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ResourceTransformerTest.java
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ResourceTransformerTest.java
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package tr.com.srdc.cda2fhir;
/*
* #%L
* CDA to FHIR Transformer Library
* %%
* Copyright (C) 2016 SRDC Yazilim Arastirma ve Gelistirme ve Danismanlik Tic. A.S.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.File;
import java.io.FileInputStream;
import java.io.FileWriter;
import java.io.IOException;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Composition.SectionComponent;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.Extension;
import org.hl7.fhir.r4.model.FamilyMemberHistory;
import org.hl7.fhir.r4.model.HumanName;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Immunization;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.MedicationStatement;
import org.hl7.fhir.r4.model.Organization;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Patient.ContactComponent;
import org.hl7.fhir.r4.model.Patient.PatientCommunicationComponent;
import org.hl7.fhir.r4.model.PractitionerRole;
import org.hl7.fhir.r4.model.Procedure;
import org.hl7.fhir.r4.model.Reference;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.openhealthtools.mdht.uml.cda.Organizer;
import org.openhealthtools.mdht.uml.cda.PatientRole;
import org.openhealthtools.mdht.uml.cda.consol.AllergyProblemAct;
import org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument;
import org.openhealthtools.mdht.uml.cda.consol.FunctionalStatusResultOrganizer;
import org.openhealthtools.mdht.uml.cda.consol.FunctionalStatusSection;
import org.openhealthtools.mdht.uml.cda.consol.ImmunizationActivity;
import org.openhealthtools.mdht.uml.cda.consol.ImmunizationsSectionEntriesOptional;
import org.openhealthtools.mdht.uml.cda.consol.MedicationActivity;
import org.openhealthtools.mdht.uml.cda.consol.ProblemConcernAct;
import org.openhealthtools.mdht.uml.cda.consol.ResultOrganizer;
import org.openhealthtools.mdht.uml.cda.consol.ResultsSection;
import org.openhealthtools.mdht.uml.cda.consol.SocialHistorySection;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignObservation;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignsOrganizer;
import org.openhealthtools.mdht.uml.cda.consol.VitalSignsSectionEntriesOptional;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil;
import org.openhealthtools.mdht.uml.hl7.datatypes.EN;
import org.openhealthtools.mdht.uml.hl7.datatypes.ENXP;
import org.openhealthtools.mdht.uml.hl7.datatypes.II;
import ca.uhn.fhir.model.api.IResource;
import tr.com.srdc.cda2fhir.transform.ResourceTransformerImpl;
import tr.com.srdc.cda2fhir.transform.ValueSetsTransformerImpl;
import tr.com.srdc.cda2fhir.transform.entry.IEntryResult;
import tr.com.srdc.cda2fhir.transform.entry.impl.EntryResult;
import tr.com.srdc.cda2fhir.transform.util.impl.BundleInfo;
import tr.com.srdc.cda2fhir.util.FHIRUtil;
public class ResourceTransformerTest {
private static final ResourceTransformerImpl rt = new ResourceTransformerImpl();
private static final ValueSetsTransformerImpl vsti = new ValueSetsTransformerImpl();
private static FileInputStream fisCCD;
private static FileInputStream fisCCD2;
private static FileWriter resultFW;
private static ContinuityOfCareDocument ccd;
private static ContinuityOfCareDocument ccd2;
private static final String resultFilePath = "src/test/resources/output/ResourceTransformerTest.txt";
private static final String transformationStartMsg = "\n# TRANSFORMATION STARTING..\n";
private static final String transformationEndMsg = "# END OF TRANSFORMATION.\n";
private static final String endOfTestMsg = "\n## END OF TEST\n";
@BeforeClass
public static void init() {
CDAUtil.loadPackages();
// read the input test file
try {
fisCCD = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD.xml");
fisCCD2 = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD2.xml"); // Original does not have authoring
// device.
