private CodeableConcept readAsCodeableConcept(Element element) { CodeableConcept cc = new CodeableConcept(); List<Element> list = new ArrayList<Element>(); element.getNamedChildren("coding", list); for (Element item : list) cc.addCoding(readAsCoding(item)); cc.setText(element.getNamedChildValue("text")); return cc; }
public org.hl7.fhir.dstu3.model.CodeableConcept convertCodeableConcept(org.hl7.fhir.instance.model.CodeableConcept src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.CodeableConcept tgt = new org.hl7.fhir.dstu3.model.CodeableConcept(); copyElement(src, tgt); for (org.hl7.fhir.instance.model.Coding t : src.getCoding()) tgt.addCoding(convertCoding(t)); tgt.setText(src.getText()); return tgt; }
public CodeableConcept makeCodeableConceptFromCD(Element cv) throws Exception { if (cv == null) return null; CodeableConcept cc = new CodeableConcept(); cc.addCoding(makeCodingFromCV(cv)); for (Element e : cda.getChildren(cv, "translation")) cc.addCoding(makeCodingFromCV(e)); if (cda.getChild(cv, "originalText") != null) { Element ote = cda.getChild(cv, "originalText"); // if (cda.getChild(ote, "reference") != null) { // if (cda.getChild(ote, "reference").getAttribute("value").startsWith("#")) { // Element t = cda.getByXmlId(cda.getChild(ote, "reference").getAttribute("value").substring(1)); // String ot = t.getTextContent().trim(); // cc.setText(Utilities.noString(ot) ? null : ot); // } else // throw new Exception("external references not handled yet "+cda.getChild(ote, "reference").getAttribute("value")); // } else { String ot = ote.getTextContent().trim(); cc.setText(Utilities.noString(ot) ? null : ot); //} } return cc; }
public static org.hl7.fhir.dstu3.model.CodeableConcept convertCodeableConcept(org.hl7.fhir.dstu2016may.model.CodeableConcept src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.CodeableConcept tgt = new org.hl7.fhir.dstu3.model.CodeableConcept(); copyElement(src, tgt); for (org.hl7.fhir.dstu2016may.model.Coding t : src.getCoding()) tgt.addCoding(convertCoding(t)); if (src.hasText()) tgt.setText(src.getText()); return tgt; }
/** * @param system - * @param code - * @param display - * @param text - * @return type, ontology code and covered text in a fhir codeable concept. */ static public CodeableConcept createSimpleCode( final String system, final String code, final String display, final String text ) { final CodeableConcept codeableConcept = new CodeableConcept(); codeableConcept.addCoding( new Coding( system, code, display ) ); codeableConcept.setText( text ); return codeableConcept; }
public static CodeableConcept readAsCodeableConcept(Element element) { CodeableConcept cc = new CodeableConcept(); List<Element> list = new ArrayList<Element>(); element.getNamedChildren("coding", list); for (Element item : list) cc.addCoding(readAsCoding(item)); cc.setText(element.getNamedChildValue("text")); return cc; }
public static CodeableConcept createServiceCategory(String sc, String shortDx, String longDx) { CodeableConcept cpt = new CodeableConcept(); cpt.setText(longDx); Coding coding = new Coding(); coding.setCode(sc); coding.setDisplay(shortDx); cpt.getCoding().add(coding); return cpt; }
private CodeableConcept readAsCodeableConcept(Element element) { CodeableConcept cc = new CodeableConcept(); List<Element> list = new ArrayList<Element>(); element.getNamedChildren("coding", list); for (Element item : list) cc.addCoding(readAsCoding(item)); cc.setText(element.getNamedChildValue("text")); return cc; }
public org.hl7.fhir.dstu3.model.ClinicalImpression convertClinicalImpression(org.hl7.fhir.instance.model.ClinicalImpression src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.ClinicalImpression tgt = new org.hl7.fhir.dstu3.model.ClinicalImpression(); copyDomainResource(src, tgt); tgt.setSubject(convertReference(src.getPatient())); tgt.setAssessor(convertReference(src.getAssessor())); tgt.setStatus(convertClinicalImpressionStatus(src.getStatus())); if (src.hasDate()) tgt.setDate(src.getDate()); tgt.setDescription(src.getDescription()); tgt.setPrevious(convertReference(src.getPrevious())); for (org.hl7.fhir.instance.model.Reference t : src.getProblem()) tgt.addProblem(convertReference(t)); // for (org.hl7.fhir.instance.model.ClinicalImpression.ClinicalImpressionInvestigationsComponent t : src.getInvestigations()) // tgt.addInvestigations(convertClinicalImpressionInvestigationsComponent(t)); tgt.addProtocol(src.getProtocol()); tgt.setSummary(src.getSummary()); for (org.hl7.fhir.instance.model.ClinicalImpression.ClinicalImpressionFindingComponent t : src.getFinding()) tgt.addFinding(convertClinicalImpressionFindingComponent(t)); if (src.hasPrognosis()) tgt.addPrognosisCodeableConcept ().setText(src.getPrognosis()); // for (org.hl7.fhir.instance.model.Reference t : src.getPlan()) // tgt.addPlan(convertReference(t)); for (org.hl7.fhir.instance.model.Reference t : src.getAction()) tgt.addAction(convertReference(t)); return tgt; }
