Examples with BaseContainedDt ca.uhn.fhir.model.base.composite.BaseContainedDt used on opensource projects

Example 1 with BaseContainedDt

use of ca.uhn.fhir.model.base.composite.BaseContainedDt in project eCRNow by drajer-health.

the class LoadingQueryDstu2Bundle method createDSTU2Bundle.

public Bundle createDSTU2Bundle(LaunchDetails launchDetails, Dstu2FhirData dstu2FhirData, Date start, Date end) {
    Bundle bundle = new Bundle();
    logger.info("Initializing FHIR Context for Version:::: {}", launchDetails.getFhirVersion());
    FhirContext context = fhirContextInitializer.getFhirContext(launchDetails.getFhirVersion());
    logger.info("Initializing Client");
    IGenericClient client = fhirContextInitializer.createClient(context, launchDetails);
    // GET Patient Details and Add to Bundle
    try {
        logger.info("Get Patient Data");
        Patient patient = (Patient) fhirContextInitializer.getResouceById(launchDetails, client, context, "Patient", launchDetails.getLaunchPatientId());
        Entry patientEntry = new Entry();
        patientEntry.setResource(patient);
        bundle.addEntry(patientEntry);
    } catch (Exception e) {
        logger.error("Error in getting Patient Data", e);
    }
    // Step 1: Get Encounters for Patient based on encId. (Create a method to get
    // encounters)
    // If encId is null, find encounters for patient within the start and end time
    // provided.
    // Add to the bundle.
    // As you are adding to the bundle within Fhir Data, add the codeable concept
    // also to the list of encounterCodes.
    Encounter encounter = null;
    try {
        logger.info("Get Encounter Data");
        encounter = dstu2ResourcesData.getEncounterData(context, client, launchDetails, dstu2FhirData, start, end);
        if (encounter.getParticipant() != null) {
            List<Participant> participants = encounter.getParticipant();
            for (Participant participant : participants) {
                if (participant.getIndividual() != null) {
                    ResourceReferenceDt practitionerReference = participant.getIndividual();
                    Practitioner practitioner = (Practitioner) fhirContextInitializer.getResouceById(launchDetails, client, context, "Practitioner", practitionerReference.getReference().getIdPart());
                    Entry practitionerEntry = new Entry().setResource(practitioner);
                    bundle.addEntry(practitionerEntry);
                }
            }
        }
        if (encounter.getServiceProvider() != null) {
            ResourceReferenceDt organizationReference = encounter.getServiceProvider();
            Organization organization = (Organization) fhirContextInitializer.getResouceById(launchDetails, client, context, "Organization", organizationReference.getReference().getIdPart());
            Entry organizationEntry = new Entry().setResource(organization);
            bundle.addEntry(organizationEntry);
        }
        if (encounter.getLocation() != null) {
            List<Location> enocunterLocations = encounter.getLocation();
            for (Location location : enocunterLocations) {
                if (location.getLocation() != null) {
                    ResourceReferenceDt locationReference = location.getLocation();
                    ca.uhn.fhir.model.dstu2.resource.Location locationResource = (ca.uhn.fhir.model.dstu2.resource.Location) fhirContextInitializer.getResouceById(launchDetails, client, context, "Location", locationReference.getReference().getIdPart());
                    Entry locationEntry = new Entry().setResource(locationResource);
                    bundle.addEntry(locationEntry);
                }
            }
        }
        Entry encounterEntry = new Entry().setResource(encounter);
        bundle.addEntry(encounterEntry);
    } catch (Exception e) {
        logger.error("Error in getting Encounter Data", e);
    }
    // also to the list of ConditionCodes.
    try {
        logger.info("Get Condition Data");
        List<Condition> conditionsList = dstu2ResourcesData.getConditionData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered ConditionsList----> {}", conditionsList.size());
        dstu2FhirData.setConditions(conditionsList);
        for (Condition condition : conditionsList) {
            Entry conditionsEntry = new Entry().setResource(condition);
            bundle.addEntry(conditionsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Condition Data", e);
    }
    // also to the list of labResultCodes.
    try {
        logger.info("Get Observation Data");
        List<Observation> observationList = dstu2ResourcesData.getObservationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered Observations----> {}", observationList.size());
        dstu2FhirData.setLabResults(observationList);
        for (Observation observation : observationList) {
            Entry observationsEntry = new Entry().setResource(observation);
            bundle.addEntry(observationsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Observation Data", e);
    }
    // Get Pregnancy Observations
    try {
        logger.info("Get Pregnancy Observation Data");
        List<Observation> observationList = dstu2ResourcesData.getPregnancyObservationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered Observations----> {}", observationList.size());
        dstu2FhirData.setPregnancyObs(observationList);
        for (Observation observation : observationList) {
            Entry observationsEntry = new Entry().setResource(observation);
            bundle.addEntry(observationsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Pregnancy Observation Data", e);
    }
    // Get Travel Observations
    try {
        logger.info("Get Travel Observation Data");
        List<Observation> observationList = dstu2ResourcesData.getTravelObservationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered Observations----> {}", observationList.size());
        dstu2FhirData.setTravelObs(observationList);