ccd = (ContinuityOfCareDocument) CDAUtil.load(fisCCD);
ccd2 = (ContinuityOfCareDocument) CDAUtil.load(fisCCD2);
} catch (Exception ex) {
ex.printStackTrace();
}
// init the output file writer
File resultFile = new File(resultFilePath);
resultFile.getParentFile().mkdirs();
try {
resultFW = new FileWriter(resultFile);
} catch (IOException e) {
e.printStackTrace();
}
}
@AfterClass
public static void finalise() {
try {
resultFW.close();
} catch (IOException e) {
e.printStackTrace();
}
}
@Test
public void referenceOrgNameStringTest() {
String name = "Organization Name";
Organization org = new Organization();
org.setName(name);
Reference ref = rt.getReference(org);
Assert.assertEquals("Organization name becomes reference display", ref.getDisplay(), name);
}
@Test
public void referenceHumanNameTest() {
String firstName = "Homer";
String lastName = "Simpson";
HumanName name = new HumanName();
name.setFamily(lastName);
name.addGiven(firstName);
Patient patient = new Patient();
patient.addName(name);
Reference ref = rt.getReference(patient);
Assert.assertEquals("Organization name becomes reference display", ref.getDisplay(),
name.getNameAsSingleString());
}
@Test
public void referenceImmunizationTest() {
CodeableConcept cc = new CodeableConcept();
String expectedDisplay = "expected display";
cc.setText(expectedDisplay);
Immunization immunization = new Immunization();
immunization.setVaccineCode(cc);
Reference ref = rt.getReference(immunization);
Assert.assertEquals("Organization name becomes reference display", ref.getDisplay(), expectedDisplay);
}
@Test
public void referenceDisplayFirstRepTest() {
Reference ref;
CodeableConcept cc = new CodeableConcept();
String expectedDisplay = "expected display";
Coding coding = new Coding();
coding.setDisplay(expectedDisplay);
cc.addCoding(coding);
PractitionerRole pracRole = new PractitionerRole();
Procedure procedure = new Procedure();
pracRole.addCode(cc);
procedure.setCode(cc);
ref = rt.getReference(pracRole);
Assert.assertEquals("Organization name becomes reference display", ref.getDisplay(), expectedDisplay);
ref = rt.getReference(procedure);
Assert.assertEquals("Organization name becomes reference display", ref.getDisplay(), expectedDisplay);
}
@Test
public void referenceCodeTest() {
Reference ref;
String expectedTestID = "testID/0";
String expectedDisplay = "expected display";
CodeableConcept cc = new CodeableConcept();
cc.setText(expectedDisplay);
Medication med = new Medication();
IdType id = new IdType("testID", "0");
med.setId(id);
med.setCode(cc);
ref = rt.getReference(med);
Assert.assertTrue(ref.getReference().contentEquals(expectedTestID));
MedicationStatement medStatement = new MedicationStatement();
medStatement.setId(id);
ref = rt.getReference(medStatement);
Assert.assertTrue(ref.getReference().contentEquals(expectedTestID));
Condition condition = new Condition();
condition.setId(id);
condition.setCode(cc);
ref = rt.getReference(condition);
Assert.assertTrue(ref.getReference().contentEquals(expectedTestID));
}
// Most of the test methods just print the transformed object in JSON form.
@Test
public void testAllergyProblemAct2AllergyIntolerance() {
appendToResultFile("## TEST: AllergyProblemAct2AllergyIntolerance\n");
// null instance test
AllergyProblemAct cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
Bundle fhirNull = rt.tAllergyProblemAct2AllergyIntolerance(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
for (AllergyProblemAct cdaAPA : ResourceTransformerTest.ccd.getAllergiesSection().getAllergyProblemActs()) {
appendToResultFile(transformationStartMsg);
Bundle allergyBundle = rt.tAllergyProblemAct2AllergyIntolerance(cdaAPA, bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(allergyBundle);
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testAssignedAuthor2Device() {
appendToResultFile("## TEST: AssignedAuthor2Device\n");
// null instance test
BundleInfo bundleInfo = new BundleInfo(rt);
org.openhealthtools.mdht.uml.cda.AssignedAuthor cdaNull = null;
Bundle fhirNull = rt.tAssignedAuthor2Device(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd2.getAuthors() != null) {
for (org.openhealthtools.mdht.uml.cda.Author author : ResourceTransformerTest.ccd2.getAuthors()) {
// traversing authors
if (author != null && author.getAssignedAuthor() != null) {
appendToResultFile(transformationStartMsg);
Bundle deviceBundle = rt.tAssignedAuthor2Device(author.getAssignedAuthor(), bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(deviceBundle);
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testAssignedAuthor2Practitioner() {
appendToResultFile("## TEST: AssignedAuthor2Practitioner\n");
// null instance test
BundleInfo bundleInfo = new BundleInfo(rt);
org.openhealthtools.mdht.uml.cda.AssignedAuthor cdaNull = null;
Bundle fhirNull = rt.tAssignedAuthor2Practitioner(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getAuthors() != null) {
