Java Code Examples for org.hl7.fhir.r4.model.Bundle#getEntry()
The following examples show how to use
org.hl7.fhir.r4.model.Bundle#getEntry() .
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Example 1
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 2
Source File: MeasureOperationsProvider.java From cqf-ruler with Apache License 2.0 | 6 votes |
private void addEvaluatedResourcesToParameters(Bundle contained, Parameters parameters) { Map<String, Resource> resourceMap = new HashMap<>(); if (contained.hasEntry()) { for (Bundle.BundleEntryComponent entry : contained.getEntry()) { if (entry.hasResource() && !(entry.getResource() instanceof ListResource)) { if (!resourceMap.containsKey(entry.getResource().getIdElement().getValue())) { parameters.addParameter(new Parameters.ParametersParameterComponent().setName("resource") .setResource(entry.getResource())); resourceMap.put(entry.getResource().getIdElement().getValue(), entry.getResource()); resolveReferences(entry.getResource(), parameters, resourceMap); } } } } }
Example 3
Source File: MeasureOperationsProvider.java From cqf-ruler with Apache License 2.0 | 6 votes |
private Bundle createTransactionBundle(Bundle bundle) { Bundle transactionBundle; if (bundle != null) { if (bundle.hasType() && bundle.getType() == Bundle.BundleType.TRANSACTION) { transactionBundle = bundle; } else { transactionBundle = new Bundle().setType(Bundle.BundleType.TRANSACTION); if (bundle.hasEntry()) { for (Bundle.BundleEntryComponent entry : bundle.getEntry()) { if (entry.hasResource()) { transactionBundle.addEntry(createTransactionEntry(entry.getResource())); } } } } } else { transactionBundle = new Bundle().setType(Bundle.BundleType.TRANSACTION).setEntry(new ArrayList<>()); } return transactionBundle; }
Example 4
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 5
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 6
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 7
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 8
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 9
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 10
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 11
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 12
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"); } } } }