use of org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent in project org.hl7.fhir.core by hapifhir.
the class ValueSetComparer method compareDefinitions.
private void compareDefinitions(ConceptSetComponent left, ConceptSetComponent right, StructuralMatch<Element> combined, ConceptSetComponent union, ConceptSetComponent intersection) {
// system must match, but the rest might not. we're going to do the full comparison whatever, so the outcome looks consistent to the user
List<CanonicalType> matchVSR = new ArrayList<>();
for (CanonicalType l : left.getValueSet()) {
CanonicalType r = findInList(right.getValueSet(), l, left.getValueSet());
if (r == null) {
union.getValueSet().add(l);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed ValueSet", "ValueSet.compose.include.valueSet")));
} else {
matchVSR.add(r);
if (l.getValue().equals(r.getValue())) {
union.getValueSet().add(l);
intersection.getValueSet().add(l);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, null);
combined.getChildren().add(sm);
} else {
union.getValueSet().add(l);
union.getValueSet().add(r);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Values are different", "ValueSet.compose.include.valueSet"));
combined.getChildren().add(sm);
}
}
}
for (CanonicalType r : right.getValueSet()) {
if (!matchVSR.contains(r)) {
union.getValueSet().add(r);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Add ValueSet", "ValueSet.compose.include.valueSet"), r));
}
}
List<ConceptReferenceComponent> matchCR = new ArrayList<>();
for (ConceptReferenceComponent l : left.getConcept()) {
ConceptReferenceComponent r = findInList(right.getConcept(), l, left.getConcept());
if (r == null) {
union.getConcept().add(l);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this Concept", "ValueSet.compose.include.concept")));
} else {
matchCR.add(r);
if (l.getCode().equals(r.getCode())) {
ConceptReferenceComponent cu = new ConceptReferenceComponent();
ConceptReferenceComponent ci = new ConceptReferenceComponent();
union.getConcept().add(cu);
intersection.getConcept().add(ci);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
combined.getChildren().add(sm);
compareConcepts(l, r, sm, cu, ci);
} else {
union.getConcept().add(l);
union.getConcept().add(r);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Concepts are different", "ValueSet.compose.include.concept"));
combined.getChildren().add(sm);
compareConcepts(l, r, sm, null, null);
}
}
}
for (ConceptReferenceComponent r : right.getConcept()) {
if (!matchCR.contains(r)) {
union.getConcept().add(r);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this Concept", "ValueSet.compose.include.concept"), r));
}
}
List<ConceptSetFilterComponent> matchFR = new ArrayList<>();
for (ConceptSetFilterComponent l : left.getFilter()) {
ConceptSetFilterComponent r = findInList(right.getFilter(), l, left.getFilter());
if (r == null) {
union.getFilter().add(l);
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this item", "ValueSet.compose.include.filter")));
} else {
matchFR.add(r);
if (l.getProperty().equals(r.getProperty()) && l.getOp().equals(r.getOp())) {
ConceptSetFilterComponent cu = new ConceptSetFilterComponent();
ConceptSetFilterComponent ci = new ConceptSetFilterComponent();
union.getFilter().add(cu);
intersection.getFilter().add(ci);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
combined.getChildren().add(sm);
compareFilters(l, r, sm, cu, ci);
} else {
union.getFilter().add(l);
union.getFilter().add(r);
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r, vmI(IssueSeverity.INFORMATION, "Codes are different", "ValueSet.compose.include.filter"));
combined.getChildren().add(sm);
compareFilters(l, r, sm, null, null);
}
}
}
for (ConceptSetFilterComponent r : right.getFilter()) {
if (!matchFR.contains(r)) {
union.getFilter().add(r);
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this item", "ValueSet.compose.include.filter"), r));
}
}
}
use of org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent in project org.hl7.fhir.core by hapifhir.
the class ValueSetComparer method addSetConceptRow.
private void addSetConceptRow(HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<Element> t) {
Row r = gen.new Row();
rows.add(r);
r.getCells().add(gen.new Cell(null, null, "Concept", null, null));
if (t.hasLeft() && t.hasRight()) {
ConceptReferenceComponent csL = (ConceptReferenceComponent) t.getLeft();
ConceptReferenceComponent csR = (ConceptReferenceComponent) t.getRight();
// we assume both have codes
if (csL.getCode().equals(csR.getCode())) {
r.getCells().add(gen.new Cell(null, null, csL.getCode(), null, null).span(2).center());
} else {
r.getCells().add(gen.new Cell(null, null, csL.getCode(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
r.getCells().add(gen.new Cell(null, null, csR.getCode(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
}
if (csL.hasDisplay() && csR.hasDisplay()) {
if (csL.getDisplay().equals(csR.getDisplay())) {
r.getCells().add(gen.new Cell(null, null, csL.getDisplay(), null, null).span(2).center());
} else {
r.getCells().add(gen.new Cell(null, null, csL.getDisplay(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
r.getCells().add(gen.new Cell(null, null, csR.getDisplay(), null, null).setStyle("background-color: " + COLOR_DIFFERENT));
}
} else if (csL.hasDisplay()) {
r.getCells().add(gen.new Cell(null, null, csL.getDisplay(), null, null));
r.getCells().add(missingCell(gen, COLOR_NO_CELL_RIGHT));
} else if (csR.hasDisplay()) {
r.getCells().add(missingCell(gen, COLOR_NO_CELL_LEFT));
r.getCells().add(gen.new Cell(null, null, csR.getDisplay(), null, null));
} else {
r.getCells().add(missingCell(gen).span(2).center());
}
} else if (t.hasLeft()) {
r.setColor(COLOR_NO_ROW_RIGHT);
ConceptReferenceComponent cs = (ConceptReferenceComponent) t.getLeft();
r.getCells().add(gen.new Cell(null, null, cs.getCode(), null, null));
r.getCells().add(missingCell(gen));
r.getCells().add(gen.new Cell(null, null, cs.hasDisplay() ? "Version: " + cs.getDisplay() : "", null, null));
r.getCells().add(missingCell(gen));
} else {
r.setColor(COLOR_NO_ROW_LEFT);
ConceptReferenceComponent cs = (ConceptReferenceComponent) t.getRight();
r.getCells().add(missingCell(gen));
r.getCells().add(gen.new Cell(null, null, cs.getCode(), null, null));
r.getCells().add(missingCell(gen));
r.getCells().add(gen.new Cell(null, null, cs.hasDisplay() ? "Version: " + cs.getDisplay() : "", null, null));
}
r.getCells().add(cellForMessages(gen, t.getMessages()));
}
use of org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent in project org.hl7.fhir.core by hapifhir.