for (org.openhealthtools.mdht.uml.cda.Author author : ResourceTransformerTest.ccd.getAuthors()) {
// traversing authors
if (author != null && author.getAssignedAuthor() != null) {
appendToResultFile(transformationStartMsg);
Bundle practitionerBundle = rt.tAssignedAuthor2Practitioner(author.getAssignedAuthor(), bundleInfo)
.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(practitionerBundle);
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testAssignedEntity2Practitioner() {
appendToResultFile("## TEST: AssignedEntity2Practitioner\n");
// null instance test
org.openhealthtools.mdht.uml.cda.AssignedEntity cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
Bundle fhirNull = rt.tAssignedEntity2Practitioner(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getProceduresSection() != null
&& !ResourceTransformerTest.ccd.getProceduresSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getProceduresSection().getProcedures() != null
&& !ResourceTransformerTest.ccd.getProceduresSection().getProcedures().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Procedure procedure : ResourceTransformerTest.ccd
.getProceduresSection().getProcedures()) {
// traversing procedures
if (procedure.getPerformers() != null && !procedure.getPerformers().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Performer2 performer : procedure.getPerformers()) {
if (performer.getAssignedEntity() != null
&& !performer.getAssignedEntity().isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirPractitionerBundle = rt
.tAssignedEntity2Practitioner(performer.getAssignedEntity(), bundleInfo)
.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirPractitionerBundle);
}
}
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testClinicalDocument2Composition() {
appendToResultFile("## TEST: ClinicalDocument2Composition\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument cdaNull = null;
Bundle fhirNull = rt.tClinicalDocument2Composition(cdaNull).getBundle();
Assert.assertNull(fhirNull);
// instance from file
if (ResourceTransformerTest.ccd != null && !ResourceTransformerTest.ccd.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirComp = rt.tClinicalDocument2Composition(ResourceTransformerTest.ccd).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirComp);
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testEncounterActivity2Encounter() {
appendToResultFile("## TEST: EncounterActivity2Encounter\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.EncounterActivities cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
Bundle fhirNull = rt.tEncounterActivity2Encounter(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getEncountersSection() != null
&& !ResourceTransformerTest.ccd.getEncountersSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getEncountersSection().getEncounterActivitiess() != null
&& !ResourceTransformerTest.ccd.getEncountersSection().getEncounterActivitiess().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.consol.EncounterActivities encounterActivity : ResourceTransformerTest.ccd
.getEncountersSection().getEncounterActivitiess()) {
if (encounterActivity != null && !encounterActivity.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirEncounterBundle = rt.tEncounterActivity2Encounter(encounterActivity, bundleInfo)
.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirEncounterBundle);
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testFamilyHistoryOrganizer2FamilyMemberHistory() {
appendToResultFile("## TEST: FamilyHistoryOrganizer2FamilyMemberHistory\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.FamilyHistoryOrganizer cdaNull = null;
FamilyMemberHistory fhirNull = rt.tFamilyHistoryOrganizer2FamilyMemberHistory(cdaNull);
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getFamilyHistorySection() != null
&& ResourceTransformerTest.ccd.getFamilyHistorySection().getFamilyHistories() != null) {
for (org.openhealthtools.mdht.uml.cda.consol.FamilyHistoryOrganizer familyHistoryOrganizer : ResourceTransformerTest.ccd
.getFamilyHistorySection().getFamilyHistories()) {
if (familyHistoryOrganizer != null) {
appendToResultFile(transformationStartMsg);
FamilyMemberHistory fmHistory = rt
.tFamilyHistoryOrganizer2FamilyMemberHistory(familyHistoryOrganizer);
appendToResultFile(transformationEndMsg);
appendToResultFile(fmHistory);
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testFunctionalStatus2Observation() {
appendToResultFile("## TEST: FunctionalStatus2Observation\n");
// null instance test
org.openhealthtools.mdht.uml.cda.Observation cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
Bundle fhirNull = rt.tFunctionalStatus2Observation(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instance from file
FunctionalStatusSection funcStatSec = ResourceTransformerTest.ccd.getFunctionalStatusSection();
if (funcStatSec != null && !funcStatSec.isSetNullFlavor()) {
