use of org.hl7.fhir.r5.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_orur01_with_encounter_present.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@Test
void test_orur01_with_encounter_present() throws IOException {
String hl7message = "MSH|^~\\&|PROSLOV|MYHOSPITAL|WHIA|IBM|20180520230000||ORU^R01|MSGID006552|T|2.6\r" + "PID|1||000065432^^^MRN^MR||ROSTENKOWSKI^BERNADETTE^||19840823|Female||1002-5|382 OTHERSTREET AVE^^PASADENA^LA^223343||4582143248||^French|S||53811||||U|||||||\r" + "PV1|1|O|||||9905^Adams^John|9906^Yellow^William^F|9907^Blue^Oren^J||||||||9908^Green^Mircea^||2462201|||||||||||||||||||||||||20180520230000\r" + "OBR|1||bbf1993ab|1122^Final Echocardiogram Report|||20180520230000|||||||||||||002|||||F|||550469^Tsadok550469^Janetary~660469^Merrit660469^Darren^F~770469^Das770469^Surjya^P~880469^Winter880469^Oscar^||||770469&Das770469&Surjya&P^^^6N^1234^A|\r" + "OBX|1|NM|2552^HRTRTMON|1|115||||||F|||20180520230000|||\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify that the right resources are created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(5);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(10);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("Final Echocardiogram Report");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1122");
assertThat(coding.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isFalse();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2018-05-20T23:00:00+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(1);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not of type TX.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference exists
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isFalse();
assertThat(obs.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.r5.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_with_multiple_observations.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@Test
// Observation resources are created instead of attachments in the diagReport because they are not type TX.
void test_oru_with_multiple_observations() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + // OBR.24 creates a DiagnosticReport.category
"OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002||||CUS|F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|ST|TS-F-01-002^Endocrine Disorders^L||obs report||||||F\r" + "OBX|2|ST|GA-F-01-024^Galactosemia^L||ECHOCARDIOGRAPHIC REPORT||||||F\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify correct resources created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(2);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(1);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(6);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).hasSize(1);
DatatypeUtils.checkCommonCodeableConceptAssertions(diag.getCategoryFirstRep(), "CUS", "Cardiac Ultrasound", "http://terminology.hl7.org/CodeSystem/v2-0074", "CUS");
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("New Born Screening");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1051-2");
assertThat(coding.hasSystem()).isTrue();
assertThat(coding.getSystem()).hasToString("http://loinc.org");
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo(// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
"2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(2);
assertThat(obsRef.get(0).isEmpty()).isFalse();
assertThat(obsRef.get(1).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX of type TX have ids.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference is not set
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isTrue();
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.r5.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_multipleOBXWithMixedType.
/**
* Verifies ORU messages with mixed OBX types
*
* @throws IOException
*/
@Test
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
void test_oru_multipleOBXWithMixedType() throws IOException {
String json = ftv.convert(new File("src/test/resources/ORU-multiline-short-mixed.hl7"), OPTIONS_PRETTYPRINT);
assertThat(json).isNotBlank();
LOGGER.debug("FHIR json result:\n" + json);
// Verify conversion
FHIRContext context = new FHIRContext();
IBaseResource bundleResource = context.getParser().parseResource(json);
Bundle b = (Bundle) bundleResource;
assertThat(bundleResource).isNotNull();
Assertions.assertSame(BundleType.COLLECTION, b.getType(), "Bundle type not expected");
List<BundleEntryComponent> e = b.getEntry();
// Verify that the right resources have been created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
assertThat(encounterResource).hasSize(1);
List<Resource> organizationResource = ResourceUtils.getResourceList(e, ResourceType.Organization);
// We expect an organization created from an Encounter.serviceProvider reference
assertThat(organizationResource).hasSize(1);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(4);
List<Resource> messageHeader = ResourceUtils.getResourceList(e, ResourceType.MessageHeader);
assertThat(messageHeader).hasSize(1);
// Verify one Observation is created (from the ST, not the TX)
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
// TODO: When NTE is implemented, then update this.
assertThat(obsResource).hasSize(1);
// Verify Diagnostic Report is created as expected
List<Resource> reportResource = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(reportResource).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
// Verify there are no extra resources created
assertThat(e).hasSize(11);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(reportResource.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).hasSize(1);
assertThat(diag.getCategory().get(0).getCoding()).hasSize(1);
assertThat(diag.getCategory().get(0).getCoding().get(0).getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/v2-0074");
assertThat(diag.getCategory().get(0).getCoding().get(0).getCode()).isEqualTo("CT");
assertThat(diag.getCategory().get(0).getCoding().get(0).getDisplay()).isEqualTo("CAT Scan");
assertThat(diag.getCategory().get(0).getText()).isEqualTo("CT");
// Verify code from OBR.4; This tests scenario of the code not being in the default loinc system.
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("ECHO CARDIOGRAM COMPLETE");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1487");
assertThat(coding.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isFalse();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2020-08-02T12:44:55+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).isEmpty();
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
List<Reference> spmRef = diag.getSpecimen();
assertThat(spmRef).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).isNotEmpty().hasSize(1);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// No attachment created since OBX with TX and no id is not first
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference exists
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isFalse();
assertThat(obs.getEncounter().getReference().substring(0, 10)).isEqualTo("Encounter/");
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.r5.model.Attachment in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_patient_diagReport.
// DiagnosticReports are only created from ORU messages so the test of DiagnosticReport content is included in this test module.
// Suppress warnings about too many assertions in a test. Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
@Test
// Test the minimum scenario where the least possible segments and resource info are provided in the message
void test_oru_patient_diagReport() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^|||||\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify correct resources created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(3);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("New Born Screening");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1051-2");
assertThat(coding.hasSystem()).isTrue();
assertThat(coding.getSystem()).hasToString("http://loinc.org");
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).isEmpty();
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag.getSpecimen()).isEmpty();
// Verify result reference
assertThat(diag.getResult()).isEmpty();
// Verify presentedForm from OBX of type TX - In this case no attachments created since there are no OBX with type TX
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
}
use of org.hl7.fhir.r5.model.Attachment in project fhir-bridge by ehrbase.
the class DocumentReferenceProcessor method process.
@Override
public void process(Exchange exchange) throws Exception {
DocumentReference documentReference = exchange.getIn().getMandatoryBody(DocumentReference.class);
Attachment attachment = documentReference.getContentFirstRep().getAttachment();
ObjectWriteResponse response = minioService.uploadObject(new ByteArrayInputStream(attachment.getData()), attachment.getContentType());
if (!attachment.hasSize()) {
attachment.setSize(attachment.getData().length);
}
attachment.setUrl(minioService.getObjectUrl(response.object()));
attachment.setData(null);
exchange.getMessage().setHeader(CamelConstants.MINIO_OBJECT, response.object());
MethodOutcome outcome = new MethodOutcome().setResource(documentReference);
exchange.setProperty(CamelConstants.OUTCOME, outcome);
}
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