use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.MEDICATIONSTATEMENT in project org.hl7.fhir.core by hapifhir.
the class ProfileUtilitiesTests method execute.
public void execute(String[] args) throws FileNotFoundException, IOException, FHIRException {
System.out.println("loading context");
context = SimpleWorkerContext.fromPack(Utilities.path(root, "validation.zip"));
comp = new ProfileComparer(context);
compare("patient-daf-dafpatient.profile.xml", "patient-qicore-qicore-patient.profile.xml");
compare("encounter-daf-dafencounter.profile.xml", "encounter-qicore-qicore-encounter.profile.xml");
compare("substance-daf-dafsubstance.profile.xml", "substance-qicore-qicore-substance.profile.xml");
compare("medication-daf-dafmedication.profile.xml", "medication-qicore-qicore-medication.profile.xml");
compare("procedure-daf-dafprocedure.profile.xml", "procedure-qicore-qicore-procedure.profile.xml");
compare("familymemberhistory-daf-daffamilymemberhistory.profile.xml", "familymemberhistory-qicore-qicore-familymemberhistory.profile.xml");
compare("immunization-daf-dafimmunization.profile.xml", "immunization-qicore-qicore-immunization.profile.xml");
compare("condition-daf-dafcondition.profile.xml", "condition-qicore-qicore-condition.profile.xml");
compare("allergyintolerance-daf-dafallergyintolerance.profile.xml", "allergyintolerance-qicore-qicore-allergyintolerance.profile.xml");
compare("medicationadministration-daf-dafmedicationadministration.profile.xml", "medicationadministration-qicore-qicore-medicationadministration.profile.xml");
compare("medicationdispense-daf-dafmedicationdispense.profile.xml", "medicationdispense-qicore-qicore-medicationdispense.profile.xml");
compare("medicationprescription-daf-dafmedicationprescription.profile.xml", "medicationprescription-qicore-qicore-medicationprescription.profile.xml");
compare("medicationstatement-daf-dafmedicationstatement.profile.xml", "medicationstatement-qicore-qicore-medicationstatement.profile.xml");
compare("observation-daf-smokingstatus-dafsmokingstatus.profile.xml", "observation-qicore-qicore-observation.profile.xml");
compare("observation-daf-vitalsigns-dafvitalsigns.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("observation-daf-results-dafresultobs.profile.xml", "observation-qicore-qicore-observation.profile.xml");
// compare("diagnosticorder-daf-dafdiagnosticorder.profile.xml", "diagnosticorder-qicore-qicore-diagnosticorder.profile.xml");
// compare("diagnosticreport-daf-dafdiagnosticreport.profile.xml", "diagnosticreport-qicore-qicore-diagnosticreport.profile.xml");
System.out.println("processing output");
for (ProfileComparison outcome : comp.getComparisons()) {
if (outcome.getSubset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "intersection-" + outcome.getId() + ".xml")), outcome.getSubset());
if (outcome.getSuperset() != null)
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "union-" + outcome.getId() + ".xml")), outcome.getSuperset());
System.out.println("\r\n" + outcome.getId() + ": Comparison of " + outcome.getLeft().getUrl() + " and " + outcome.getRight().getUrl());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.INFORMATION)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.WARNING)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.ERROR)
System.out.println(vm.summary());
for (ValidationMessage vm : outcome.getMessages()) if (vm.getLevel() == IssueSeverity.FATAL)
System.out.println(vm.summary());
System.out.println("done. " + Integer.toString(outcome.getMessages().size()) + " messages");
System.out.println("=================================================================");
}
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.MEDICATIONSTATEMENT in project eCRNow by drajer-health.
the class R4ResourcesData method getMedicationStatementData.