if (funcStatSec.getOrganizers() != null && !funcStatSec.getOrganizers().isEmpty()) {
for (Organizer funcStatOrg : funcStatSec.getOrganizers()) {
if (funcStatOrg != null && !funcStatOrg.isSetNullFlavor()) {
if (funcStatOrg instanceof FunctionalStatusResultOrganizer) {
if (((FunctionalStatusResultOrganizer) funcStatOrg).getObservations() != null
&& !((FunctionalStatusResultOrganizer) funcStatOrg).getObservations().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Observation cdaObs : ((FunctionalStatusResultOrganizer) funcStatOrg)
.getObservations()) {
appendToResultFile(transformationStartMsg);
Bundle fhirObs = rt.tFunctionalStatus2Observation(cdaObs, bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirObs);
}
}
}
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testGuardian2Contact() {
appendToResultFile("## TEST: Guardian2Contact\n");
// null instance test
org.openhealthtools.mdht.uml.cda.Guardian cdaNull = null;
ContactComponent fhirNull = rt.tGuardian2Contact(cdaNull);
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getPatientRoles() != null
&& !ResourceTransformerTest.ccd.getPatientRoles().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.PatientRole patientRole : ResourceTransformerTest.ccd
.getPatientRoles()) {
if (patientRole != null && !patientRole.isSetNullFlavor() && patientRole.getPatient() != null
&& !patientRole.getPatient().isSetNullFlavor()) {
for (org.openhealthtools.mdht.uml.cda.Guardian guardian : patientRole.getPatient().getGuardians()) {
if (guardian != null && !guardian.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
ContactComponent contact = rt.tGuardian2Contact(guardian);
appendToResultFile(transformationEndMsg);
org.hl7.fhir.r4.model.Patient patient = new Patient().addContact(contact);
appendToResultFile(patient);
}
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testImmunizationActivity2Immunization() {
appendToResultFile("## TEST: ImmunizationActivity2Immunization\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.ImmunizationActivity cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
Bundle fhirNull = rt.tImmunizationActivity2Immunization(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
ImmunizationsSectionEntriesOptional immSec = ResourceTransformerTest.ccd
.getImmunizationsSectionEntriesOptional();
if (immSec != null && !immSec.isSetNullFlavor()) {
for (ImmunizationActivity immAct : immSec.getImmunizationActivities()) {
if (immAct != null && !immAct.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirImm = rt.tImmunizationActivity2Immunization(immAct, bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirImm);
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testLanguageCommunication2Communication() {
appendToResultFile("## TEST: LanguageCommunication2Communication\n");
// null instance test
org.openhealthtools.mdht.uml.cda.LanguageCommunication cdaNull = null;
PatientCommunicationComponent fhirNull = rt.tLanguageCommunication2Communication(cdaNull);
Assert.assertNull(fhirNull);
// instances from file
for (org.openhealthtools.mdht.uml.cda.Patient patient : ResourceTransformerTest.ccd.getPatients()) {
for (org.openhealthtools.mdht.uml.cda.LanguageCommunication LC : patient.getLanguageCommunications()) {
appendToResultFile(transformationStartMsg);
PatientCommunicationComponent fhirCommunication = rt.tLanguageCommunication2Communication(LC);
appendToResultFile(transformationEndMsg);
org.hl7.fhir.r4.model.Patient fhirPatient = new org.hl7.fhir.r4.model.Patient();
fhirPatient.addCommunication(fhirCommunication);
appendToResultFile(fhirPatient);
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testManufacturedProduct2Medication() {
appendToResultFile("## TEST: ManufacturedProduct2Medication\n");
// null instance test
org.openhealthtools.mdht.uml.cda.ManufacturedProduct cdaNull = null;
BundleInfo bundleInfo = new BundleInfo(rt);
EntryResult nullResult = rt.tManufacturedProduct2Medication(cdaNull, bundleInfo);
Assert.assertFalse(nullResult.hasResult());
// instances from file
ImmunizationsSectionEntriesOptional immSection = ResourceTransformerTest.ccd
.getImmunizationsSectionEntriesOptional();
if (immSection != null && !immSection.isSetNullFlavor()) {
if (immSection.getImmunizationActivities() != null && !immSection.getImmunizationActivities().isEmpty()) {
for (ImmunizationActivity immAct : immSection.getImmunizationActivities()) {
if (immAct != null && !immAct.isSetNullFlavor()) {
if (immAct.getConsumable() != null && !immAct.getConsumable().isSetNullFlavor()) {
if (immAct.getConsumable().getManufacturedProduct() != null
&& !immAct.getConsumable().getManufacturedProduct().isSetNullFlavor()) {
// immAct.immSection.immAct.consumable.manuProd
appendToResultFile(transformationStartMsg);
EntryResult fhirMed = rt.tManufacturedProduct2Medication(
immAct.getConsumable().getManufacturedProduct(), bundleInfo);
