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Merge pull request #911 from Shreeja-dev/745-csv-validate-new
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feat:fix issue in bundle and patient#745
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@ratheesh-kr
ratheesh-kr authored Dec 18, 2024
2 parents abfe860 + 4ac2ce8 commit 8f54e84
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Showing 5 changed files with 73 additions and 181 deletions.
2 changes: 1 addition & 1 deletion hub-prime/pom.xml
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Expand Up @@ -11,7 +11,7 @@
</parent>
<groupId>org.techbd</groupId>
<artifactId>hub-prime</artifactId>
<version>0.392.0</version>
<version>0.393.0</version>
<packaging>war</packaging>
<name>Tech by Design Hub (Prime)</name>
<description>Tech by Design Hub (Primary)</description>
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2 changes: 1 addition & 1 deletion hub-prime/src/main/java/org/techbd/service/converters/csv/CsvToFhirConverter.java
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Expand Up @@ -39,7 +39,7 @@ public String convert(DemographicData demographicData,
Bundle bundle = null;
try {
LOG.info("CsvToFhirConvereter::convert - BEGIN for interactionId :{}", interactionId);
bundle = bundleConverter.generateEmptyBundle(interactionId, appConfig.getIgVersion());
bundle = bundleConverter.generateEmptyBundle(interactionId, appConfig.getIgVersion(),demographicData);
LOG.debug("CsvToFhirConvereter::convert - Bundle entry created :{}", interactionId);
LOG.debug("Conversion of resources - BEGIN for interactionId :{}", interactionId);
addEntries(bundle, demographicData, screeningDataList, qeAdminData, screeningProfileData,interactionId);
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13 changes: 11 additions & 2 deletions hub-prime/src/main/java/org/techbd/service/converters/shinny/BundleConverter.java
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@@ -1,11 +1,17 @@
package org.techbd.service.converters.shinny;

import java.util.List;

import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.CanonicalType;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.ResourceType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import org.techbd.model.csv.DemographicData;
import org.techbd.util.CsvConversionUtil;
import org.techbd.util.DateUtil;

@Component
public class BundleConverter {
Expand All @@ -22,11 +28,14 @@ public ResourceType getResourceType() {
* @return a Bundle with type set to COLLECTION, one empty entry, and Meta
* information.
*/
public Bundle generateEmptyBundle(String interactionId,String igVersion) {
public Bundle generateEmptyBundle(String interactionId,String igVersion,DemographicData demographicData) {
Bundle bundle = new Bundle();
bundle.setType(Bundle.BundleType.COLLECTION);
bundle.setId("AHCHRSNScreeningResponse-"+CsvConversionUtil.sha256(demographicData.getPatientMrIdValue()));
bundle.setType(Bundle.BundleType.TRANSACTION);
Meta meta = new Meta();
meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));
meta.setVersionId(igVersion);
meta.setProfile(List.of(new CanonicalType("http://shinny.org/us/ny/hrsn/StructureDefinition/SHINNYBundleProfile")));
bundle.setMeta(meta);
LOG.info("Empty FHIR Bundle template generated with Meta and one empty entry for interactionId : {}.",
interactionId);
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22 changes: 0 additions & 22 deletions hub-prime/src/main/java/org/techbd/service/converters/shinny/IPatientConverter.java
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215 changes: 60 additions & 155 deletions hub-prime/src/main/java/org/techbd/service/converters/shinny/PatientConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@

@Component
@Order(2)
public class PatientConverter extends BaseConverter implements IPatientConverter {
public class PatientConverter extends BaseConverter {
private static final Logger LOG = LoggerFactory.getLogger(PatientConverter.class.getName());

