org.hl7.fhir.r4.model.Bundle.BundleEntryComponent Java Examples
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org.hl7.fhir.r4.model.Bundle.BundleEntryComponent.
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Example #1
Source File: FhirR4.java From synthea with Apache License 2.0 | 6 votes |
/** * Helper function to create an Entry for the given Resource within the given Bundle. Sets the * resourceID to a random UUID, sets the entry's fullURL to that resourceID, and adds the entry to * the bundle. * * @param bundle The Bundle to add the Entry to * @param resource Resource the new Entry should contain * @param resourceID The Resource ID to assign * @return the created Entry */ private static BundleEntryComponent newEntry(Bundle bundle, Resource resource, String resourceID) { BundleEntryComponent entry = bundle.addEntry(); resource.setId(resourceID); entry.setFullUrl(getUrlPrefix(resource.fhirType()) + resourceID); entry.setResource(resource); if (TRANSACTION_BUNDLE) { BundleEntryRequestComponent request = entry.getRequest(); request.setMethod(HTTPVerb.POST); request.setUrl(resource.getResourceType().name()); entry.setRequest(request); } return entry; }
Example #2
Source File: Unbundler.java From org.hl7.fhir.core with Apache License 2.0 | 6 votes |
private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException { String folder = Utilities.getDirectoryForFile(src); Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src)); for (BundleEntryComponent be : bnd.getEntry()) { Resource r = be.getResource(); if (r != null) { if (StringUtils.isBlank(r.getId())) { if (r instanceof MetadataResource) r.setId(tail((MetadataResource) r)); } if (!StringUtils.isBlank(r.getId())) { String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json"); if (!new File(tgt).exists()) new JsonParser().compose(new FileOutputStream(tgt), r); } } } }
Example #3
Source File: GraphQLEngineTests.java From org.hl7.fhir.core with Apache License 2.0 | 6 votes |
@Override public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException { try { Bundle bnd = new Bundle(); BundleLinkComponent bl = bnd.addLink(); bl.setRelation("next"); bl.setUrl("http://test.fhir.org/r4/Patient?_format=text/xhtml&search-id=77c97e03-8a6c-415f-a63d-11c80cf73f&&active=true&_sort=_id&search-offset=50&_count=50"); bl = bnd.addLink(); bl.setRelation("self"); bl.setUrl("http://test.fhir.org/r4/Patient?_format=text/xhtml&search-id=77c97e03-8a6c-415f-a63d-11c80cf73f&&active=true&_sort=_id&search-offset=0&_count=50"); BundleEntryComponent be = bnd.addEntry(); be.setFullUrl("http://hl7.org/fhir/Patient/example"); be.setResource(new XmlParser().parse(new FileInputStream(Utilities.path(TestingUtilities.resourceNameToFile("patient-example.xml"))))); be = bnd.addEntry(); be.setFullUrl("http://hl7.org/fhir/Patient/example"); be.setResource(new XmlParser().parse(new FileInputStream(Utilities.path(TestingUtilities.resourceNameToFile("patient-example-xds.xml"))))); be.getSearch().setScore(0.5); be.getSearch().setMode(SearchEntryMode.MATCH); bnd.setTotal(50); return bnd; } catch (Exception e) { throw new FHIRException(e); } }
Example #4
Source File: FhirR4.java From synthea with Apache License 2.0 | 6 votes |
/** * Map the JsonObject for a Supply into a FHIR SupplyDelivery and add it to the Bundle. * * @param personEntry The Person entry. * @param bundle Bundle to add to. * @param supply The supplied object to add. * @param encounter The encounter during which the supplies were delivered * @return The added Entry. */ private static BundleEntryComponent supplyDelivery(BundleEntryComponent personEntry, Bundle bundle, HealthRecord.Supply supply, Encounter encounter) { SupplyDelivery supplyResource = new SupplyDelivery(); supplyResource.setStatus(SupplyDeliveryStatus.COMPLETED); supplyResource.setPatient(new Reference(personEntry.getFullUrl())); CodeableConcept type = new CodeableConcept(); type.addCoding() .setCode("device") .setDisplay("Device") .setSystem("http://terminology.hl7.org/CodeSystem/supply-item-type"); supplyResource.setType(type); SupplyDeliverySuppliedItemComponent suppliedItem = new SupplyDeliverySuppliedItemComponent(); suppliedItem.setItem(mapCodeToCodeableConcept(supply.codes.get(0), SNOMED_URI)); suppliedItem.setQuantity(new Quantity(supply.quantity)); supplyResource.setSuppliedItem(suppliedItem); supplyResource.setOccurrence(convertFhirDateTime(supply.start, true)); return newEntry(bundle, supplyResource); }
Example #5
Source File: ResourceUtilities.java From org.hl7.fhir.core with Apache License 2.0 | 5 votes |
public static Resource getById(Bundle feed, ResourceType type, String reference) { for (BundleEntryComponent item : feed.getEntry()) { if (item.getResource().getId().equals(reference) && item.getResource().getResourceType() == type) return item.getResource(); } return null; }
Example #6
Source File: R4ApelonFhirTerminologyProvider.java From cqf-ruler with Apache License 2.0 | 5 votes |