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirMed.getBundle());
}
}
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testMedicationActivity2MedicationStatement() {
BundleInfo bundleInfo = new BundleInfo(rt);
appendToResultFile("## TEST: MedicationActivity2MedicationStatement\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.MedicationActivity cdaNull = null;
Bundle fhirNull = rt.tMedicationActivity2MedicationStatement(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getMedicationsSection() != null
&& !ResourceTransformerTest.ccd.getMedicationsSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getMedicationsSection().getMedicationActivities() != null
&& !ResourceTransformerTest.ccd.getMedicationsSection().getMedicationActivities().isEmpty()) {
for (MedicationActivity cdaMedAct : ResourceTransformerTest.ccd.getMedicationsSection()
.getMedicationActivities()) {
if (cdaMedAct != null && !cdaMedAct.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirMedStBundle = rt.tMedicationActivity2MedicationStatement(cdaMedAct, bundleInfo)
.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirMedStBundle);
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testMedicationDispense2MedicationDispense() {
BundleInfo bundleInfo = new BundleInfo(rt);
appendToResultFile("## TEST: MedicationDispense2MedicationDispense\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.MedicationDispense cdaNull = null;
Bundle fhirNull = rt.tMedicationDispense2MedicationDispense(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
// medicationsSection.medicationActivities.medicationDispense
if (ResourceTransformerTest.ccd.getMedicationsSection() != null
&& !ResourceTransformerTest.ccd.getMedicationsSection().isSetNullFlavor()) {
org.openhealthtools.mdht.uml.cda.consol.MedicationsSection medSec = ResourceTransformerTest.ccd
.getMedicationsSection();
if (medSec.getMedicationActivities() != null && !medSec.getMedicationActivities().isEmpty()) {
for (MedicationActivity medAct : medSec.getMedicationActivities()) {
if (medAct != null && !medAct.isSetNullFlavor()) {
if (medAct.getMedicationDispenses() != null && !medAct.getMedicationDispenses().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.consol.MedicationDispense medDisp : medAct
.getMedicationDispenses()) {
if (medDisp != null && !medDisp.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirMedDispBundle = rt
.tMedicationDispense2MedicationDispense(medDisp, bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirMedDispBundle);
}
}
}
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testObservation2Observation() {
appendToResultFile("## TEST: Observation2Observation\n");
BundleInfo bundleInfo = new BundleInfo(rt);
// null instance test
org.openhealthtools.mdht.uml.cda.Observation cdaNull = null;
Bundle fhirNull = rt.tObservation2Observation(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getSocialHistorySection() != null
&& !ResourceTransformerTest.ccd.getSocialHistorySection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getSocialHistorySection().getObservations() != null
&& !ResourceTransformerTest.ccd.getSocialHistorySection().getObservations().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Observation cdaObs : ResourceTransformerTest.ccd
.getSocialHistorySection().getObservations()) {
if (cdaObs != null && !cdaObs.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle obsBundle = rt.tObservation2Observation(cdaObs, bundleInfo).getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(obsBundle);
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testOrganization2Organization() {
appendToResultFile("## TEST: Organization2Organization\n");
// null instance test
org.openhealthtools.mdht.uml.cda.Organization cdaNull = null;
IEntryResult result1 = rt.tOrganization2Organization(cdaNull, new BundleInfo(rt));
Assert.assertFalse(result1.hasResult());
// instances from file
for (org.openhealthtools.mdht.uml.cda.PatientRole patRole : ResourceTransformerTest.ccd.getPatientRoles()) {
org.openhealthtools.mdht.uml.cda.Organization cdaOrg = patRole.getProviderOrganization();
appendToResultFile(transformationStartMsg);
IEntryResult result2 = rt.tOrganization2Organization(cdaOrg, new BundleInfo(rt));
org.hl7.fhir.r4.model.Organization fhirOrg = FHIRUtil.findFirstResource(result2.getBundle(),
org.hl7.fhir.r4.model.Organization.class);
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirOrg);
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testPatientRole2Patient() {
appendToResultFile("## TEST: PatientRole2Patient\n");
// null instance test
org.openhealthtools.mdht.uml.cda.PatientRole cdaNull = null;
IEntryResult patientResult1 = rt.tPatientRole2Patient(cdaNull, new BundleInfo(rt));
Assert.assertFalse(patientResult1.hasResult());
// instances from file
for (PatientRole pr : ResourceTransformerTest.ccd.getPatientRoles()) {