public List<MedicationStatement> getMedicationStatementData(FhirContext context, IGenericClient client, LaunchDetails launchDetails, R4FhirData r4FhirData, Encounter encounter, Date start, Date end) {
logger.trace("Get MedicationStatement Data");
Bundle bundle = (Bundle) resourceData.getResourceByPatientId(launchDetails, client, context, "MedicationStatement");
List<MedicationStatement> medStatements = new ArrayList<>();
List<CodeableConcept> medicationCodes = new ArrayList<>();
if (bundle != null && bundle.getEntry() != null) {
// Filter MedicationStatement based on Encounter Reference
if (encounter != null && !encounter.getIdElement().getValue().isEmpty()) {
for (BundleEntryComponent entry : bundle.getEntry()) {
MedicationStatement medStatement = (MedicationStatement) entry.getResource();
if (!medStatement.getContext().isEmpty() && medStatement.getContext().getReferenceElement().getIdPart().equals(encounter.getIdElement().getIdPart())) {
medStatements.add(medStatement);
medicationCodes.addAll(findMedicationStatementCodes(medStatement));
}
}
// If Encounter Id is not present using start and end dates to filter
// MedicationStatement
} else {
for (BundleEntryComponent entry : bundle.getEntry()) {
MedicationStatement medStatement = (MedicationStatement) entry.getResource();
// Checking If Effective Date is present in MedicationStatement resource
if (medStatement.hasEffectiveDateTimeType()) {
Type effectiveDateTime = medStatement.getEffectiveDateTimeType();
Date effDate = effectiveDateTime.dateTimeValue().getValue();
if (isResourceWithinDateTime(start, end, effDate)) {
medStatements.add(medStatement);
medicationCodes.addAll(findMedicationStatementCodes(medStatement));
}
} else // If Effective Date is not present looking for LastUpdatedDate
{
Date lastUpdatedDateTime = medStatement.getMeta().getLastUpdated();
if (isResourceWithinDateTime(start, end, lastUpdatedDateTime)) {
medStatements.add(medStatement);
medicationCodes.addAll(findMedicationStatementCodes(medStatement));
}
}
}
}
r4FhirData.setR4MedicationCodes(medicationCodes);
}
logger.info("Filtered MedicationStatement -----------> {}", medStatements.size());
return medStatements;
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.MEDICATIONSTATEMENT in project eCRNow by drajer-health.
the class CdaMedicationGenerator method generateMedicationSection.
public static String generateMedicationSection(R4FhirData data, LaunchDetails details) {
StringBuilder sb = new StringBuilder(2000);
List<Medication> medList = data.getMedicationList();
List<MedicationStatement> meds = data.getMedications();
List<MedicationAdministration> medAdms = data.getMedicationAdministrations();
List<MedicationRequest> medReqs = getValidMedicationRequests(data, medList);
if ((meds != null && !meds.isEmpty()) || (medAdms != null && !medAdms.isEmpty()) || (medReqs != null && !medReqs.isEmpty())) {
// Generate the component and section end tags
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.COMP_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.SECTION_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.MED_ADM_SEC_TEMPLATE_ID));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.MED_ADM_SEC_TEMPLATE_ID, CdaGeneratorConstants.MED_SEC_TEMPLATE_ID_EXT));
sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.CODE_EL_NAME, CdaGeneratorConstants.MED_ADM_SEC_CODE, CdaGeneratorConstants.LOINC_CODESYSTEM_OID, CdaGeneratorConstants.LOINC_CODESYSTEM_NAME, CdaGeneratorConstants.MED_ADM_SEC_NAME));
// add Title
sb.append(CdaGeneratorUtils.getXmlForText(CdaGeneratorConstants.TITLE_EL_NAME, CdaGeneratorConstants.MED_ADM_SEC_TITLE));
// add Narrative Text
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TEXT_EL_NAME));
// Create Table Header.
List<String> list = new ArrayList<>();
list.add(CdaGeneratorConstants.MED_TABLE_COL_1_TITLE);
list.add(CdaGeneratorConstants.MED_TABLE_COL_2_TITLE);
sb.append(CdaGeneratorUtils.getXmlForTableHeader(list, CdaGeneratorConstants.TABLE_BORDER, CdaGeneratorConstants.TABLE_WIDTH));
// add Table Body
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
// add Body Rows
int rowNum = 1;
StringBuilder medEntries = new StringBuilder();
for (MedicationStatement med : meds) {
String medDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
if (med.getMedication() != null) {
medDisplayName = CdaFhirUtilities.getStringForMedicationType(med);
}
String dt = null;
if (med.getEffective() != null) {
dt = CdaFhirUtilities.getStringForType(med.getEffective());
}
Map<String, String> bodyvals = new LinkedHashMap<>();
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_1_BODY_CONTENT, medDisplayName);
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_2_BODY_CONTENT, dt);
sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
// TODO: ++rowNum or rowNum++
++rowNum;
// Create the Med Entry for the Medication Statement.