        for (Observation observation : observationList) {
            Entry observationsEntry = new Entry().setResource(observation);
            bundle.addEntry(observationsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Travel Observation Data", e);
    }
    // also to the list of medicationCodes.
    try {
        logger.info("Get MedicationAdministration Data");
        List<MedicationAdministration> medAdministrationsList = dstu2ResourcesData.getMedicationAdministrationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered MedicationAdministration-----------> {}", medAdministrationsList.size());
        dstu2FhirData.setMedicationAdministrations(medAdministrationsList);
        for (MedicationAdministration medAdministration : medAdministrationsList) {
            if (medAdministration.getMedication() != null && !medAdministration.getMedication().isEmpty() && medAdministration.getMedication() instanceof ResourceReferenceDt) {
                BaseResourceReferenceDt medRef = (BaseResourceReferenceDt) medAdministration.getMedication();
                String medReference = medRef.getReference().getValue();
                if (medReference.startsWith("#")) {
                    BaseContainedDt medAdministrationContained = medAdministration.getContained();
                    List<Medication> containedResources = (List<Medication>) medAdministrationContained.getContainedResources();
                    if (containedResources.stream().anyMatch(resource -> resource.getIdElement().getValue().equals(medReference))) {
                        logger.info("Medication Resource exists in MedicationAdministration.contained. So no need to add again in Bundle.");
                    }
                } else {
                    logger.info("Medication Reference Found=============>");
                    Medication medication = dstu2ResourcesData.getMedicationData(context, client, launchDetails, dstu2FhirData, medReference);
                    Entry medicationEntry = new Entry().setResource(medication);
                    bundle.addEntry(medicationEntry);
                    if (medication != null) {
                        List<Medication> medicationList = new ArrayList<>();
                        medicationList.add(medication);
                        dstu2FhirData.setMedicationList(medicationList);
                    }
                }
            }
            Entry medAdministrationEntry = new Entry().setResource(medAdministration);
            bundle.addEntry(medAdministrationEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the MedicationAdministration Data", e);
    }
    try {
        logger.info("Get MedicationStatement Data");
        List<MedicationStatement> medStatementsList = dstu2ResourcesData.getMedicationStatementData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered MedicationStatement-----------> {}", medStatementsList.size());
        for (MedicationStatement medStatement : medStatementsList) {
            Entry medStatementEntry = new Entry().setResource(medStatement);
            bundle.addEntry(medStatementEntry);
        }
        dstu2FhirData.setMedications(medStatementsList);
    } catch (Exception e) {
        logger.error("Error in getting the MedicationStatement Data", e);
    }
    try {
        logger.info("Get DiagnosticOrder Data");
        List<DiagnosticOrder> diagnosticOrdersList = dstu2ResourcesData.getDiagnosticOrderData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered DiagnosticOrders-----------> {}", diagnosticOrdersList.size());
        dstu2FhirData.setDiagOrders(diagnosticOrdersList);
        for (DiagnosticOrder diagnosticOrder : diagnosticOrdersList) {
            Entry diagnosticOrderEntry = new Entry().setResource(diagnosticOrder);
            bundle.addEntry(diagnosticOrderEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the DiagnosticOrder Data", e);
    }
    // Add to the bundle
    try {
        List<Immunization> immunizationsList = dstu2ResourcesData.getImmunizationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered Immunizations-----------> {}", immunizationsList.size());
        dstu2FhirData.setImmunizations(immunizationsList);
        for (Immunization immunization : immunizationsList) {
            Entry immunizationEntry = new Entry().setResource(immunization);
            bundle.addEntry(immunizationEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the Immunization Data", e);
    }
    // Add to the bundle
    try {
        List<DiagnosticReport> diagnosticReportList = dstu2ResourcesData.getDiagnosticReportData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered DiagnosticReports-----------> {}", diagnosticReportList.size());
        dstu2FhirData.setDiagReports(diagnosticReportList);
        for (DiagnosticReport diagnosticReport : diagnosticReportList) {
            Entry diagnosticReportEntry = new Entry().setResource(diagnosticReport);
            bundle.addEntry(diagnosticReportEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the DiagnosticReport Data", e);
    }
    // Setting bundle to FHIR Data
    logger.info("------------------------------CodeableConcept Codes------------------------------");
    logger.info("Encounter Codes Size=====> {}", dstu2FhirData.getEncounterCodes().size());
    logger.info("Conditions Codes Size=====> {}", dstu2FhirData.getConditionCodes().size());
    logger.info("Observation Codes Size=====> {}", dstu2FhirData.getLabResultCodes().size());
    logger.info("Medication Codes Size=====> {}", dstu2FhirData.getMedicationCodes().size());
    logger.info("Immunization Codes Size=====> {}", dstu2FhirData.getImmuniationCodes().size());
    logger.info("DiagnosticReport Codes Size=====> {}", dstu2FhirData.getDiagnosticReportCodes().size());
    String fileName = ActionRepo.getInstance().getLogFileDirectory() + "/LoadingQueryDSTU2Bundle-" + launchDetails.getLaunchPatientId() + ".json";
    ApplicationUtils.saveDataToFile(context.newJsonParser().encodeResourceToString(bundle), fileName);
    return bundle;
}