public String resolveByIdentifier(ValueSetInfo valueSet) { String valueSetId = valueSet.getId(); // Turns out we got a FHIR url. Let's use that. if (valueSetId.startsWith("http")) { return valueSetId; } valueSetId = valueSetId.replace("urn:oid:", ""); IQuery<Bundle> bundleQuery = this.getFhirClient() .search() .byUrl("ValueSet?identifier=" + valueSetId) .returnBundle(Bundle.class) .accept("application/fhir+xml"); Bundle searchResults = bundleQuery.execute(); if (searchResults.hasEntry()) { for (BundleEntryComponent bec : searchResults.getEntry()) { if (bec.hasResource()) { String id = bec.getResource().getIdElement().getIdPart(); if (id.equals(valueSetId)) { return ((ValueSet)bec.getResource()).getUrl(); } } } } return null; }
Example #7
Source File: ValidationSupportR4.java From synthea with Apache License 2.0 | 5 votes |
private void handleResource(IBaseResource resource) { if (resource instanceof Bundle) { Bundle bundle = (Bundle) resource; for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.hasResource()) { handleResource(entry.getResource()); } } } else { resources.add(resource); if (resource instanceof CodeSystem) { CodeSystem cs = (CodeSystem) resource; resourcesMap.put(cs.getUrl(), cs); codeSystemMap.put(cs.getUrl(), cs); } else if (resource instanceof ValueSet) { ValueSet vs = (ValueSet) resource; resourcesMap.put(vs.getUrl(), vs); if (vs.hasExpansion() && vs.getExpansion().hasContains()) { processExpansion(vs.getExpansion().getContains()); } } else if (resource instanceof StructureDefinition) { StructureDefinition sd = (StructureDefinition) resource; resourcesMap.put(sd.getUrl(), sd); definitions.add(sd); definitionsMap.put(sd.getUrl(), sd); } } }
Example #8
Source File: HospitalExporterR4.java From synthea with Apache License 2.0 | 5 votes |
/** * Export the hospital in FHIR R4 format. */ public static void export(long stop) { if (Boolean.parseBoolean(Config.get("exporter.hospital.fhir.export"))) { Bundle bundle = new Bundle(); if (Boolean.parseBoolean(Config.get("exporter.fhir.transaction_bundle"))) { bundle.setType(BundleType.TRANSACTION); } else { bundle.setType(BundleType.COLLECTION); } for (Provider h : Provider.getProviderList()) { // filter - exports only those hospitals in use Table<Integer, String, AtomicInteger> utilization = h.getUtilization(); int totalEncounters = utilization.column(Provider.ENCOUNTERS).values().stream() .mapToInt(ai -> ai.get()).sum(); if (totalEncounters > 0) { BundleEntryComponent entry = FhirR4.provider(bundle, h); addHospitalExtensions(h, (Organization) entry.getResource()); } } String bundleJson = FHIR_CTX.newJsonParser().setPrettyPrint(true) .encodeResourceToString(bundle); // get output folder List<String> folders = new ArrayList<>(); folders.add("fhir"); String baseDirectory = Config.get("exporter.baseDirectory"); File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile(); f.mkdirs(); Path outFilePath = f.toPath().resolve("hospitalInformation" + stop + ".json"); try { Files.write(outFilePath, Collections.singleton(bundleJson), StandardOpenOption.CREATE_NEW); } catch (IOException e) { e.printStackTrace(); } } }
Example #9
Source File: FhirR4.java From synthea with Apache License 2.0 | 5 votes |
/** * Find the Location entry in this bundle for the given provider, and return the * "fullUrl" attribute. * * @param provider A given provider. * @param bundle The current bundle being generated. * @return Location.fullUrl if found, otherwise null. */ private static String findLocationUrl(Provider provider, Bundle bundle) { for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.getResource().fhirType().equals("Location")) { org.hl7.fhir.r4.model.Location location = (org.hl7.fhir.r4.model.Location) entry.getResource(); if (location.getManagingOrganization() .getReference().endsWith(provider.getResourceID())) { return entry.getFullUrl(); } } } return null; }
Example #10
Source File: FhirR4.java From synthea with Apache License 2.0 | 5 votes |
/** * Find the provider entry in this bundle, and return the associated "fullUrl" attribute. * * @param provider A given provider. * @param bundle The current bundle being generated. * @return Provider.fullUrl if found, otherwise null. */ private static String findProviderUrl(Provider provider, Bundle bundle) { for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.getResource().fhirType().equals("Organization")) { Organization org = (Organization) entry.getResource(); if (org.getIdentifierFirstRep().getValue() != null && org.getIdentifierFirstRep().getValue().equals(provider.getResourceID())) { return entry.getFullUrl(); } } } return null; }
Example #11
Source File: ResourceUtilities.java From org.hl7.fhir.core with Apache License 2.0 | 5 votes |
