use of org.hl7.fhir.dstu2016may.model.DomainResource in project org.hl7.fhir.core by hapifhir.
the class XmlParserBase method parseDomainResourceContained.
protected DomainResource parseDomainResourceContained(XmlPullParser xpp) throws IOException, FHIRFormatError, XmlPullParserException {
next(xpp);
int eventType = nextNoWhitespace(xpp);
if (eventType == XmlPullParser.START_TAG) {
DomainResource dr = (DomainResource) parseResource(xpp);
nextNoWhitespace(xpp);
next(xpp);
return dr;
} else {
unknownContent(xpp);
return null;
}
}
use of org.hl7.fhir.dstu2016may.model.DomainResource in project org.hl7.fhir.core by hapifhir.
the class NarrativeGeneratorTests method process.
private void process(String path) throws IOException, EOperationOutcome, FHIRException {
XmlParser p = new XmlParser();
DomainResource r = (DomainResource) p.parse(new FileInputStream(path));
gen.generate(r);
FileOutputStream s = new FileOutputStream(Utilities.path("[tmp]", "gen.xml"));
new XmlParser().compose(s, r, true);
s.close();
}
use of org.hl7.fhir.dstu2016may.model.DomainResource in project org.hl7.fhir.core by hapifhir.
the class DomainResource method copyValues.
public void copyValues(DomainResource dst) {
super.copyValues(dst);
dst.text = text == null ? null : text.copy();
if (contained != null) {
dst.contained = new ArrayList<Resource>();
for (Resource i : contained) dst.contained.add(i.copy());
}
;
if (extension != null) {
dst.extension = new ArrayList<Extension>();
for (Extension i : extension) dst.extension.add(i.copy());
}
;
if (modifierExtension != null) {
dst.modifierExtension = new ArrayList<Extension>();
for (Extension i : modifierExtension) dst.modifierExtension.add(i.copy());
}
;
}
use of org.hl7.fhir.dstu2016may.model.DomainResource 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);
}
}
}
use of org.hl7.fhir.dstu2016may.model.DomainResource in project org.hl7.fhir.core by hapifhir.
the class DomainResource method copyValues.
public void copyValues(DomainResource dst) {
super.copyValues(dst);
dst.text = text == null ? null : text.copy();
if (contained != null) {
dst.contained = new ArrayList<Resource>();
for (Resource i : contained) dst.contained.add(i.copy());
}
;
if (extension != null) {
dst.extension = new ArrayList<Extension>();
for (Extension i : extension) dst.extension.add(i.copy());
}
;
if (modifierExtension != null) {
dst.modifierExtension = new ArrayList<Extension>();
for (Extension i : modifierExtension) dst.modifierExtension.add(i.copy());
}
;
}
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