String medstatus = "";
if (med.getStatus() != null) {
medstatus = CdaFhirUtilities.getStatusCodeForFhirMedStatusCodes(med.getStatus().toString());
} else {
medstatus = COMPLETED;
}
Dosage dosage = null;
if (med.getDosageFirstRep() != null)
dosage = med.getDosageFirstRep();
medEntries.append(getEntryForMedication(med.getId(), med.getMedication(), med.getEffective(), medstatus, dosage, details, null, null, CdaGeneratorConstants.MOOD_CODE_DEF, med));
}
// Add Medication Administration
for (MedicationAdministration medAdm : medAdms) {
String medDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
if (medAdm.getMedication() != null) {
medDisplayName = CdaFhirUtilities.getStringForMedicationType(medAdm);
}
String dt = null;
if (medAdm.getEffective() != null) {
dt = CdaFhirUtilities.getStringForType(medAdm.getEffective());
}
Map<String, String> bodyvals = new HashMap<>();
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_1_BODY_CONTENT, medDisplayName);
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_2_BODY_CONTENT, dt);
sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
// TODO: ++rowNum or rowNum++
++rowNum;
// Create the Med Entry for the Medication Statement.
String medstatus = "";
if (medAdm.getStatus() != null) {
medstatus = CdaFhirUtilities.getStatusCodeForFhirMedStatusCodes(medAdm.getStatus());
} else {
medstatus = COMPLETED;
}
Quantity dose = null;
if (medAdm.getDosage() != null && medAdm.getDosage().getDose() != null)
dose = medAdm.getDosage().getDose();
medEntries.append(getEntryForMedication(medAdm.getId(), medAdm.getMedication(), medAdm.getEffective(), medstatus, null, details, dose, null, CdaGeneratorConstants.MOOD_CODE_DEF, medAdm));
}
// Add Medication Requests
for (MedicationRequest medReq : medReqs) {
String medDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
if (medReq.getMedication() != null) {
medDisplayName = CdaFhirUtilities.getStringForMedicationType(medReq);
}
DateTimeType startDate = null;
Dosage dosage = null;
if (medReq.getDosageInstructionFirstRep() != null && medReq.getDosageInstructionFirstRep().getTiming() != null) {
dosage = medReq.getDosageInstructionFirstRep();
Timing t = medReq.getDosageInstructionFirstRep().getTiming();
if (t != null && t.getRepeat() != null && t.getRepeat().getBoundsPeriod() != null) {
startDate = t.getRepeat().getBoundsPeriod().getStartElement();
}
}
String dt = CdaGeneratorConstants.UNKNOWN_VALUE;
if (startDate != null) {
dt = CdaFhirUtilities.getDisplayStringForDateTimeType(startDate);
} else {
logger.error(" Dosage field does not have a valid period either due to datetime or timezone being null ");
}
Map<String, String> bodyvals = new HashMap<>();
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_1_BODY_CONTENT, medDisplayName);
bodyvals.put(CdaGeneratorConstants.MED_TABLE_COL_2_BODY_CONTENT, dt);
sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
// TODO: ++rowNum or rowNum++
++rowNum;
// Create the Med Entry for the Medication Request.
String medstatus = "";
String moodCode = CdaGeneratorConstants.MOOD_CODE_INT;
if (medReq.getStatus() != null) {
medstatus = CdaFhirUtilities.getStatusCodeForFhirMedStatusCodes(medReq.getStatus().toString());
if (medstatus.equalsIgnoreCase(COMPLETED)) {
moodCode = CdaGeneratorConstants.MOOD_CODE_DEF;
}
} else {
medstatus = "active";
}
medEntries.append(getEntryForMedication(medReq.getId(), medReq.getMedication(), null, medstatus, dosage, details, null, startDate, moodCode, medReq));
}
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_BODY_EL_NAME));
// End Table.
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TABLE_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.TEXT_EL_NAME));
// Add Medication Entries
sb.append(medEntries);
// Complete the section end tags.
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.SECTION_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.COMP_EL_NAME));
} else {
sb.append(generateEmptyMedications());
}
return sb.toString();
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.MEDICATIONSTATEMENT in project eCRNow by drajer-health.
the class CdaFhirUtilities method getStringForMedicationType.
public static String getStringForMedicationType(Resource r) {
String retVal = CdaGeneratorConstants.UNKNOWN_VALUE;
if (r instanceof MedicationRequest) {
logger.debug("Found Med Request ");
MedicationRequest mr = (MedicationRequest) r;
if (mr.getMedication() instanceof Reference) {
logger.debug("Found Med Request.Medication Reference ");
Reference med = (Reference) mr.getMedication();
if (med.getReference().startsWith(CdaGeneratorConstants.FHIR_CONTAINED_REFERENCE)) {
logger.debug("Found Med Request.Medication which is a contained reference");
// Check contained.