public static BundleEntryComponent getEntryById(Bundle feed, ResourceType type, String reference) { for (BundleEntryComponent item : feed.getEntry()) { if (item.getResource().getId().equals(reference) && item.getResource().getResourceType() == type) return item; } return null; }
Example #12
Source File: FhirR4.java From synthea with Apache License 2.0 | 4 votes |
/** * Map the clinician into a FHIR Practitioner resource, and add it to the given Bundle. * @param bundle The Bundle to add to * @param clinician The clinician * @return The added Entry */ protected static BundleEntryComponent practitioner(Bundle bundle, Clinician clinician) { Practitioner practitionerResource = new Practitioner(); if (USE_US_CORE_IG) { Meta meta = new Meta(); meta.addProfile( "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"); practitionerResource.setMeta(meta); } practitionerResource.addIdentifier().setSystem("http://hl7.org/fhir/sid/us-npi") .setValue("" + (9_999_999_999L - clinician.identifier)); practitionerResource.setActive(true); practitionerResource.addName().setFamily( (String) clinician.attributes.get(Clinician.LAST_NAME)) .addGiven((String) clinician.attributes.get(Clinician.FIRST_NAME)) .addPrefix((String) clinician.attributes.get(Clinician.NAME_PREFIX)); String email = (String) clinician.attributes.get(Clinician.FIRST_NAME) + "." + (String) clinician.attributes.get(Clinician.LAST_NAME) + "@example.com"; practitionerResource.addTelecom() .setSystem(ContactPointSystem.EMAIL) .setUse(ContactPointUse.WORK) .setValue(email); if (USE_US_CORE_IG) { practitionerResource.getTelecomFirstRep().addExtension() .setUrl("http://hl7.org/fhir/us/core/StructureDefinition/us-core-direct") .setValue(new BooleanType(true)); } Address address = new Address() .addLine((String) clinician.attributes.get(Clinician.ADDRESS)) .setCity((String) clinician.attributes.get(Clinician.CITY)) .setPostalCode((String) clinician.attributes.get(Clinician.ZIP)) .setState((String) clinician.attributes.get(Clinician.STATE)); if (COUNTRY_CODE != null) { address.setCountry(COUNTRY_CODE); } practitionerResource.addAddress(address); if (clinician.attributes.get(Person.GENDER).equals("M")) { practitionerResource.setGender(AdministrativeGender.MALE); } else if (clinician.attributes.get(Person.GENDER).equals("F")) { practitionerResource.setGender(AdministrativeGender.FEMALE); } BundleEntryComponent practitionerEntry = newEntry(bundle, practitionerResource, clinician.getResourceID()); if (USE_US_CORE_IG) { // generate an accompanying PractitionerRole resource PractitionerRole practitionerRole = new PractitionerRole(); Meta meta = new Meta(); meta.addProfile( "http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitionerrole"); practitionerRole.setMeta(meta); practitionerRole.setPractitioner(new Reference() .setReference(practitionerEntry.getFullUrl()) .setDisplay(practitionerResource.getNameFirstRep().getNameAsSingleString())); practitionerRole.setOrganization(new Reference() .setReference( getUrlPrefix("Organization") + clinician.getOrganization().getResourceID()) .setDisplay(clinician.getOrganization().name)); practitionerRole.addCode( mapCodeToCodeableConcept( new Code("http://nucc.org/provider-taxonomy", "208D00000X", "General Practice"), null)); practitionerRole.addSpecialty( mapCodeToCodeableConcept( new Code("http://nucc.org/provider-taxonomy", "208D00000X", "General Practice"), null)); practitionerRole.addLocation() .setReference(findLocationUrl(clinician.getOrganization(), bundle)) .setDisplay(clinician.getOrganization().name); if (clinician.getOrganization().phone != null && !clinician.getOrganization().phone.isEmpty()) { practitionerRole.addTelecom(new ContactPoint() .setSystem(ContactPointSystem.PHONE) .setValue(clinician.getOrganization().phone)); } practitionerRole.addTelecom(practitionerResource.getTelecomFirstRep()); newEntry(bundle, practitionerRole); } return practitionerEntry; }
Example #13
Source File: FhirChCrlDocumentBundle.java From elexis-3-core with Eclipse Public License 1.0 | 4 votes |
@SuppressWarnings("unchecked") private void createBundle(){ try { Date now = new Date(); this.bundle = new Bundle(); bundle.setId("BundleFromPractitioner"); bundle.setMeta(new Meta().setLastUpdated(now).setProfile(Collections.singletonList( new CanonicalType("http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-bundle")))); bundle.setType(BundleType.DOCUMENT); BundleEntryComponent compositionEntry = bundle.addEntry(); Composition composition = new Composition(); compositionEntry.setResource(composition); composition.setId("CompFromPractitioner"); composition.setMeta(new Meta().setLastUpdated(now) .setProfile(Collections.singletonList(new CanonicalType( "http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-composition")))); composition.setStatus(CompositionStatus.FINAL); composition.setType(new CodeableConcept( new Coding("http://loinc.org", "72134-0", "Cancer event report"))); composition.setDate(now); composition.setTitle("Report to the Cancer Registry"); BundleEntryComponent