Merge pull request #915 from Shreeja-dev/745-csv-validate-new

feat:added missing fields#745

hub-prime/src/main/java/org/techbd/service/converters/shinny/BundleConverter.java

@@ -30,7 +30,7 @@ public ResourceType getResourceType() {
      */
     public Bundle generateEmptyBundle(String interactionId,String igVersion,DemographicData demographicData) {
         Bundle bundle = new Bundle();
-        bundle.setId("AHCHRSNScreeningResponse-"+CsvConversionUtil.sha256(demographicData.getPatientMrIdValue()));
+        bundle.setId(CsvConversionUtil.sha256(demographicData.getPatientMrIdValue()));
         bundle.setType(Bundle.BundleType.TRANSACTION);
         Meta meta = new Meta();
         meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));

hub-prime/src/main/java/org/techbd/service/converters/shinny/ConsentConverter.java

@@ -1,15 +1,13 @@
 package org.techbd.service.converters.shinny;
 
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
-import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
 import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Consent;
@@ -78,7 +76,7 @@ public List<BundleEntryComponent>  convert(Bundle bundle,DemographicData demogra
         consent.setId(CsvConversionUtil.sha256(screeningProfileData.getEncounterId()));
 
         Meta meta = consent.getMeta();
-        meta.setLastUpdated(getLastUpdatedDate(screeningProfileData));
+        meta.setLastUpdated(DateUtil.parseDate(screeningProfileData.getConsentLastUpdated()));
 
         populateConsentStatusAndScope(consent, screeningProfileData);
 
@@ -103,6 +101,7 @@ public List<BundleEntryComponent>  convert(Bundle bundle,DemographicData demogra
         String fullUrl = "http://shinny.org/us/ny/hrsn/Consent/" + consent.getId();
         BundleEntryComponent bundleEntryComponent = new BundleEntryComponent();
         bundleEntryComponent.setFullUrl(fullUrl);
+        bundleEntryComponent.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Consent/" + consent.getId()));
         bundleEntryComponent.setResource(consent);
         return List.of(bundleEntryComponent);
     }
@@ -193,26 +192,6 @@ public static void populateConsentDateTime(Consent consent, ScreeningProfileData
         consent.setDateTime(DateUtil.convertStringToDate(consentDateTime));
     }
 
-    /**
-     * Get the last updated date for the consent based on its data from QeAdminData.
-     *
-     * @param qrAdminData The QeAdminData object containing the consent's last
-     *                    updated date.
-     * @return The last updated date.
-     */
-    private Date getLastUpdatedDate(ScreeningProfileData screeningResourceData) {
-        if (screeningResourceData != null && screeningResourceData.getConsentLastUpdated() != null
-                && !screeningResourceData.getConsentLastUpdated().isEmpty()) {
-            try {
-                SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
-                return dateFormat.parse(screeningResourceData.getConsentLastUpdated());
-            } catch (ParseException e) {
-                LOG.error("Error parsing last updated date", e);
-            }
-        }
-        return new Date();
-    }
-
     private void populateSourceAttachment(Consent consent) {
         Attachment attachment = new Attachment();
         attachment.setContentType("application/pdf");

hub-prime/src/main/java/org/techbd/service/converters/shinny/EncounterConverter.java

@@ -1,13 +1,11 @@
 package org.techbd.service.converters.shinny;
 
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Encounter;
@@ -76,7 +74,7 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
         String fullUrl = "http://shinny.org/us/ny/hrsn/Encounter/" + encounter.getId();
 
         Meta meta = encounter.getMeta();
-        meta.setLastUpdated(getLastUpdatedDate(qeAdminData));
+        meta.setLastUpdated(DateUtil.parseDate(qeAdminData.getFacilityLastUpdated()));
 
         populateEncounterStatus(encounter, screeningProfileData);
 
