Examples with Organization org.hl7.fhir.r4.model.Organization used on opensource projects

Example 71 with Organization

use of org.hl7.fhir.r4.model.Organization in project odm2fhir by num-codex.

the class Subject method map.

public Stream<DomainResource> map(SubjectData subjectData) {
    var value = getIdentifierAssigner();
    if (!ENVIRONMENT.containsProperty("debug")) {
        value = sha256Hex(value);
    }
    var organizationIdentifier = new Identifier().setSystem(getIdentifierSystem(ORGANIZATION)).setValue(value);
    var organization = (Organization) new Organization().setName(getIdentifierAssigner()).addIdentifier(organizationIdentifier).setId(sha256Hex(organizationIdentifier.getSystem() + organizationIdentifier.getValue()));
    organizationReference = new Reference(format("%s/%s", ORGANIZATION.toCode(), organization.getId()));
    value = subjectData.getSubjectKey();
    if (!ENVIRONMENT.containsProperty("debug")) {
        value = sha256Hex(value);
    }
    var patientIdentifier = new Identifier().setSystem(getIdentifierSystem(PATIENT)).setValue(value).setType(new CodeableConcept(new Coding().setSystem(IDENTIFIER_TYPE_CODES.getUrl()).setCode(MR.toCode()))).setAssigner(organizationReference);
    patient = (Patient) new Patient().addIdentifier(patientIdentifier).setId(sha256Hex(patientIdentifier.getSystem() + patientIdentifier.getValue())).setMeta(new Meta().addProfile(NUMStructureDefinition.PATIENT.getUrl()));
    patientReference = new Reference(format("%s/%s", PATIENT.toCode(), patient.getId()));
    return Stream.concat(Stream.of(patient, organization), subjectData.getMergedStudyEventData().stream().flatMap(studyEventData -> new StudyEvent().map(this, studyEventData)).peek(this::setId).peek(this::setPatientSubject));
}

Example 72 with Organization

use of org.hl7.fhir.r4.model.Organization in project geoprism-registry by terraframe.

the class AbstractFhirDataPopulator method getLiteralIdentifier.

private String getLiteralIdentifier(String code) {
    if (this.resolveIds) {
        if (!this.identifiers.containsKey(code)) {
            IGenericClient client = context.getClient();
            IBaseBundle result = client.search().forResource(Organization.class).count(1).where(Organization.IDENTIFIER.exactly().systemAndValues(context.getSystem(), code)).execute();
            List<IBaseResource> resources = BundleUtil.toListOfResources(client.getFhirContext(), result);
            if (resources.size() > 0) {
                IBaseResource resource = resources.get(0);
                IIdType idElement = resource.getIdElement();
                this.identifiers.put(code, idElement.getResourceType() + "/" + idElement.getIdPart());
            }
        }
        return this.identifiers.get(code);
    }
    return "Organization/" + code;
}

Example 73 with Organization

use of org.hl7.fhir.r4.model.Organization in project geoprism-registry by terraframe.

the class BasicFhirDataPopulator method populate.

@Override
public void populate(Business row, Facility facility) {
    Organization org = facility.getOrganization();
    org.addAlias(row.getValue(DefaultAttribute.DISPLAY_LABEL.getName() + ListTypeVersion.DEFAULT_LOCALE));
    Location location = facility.getLocation();
    location.setMode(LocationMode.INSTANCE);
    location.setStatus(LocationStatus.ACTIVE);
    location.addAlias(row.getValue(DefaultAttribute.DISPLAY_LABEL.getName() + ListTypeVersion.DEFAULT_LOCALE));
    Collection<Locale> locales = LocalizationFacade.getInstalledLocales();
    for (Locale locale : locales) {
        String attributeName = DefaultAttribute.DISPLAY_LABEL.getName() + locale.toString();
        if (row.hasAttribute(attributeName)) {
            String value = row.getValue(attributeName);
            if (value != null) {
                org.addAlias(value);
                location.addAlias(value);
            }
        }
    }
}

Example 74 with Organization

use of org.hl7.fhir.r4.model.Organization in project geoprism-registry by terraframe.

the class FhirBulkDataImporter method synchronize.

public void synchronize() {
    PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
    HttpClientBuilder builder = HttpClientBuilder.create();
    builder.setConnectionManager(connectionManager);
    CloseableHttpClient myClient = builder.build();
    FhirContext ctx = FhirContext.forR4();
    String statusUrl = initiateBulkExport(myClient, ctx);
    if (statusUrl != null) {
        final List<String> outputs = getExportResults(myClient, statusUrl);
        IGenericClient client = ctx.newRestfulGenericClient(this.system.getUrl());
        for (String binaryUrl : outputs) {
            Binary binary = client.fetchResourceFromUrl(Binary.class, binaryUrl);
            String base64 = binary.getContentAsBase64();
            byte[] result = Base64.getDecoder().decode(base64);
            IParser parser = ctx.newJsonParser();
            String message = new String(result);
            try (BufferedReader reader = new BufferedReader(new StringReader(message))) {
                String line = null;
                while ((line = reader.readLine()) != null) {
                    IBaseResource resource = parser.parseResource(line);
                    IIdType id = resource.getIdElement();
                    String resourceType = id.getResourceType();
                    if (resourceType.equals(ResourceTypes.LOCATION.toCode())) {
                        Location location = (Location) resource;
                        this.processor.process(location);
                    } else if (resourceType.equals(ResourceTypes.ORGANIZATION.toCode())) {
                        Organization organization = (Organization) resource;
                        this.processor.process(organization);
                    }
                }
            } catch (IOException e) {
                throw new ProgrammingErrorException(e);
            }
        }
    }
}

Example 75 with Organization

use of org.hl7.fhir.r4.model.Organization in project geoprism-registry by terraframe.

the class FhirResourceImporter method process.

private void process(Bundle bundle) {
    FhirPathR4 path = new FhirPathR4(FhirContext.forR4());
    List<Location> locations = path.evaluate(bundle, "Bundle.entry.resource.ofType(Location)", Location.class);
    for (Location location : locations) {
        try {
            handleLocation(location);
            if (this.history != null) {
                this.history.appLock();
                this.history.setWorkProgress(count++);
                this.history.setExportedRecords(exportCount++);
                this.history.apply();
            }
        } catch (Exception e) {
            if (this.history != null) {
                this.recordExportError(e, this.history, location);
                this.history.appLock();
                this.history.setWorkProgress(count++);
                this.history.apply();
            } else {
                throw new ProgrammingErrorException(e);
            }
        }
    }
    List<Organization> organizations = path.evaluate(bundle, "Bundle.entry.resource.ofType(Organization)", Organization.class);
    for (Organization organization : organizations) {
        try {
            handleOrganization(organization);
            if (this.history != null) {
                this.history.appLock();
                this.history.setWorkProgress(count++);
                this.history.setExportedRecords(exportCount++);
                this.history.apply();
            }
        } catch (Exception e) {
            if (this.history != null) {
                this.recordExportError(e, this.history, organization);
                this.history.appLock();
                this.history.setWorkProgress(count++);
                this.history.apply();
            } else {
                throw new ProgrammingErrorException(e);
            }
        }
    }
}