fhir.r4.model.Identifier)7
Test (org.junit.jupiter.api.Test)7
COCTMT090003UV01AssignedEntity (net.ihe.gazelle.hl7v3.coctmt090003UV01.COCTMT090003UV01AssignedEntity)6
COCTMT090003UV01Organization (net.ihe.gazelle.hl7v3.coctmt090003UV01.COCTMT090003UV01Organization)6