/**
Expand Down Expand Up @@ -79,7 +79,7 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated())); // max date available in all
// screening records
patient.setLanguage("en");
populateExtensions(patient, demographicData);
populatePatientWithExtensions(patient, demographicData);
populateMrIdentifier(patient, demographicData,idsGenerated );
populateMaIdentifier(patient, demographicData);
populateSsnIdentifier(patient, demographicData);
Expand All @@ -102,6 +102,63 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
return List.of(bundleEntryComponent);
}

public static void populatePatientWithExtensions(Patient patient,DemographicData demographicData) {
if (demographicData.getExtensionOmbCategoryRaceCode() != null) {
Extension raceExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race");
Extension ombCategoryExtension = new Extension("ombCategory");
ombCategoryExtension.setValue(new Coding()
.setSystem("urn:oid:2.16.840.1.113883.6.238")
.setCode(demographicData.getExtensionOmbCategoryRaceCode())
.setDisplay(demographicData.getExtensionOmbCategoryRaceCodeDescription()));
raceExtension.addExtension(ombCategoryExtension);
Extension textExtension = new Extension("text");
textExtension.setValue(new org.hl7.fhir.r4.model.StringType(demographicData.getExtensionOmbCategoryRaceCodeDescription()));
raceExtension.addExtension(textExtension);

patient.addExtension(raceExtension);
}

if (demographicData.getExtensionOmbCategoryEthnicityCode() != null) {
Extension ethnicityExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity");

Extension ombCategoryExtension = new Extension("ombCategory");
ombCategoryExtension.setValue(new Coding()
.setSystem("urn:oid:2.16.840.1.113883.6.238")
.setCode(demographicData.getExtensionOmbCategoryEthnicityCode())
.setDisplay(demographicData.getExtensionOmbCategoryEthnicityCodeDescription()));
ethnicityExtension.addExtension(ombCategoryExtension);

Extension textExtension = new Extension("text");
textExtension.setValue(new org.hl7.fhir.r4.model.StringType(demographicData.getExtensionOmbCategoryEthnicityCodeDescription()));
ethnicityExtension.addExtension(textExtension);

patient.addExtension(ethnicityExtension);
}

if (demographicData.getExtensionSexAtBirthCodeValue() != null) {
Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
birthSexExtension.setValue(new org.hl7.fhir.r4.model.CodeType(demographicData.getExtensionSexAtBirthCodeValue()));
patient.addExtension(birthSexExtension);
}

if (demographicData.getExtensionPersonalPronounsCode() != null) {
Extension pronounsExtension = new Extension("http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-personal-pronouns");
pronounsExtension.setValue(new CodeableConcept().addCoding(new Coding()
.setSystem("http://loinc.org")
.setCode(demographicData.getExtensionPersonalPronounsCode())
.setDisplay(demographicData.getExtensionPersonalPronounsDisplay())));
patient.addExtension(pronounsExtension);
}

if (demographicData.getExtensionGenderIdentityCode() != null) {
Extension genderIdentityExtension = new Extension("http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-gender-identity");
genderIdentityExtension.setValue(new CodeableConcept().addCoding(new Coding()
.setSystem("http://snomed.info/sct")
.setCode(demographicData.getExtensionGenderIdentityCode())
.setDisplay(demographicData.getExtensionGenderIdentityDisplay())));
patient.addExtension(genderIdentityExtension);
}
}
private static Patient populatePatientName(Patient patient, DemographicData demographicData) {
HumanName name = new HumanName();
if (demographicData.getGivenName() != null) {
Expand Down Expand Up @@ -144,113 +201,7 @@ private String generateUniqueId(String encounterId, String facilityId, String pa
.toString();
}

private void populateExtensions(Patient patient, DemographicData demographicData) {
if (StringUtils.isNotEmpty("ombCategory") || // TODO : remove static reference
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryRaceCode()) ||
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryRaceCodeDescription()) ||
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryRaceCodeSystemName())) {
Extension raceOmbExtension = getRaceOmbExtension(
"ombCategory", // TODO : remove static reference
null,
demographicData.getExtensionOmbCategoryRaceCodeSystemName(),
demographicData.getExtensionOmbCategoryRaceCode(),
demographicData.getExtensionOmbCategoryRaceCodeDescription());
patient.addExtension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", raceOmbExtension); // TODO
// :
// remove
// static
// reference
}

if (StringUtils.isNotEmpty("text") || // TODO : remove static reference
StringUtils.isNotEmpty("Asian")) { // TODO : remove static reference

Extension raceDetailedExtension = getRaceDetailedExtension(
"text", // TODO : remove static reference
"Asian", // TODO : remove static reference
null,
null,
null);
patient.addExtension(raceDetailedExtension);
}

if (StringUtils.isNotEmpty("ombCategory") || // TODO : remove static reference
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryEthnicityCode()) ||
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryEthnicityCodeDescription()) ||
StringUtils.isNotEmpty(demographicData.getExtensionOmbCategoryEthnicityCodeSystemName())) {