subjectEntry = bundle.addEntry(); IFhirTransformer<Patient, IPatient> patientTransformer = (IFhirTransformer<Patient, IPatient>) FhirTransformersHolder .getTransformerFor(Patient.class, IPatient.class); Patient subject = patientTransformer.getFhirObject(patient) .orElseThrow(() -> new IllegalStateException("Could not create subject")); subject.getExtension().clear(); fixAhvIdentifier(subject); subjectEntry.setResource(subject); BundleEntryComponent practitionerEntry = bundle.addEntry(); IFhirTransformer<Practitioner, IMandator> practitionerTransformer = (IFhirTransformer<Practitioner, IMandator>) FhirTransformersHolder .getTransformerFor(Practitioner.class, IMandator.class); Practitioner practitioner = practitionerTransformer.getFhirObject(author) .orElseThrow(() -> new IllegalStateException("Could not create autor")); practitioner.getExtension().clear(); practitioner.getIdentifier().clear(); practitionerEntry.setResource(practitioner); BundleEntryComponent documentReferenceEntry = bundle.addEntry(); DocumentReference documentReference = new DocumentReference(); documentReferenceEntry.setResource(documentReference); documentReference.setId(document.getId()); DocumentReferenceContentComponent content = documentReference.addContent(); content.setAttachment(new Attachment().setContentType("application/pdf") .setData(IOUtils.toByteArray(document.getContent()))); composition.setSubject(new Reference(subject)); composition.setAuthor(Collections.singletonList(new Reference(practitioner))); SectionComponent section = composition.addSection(); section.addEntry(new Reference(documentReference)); } catch (IOException e) { LoggerFactory.getLogger(getClass()).error("Error creating FHIR bundle", e); throw new IllegalStateException("Error creating FHIR bundle", e); } }
Example #14
Source File: BatchLoader.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
private static void sendFile(FHIRToolingClient client, File f, int size, IniFile ini) throws FHIRFormatError, FileNotFoundException, IOException { long ms = System.currentTimeMillis(); System.out.print("Loading "+f.getName()+".. "); IParser parser = f.getName().endsWith(".json") ? new JsonParser() : new XmlParser(); Resource res = parser.parse(new FileInputStream(f)); System.out.println(" done: ("+Long.toString(System.currentTimeMillis()-ms)+" ms)"); if (res instanceof Bundle) { Bundle bnd = (Bundle) res; int cursor = ini.hasProperty("progress", f.getName()) ? ini.getIntegerProperty("progress", f.getName()) : 0; while (cursor < bnd.getEntry().size()) { Bundle bt = new Bundle(); bt.setType(BundleType.BATCH); bt.setId(UUID.randomUUID().toString().toLowerCase()); for (int i = cursor; i < Math.min(bnd.getEntry().size(), cursor+size); i++) { BundleEntryComponent be = bt.addEntry(); be.setResource(bnd.getEntry().get(i).getResource()); be.getRequest().setMethod(HTTPVerb.PUT); be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId()); } System.out.print(f.getName()+" ("+cursor+"/"+bnd.getEntry().size()+"): "); ms = System.currentTimeMillis(); Bundle resp = client.transaction(bt); int ncursor = cursor+size; for (int i = 0; i < resp.getEntry().size(); i++) { BundleEntryComponent t = resp.getEntry().get(i); if (!t.getResponse().getStatus().startsWith("2")) { System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus()); ncursor = cursor+i-1; break; } } cursor = ncursor; System.out.println(" .. done: ("+Long.toString(System.currentTimeMillis()-ms)+" ms) "+SimpleDateFormat.getInstance().format(new Date())); ini.setIntegerProperty("progress", f.getName(), cursor, null); ini.save(); } ini.setBooleanProperty("finished", f.getName(), true, null); ini.save(); } else { client.update(res); ini.setBooleanProperty("finished", f.getName(), true, null); ini.save(); } }
Example #15
Source File: FHIRR4ExporterTest.java From synthea with Apache License 2.0 | 4 votes |
@Test public void testObservationAttachment() throws Exception { Person person = new Person(0L); person.attributes.put(Person.GENDER, "F"); person.attributes.put(Person.FIRST_LANGUAGE, "spanish"); person.attributes.put(Person.RACE, "other"); person.attributes.put(Person.ETHNICITY, "hispanic"); person.attributes.put(Person.INCOME, Integer.parseInt(Config .get("generate.demographics.socioeconomic.income.poverty")) * 2); person.attributes.put(Person.OCCUPATION_LEVEL, 1.0); person.attributes.put("Pulmonary Resistance", 0.1552); person.attributes.put("BMI Multiplier", 0.055); person.setVitalSign(VitalSign.BMI, 21.0); person.history = new LinkedList<>(); Provider mock = Mockito.mock(Provider.class); mock.uuid = "Mock-UUID"; person.setProvider(EncounterType.AMBULATORY, mock); person.setProvider(EncounterType.WELLNESS, mock); person.setProvider(EncounterType.EMERGENCY, mock); person.setProvider(EncounterType.INPATIENT, mock); Long time = System.currentTimeMillis(); long birthTime = time - Utilities.convertTime("years", 