String refId = med.getReference().substring(1);
logger.debug("Ref Id {} ", refId);
if (mr.getContained() != null) {
retVal = getStringForMedicationFromContainedResources(mr.getContained(), refId);
logger.debug("Return Val = {}", retVal);
}
// contained present
}
return retVal;
} else if (mr.getMedication() instanceof CodeableConcept) {
CodeableConcept cc = (CodeableConcept) mr.getMedication();
return getStringForType(cc);
}
} else if (r instanceof MedicationAdministration) {
MedicationAdministration medAdminRef = (MedicationAdministration) r;
if (medAdminRef.getMedication() instanceof Reference) {
Reference med = (Reference) medAdminRef.getMedication();
if (med.getReference().startsWith(CdaGeneratorConstants.FHIR_CONTAINED_REFERENCE)) {
// Check contained.
String refId = med.getReference().substring(1);
if (medAdminRef.getContained() != null) {
retVal = getStringForMedicationFromContainedResources(medAdminRef.getContained(), refId);
}
// contained present
}
return retVal;
} else if (medAdminRef.getMedication() instanceof CodeableConcept) {
CodeableConcept cc = (CodeableConcept) medAdminRef.getMedication();
return getStringForType(cc);
}
} else if (r instanceof MedicationStatement) {
MedicationStatement medStmtRef = (MedicationStatement) r;
if (medStmtRef.getMedication() instanceof Reference) {
Reference med = (Reference) medStmtRef.getMedication();
if (med.getReference().startsWith(CdaGeneratorConstants.FHIR_CONTAINED_REFERENCE)) {
// Check contained.
String refId = med.getReference().substring(1);
if (medStmtRef.getContained() != null) {
retVal = getStringForMedicationFromContainedResources(medStmtRef.getContained(), refId);
}
// contained present
}
return retVal;
} else if (medStmtRef.getMedication() instanceof CodeableConcept) {
CodeableConcept cc = (CodeableConcept) medStmtRef.getMedication();
return getStringForType(cc);
}
}
return retVal;
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.MEDICATIONSTATEMENT in project nia-patient-switching-standard-adaptor by NHSDigital.
the class MedicationRequestOrderMapperTest method When_MappingPrescribeResourceWithNoOptionals_Expect_AllFieldsToBeMappedCorrectly.
@Test
public void When_MappingPrescribeResourceWithNoOptionals_Expect_AllFieldsToBeMappedCorrectly() {
var medicationStatement = unmarshallMedicationStatement("medicationStatementPrescribeNoOptionals.xml");
var prescribe = medicationStatement.getComponent().stream().filter(RCMRMT030101UK04Component2::hasEhrSupplyPrescribe).map(RCMRMT030101UK04Component2::getEhrSupplyPrescribe).findFirst();
when(medicationMapper.extractMedicationReference(any())).thenReturn(Optional.of(new Reference(new IdType(ResourceType.Medication.name(), MEDICATION_ID))));
assertThat(prescribe.isPresent()).isTrue();
var medicationRequest = medicationRequestOrderMapper.mapToOrderMedicationRequest(new RCMRMT030101UK04EhrExtract(), medicationStatement, prescribe.get(), PRACTISE_CODE);
assertCommonValues(medicationRequest);
medicationRequest.getExtensionsByUrl("https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-PrescriptionType-1").forEach(extension -> assertPrescriptionType(extension, "Repeat"));
assertThat(medicationRequest.getBasedOnFirstRep().getReferenceElement().getIdPart()).isEqualTo(TEST_ID);
assertThat(medicationRequest.getNote().size()).isEqualTo(1);
assertThat(medicationRequest.getDosageInstructionFirstRep().getText()).isEqualTo(TAKE_ONE_DAILY);
assertThat(medicationRequest.getDispenseRequest().getQuantity().getValue()).isNull();
assertThat(medicationRequest.getDispenseRequest().getValidityPeriod().getStartElement().getValue()).isEqualTo(DateFormatUtil.parseToDateTimeType(AVAILABILITY_TIME).getValue());
}
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