@@ -95,6 +93,7 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
 
         BundleEntryComponent bundleEntryComponent = new BundleEntryComponent();
         bundleEntryComponent.setFullUrl(fullUrl);
+        bundleEntryComponent.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Encounter/" + encounter.getId()));
         bundleEntryComponent.setResource(encounter);
         return List.of(bundleEntryComponent);
     }
@@ -161,25 +160,4 @@ private void populateLocationReference(Encounter encounter, ScreeningProfileData
                     .setLocation(new Reference("Location/" + "LocationExample-SCN")));
         }
     }
-
-    /**
-     * Get the last updated date for the encounter based on its data from
-     * QeAdminData.
-     *
-     * @param qrAdminData The QeAdminData object containing the encounter's last
-     *                    updated date.
-     * @return The last updated date.
-     */
-    private Date getLastUpdatedDate(QeAdminData qrAdminData) {
-        if (qrAdminData != null && qrAdminData.getFacilityLastUpdated() != null
-                && !qrAdminData.getFacilityLastUpdated().isEmpty()) {
-            try {
-                SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
-                return dateFormat.parse(qrAdminData.getFacilityLastUpdated());
-            } catch (ParseException e) {
-                LOG.error("Error parsing last updated date", e);
-            }
-        }
-        return new Date();
-    }
 }

hub-prime/src/main/java/org/techbd/service/converters/shinny/OrganizationConverter.java

@@ -1,17 +1,15 @@
 package org.techbd.service.converters.shinny;
 
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.Date;
 import java.util.List;
 import java.util.Map;
 
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.r4.model.Address;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Identifier;
@@ -28,6 +26,7 @@
 import org.techbd.model.csv.ScreeningProfileData;
 import org.techbd.util.CsvConstants;
 import org.techbd.util.CsvConversionUtil;
+import org.techbd.util.DateUtil;
 
 /**
  * Converts data related to an Organization into a FHIR Organization resource.
@@ -70,14 +69,17 @@ public List<BundleEntryComponent>  convert(Bundle bundle,DemographicData demogra
         setMeta(organization);
         organization.setId(CsvConversionUtil.sha256(qeAdminData.getFacilityId())); // Assuming qrAdminData contains orgId
         idsGenerated.put(CsvConstants.ORGANIZATION_ID,organization.getId());
+        String fullUrl = "http://shinny.org/us/ny/hrsn/Organization/" + organization.getId();
         Meta meta = organization.getMeta();
-        meta.setLastUpdated(getLastUpdatedDate(qeAdminData));
+        meta.setLastUpdated(DateUtil.parseDate(qeAdminData.getFacilityLastUpdated()));
         populateOrganizationName(organization, qeAdminData);
         populateOrganizationIdentifier(organization, qeAdminData);
         populateIsActive(organization, qeAdminData);
         populateOrganizationType(organization, qeAdminData);
         populateOrganizationAddress(organization, qeAdminData);
         BundleEntryComponent bundleEntryComponent = new BundleEntryComponent();
+        bundleEntryComponent.setFullUrl(fullUrl);
+        bundleEntryComponent.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Organization/" + organization.getId()));
         bundleEntryComponent.setResource(organization);
         return List.of(bundleEntryComponent);
     }
@@ -155,28 +157,4 @@ private static void populateIsActive(Organization organization, QeAdminData qrAd
             organization.setActive(Boolean.parseBoolean("TRUE"));
         }
     }
-
-    /**
-     * Get the last updated date for the organization based on its data from
-     * QeAdminData.
-     *
-     * @param qrAdminData The QeAdminData object containing the facility's last
-     *                    updated date.
-     * @return The last updated date.
-     */
-    private Date getLastUpdatedDate(QeAdminData qrAdminData) {
-        // Check if the facilityLastUpdated field in QeAdminData is not null or empty
-        if (qrAdminData != null && qrAdminData.getFacilityLastUpdated() != null
-                && !qrAdminData.getFacilityLastUpdated().isEmpty()) {
-            try {
-                // Example: Assuming the format is "yyyy-MM-dd'T'HH:mm:ss'Z'" (ISO 8601 format)
-                SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'");
-                return dateFormat.parse(qrAdminData.getFacilityLastUpdated()); // Return the parsed date
-            } catch (ParseException e) {
-                return new Date();
-            }
-        }
-        return new Date();
-    }
-
 }

hub-prime/src/main/java/org/techbd/service/converters/shinny/PatientConverter.java