35); person.attributes.put(Person.BIRTHDATE, birthTime); Payer.loadNoInsurance(); for (int i = 0; i < person.payerHistory.length; i++) { person.setPayerAtAge(i, Payer.noInsurance); } Module module = TestHelper.getFixture("observation.json"); State physiology = module.getState("Simulate_CVS"); assertTrue(physiology.process(person, time)); person.history.add(physiology); State encounter = module.getState("SomeEncounter"); assertTrue(encounter.process(person, time)); person.history.add(encounter); State chartState = module.getState("ChartObservation"); assertTrue(chartState.process(person, time)); person.history.add(chartState); State urlState = module.getState("UrlObservation"); assertTrue(urlState.process(person, time)); person.history.add(urlState); FhirContext ctx = FhirContext.forR4(); IParser parser = ctx.newJsonParser().setPrettyPrint(true); String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis()); Bundle bundle = parser.parseResource(Bundle.class, fhirJson); for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.getResource() instanceof Media) { Media media = (Media) entry.getResource(); if (media.getContent().getData() != null) { assertEquals(400, media.getWidth()); assertEquals(200, media.getHeight()); assertEquals("Invasive arterial pressure", media.getReasonCode().get(0).getText()); assertTrue(Base64.isBase64(media.getContent().getDataElement().getValueAsString())); } else if (media.getContent().getUrl() != null) { assertEquals("https://example.com/image/12498596132", media.getContent().getUrl()); assertEquals("en-US", media.getContent().getLanguage()); assertTrue(media.getContent().getSize() > 0); } else { fail("Invalid Media element in output JSON"); } } } }
Example #16
Source File: FHIRR4ExporterTest.java From synthea with Apache License 2.0 | 4 votes |
@Test public void testSampledDataExport() throws Exception { Person person = new Person(0L); person.attributes.put(Person.GENDER, "F"); person.attributes.put(Person.FIRST_LANGUAGE, "spanish"); person.attributes.put(Person.RACE, "other"); person.attributes.put(Person.ETHNICITY, "hispanic"); person.attributes.put(Person.INCOME, Integer.parseInt(Config .get("generate.demographics.socioeconomic.income.poverty")) * 2); person.attributes.put(Person.OCCUPATION_LEVEL, 1.0); person.history = new LinkedList<>(); Provider mock = Mockito.mock(Provider.class); mock.uuid = "Mock-UUID"; person.setProvider(EncounterType.AMBULATORY, mock); person.setProvider(EncounterType.WELLNESS, mock); person.setProvider(EncounterType.EMERGENCY, mock); person.setProvider(EncounterType.INPATIENT, mock); Long time = System.currentTimeMillis(); long birthTime = time - Utilities.convertTime("years", 35); person.attributes.put(Person.BIRTHDATE, birthTime); Payer.loadNoInsurance(); for (int i = 0; i < person.payerHistory.length; i++) { person.setPayerAtAge(i, Payer.noInsurance); } Module module = TestHelper.getFixture("observation.json"); State encounter = module.getState("SomeEncounter"); assertTrue(encounter.process(person, time)); person.history.add(encounter); State physiology = module.getState("Simulate_CVS"); assertTrue(physiology.process(person, time)); person.history.add(physiology); State sampleObs = module.getState("SampledDataObservation"); assertTrue(sampleObs.process(person, time)); person.history.add(sampleObs); FhirContext ctx = FhirContext.forR4(); IParser parser = ctx.newJsonParser().setPrettyPrint(true); String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis()); Bundle bundle = parser.parseResource(Bundle.class, fhirJson); for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.getResource() instanceof Observation) { Observation obs = (Observation) entry.getResource(); assertTrue(obs.getValue() instanceof SampledData); SampledData data = (SampledData) obs.getValue(); assertEquals(10, data.getPeriod().doubleValue(), 0.001); // 0.01s == 10ms assertEquals(3, (int) data.getDimensions()); } } }
Example #17
Source File: FHIRR4ExporterTest.java From synthea with Apache License 2.0 | 4 votes |
@Test public void testFHIRR4Export() throws Exception { TestHelper.loadTestProperties(); Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts"); Config.set("exporter.baseDirectory", tempFolder.newFolder().toString()); FhirContext ctx = FhirContext.forR4(); IParser parser = ctx.newJsonParser().setPrettyPrint(true); ValidationResources validator = new ValidationResources(); List<String> validationErrors = new ArrayList<String>(); int numberOfPeople = 10; Generator generator = new Generator(numberOfPeople); generator.options.overflow = false; for (int i = 0; i < numberOfPeople; i++) { int x = validationErrors.size(); TestHelper.exportOff(); Person person = generator.generatePerson(i); FhirR4.TRANSACTION_BUNDLE = person.random.nextBoolean(); FhirR4.USE_US_CORE_IG = person.random.nextBoolean(); FhirR4.USE_SHR_EXTENSIONS = false; String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis()); // Check