the class ValueSetCheckerSimple method validateCode.
private ValidationResult validateCode(Coding code, CodeSystem cs) {
ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
if (cc == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
} else {
return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
}
}
if (code.getDisplay() == null) {
return new ValidationResult(code.getSystem(), cc);
}
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (cc.hasDisplay()) {
b.append(cc.getDisplay());
if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
return new ValidationResult(code.getSystem(), cc);
}
}
for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
b.append(ds.getValue());
if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
return new ValidationResult(code.getSystem(), cc);
}
}
// also check to see if the value set has another display
ConceptReferenceComponent vs = findValueSetRef(code.getSystem(), code.getCode());
if (vs != null && (vs.hasDisplay() || vs.hasDesignation())) {
if (vs.hasDisplay()) {
b.append(vs.getDisplay());
if (code.getDisplay().equalsIgnoreCase(vs.getDisplay())) {
return new ValidationResult(code.getSystem(), cc);
}
}
for (ConceptReferenceDesignationComponent ds : vs.getDesignation()) {
b.append(ds.getValue());
if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
return new ValidationResult(code.getSystem(), cc);
}
}
}
return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_, code.getSystem(), code.getCode(), b.toString(), code.getDisplay()), code.getSystem(), cc);
}
use of org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent in project org.hl7.fhir.core by hapifhir.
the class ValueSetCheckerSimple method findValueSetRef.
private ConceptReferenceComponent findValueSetRef(String system, String code) {
if (valueset == null)
return null;
// if it has an expansion
for (ValueSetExpansionContainsComponent exp : valueset.getExpansion().getContains()) {
if (system.equals(exp.getSystem()) && code.equals(exp.getCode())) {
ConceptReferenceComponent cc = new ConceptReferenceComponent();
cc.setDisplay(exp.getDisplay());
cc.setDesignation(exp.getDesignation());
return cc;
}
}
for (ConceptSetComponent inc : valueset.getCompose().getInclude()) {
if (system.equals(inc.getSystem())) {
for (ConceptReferenceComponent cc : inc.getConcept()) {
if (cc.getCode().equals(code)) {
return cc;
}
}
}
for (CanonicalType url : inc.getValueSet()) {
ConceptReferenceComponent cc = getVs(url.asStringValue()).findValueSetRef(system, code);
if (cc != null) {
return cc;
}
}
}
return null;
}
use of org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent in project org.hl7.fhir.core by hapifhir.
the class ValueSetExpanderSimple method doInternalIncludeCodes.
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
if (cs == null) {
if (context.isNoTerminologyServer())
throw failTSE("Unable to find code system " + inc.getSystem().toString());
else
throw failTSE("Unable to find code system " + inc.getSystem().toString());
}
cs.checkNoModifiers("Code System", "expanding");
if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)
throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion())
if (!existsInParams(exp.getParameter(), "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
}
}
if (!inc.getConcept().isEmpty()) {
canBeHeirarchy = false;
for (ConceptReferenceComponent c : inc.getConcept()) {
c.checkNoModifiers("Code in Code System", "expanding");
ConceptDefinitionComponent def = CodeSystemUtilities.findCode(cs.getConcept(), c.getCode());
// default is true if we're a fragment and
Boolean inactive = false;
if (def == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
} else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
} else {
if (checkCodesWhenExpanding) {
throw failTSE("Unable to find code '" + c.getCode() + "' in code system " + cs.getUrl());
}
}
} else {
inactive = CodeSystemUtilities.isInactive(cs, def);
}
addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, inactive, imports, noInactive);
}
}
if (inc.getFilter().size() > 1) {
// which will bt the case if we get around to supporting this
canBeHeirarchy = false;
// need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
throw failTSE("Multiple filters not handled yet");
}
if (inc.getFilter().size() == 1) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
ConceptSetFilterComponent fc = inc.getFilter().get(0);
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
// special: all codes in the target code system that are not under the value
ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
if (defEx == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(), noInactive);
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
// gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
canBeHeirarchy = false;
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports, noInactive);
}
}
}
} else if (isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())), noInactive);
}
} else {
throw fail("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
}
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