@@ -8,6 +8,7 @@
 import org.hl7.fhir.r4.model.Address;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ContactPoint;
@@ -97,6 +98,7 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
         // populatePatientText(patient, demographicData);
         BundleEntryComponent bundleEntryComponent = new BundleEntryComponent();
         bundleEntryComponent.setFullUrl(fullUrl);
+        bundleEntryComponent.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Patient/" + patient.getId()));
         bundleEntryComponent.setResource(patient);
         LOG.info("PatientConverter :: convert  END for transaction id :{}", interactionId);
         return List.of(bundleEntryComponent);
@@ -246,7 +248,7 @@ private static void populateSsnIdentifier(Patient patient, DemographicData data)
             Identifier identifier = new Identifier();
             Coding coding = new Coding();
             coding.setSystem("http://terminology.hl7.org/CodeSystem/v2-0203"); // TODO : remove static reference
-            coding.setCode("SSN");
+            coding.setCode("SS");
             coding.setDisplay("Social Security Number");
             CodeableConcept type = new CodeableConcept();
             type.addCoding(coding);

hub-prime/src/main/java/org/techbd/service/converters/shinny/ScreeningResponseObservationConverter.java

@@ -6,6 +6,7 @@
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DateTimeType;
@@ -52,8 +53,9 @@ public List<BundleEntryComponent> convert(
 
         for (ScreeningObservationData data : screeningObservationDataList) {
             Observation observation = new Observation();
-            String observationId = CsvConversionUtil.sha256(data.getEncounterId()+data.getScreeningCode()); // Use screening code as ID
-            String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/" + observationId;
+            String observationId = CsvConversionUtil.sha256(data.getEncounterId()+data.getScreeningCode()); // Use screening code as ID'
+            observation.setId(observationId);
+            String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/" + data.getQuestionCode();
             setMeta(observation);
             Meta meta = observation.getMeta();
             meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated())); // max date available in all
@@ -70,7 +72,7 @@ public List<BundleEntryComponent> convert(
             observation.addCategory(createCategory("http://terminology.hl7.org/CodeSystem/observation-category",
                     "survey", null));
             CodeableConcept code = new CodeableConcept();
-            code.addCoding(new Coding("http://loinc.org", data.getScreeningCode(), data.getScreeningCodeDescription()));
+            code.addCoding(new Coding("http://loinc.org", data.getQuestionCode(), data.getQuestionCodeDisplay()));
             code.setText(data.getQuestionCodeText());
             observation.setCode(code);
             observation.setSubject(new Reference("Patient/" +idsGenerated.get(CsvConstants.PATIENT_ID)));
@@ -83,6 +85,7 @@ public List<BundleEntryComponent> convert(
             observation.setValue(value);
             BundleEntryComponent entry = new BundleEntryComponent();
             entry.setFullUrl(fullUrl);
+            entry.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Observation/" + observationId));
             entry.setResource(observation);
             bundleEntryComponents.add(entry);
         }    

hub-prime/src/main/java/org/techbd/service/converters/shinny/SexualOrientationObservationConverter.java

@@ -5,6 +5,7 @@
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
+import org.hl7.fhir.r4.model.Bundle.HTTPVerb;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
@@ -48,8 +49,7 @@ public List<BundleEntryComponent>   convert(Bundle bundle,DemographicData demogr
         setMeta(observation);
         observation.setId("SexualOrientation-" +CsvConversionUtil.sha256(screeningProfileData.getEncounterId()));
         Meta meta = observation.getMeta();
-        String fullUrl = "http://shinny.org/us/ny/hrsn/Observation" + observation.getId();
-        meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));
+        String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/" + observation.getId();
         meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));
         observation.setStatus(Observation.ObservationStatus.fromCode("final"));  //TODO : remove static reference
         Reference subjectReference = new Reference();
@@ -71,6 +71,7 @@ public List<BundleEntryComponent>   convert(Bundle bundle,DemographicData demogr
         observation.setText(text);
         BundleEntryComponent entry = new BundleEntryComponent();
         entry.setFullUrl(fullUrl);
+        entry.setRequest(new Bundle.BundleEntryRequestComponent().setMethod(HTTPVerb.POST).setUrl("http://shinny.org/us/ny/hrsn/Observation/" + observation.getId()));
         entry.setResource(observation);
         LOG.info("SexualOrientationObservationConverter:: convert END for interaction id :{} ", interactionId);
         return List.of(entry);

hub-prime/src/test/java/org/techbd/service/csv/ConsentConverterTest.java

@@ -3,7 +3,9 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.assertj.core.api.SoftAssertions;
 import org.hl7.fhir.r4.model.Bundle;
@@ -40,11 +42,12 @@ void testConvert() throws Exception {
         final DemographicData demographicData = CsvTestHelper.createDemographicData();
         final List<ScreeningObservationData> screeningDataList = CsvTestHelper.createScreeningObservationData();
         final QeAdminData qrAdminData = CsvTestHelper.createQeAdminData();
+        final Map<String, String> idsGenerated = new HashMap<>();
         final ScreeningProfileData screeningResourceData = CsvTestHelper.createScreeningProfileData();
 