that the fhirJSON doesn't contain unresolved SNOMED-CT strings // (these should have been converted into URIs) if (fhirJson.contains("SNOMED-CT")) { validationErrors.add( "JSON contains unconverted references to 'SNOMED-CT' (should be URIs)"); } // Now validate the resource... IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson); ValidationResult result = validator.validateR4(resource); if (!result.isSuccessful()) { // If the validation failed, let's crack open the Bundle and validate // each individual entry.resource to get context-sensitive error // messages... Bundle bundle = parser.parseResource(Bundle.class, fhirJson); for (Bundle.BundleEntryComponent entry : bundle.getEntry()) { ValidationResult eresult = validator.validateR4(entry.getResource()); if (!eresult.isSuccessful()) { for (SingleValidationMessage emessage : eresult.getMessages()) { boolean valid = false; if (emessage.getMessage().contains("@ AllergyIntolerance ait-2")) { /* * The ait-2 invariant: * Description: * AllergyIntolerance.clinicalStatus SHALL NOT be present * if verification Status is entered-in-error * Expression: * verificationStatus!='entered-in-error' or clinicalStatus.empty() */ valid = true; } else if (emessage.getMessage().contains("@ ExplanationOfBenefit dom-3")) { /* * For some reason, it doesn't like the contained ServiceRequest and contained * Coverage resources in the ExplanationOfBenefit, both of which are * properly referenced. Running $validate on test servers finds this valid... */ valid = true; } else if (emessage.getMessage().contains( "per-1: If present, start SHALL have a lower value than end")) { /* * The per-1 invariant does not account for daylight savings time... so, if the * daylight savings switch happens between the start and end, the validation * fails, even if it is valid. */ valid = true; // ignore this error } else if (emessage.getMessage().contains("[active, inactive, entered-in-error]") || emessage.getMessage().contains("MedicationStatusCodes-list")) { /* * MedicationStatement.status has more legal values than this... including * completed and stopped. */ valid = true; } if (!valid) { System.out.println(parser.encodeResourceToString(entry.getResource())); System.out.println("ERROR: " + emessage.getMessage()); validationErrors.add(emessage.getMessage()); } } } } } int y = validationErrors.size(); if (x != y) { Exporter.export(person, System.currentTimeMillis()); } } assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", validationErrors), validationErrors.size() == 0); }
Example #18
Source File: GraphQLEngine.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
SearchEdge(String type, BundleEntryComponent be) { this.type = type; this.be = be; }
Example #19
Source File: GraphQLEngine.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
private List<Base> getEdges() { List<Base> list = new ArrayList<>(); for (BundleEntryComponent be : bnd.getEntry()) list.add(new SearchEdge(type.substring(0, type.length() - 10) + "Edge", be)); return list; }
Example #20
Source File: R3ToR4Loader.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
@Override public boolean ignoreEntry(BundleEntryComponent src) { return false; }
Example #21
Source File: FhirR4.java From synthea with Apache License 2.0 | 4 votes |
/** * Map the given Observation with attachment element to a FHIR Media resource, and add it to the * given Bundle. * * @param personEntry The Entry for the Person * @param bundle Bundle to add the Media to * @param encounterEntry Current Encounter entry * @param obs The Observation to map to FHIR and add to the bundle * @return The added Entry */ private static BundleEntryComponent media(BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Observation obs) { org.hl7.fhir.r4.model.Media mediaResource = new org.hl7.fhir.r4.model.Media(); // Hard code as Image since we don't anticipate using video or audio any time soon Code mediaType = new Code("http://terminology.hl7.org/CodeSystem/media-type", "image", "Image"); if (obs.codes != null && obs.codes.size() > 0) { List<CodeableConcept> reasonList = obs.codes.stream() .map(code -> mapCodeToCodeableConcept(code, SNOMED_URI)).collect(Collectors.toList()); mediaResource.setReasonCode(reasonList); } mediaResource.setType(mapCodeToCodeableConcept(mediaType, MEDIA_TYPE_URI)); mediaResource.setStatus(MediaStatus.COMPLETED); mediaResource.setSubject(new Reference(personEntry.getFullUrl())); mediaResource.setEncounter(new Reference(encounterEntry.getFullUrl())); Attachment content = (Attachment) obs.value; org.hl7.fhir.r4.model.Attachment contentResource = new org.hl7.fhir.r4.model.Attachment(); contentResource.setContentType(content.contentType); contentResource.setLanguage(content.language); if (content.data != null) { contentResource.setDataElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.data)); } contentResource.setUrl(content.url); contentResource.setSize(content.size); contentResource.setTitle(content.title); if (content.hash != null) { contentResource.setHashElement(new org.hl7.fhir.r4.model.Base64BinaryType(content.hash)); } mediaResource.setWidth(content.width); mediaResource.setHeight(content.height); mediaResource.setContent(contentResource); return newEntry(bundle, mediaResource); }