Example 2 with BaseContainedDt

use of ca.uhn.fhir.model.base.composite.BaseContainedDt in project eCRNow by drajer-health.

the class TriggerQueryDstu2Bundle method createDSTU2Bundle.

public Bundle createDSTU2Bundle(LaunchDetails launchDetails, Dstu2FhirData dstu2FhirData, Date start, Date end) {
    Bundle bundle = new Bundle();
    logger.info("Initializing FHIR Context for Version:::: {}", launchDetails.getFhirVersion());
    FhirContext context = fhirContextInitializer.getFhirContext(launchDetails.getFhirVersion());
    logger.info("Initializing Client");
    IGenericClient client = fhirContextInitializer.createClient(context, launchDetails);
    // GET Patient Details and Add to Bundle
    try {
        logger.info("Get Patient Data");
        Patient patient = (Patient) fhirContextInitializer.getResouceById(launchDetails, client, context, "Patient", launchDetails.getLaunchPatientId());
        Entry patientEntry = new Entry();
        patientEntry.setResource(patient);
        bundle.addEntry(patientEntry);
    } catch (Exception e) {
        logger.error("Error in getting Patient Data", e);
    }
    // Step 1: Get Encounters for Patient based on encId. (Create a method to get
    // encounters)
    // If encId is null, find encounters for patient within the start and end time
    // provided.
    // Add to the bundle.
    // As you are adding to the bundle within Fhir Data, add the codeable concept
    // also to the list of encounterCodes.
    Encounter encounter = null;
    try {
        logger.info("Get Encounter Data");
        encounter = dstu2ResourcesData.getEncounterData(context, client, launchDetails, dstu2FhirData, start, end);
        if (encounter.getParticipant() != null) {
            List<Participant> participants = encounter.getParticipant();
            for (Participant participant : participants) {
                if (participant.getIndividual() != null) {
                    ResourceReferenceDt practitionerReference = participant.getIndividual();
                    Practitioner practitioner = (Practitioner) fhirContextInitializer.getResouceById(launchDetails, client, context, "Practitioner", practitionerReference.getReference().getIdPart());
                    Entry practitionerEntry = new Entry().setResource(practitioner);
                    bundle.addEntry(practitionerEntry);
                }
            }
        }
        if (encounter.getServiceProvider() != null) {
            ResourceReferenceDt organizationReference = encounter.getServiceProvider();
            Organization organization = (Organization) fhirContextInitializer.getResouceById(launchDetails, client, context, "Organization", organizationReference.getReference().getIdPart());
            Entry organizationEntry = new Entry().setResource(organization);
            bundle.addEntry(organizationEntry);
        }
        if (encounter.getLocation() != null) {
            List<Location> enocunterLocations = encounter.getLocation();
            for (Location location : enocunterLocations) {
                if (location.getLocation() != null) {
                    ResourceReferenceDt locationReference = location.getLocation();
                    ca.uhn.fhir.model.dstu2.resource.Location locationResource = (ca.uhn.fhir.model.dstu2.resource.Location) fhirContextInitializer.getResouceById(launchDetails, client, context, "Location", locationReference.getReference().getIdPart());
                    Entry locationEntry = new Entry().setResource(locationResource);
                    bundle.addEntry(locationEntry);
                }
            }
        }
        Entry encounterEntry = new Entry().setResource(encounter);
        bundle.addEntry(encounterEntry);
    } catch (Exception e) {
        logger.error("Error in getting Encounter Data", e);
    }
    // also to the list of ConditionCodes.
    try {
        logger.info("Get Condition Data");
        List<Condition> conditionsList = dstu2ResourcesData.getConditionData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered ConditionsList----> {}", conditionsList.size());
        dstu2FhirData.setConditions(conditionsList);
        for (Condition condition : conditionsList) {
            Entry conditionsEntry = new Entry().setResource(condition);
            bundle.addEntry(conditionsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Condition Data", e);
    }
    // also to the list of labResultCodes.
    try {
        logger.info("Get Observation Data");
        List<Observation> observationList = dstu2ResourcesData.getObservationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered Observations----> {}", observationList.size());
        dstu2FhirData.setLabResults(observationList);
        for (Observation observation : observationList) {
            Entry observationsEntry = new Entry().setResource(observation);