// here we do the transformation by calling the method rt.PatientRole2Patient
Patient patient = null;
appendToResultFile(transformationStartMsg);
IEntryResult patientResult2 = rt.tPatientRole2Patient(pr, new BundleInfo(rt));
appendToResultFile(transformationEndMsg);
appendToResultFile(patientResult2.getBundle());
for (BundleEntryComponent entry : patientResult2.getFullBundle().getEntry()) {
if (entry.getResource() instanceof Patient) {
patient = (Patient) entry.getResource();
}
}
// patient.identifier
int idCount = 0;
for (II id : pr.getIds()) {
if (id.getRoot() != null && id.getExtension() != null) {
// since extension may contain "urn:oid:" or "urn:uuid:", assertion is about
// containing the value as a piece
Assert.assertTrue("pr.id.extension #" + idCount + " was not transformed",
patient.getIdentifier().get(idCount).getValue().contains(id.getExtension()));
Assert.assertTrue("pr.id.root #" + idCount + " was not transformed",
patient.getIdentifier().get(idCount).getSystem().contains(id.getRoot()));
} else if (id.getRoot() != null) {
Assert.assertTrue("pr.id.root #" + idCount + " was not transformed",
patient.getIdentifier().get(idCount).getValue().contains(id.getRoot()));
} else if (id.getExtension() != null) {
Assert.assertTrue("pr.id.root #" + idCount + " was not transformed",
patient.getIdentifier().get(idCount).getValue().contains(id.getExtension()));
}
// codeSystem method is changed and tested
idCount++;
}
// patient.name
// Notice that patient.name is fullfilled by the method EN2HumanName.
int nameCount = 0;
for (EN pn : pr.getPatient().getNames()) {
// patient.name.use
if (pn.getUses() == null || pn.getUses().isEmpty()) {
Assert.assertNull(patient.getName().get(nameCount).getUse().toCode());
} else {
Assert.assertEquals("pr.patient.name[" + nameCount + "]" + ".use was not transformed",
vsti.tEntityNameUse2NameUse(pn.getUses().get(0)).toString().toLowerCase(),
patient.getName().get(nameCount).getUse().toCode());
}
// patient.name.text
Assert.assertEquals("pr.patient.name[" + nameCount + "].text was not transformed", pn.getText(),
patient.getName().get(nameCount).getText());
// patient.name.family
for (ENXP family : pn.getFamilies()) {
if (family == null || family.isSetNullFlavor()) {
// It can return null or an empty list
Assert.assertTrue(patient.getName().get(nameCount).getFamily() == null
|| !patient.getName().get(nameCount)
.hasFamily()/* patient.getName().get(nameCount).getFamily().size() == 0 */);
} else {
Assert.assertEquals("pr.patient.name[" + nameCount + "].family was not transformed",
family.getText(),
patient.getName().get(nameCount).getFamily()/* .get(familyCount).getValue() */);
}
}
// patient.name.given
int givenCount = 0;
for (ENXP given : pn.getGivens()) {
if (given == null || given.isSetNullFlavor()) {
// It can return null or an empty list
Assert.assertTrue(patient.getName().get(nameCount).getGiven() == null
|| patient.getName().get(nameCount).getGiven().size() == 0);
} else {
Assert.assertEquals("pr.patient.name[" + nameCount + "].given was not transformed",
given.getText(),
patient.getName().get(nameCount).getGiven().get(givenCount).getValue());
}
givenCount++;
}
// patient.name.prefix
int prefixCount = 0;
for (ENXP prefix : pn.getPrefixes()) {
if (prefix == null || prefix.isSetNullFlavor()) {
// It can return null or an empty list
Assert.assertTrue(patient.getName().get(nameCount).getPrefix() == null
|| patient.getName().get(nameCount).getPrefix().size() == 0);
} else {
Assert.assertEquals("pr.patient.name[" + nameCount + "].prefix was not transformed",
prefix.getText(),
patient.getName().get(nameCount).getPrefix().get(prefixCount).getValue());
}
prefixCount++;
}
// patient.name.suffix
int suffixCount = 0;
for (ENXP suffix : pn.getPrefixes()) {
if (suffix == null || suffix.isSetNullFlavor()) {
// It can return null or an empty list
Assert.assertTrue(patient.getName().get(nameCount).getSuffix() == null
|| patient.getName().get(nameCount).getSuffix().size() == 0);
} else {
Assert.assertEquals("pr.patient.name[" + nameCount + "].suffix was not transformed",
suffix.getText(),
patient.getName().get(nameCount).getSuffix().get(suffixCount).getValue());
}
suffixCount++;
}
// patient.name.period
if (pn.getValidTime() == null || pn.getValidTime().isSetNullFlavor()) {
// It can return null or an empty list
Assert.assertTrue(patient.getName().get(nameCount).getPeriod() == null
|| patient.getName().get(nameCount).getPeriod().isEmpty());
}
}
// patient.telecom
// Notice that patient.telecom is fullfilled by the method dtt.TEL2ContactPoint
if (pr.getTelecoms() == null || pr.getTelecoms().isEmpty()) {
Assert.assertTrue(patient.getTelecom() == null || patient.getTelecom().isEmpty());
} else {
// size check
Assert.assertTrue(pr.getTelecoms().size() == patient.getTelecom().size());
// We have already tested the method TEL2ContactPoint. Therefore, null-check and
// size-check is enough for now.