Example #22
Source File: FhirR4.java From synthea with Apache License 2.0 | 4 votes |
/** * Add a MedicationAdministration if needed for the given medication. * * @param personEntry The Entry for the Person * @param bundle Bundle to add the MedicationAdministration to * @param encounterEntry Current Encounter entry * @param medication The Medication * @param medicationRequest The related medicationRequest * @return The added Entry */ private static BundleEntryComponent medicationAdministration( BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Medication medication, MedicationRequest medicationRequest) { MedicationAdministration medicationResource = new MedicationAdministration(); medicationResource.setSubject(new Reference(personEntry.getFullUrl())); medicationResource.setContext(new Reference(encounterEntry.getFullUrl())); Code code = medication.codes.get(0); String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI; medicationResource.setMedication(mapCodeToCodeableConcept(code, system)); medicationResource.setEffective(new DateTimeType(new Date(medication.start))); medicationResource.setStatus("completed"); if (medication.prescriptionDetails != null) { JsonObject rxInfo = medication.prescriptionDetails; MedicationAdministrationDosageComponent dosage = new MedicationAdministrationDosageComponent(); // as_needed is false if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) { Quantity dose = new SimpleQuantity() .setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble()); dosage.setDose((SimpleQuantity) dose); if (rxInfo.has("instructions")) { for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) { JsonObject instruction = instructionElement.getAsJsonObject(); dosage.setText(instruction.get("display").getAsString()); } } } if (rxInfo.has("refills")) { SimpleQuantity rate = new SimpleQuantity(); rate.setValue(rxInfo.get("refills").getAsLong()); dosage.setRate(rate); } medicationResource.setDosage(dosage); } if (!medication.reasons.isEmpty()) { // Only one element in list Code reason = medication.reasons.get(0); for (BundleEntryComponent entry : bundle.getEntry()) { if (entry.getResource().fhirType().equals("Condition")) { Condition condition = (Condition) entry.getResource(); // Only one element in list Coding coding = condition.getCode().getCoding().get(0); if (reason.code.equals(coding.getCode())) { medicationResource.addReasonReference().setReference(entry.getFullUrl()); } } } } BundleEntryComponent medicationAdminEntry = newEntry(bundle, medicationResource); return medicationAdminEntry; }
Example #23
Source File: NpmPackageVersionConverter.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
@Override public boolean ignoreEntry(BundleEntryComponent src) { return false; }
Example #24
Source File: FhirR4.java From synthea with Apache License 2.0 | 4 votes |
/** * Create an entry for the given Claim, which references a Medication. * * @param person The person being prescribed medication * @param personEntry Entry for the person * @param bundle The Bundle to add to * @param encounterEntry The current Encounter * @param claim the Claim object * @param medicationEntry The Entry for the Medication object, previously created * @return the added Entry */ private static BundleEntryComponent medicationClaim( Person person, BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry, Claim claim, BundleEntryComponent medicationEntry) { org.hl7.fhir.r4.model.Claim claimResource = new org.hl7.fhir.r4.model.Claim(); org.hl7.fhir.r4.model.Encounter encounterResource = (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource(); claimResource.setStatus(ClaimStatus.ACTIVE); CodeableConcept type = new CodeableConcept(); type.getCodingFirstRep() .setSystem("http://terminology.hl7.org/CodeSystem/claim-type") .setCode("pharmacy"); claimResource.setType(type); claimResource.setUse(org.hl7.fhir.r4.model.Claim.Use.CLAIM); // Get the insurance info at the time that the encounter occurred. InsuranceComponent insuranceComponent = new InsuranceComponent(); insuranceComponent.setSequence(1); insuranceComponent.setFocal(true); insuranceComponent.setCoverage(new Reference().setDisplay(claim.payer.getName())); claimResource.addInsurance(insuranceComponent); // duration of encounter claimResource.setBillablePeriod(encounterResource.getPeriod()); claimResource.setCreated(encounterResource.getPeriod().getEnd()); claimResource.setPatient(new Reference(personEntry.getFullUrl())); claimResource.setProvider(encounterResource.getServiceProvider()); // set the required priority CodeableConcept priority = new CodeableConcept(); priority.getCodingFirstRep() .setSystem("http://terminology.hl7.org/CodeSystem/processpriority") .setCode("normal"); claimResource.setPriority(priority); // add item for encounter claimResource.addItem(new ItemComponent(new PositiveIntType(1), encounterResource.getTypeFirstRep()) .addEncounter(new Reference(encounterEntry.getFullUrl()))); // add prescription. claimResource.setPrescription(new Reference(medicationEntry.getFullUrl())); Money moneyResource = new Money(); moneyResource.setValue(claim.getTotalClaimCost()); moneyResource.setCurrency("USD"); claimResource.setTotal(moneyResource); return newEntry(bundle, claimResource); }