            bundle.addEntry(observationsEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting Observation Data", e);
    }
    // also to the list of medicationCodes.
    try {
        logger.info("Get MedicationAdministration Data");
        List<MedicationAdministration> medAdministrationsList = dstu2ResourcesData.getMedicationAdministrationData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered MedicationAdministration-----------> {}", medAdministrationsList.size());
        dstu2FhirData.setMedicationAdministrations(medAdministrationsList);
        for (MedicationAdministration medAdministration : medAdministrationsList) {
            if (!medAdministration.getMedication().isEmpty() && medAdministration.getMedication() != null) {
                if (medAdministration.getMedication() instanceof ResourceReferenceDt) {
                    BaseResourceReferenceDt medRef = (BaseResourceReferenceDt) medAdministration.getMedication();
                    String medReference = medRef.getReference().getValue();
                    if (medReference.startsWith("#")) {
                        BaseContainedDt medAdministrationContained = medAdministration.getContained();
                        List<Medication> containedResources = (List<Medication>) medAdministrationContained.getContainedResources();
                        if (containedResources.stream().anyMatch(resource -> resource.getIdElement().getValue().equals(medReference))) {
                            logger.info("Medication Resource exists in MedicationAdministration.contained. So no need to add again in Bundle.");
                        }
                    } else {
                        logger.info("Medication Reference Found=============>");
                        Medication medication = dstu2ResourcesData.getMedicationData(context, client, launchDetails, dstu2FhirData, medReference);
                        Entry medicationEntry = new Entry().setResource(medication);
                        bundle.addEntry(medicationEntry);
                        if (medication != null) {
                            List<Medication> medicationList = new ArrayList<>();
                            medicationList.add(medication);
                            dstu2FhirData.setMedicationList(medicationList);
                        }
                    }
                }
            }
            Entry medAdministrationEntry = new Entry().setResource(medAdministration);
            bundle.addEntry(medAdministrationEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the MedicationAdministration Data", e);
    }
    try {
        logger.info("Get DiagnosticOrder Data");
        List<DiagnosticOrder> diagnosticOrdersList = dstu2ResourcesData.getDiagnosticOrderData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered DiagnosticOrders-----------> {}", diagnosticOrdersList.size());
        dstu2FhirData.setDiagOrders(diagnosticOrdersList);
        for (DiagnosticOrder diagnosticOrder : diagnosticOrdersList) {
            Entry diagnosticOrderEntry = new Entry().setResource(diagnosticOrder);
            bundle.addEntry(diagnosticOrderEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the DiagnosticOrder Data", e);
    }
    try {
        List<DiagnosticReport> diagnosticReportList = dstu2ResourcesData.getDiagnosticReportData(context, client, launchDetails, dstu2FhirData, encounter, start, end);
        logger.info("Filtered DiagnosticReports-----------> {}", diagnosticReportList.size());
        dstu2FhirData.setDiagReports(diagnosticReportList);
        for (DiagnosticReport diagnosticReport : diagnosticReportList) {
            Entry diagnosticReportEntry = new Entry().setResource(diagnosticReport);
            bundle.addEntry(diagnosticReportEntry);
        }
    } catch (Exception e) {
        logger.error("Error in getting the DiagnosticReport Data", e);
    }
    // Setting bundle to FHIR Data
    logger.info("------------------------------CodeableConcept Codes------------------------------");
    logger.info("Encounter Codes Size=====> {}", dstu2FhirData.getEncounterCodes().size());
    logger.info("Conditions Codes Size=====> {}", dstu2FhirData.getConditionCodes().size());
    logger.info("Observation Codes Size=====> {}", dstu2FhirData.getLabResultCodes().size());
    logger.info("Medication Codes Size=====> {}", dstu2FhirData.getMedicationCodes().size());
    logger.info("DiagnosticReport Codes Size=====> {}", dstu2FhirData.getDiagnosticReportCodes().size());
    logger.info("DiagnosticOrders Codes Size=====> {}", dstu2FhirData.getDiagnosticOrderCodes().size());
    String fileName = ActionRepo.getInstance().getLogFileDirectory() + "/TriggerQueryDSTU2Bundle-" + launchDetails.getLaunchPatientId() + ".json";
    ApplicationUtils.saveDataToFile(context.newJsonParser().encodeResourceToString(bundle), fileName);
    return bundle;
}