}
// patient.gender
// vst.AdministrativeGenderCode2AdministrativeGenderEnum is used in this
// transformation.
// Following test aims to test that ValueSetTransformer method.
if (pr.getPatient().getAdministrativeGenderCode() == null
|| pr.getPatient().getAdministrativeGenderCode().isSetNullFlavor()) {
Assert.assertTrue(patient.getGender() == null || !patient.getGenderElement().hasValue());
}
// patient.birthDate
// Notice that patient.birthDate is fullfilled by the method dtt.TS2Date
if (pr.getPatient().getBirthTime() == null || pr.getPatient().getBirthTime().isSetNullFlavor()) {
Assert.assertTrue(patient.getBirthDate() == null);
}
// patient.address
// Notice that patient.address is fullfilled by the method dtt.AD2Address
if (pr.getAddrs() == null || pr.getAddrs().isEmpty()) {
Assert.assertTrue(patient.getAddress() == null || patient.getAddress().isEmpty());
} else {
// We have already tested the method AD2Address. Therefore, null-check and
// size-check is enough for now.
Assert.assertTrue(pr.getAddrs().size() == patient.getAddress().size());
}
// patient.maritalStatus
// vst.MaritalStatusCode2MaritalStatusCodesEnum is used in this transformation.
// Following test aims to test that ValueSetTransformer method.
if (pr.getPatient().getMaritalStatusCode() == null
|| pr.getPatient().getMaritalStatusCode().isSetNullFlavor()) {
Assert.assertTrue(patient.getMaritalStatus() == null || patient.getMaritalStatus().isEmpty());
} else {
Assert.assertTrue(patient.getMaritalStatus().getCoding().get(0).getCode().toLowerCase().charAt(0) == pr
.getPatient().getMaritalStatusCode().getCode().toLowerCase().charAt(0));
}
// patient.languageCommunication
if (pr.getPatient().getLanguageCommunications() == null
|| pr.getPatient().getLanguageCommunications().isEmpty()) {
Assert.assertTrue(patient.getCommunication() == null || patient.getCommunication().isEmpty());
} else {
Assert.assertTrue(
pr.getPatient().getLanguageCommunications().size() == patient.getCommunication().size());
int sizeCommunication = pr.getPatient().getLanguageCommunications().size();
while (sizeCommunication != 0) {
// language
if (pr.getPatient().getLanguageCommunications().get(sizeCommunication - 1).getLanguageCode() == null
|| pr.getPatient().getLanguageCommunications().get(0).getLanguageCode().isSetNullFlavor()) {
Assert.assertTrue(patient.getCommunication().get(sizeCommunication - 1).getLanguage() == null
|| patient.getCommunication().get(sizeCommunication - 1).getLanguage().isEmpty());
} else {
// We have already tested the method CD2CodeableConcept. Therefore, null-check
// is enough for now.
}
// preference
if (pr.getPatient().getLanguageCommunications().get(sizeCommunication - 1)
.getPreferenceInd() == null
|| pr.getPatient().getLanguageCommunications().get(sizeCommunication - 1).getPreferenceInd()
.isSetNullFlavor()) {
// Assert.assertTrue(patient.getCommunication().get(sizeCommunication -
// 1).getPreferred() == null);
Assert.assertTrue(!patient.getCommunication().get(sizeCommunication - 1).hasPreferred());
} else {
Assert.assertEquals(
pr.getPatient().getLanguageCommunications().get(sizeCommunication - 1)
.getPreferenceInd().getValue(),
patient.getCommunication().get(sizeCommunication - 1).getPreferred());
}
sizeCommunication--;
}
}
// providerOrganization
if (pr.getProviderOrganization() == null || pr.getProviderOrganization().isSetNullFlavor()) {
Assert.assertTrue(
patient.getManagingOrganization() == null || patient.getManagingOrganization().isEmpty());
} else {
if (pr.getProviderOrganization().getNames() == null) {
Assert.assertTrue(patient.getManagingOrganization().getDisplay() == null);
}
}
// guardian
if (pr.getPatient().getGuardians() == null || pr.getPatient().getGuardians().isEmpty()) {
Assert.assertTrue(patient.getContact() == null || patient.getContact().isEmpty());
} else {
// Notice that, inside this mapping, the methods dtt.TEL2ContactPoint and
// dtt.AD2Address are used.