Example #25
Source File: IGR2ConvertorAdvisor.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
@Override public boolean ignoreEntry(BundleEntryComponent src) { return false; }
Example #26
Source File: R2016MayToR4Loader.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
@Override public boolean ignoreEntry(BundleEntryComponent src) { return false; }
Example #27
Source File: FhirR4.java From synthea with Apache License 2.0 | 4 votes |
/** * Convert the given Person into a FHIR Bundle of the Patient and the * associated entries from their health record. * * @param person Person to generate the FHIR JSON for * @param stopTime Time the simulation ended * @return FHIR Bundle containing the Person's health record */ public static Bundle convertToFHIR(Person person, long stopTime) { Bundle bundle = new Bundle(); if (TRANSACTION_BUNDLE) { bundle.setType(BundleType.TRANSACTION); } else { bundle.setType(BundleType.COLLECTION); } BundleEntryComponent personEntry = basicInfo(person, bundle, stopTime); for (Encounter encounter : person.record.encounters) { BundleEntryComponent encounterEntry = encounter(person, personEntry, bundle, encounter); for (HealthRecord.Entry condition : encounter.conditions) { condition(personEntry, bundle, encounterEntry, condition); } for (HealthRecord.Entry allergy : encounter.allergies) { allergy(personEntry, bundle, encounterEntry, allergy); } for (Observation observation : encounter.observations) { // If the Observation contains an attachment, use a Media resource, since // Observation resources in v4 don't support Attachments if (observation.value instanceof Attachment) { media(personEntry, bundle, encounterEntry, observation); } else { observation(personEntry, bundle, encounterEntry, observation); } } for (Procedure procedure : encounter.procedures) { procedure(personEntry, bundle, encounterEntry, procedure); } for (HealthRecord.Device device : encounter.devices) { device(personEntry, bundle, device); } for (HealthRecord.Supply supply : encounter.supplies) { supplyDelivery(personEntry, bundle, supply, encounter); } for (Medication medication : encounter.medications) { medicationRequest(person, personEntry, bundle, encounterEntry, medication); } for (HealthRecord.Entry immunization : encounter.immunizations) { immunization(personEntry, bundle, encounterEntry, immunization); } for (Report report : encounter.reports) { report(personEntry, bundle, encounterEntry, report); } for (CarePlan careplan : encounter.careplans) { BundleEntryComponent careTeamEntry = careTeam(personEntry, bundle, encounterEntry, careplan); carePlan(personEntry, bundle, encounterEntry, encounter.provider, careTeamEntry, careplan); } for (ImagingStudy imagingStudy : encounter.imagingStudies) { imagingStudy(personEntry, bundle, encounterEntry, imagingStudy); } if (USE_US_CORE_IG) { String clinicalNoteText = ClinicalNoteExporter.export(person, encounter); boolean lastNote = (encounter == person.record.encounters.get(person.record.encounters.size() - 1)); clinicalNote(personEntry, bundle, encounterEntry, clinicalNoteText, lastNote); } // one claim per encounter BundleEntryComponent encounterClaim = encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim); explanationOfBenefit(personEntry, bundle, encounterEntry, person, encounterClaim, encounter); } if (USE_US_CORE_IG) { // Add Provenance to the Bundle provenance(bundle, person, stopTime); } return bundle; }
Example #28
Source File: R2ToR4Loader.java From org.hl7.fhir.core with Apache License 2.0 | 4 votes |
@Override public boolean ignoreEntry(BundleEntryComponent src) { return false; }
Example #29
Source File: FhirR4.java From synthea with Apache License 2.0 | 2 votes |
/** * Helper function to create an Entry for the given Resource within the given Bundle. Sets the * resourceID to a random UUID, sets the entry's fullURL to that resourceID, and adds the entry to * the bundle. * * @param bundle The Bundle to add the Entry to * @param resource Resource the new Entry should contain * @return the created Entry */ private static BundleEntryComponent newEntry(Bundle bundle, Resource resource) { String resourceID = UUID.randomUUID().toString(); return newEntry(bundle, resource, resourceID); }