         // Call the convert method of the consent converter
         final BundleEntryComponent result = consentConverter.convert(bundle, demographicData, qrAdminData, screeningResourceData,
-                 screeningDataList, "interactionId",null).get(0);
+                 screeningDataList, "interactionId", idsGenerated).get(0);
 
         // Create soft assertions to verify the result
         final SoftAssertions softly = new SoftAssertions();
@@ -80,11 +83,12 @@ void testGeneratedJson() throws Exception {
         final var demographicData = CsvTestHelper.createDemographicData();
         final var screeningDataList = CsvTestHelper.createScreeningObservationData();
         final var qrAdminData = CsvTestHelper.createQeAdminData();
+        final Map<String, String> idsGenerated = new HashMap<>();
         final ScreeningProfileData screeningResourceData = CsvTestHelper.createScreeningProfileData();
 
         final var result = consentConverter.convert(bundle, demographicData, qrAdminData, screeningResourceData,
                 screeningDataList,
-                "interactionId",null);
+                "interactionId", idsGenerated);
 
         final Consent consent = (Consent) result.get(0).getResource();
         final var filePath = "src/test/resources/org/techbd/csv/generated-json/consent.json";

hub-prime/src/test/java/org/techbd/service/csv/EncounterConverterTest.java

@@ -3,7 +3,9 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import org.assertj.core.api.SoftAssertions;
 import org.hl7.fhir.r4.model.Bundle;
@@ -36,18 +38,19 @@ class EncounterConverterTest {
     @Disabled
     void testConvert() throws Exception {
         // Create necessary data objects for the test
-        final Bundle bundle = new Bundle();  // Ensure this is populated with relevant data
-        final DemographicData demographicData = CsvTestHelper.createDemographicData();  // Create DemographicData instance
-        final List<ScreeningObservationData> screeningDataList = CsvTestHelper.createScreeningObservationData();  // Create list of ScreeningData
-        final QeAdminData qrAdminData = CsvTestHelper.createQeAdminData();  // Create QeAdminData instance
-        final ScreeningProfileData screeningResourceData = CsvTestHelper.createScreeningProfileData();  // Create ScreeningResourceData
+        final Bundle bundle = new Bundle();
+        final DemographicData demographicData = CsvTestHelper.createDemographicData();
+        final List<ScreeningObservationData> screeningDataList = CsvTestHelper.createScreeningObservationData();
+        final QeAdminData qrAdminData = CsvTestHelper.createQeAdminData();
+        final ScreeningProfileData screeningResourceData = CsvTestHelper.createScreeningProfileData();
+        final Map<String, String> idsGenerated = new HashMap<>();
 
         // Instantiate the EncounterConverter
         EncounterConverter encounterConverter = new EncounterConverter();
 
         // Call the convert method of the encounter converter
         final BundleEntryComponent result = encounterConverter.convert(bundle, demographicData, qrAdminData, screeningResourceData,
-                 screeningDataList, "interactionId", null).get(0);;
+                 screeningDataList, "interactionId", idsGenerated).get(0);;
 
         // Create soft assertions to verify the result
         final SoftAssertions softly = new SoftAssertions();
@@ -84,11 +87,12 @@ void testGeneratedJson() throws Exception {
         final var demographicData = CsvTestHelper.createDemographicData();
         final var screeningDataList = CsvTestHelper.createScreeningObservationData();
         final var qrAdminData = CsvTestHelper.createQeAdminData();
+        final Map<String, String> idsGenerated = new HashMap<>();
         final ScreeningProfileData screeningResourceData = CsvTestHelper.createScreeningProfileData();
 
         final var result = encounterConverter.convert(bundle, demographicData, qrAdminData, screeningResourceData,
                 screeningDataList,
-                "interactionId", null);
+                "interactionId", idsGenerated);
 
         final Encounter encounter = (Encounter) result.get(0).getResource();
         final var filePath = "src/test/resources/org/techbd/csv/generated-json/encounter.json";