// Therefore, null-check and size-check are enough
Assert.assertTrue(pr.getPatient().getGuardians().size() == patient.getContact().size());
}
// extensions
for (Extension extension : patient.getExtension()) {
Assert.assertTrue(extension.getUrl() != null);
Assert.assertTrue(extension.getValue() != null);
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testProblemConcernAct2Condition() {
BundleInfo bundleInfo = new BundleInfo(rt);
appendToResultFile("## TEST: ProblemConcernAct2Condition\n");
// null instance test
org.openhealthtools.mdht.uml.cda.consol.ProblemConcernAct cdaNull = null;
Bundle fhirNull = rt.tProblemConcernAct2Condition(cdaNull, bundleInfo).getBundle();
Assert.assertNull(fhirNull);
// instances from file
if (ResourceTransformerTest.ccd.getProblemSection() != null
&& !ResourceTransformerTest.ccd.getProblemSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getProblemSection().getProblemConcerns() != null
&& !ResourceTransformerTest.ccd.getProblemSection().getProblemConcerns().isEmpty()) {
for (ProblemConcernAct problemConcernAct : ResourceTransformerTest.ccd.getProblemSection()
.getProblemConcerns()) {
if (problemConcernAct != null && !problemConcernAct.isSetNullFlavor()) {
appendToResultFile(transformationStartMsg);
Bundle fhirConditionBundle = rt.tProblemConcernAct2Condition(problemConcernAct, bundleInfo)
.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirConditionBundle);
}
}
}
}
appendToResultFile(endOfTestMsg);
}
@Test
public void testProcedure2Procedure() {
BundleInfo bundleInfo = new BundleInfo(rt);
appendToResultFile("## TEST: Procedure2Procedure\n");
// null instance test
org.openhealthtools.mdht.uml.cda.Procedure cdaNull = null;
EntryResult entryResultNull = rt.tProcedure2Procedure(cdaNull, bundleInfo);
Assert.assertNull(entryResultNull.getBundle());
// instances from file
if (ResourceTransformerTest.ccd.getProceduresSection() != null
&& !ResourceTransformerTest.ccd.getProceduresSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getProceduresSection().getProcedures() != null
&& !ResourceTransformerTest.ccd.getProceduresSection().getProcedures().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Procedure cdaProcedure : ResourceTransformerTest.ccd
.getProceduresSection().getProcedures()) {
// traversing procedures
appendToResultFile(transformationStartMsg);
EntryResult entryResult = rt.tProcedure2Procedure(cdaProcedure, bundleInfo);
Bundle fhirProcedureBundle = entryResult.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirProcedureBundle);
}
}
}
if (ResourceTransformerTest.ccd.getEncountersSection() != null
&& !ResourceTransformerTest.ccd.getEncountersSection().isSetNullFlavor()) {
if (ResourceTransformerTest.ccd.getEncountersSection().getProcedures() != null
&& !ResourceTransformerTest.ccd.getEncountersSection().getProcedures().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Procedure cdaProcedure : ResourceTransformerTest.ccd
.getEncountersSection().getProcedures()) {
// traversing procedures
appendToResultFile(transformationStartMsg);
EntryResult entryResult = rt.tProcedure2Procedure(cdaProcedure, bundleInfo);
Bundle fhirProcedureBundle = entryResult.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirProcedureBundle);
}
}
}
if (ResourceTransformerTest.ccd.getAllSections() != null
&& !ResourceTransformerTest.ccd.getAllSections().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Section section : ResourceTransformerTest.ccd.getAllSections()) {
if (section.getProcedures() != null && !section.getProcedures().isEmpty()) {
for (org.openhealthtools.mdht.uml.cda.Procedure cdaProcedure : section.getProcedures()) {
// traversing procedures
appendToResultFile(transformationStartMsg);
EntryResult entryResult = rt.tProcedure2Procedure(cdaProcedure, bundleInfo);
Bundle fhirProcedureBundle = entryResult.getBundle();
appendToResultFile(transformationEndMsg);
appendToResultFile(fhirProcedureBundle);
}
}
}
}