Extension ethnicityOmbExtension = getEthnicityOmbExtension(
"ombCategory",
null,
demographicData.getExtensionOmbCategoryEthnicityCodeSystemName(),
demographicData.getExtensionOmbCategoryEthnicityCode(),
demographicData.getExtensionOmbCategoryEthnicityCodeDescription());
patient.addExtension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
ethnicityOmbExtension); // TODO : remove static reference
}

if (StringUtils.isNotEmpty("text") ||
StringUtils.isNotEmpty("Hispanic or Latino")) { // TODO : remove static reference

Extension ethnicityDetailedExtension = getEthnicityDetailedExtension(
"text", // TODO : remove static reference
"Hispanic or Latino",
null, null, null);
patient.addExtension(ethnicityDetailedExtension);
}

if (StringUtils.isNotEmpty("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex") || // TODO :
// remove
// static
// reference
StringUtils.isNotEmpty(demographicData.getExtensionSexAtBirthCodeValue())) {

Extension ethnicityDetailedExtension = getEthnicityDetailedExtension(
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", // TODO : remove static
// reference
demographicData.getExtensionSexAtBirthCodeValue(),
null, null, null);
patient.addExtension(ethnicityDetailedExtension);
}

if (StringUtils.isNotEmpty("http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-personal-pronouns") || // TODO
// :
// remove
// static
// reference
StringUtils.isNotEmpty(demographicData.getExtensionPersonalPronounsCode()) ||
StringUtils.isNotEmpty(demographicData.getExtensionPersonalPronounsDisplay()) ||
StringUtils.isNotEmpty(demographicData.getExtensionPersonalPronounsSystem())) {

Extension personalPronounsExtension = getShinnyPersonalPronounsExtension(
"http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-personal-pronouns", // TODO : remove static
// reference
null,
demographicData.getExtensionPersonalPronounsSystem(),
demographicData.getExtensionPersonalPronounsCode(),
demographicData.getExtensionPersonalPronounsDisplay());
patient.addExtension(personalPronounsExtension);
}

if (StringUtils.isNotEmpty("http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-gender-identity") || // TODO
// :
// remove
// static
// reference
StringUtils.isNotEmpty(demographicData.getExtensionGenderIdentityCode()) ||
StringUtils.isNotEmpty(demographicData.getExtensionGenderIdentityDisplay()) ||
StringUtils.isNotEmpty(demographicData.getExtensionGenderIdentitySystem())) {

Extension genderIdentityExtension = getShinnyGenderIdentityExtension(
"http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-gender-identity", // TODO : remove static
// reference
null,
demographicData.getExtensionGenderIdentitySystem(),
demographicData.getExtensionGenderIdentityCode(),
demographicData.getExtensionGenderIdentityDisplay());
patient.addExtension(genderIdentityExtension);
}
}


private static void populateMrIdentifier(Patient patient, DemographicData data,Map<String,String> idsGenerated) {
if (StringUtils.isNotEmpty(data.getPatientMrIdValue())) {
Expand Down Expand Up @@ -408,50 +359,4 @@ private static void populatePatientRelationContact(Patient patient, DemographicD
});
}

private static void populatePatientText(Patient patient, DemographicData data) {
Optional.ofNullable("generated") // TODO : remove static reference
.filter(StringUtils::isNotEmpty)
.ifPresent(status -> {
Narrative text = new Narrative();
text.setStatus(NarrativeStatus.fromCode(status.toLowerCase()));
});
}

@Override
public Extension getRaceOmbExtension(String url, String value, String system, String code, String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getRaceDetailedExtension(String url, String value, String system, String code, String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getEthnicityOmbExtension(String url, String value, String system, String code, String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getEthnicityDetailedExtension(String url, String value, String system, String code,
String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getSexAtBirthExtension(String url, String value, String system, String code, String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getShinnyPersonalPronounsExtension(String url, String value, String system, String code,
String display) {
return createExtension(url, value, system, code, display);
}

@Override
public Extension getShinnyGenderIdentityExtension(String url, String value, String system, String code,
String display) {
return createExtension(url, value, system, code, display);
}
}

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