public CodeableConcept makeCodeableConceptFromCD(Element cv) throws Exception { if (cv == null) return null; CodeableConcept cc = new CodeableConcept(); cc.addCoding(makeCodingFromCV(cv)); for (Element e : cda.getChildren(cv, "translation")) cc.addCoding(makeCodingFromCV(e)); if (cda.getChild(cv, "originalText") != null) { Element ote = cda.getChild(cv, "originalText"); // if (cda.getChild(ote, "reference") != null) { // if (cda.getChild(ote, "reference").getAttribute("value").startsWith("#")) { // Element t = cda.getByXmlId(cda.getChild(ote, "reference").getAttribute("value").substring(1)); // String ot = t.getTextContent().trim(); // cc.setText(Utilities.noString(ot) ? null : ot); // } else // throw new Exception("external references not handled yet "+cda.getChild(ote, "reference").getAttribute("value")); // } else { String ot = ote.getTextContent().trim(); cc.setText(Utilities.noString(ot) ? null : ot); //} } return cc; }
public org.hl7.fhir.dstu3.model.CodeableConcept convertCodeableConcept(org.hl7.fhir.instance.model.CodeableConcept src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.CodeableConcept tgt = new org.hl7.fhir.dstu3.model.CodeableConcept(); copyElement(src, tgt); for (org.hl7.fhir.instance.model.Coding t : src.getCoding()) tgt.addCoding(convertCoding(t)); tgt.setText(src.getText()); return tgt; }
public static org.hl7.fhir.dstu3.model.CodeableConcept convertCodeableConcept(org.hl7.fhir.dstu2016may.model.CodeableConcept src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.CodeableConcept tgt = new org.hl7.fhir.dstu3.model.CodeableConcept(); copyElement(src, tgt); for (org.hl7.fhir.dstu2016may.model.Coding t : src.getCoding()) tgt.addCoding(convertCoding(t)); if (src.hasText()) tgt.setText(src.getText()); return tgt; }
/** * {@inheritDoc} */ @Override public Basic createResource( final JCas jCas, final Segment section, final FhirPractitioner practitioner, final FhirNoteSpecs noteSpecs ) { final Basic basic = createAnnotationBasic( jCas, section, practitioner ); // The 'code' is the normalized section name PLUS section tag text. final CodeableConcept codeableConcept = FhirElementFactory.createSimpleCode( section ); codeableConcept.addCoding( new Coding( CODING_SECTION_NAME, section.getPreferredText(), null ) ); if ( !section.getPreferredText() .equals( section.getId() ) ) { codeableConcept.addCoding( new Coding( CODING_SECTION_ID, section.getId(), null ) ); } codeableConcept.setText( section.getTagText() ); basic.setCode( codeableConcept ); return basic; }
public static Encounter create(Patient patient, Date date, Location location, String sc) { Encounter encounter = new Encounter(); Reference pat = new Reference(patient); encounter.setSubject(pat); Period period = new Period(); period.setStart(date); encounter.setPeriod(period); Reference loc = new Reference(location); EncounterLocationComponent encloc = encounter.addLocation(); encloc.setPeriod(period); encloc.setLocation(loc); CodeableConcept type = encounter.addType(); CodeableConcept cat = getServiceCategory(sc); type.setText(cat.getText()); type.getCoding().addAll(cat.getCoding()); return encounter; }
private static synchronized void loadServiceCategories() { if (serviceCategories == null) { Map<String, CodeableConcept> map = new LinkedHashMap<>(); Bundle bundle = ClientUtil.getFhirClient().search().forResource(ValueSet.class) .where(CodeSystem.NAME.matchesExactly().value("EncounterType")).returnBundle(Bundle.class).execute(); for (CodeSystem cs : FhirUtil.getEntries(bundle, CodeSystem.class)) { UriType system = cs.getUrlElement(); for (ConceptDefinitionComponent concept : cs.getConcept()) { CodeableConcept cc = new CodeableConcept(); Coding coding = cc.addCoding(); coding.setCode(concept.getCode()); coding.setDisplay(concept.getDisplay()); coding.setSystemElement(system); cc.setText(concept.getDefinition()); map.put(coding.getCode(), cc); } } serviceCategories = map; } return; }
