use of ca.uhn.fhir.model.dstu2.resource.Medication in project eCRNow by drajer-health.
the class Dstu2CdaImmunizationGenerator method generateImmunizationSection.
public static String generateImmunizationSection(Dstu2FhirData data, LaunchDetails details) {
StringBuilder sb = new StringBuilder(2000);
List<Immunization> imms = data.getImmunizations();
if (imms != null && imms.size() > 0) {
// 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.IMMUNIZATION_SEC_TEMPLATE_ID));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_SEC_TEMPLATE_ID, CdaGeneratorConstants.IMMUNIZATION_SEC_TEMPLATE_ID_EXT));
sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.CODE_EL_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_CODE, CdaGeneratorConstants.LOINC_CODESYSTEM_OID, CdaGeneratorConstants.LOINC_CODESYSTEM_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_NAME));
// add Title
sb.append(CdaGeneratorUtils.getXmlForText(CdaGeneratorConstants.TITLE_EL_NAME, CdaGeneratorConstants.IMMUNIZATION_SEC_TITLE));
// add Narrative Text
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.TEXT_EL_NAME));
// Create Table Header.
List<String> list = new ArrayList<String>();
list.add(CdaGeneratorConstants.IMM_TABLE_COL_1_TITLE);
list.add(CdaGeneratorConstants.IMM_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;
for (Immunization imm : imms) {
String medDisplayName = CdaGeneratorConstants.UNKNOWN_VALUE;
if (imm.getVaccineCode() != null && imm.getVaccineCode().getCodingFirstRep() != null && !StringUtils.isEmpty(imm.getVaccineCode().getCodingFirstRep().getDisplay())) {
medDisplayName = imm.getVaccineCode().getCodingFirstRep().getDisplay();
}
String dt = null;
if (imm.getDate() != null) {
dt = imm.getDate().toString();
}
Map<String, String> bodyvals = new HashMap<String, String>();
bodyvals.put(CdaGeneratorConstants.IMM_TABLE_COL_1_BODY_CONTENT, medDisplayName);
bodyvals.put(CdaGeneratorConstants.IMM_TABLE_COL_2_BODY_CONTENT, dt);
sb.append(CdaGeneratorUtils.addTableRow(bodyvals, rowNum));
// TODO: ++rowNum or rowNum++
++rowNum;
}
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));
for (Immunization imm : imms) {
// add the Entries.
sb.append(CdaGeneratorUtils.getXmlForActEntry(CdaGeneratorConstants.TYPE_CODE_DEF));
// add the medication Act
sb.append(CdaGeneratorUtils.getXmlForAct(CdaGeneratorConstants.MED_ACT_EL_NAME, CdaGeneratorConstants.MED_CLASS_CODE, CdaGeneratorConstants.MOOD_CODE_DEF));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID, CdaGeneratorConstants.IMMUNIZATION_ACTIVITY_TEMPLATE_ID_EXT));
sb.append(CdaGeneratorUtils.getXmlForII(details.getAssigningAuthorityId(), imm.getId().getIdPart()));
// set status code
sb.append(CdaGeneratorUtils.getXmlForCD(CdaGeneratorConstants.STATUS_CODE_EL_NAME, CdaGeneratorConstants.COMPLETED_STATUS));
// Set up Effective Time for start and End time.
sb.append(Dstu2CdaFhirUtilities.getDateTimeTypeXml(imm.getDateElement(), CdaGeneratorConstants.EFF_TIME_EL_NAME));
// add the consumable presentation.
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.CONSUMABLE_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForStartElementWithClassCode(CdaGeneratorConstants.MAN_PROD_EL_NAME, CdaGeneratorConstants.MANU_CLASS_CODE));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION));
sb.append(CdaGeneratorUtils.getXmlForTemplateId(CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION, CdaGeneratorConstants.IMMUNIZATION_MEDICATION_INFORMATION_EXT));
sb.append(CdaGeneratorUtils.getXmlForIIUsingGuid());
sb.append(CdaGeneratorUtils.getXmlForStartElement(CdaGeneratorConstants.MANU_MAT_EL_NAME));
List<CodeableConceptDt> cds = new ArrayList<CodeableConceptDt>();
cds.add(imm.getVaccineCode());
sb.append(Dstu2CdaFhirUtilities.getCodeableConceptXml(cds, CdaGeneratorConstants.CODE_EL_NAME, false));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MANU_MAT_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MAN_PROD_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.CONSUMABLE_EL_NAME));
// End Tags for Entries
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.MED_ACT_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.ENTRY_EL_NAME));
}
// Complete the section end tags.
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.SECTION_EL_NAME));
sb.append(CdaGeneratorUtils.getXmlForEndElement(CdaGeneratorConstants.COMP_EL_NAME));
} else {
sb.append(generateEmptyImmunizations());
}
return sb.toString();
}
use of ca.uhn.fhir.model.dstu2.resource.Medication 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;
}
use of ca.uhn.fhir.model.dstu2.resource.Medication in project synthea by synthetichealth.
the class FhirDstu2 method convertToFHIR.
/**
* Convert the given Person into a FHIR Bundle with the Patient and the
* associated entries from their health record.