public static void main(String[] theArgs) { Patient pat = new Patient(); pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J"); // Add an extension on the resource pat.addExtension() .setUrl("http://hl7.org/fhir/StructureDefinition/patient-importance") .setValue(new CodeableConcept().setText("Patient is a VIP")); // Add an extension on a primitive pat.getBirthDateElement().setValueAsString("1955-02-22"); pat.getBirthDateElement().addExtension() .setUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime") .setValue(new TimeType("23:30")); IParser parser = FhirContext.forDstu3().newJsonParser().setPrettyPrint(true); System.out.println(parser.encodeResourceToString(pat)); } }
@SuppressWarnings("Duplicates") @Override public CapabilityStatement addCapabilityStatement(CapabilityStatement capabilityStatement) { if (metadataRepositoryConfig.isSecured()) { List<CapabilityStatement.CapabilityStatementRestComponent> restList = capabilityStatement.getRest(); CapabilityStatement.CapabilityStatementRestComponent rest = restList.get(0); CapabilityStatement.CapabilityStatementRestSecurityComponent restSecurity = rest.getSecurity(); Extension conformanceExtension = new Extension(metadataRepositoryConfig.getUrisEndpointExtensionUrl()); conformanceExtension.addExtension(new Extension("authorize", new UriType(metadataRepositoryConfig.getAuthorizeUrl()))); conformanceExtension.addExtension(new Extension("token", new UriType(metadataRepositoryConfig.getTokenUrl()))); conformanceExtension.addExtension(new Extension("register", new UriType(metadataRepositoryConfig.getRegistrationEndpointUrl()))); conformanceExtension.addExtension(new Extension("launch-registration", new UriType(metadataRepositoryConfig.getLaunchRegistrationUrl()))); restSecurity.addExtension(conformanceExtension); CodeableConcept codeableConcept = new CodeableConcept(); Coding smartOnFhirCoding = new Coding("http://hl7.org/fhir/restful-security-service", "SMART-on-FHIR", "SMART-on-FHIR"); codeableConcept.getCoding().add(smartOnFhirCoding); codeableConcept.setText("OAuth2 using SMART-on-FHIR profile (see http://docs.smarthealthit.org)"); restSecurity.getService().add(codeableConcept); } return capabilityStatement; } }
/** * @param jCas ye olde ... * @param segment uima type system representation of a clinical note section. * @return fhir SectionComponent, part of the Composition. */ static public SectionComponent createSectionComponent( final JCas jCas, final Segment segment ) { final SectionComponent sectionComponent = new SectionComponent(); sectionComponent.setId( FhirElementFactory.createId( jCas, segment.getId(), segment.hashCode() ) ); sectionComponent.setMode( Composition.SectionMode.SNAPSHOT ); sectionComponent.setTitle( segment.getPreferredText() ); // The 'code' is the normalized section name PLUS section tag text. final CodeableConcept codeableConcept = FhirElementFactory.createSimpleCode( segment ); codeableConcept.addCoding( new Coding( "section-name", segment.getPreferredText(), null ) ); if ( !segment.getPreferredText() .equals( segment.getId() ) ) { codeableConcept.addCoding( new Coding( "id", segment.getId(), null ) ); } codeableConcept.setText( segment.getTagText() ); sectionComponent.setCode( codeableConcept ); // Add text span as an extension. sectionComponent.addExtension( FhirElementFactory.createSpanBegin( segment ) ); sectionComponent.addExtension( FhirElementFactory.createSpanEnd( segment ) ); return sectionComponent; }
public org.hl7.fhir.dstu3.model.ClinicalImpression convertClinicalImpression(org.hl7.fhir.instance.model.ClinicalImpression src) throws FHIRException { if (src == null || src.isEmpty()) return null; org.hl7.fhir.dstu3.model.ClinicalImpression tgt = new org.hl7.fhir.dstu3.model.ClinicalImpression(); copyDomainResource(src, tgt); tgt.setSubject(convertReference(src.getPatient())); tgt.setAssessor(convertReference(src.getAssessor())); tgt.setStatus(convertClinicalImpressionStatus(src.getStatus())); if (src.hasDate()) tgt.setDate(src.getDate()); tgt.setDescription(src.getDescription()); tgt.setPrevious(convertReference(src.getPrevious())); for (org.hl7.fhir.instance.model.Reference t : src.getProblem()) tgt.addProblem(convertReference(t)); // for (org.hl7.fhir.instance.model.ClinicalImpression.ClinicalImpressionInvestigationsComponent t : src.getInvestigations()) // tgt.addInvestigations(convertClinicalImpressionInvestigationsComponent(t)); tgt.addProtocol(src.getProtocol()); tgt.setSummary(src.getSummary()); for (org.hl7.fhir.instance.model.ClinicalImpression.ClinicalImpressionFindingComponent t : src.getFinding()) tgt.addFinding(convertClinicalImpressionFindingComponent(t)); if (src.hasPrognosis()) tgt.addPrognosisCodeableConcept ().setText(src.getPrognosis()); // for (org.hl7.fhir.instance.model.Reference t : src.getPlan()) // tgt.addPlan(convertReference(t)); for (org.hl7.fhir.instance.model.Reference t : src.getAction()) tgt.addAction(convertReference(t)); return tgt; }