*
* @param person Person to generate the FHIR Bundle
* @param stopTime Time the simulation ended
* @return String containing a FHIR Bundle containing the Person's health record
*/
public static Bundle convertToFHIR(Person person, long stopTime) {
Bundle bundle = new Bundle();
if (TRANSACTION_BUNDLE) {
bundle.setType(BundleTypeEnum.TRANSACTION);
} else {
bundle.setType(BundleTypeEnum.COLLECTION);
}
Entry personEntry = basicInfo(person, bundle, stopTime);
for (Encounter encounter : person.record.encounters) {
Entry encounterEntry = encounter(person, personEntry, bundle, encounter);
for (HealthRecord.Entry condition : encounter.conditions) {
condition(person, personEntry, bundle, encounterEntry, condition);
}
for (HealthRecord.Entry allergy : encounter.allergies) {
allergy(person, personEntry, bundle, encounterEntry, allergy);
}
for (Observation observation : encounter.observations) {
// Observation resources in stu3 don't support Attachments
if (observation.value instanceof Attachment) {
media(person, personEntry, bundle, encounterEntry, observation);
} else {
observation(person, personEntry, bundle, encounterEntry, observation);
}
}
for (Procedure procedure : encounter.procedures) {
procedure(person, personEntry, bundle, encounterEntry, procedure);
}
for (Medication medication : encounter.medications) {
medication(person, personEntry, bundle, encounterEntry, medication);
}
for (HealthRecord.Entry immunization : encounter.immunizations) {
immunization(person, personEntry, bundle, encounterEntry, immunization);
}
for (Report report : encounter.reports) {
report(person, personEntry, bundle, encounterEntry, report);
}
for (CarePlan careplan : encounter.careplans) {
careplan(person, personEntry, bundle, encounterEntry, careplan);
}
for (ImagingStudy imagingStudy : encounter.imagingStudies) {
imagingStudy(person, personEntry, bundle, encounterEntry, imagingStudy);
}
for (HealthRecord.Device device : encounter.devices) {
device(person, personEntry, bundle, device);
}
for (HealthRecord.Supply supply : encounter.supplies) {
supplyDelivery(person, personEntry, bundle, supply, encounter);
}
// one claim per encounter
encounterClaim(person, personEntry, bundle, encounterEntry, encounter.claim);
}
return bundle;
}
use of ca.uhn.fhir.model.dstu2.resource.Medication in project synthea by synthetichealth.
the class FhirDstu2 method medicationAdministration.
/**
* Add a MedicationAdministration if needed for the given medication.
*
* @param rand Source of randomness to use when generating ids etc
* @param personEntry The Entry for the Person
* @param bundle Bundle to add the MedicationAdministration to
* @param encounterEntry Current Encounter entry
* @param medication The Medication
* @return The added Entry
*/
private static Entry medicationAdministration(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Medication medication) {
MedicationAdministration medicationResource = new MedicationAdministration();
medicationResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
medicationResource.setEncounter(new ResourceReferenceDt(encounterEntry.getFullUrl()));
Code code = medication.codes.get(0);
String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;
medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
medicationResource.setEffectiveTime(new DateTimeDt(new Date(medication.start)));
medicationResource.setStatus(MedicationAdministrationStatusEnum.COMPLETED);
if (medication.prescriptionDetails != null) {
JsonObject rxInfo = medication.prescriptionDetails;
MedicationAdministration.Dosage dosage = new MedicationAdministration.Dosage();
// as_needed is true if present
if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
SimpleQuantityDt dose = new SimpleQuantityDt();
dose.setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
dosage.setQuantity(dose);
if (rxInfo.has("instructions")) {
for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
JsonObject instruction = instructionElement.getAsJsonObject();
dosage.setText(instruction.get("display").getAsString());
}
}
}
medicationResource.setDosage(dosage);
}
if (!medication.reasons.isEmpty()) {
// Only one element in list
Code reason = medication.reasons.get(0);
for (Entry entry : bundle.getEntry()) {
if (entry.getResource().getResourceName().equals("Condition")) {
Condition condition = (Condition) entry.getResource();
// Only one element in list
CodeableConceptDt coding = condition.getCode();
if (reason.code.equals(coding.getCodingFirstRep().getCode())) {
medicationResource.addReasonGiven(coding);
}
}
}
}
Entry medicationAdminEntry = newEntry(rand, bundle, medicationResource);
return medicationAdminEntry;
}
use of ca.uhn.fhir.model.dstu2.resource.Medication in project synthea by synthetichealth.
the class FhirDstu2 method medicationClaim.
/**
* Create an entry for the given Claim, which references a Medication.
*
* @param rand
* Source of randomness to use when generating ids etc
* @param personEntry
* Entry for the person
* @param bundle
* The Bundle to add to
* @param encounterEntry
* The current Encounter
* @param claim
* the Claim object
* @param medicationEntry
* The Entry for the Medication object, previously created
* @return the added Entry
*/
private static Entry medicationClaim(RandomNumberGenerator rand, Entry personEntry, Bundle bundle, Entry encounterEntry, Claim claim, Entry medicationEntry) {
ca.uhn.fhir.model.dstu2.resource.Claim claimResource = new ca.uhn.fhir.model.dstu2.resource.Claim();
ca.uhn.fhir.model.dstu2.resource.Encounter encounterResource = (ca.uhn.fhir.model.dstu2.resource.Encounter) encounterEntry.getResource();
// assume institutional claim
// TODO review claim type
claimResource.setType(ClaimTypeEnum.INSTITUTIONAL);
claimResource.setUse(UseEnum.COMPLETE);
claimResource.setPatient(new ResourceReferenceDt(personEntry.getFullUrl()));
claimResource.setOrganization(encounterResource.getServiceProvider());
// add prescription.
claimResource.setPrescription(new ResourceReferenceDt(medicationEntry.getFullUrl()));
return newEntry(rand, bundle, claimResource);
}
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