Merge branch 'tech-by-design:main' into jb-jb-feature-techbdspring-cs…

…vfix-fourfilesmissinggroup
tech-by-design · Dec 20, 2024 · 9f038a2 · 9f038a2
2 parents 0d703af + f5020b6
commit 9f038a2
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Showing 12 changed files with 80 additions and 57 deletions.
diff --git a/hub-prime/lib/techbd-udi-jooq-ingress.auto.jar b/hub-prime/lib/techbd-udi-jooq-ingress.auto.jar
diff --git a/hub-prime/pom.xml b/hub-prime/pom.xml
@@ -11,7 +11,7 @@
 	</parent>
 	<groupId>org.techbd</groupId>
 	<artifactId>hub-prime</artifactId>
-	<version>0.397.0</version>
+	<version>0.398.0</version>
 	<packaging>war</packaging>
 	<name>Tech by Design Hub (Prime)</name>
 	<description>Tech by Design Hub (Primary)</description>

diff --git a/hub-prime/src/main/java/org/techbd/service/converters/shinny/BundleConverter.java b/hub-prime/src/main/java/org/techbd/service/converters/shinny/BundleConverter.java
@@ -1,6 +1,7 @@
 package org.techbd.service.converters.shinny;
 
 import java.util.List;
+import java.util.UUID;
 
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.CanonicalType;
@@ -30,7 +31,7 @@ public ResourceType getResourceType() {
      */
     public Bundle generateEmptyBundle(String interactionId,String igVersion,DemographicData demographicData) {
         Bundle bundle = new Bundle();
-        bundle.setId(CsvConversionUtil.sha256(demographicData.getPatientMrIdValue()));
+        bundle.setId(CsvConversionUtil.sha256(UUID.randomUUID().toString()));
         bundle.setType(Bundle.BundleType.TRANSACTION);
         Meta meta = new Meta();
         meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));

diff --git a/hub-prime/src/main/java/org/techbd/service/converters/shinny/ConsentConverter.java b/hub-prime/src/main/java/org/techbd/service/converters/shinny/ConsentConverter.java
@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
+import java.util.UUID;
 
 import org.hl7.fhir.r4.model.Attachment;
 import org.hl7.fhir.r4.model.Bundle;
@@ -73,7 +74,7 @@ public List<BundleEntryComponent>  convert(Bundle bundle,DemographicData demogra
         Consent consent = new Consent();
         setMeta(consent);
 
-        consent.setId(CsvConversionUtil.sha256(screeningProfileData.getEncounterId()));
+        consent.setId(CsvConversionUtil.sha256(UUID.randomUUID().toString()));
 
         Meta meta = consent.getMeta();
         meta.setLastUpdated(DateUtil.parseDate(screeningProfileData.getConsentLastUpdated()));

diff --git a/hub-prime/src/main/java/org/techbd/service/converters/shinny/EncounterConverter.java b/hub-prime/src/main/java/org/techbd/service/converters/shinny/EncounterConverter.java
@@ -88,7 +88,7 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
 
         populatePatientReference(encounter, idsGenerated);
 
-        populateLocationReference(encounter, screeningProfileData, idsGenerated);
+    //    populateLocationReference(encounter, screeningProfileData, idsGenerated);
         Narrative text = new Narrative();
         text.setStatus(NarrativeStatus.GENERATED);
         encounter.setText(text);

diff --git a/hub-prime/src/main/java/org/techbd/service/converters/shinny/OrganizationConverter.java b/hub-prime/src/main/java/org/techbd/service/converters/shinny/OrganizationConverter.java
@@ -108,7 +108,7 @@ private static void populateOrganizationIdentifier(Organization organization, Qe
             CodeableConcept type = new CodeableConcept();
             type.addCoding(coding);
             identifier.setType(type);
-            identifier.setSystem("http://www.scn.ny.gov/");
+            identifier.setSystem(data.getFacilityIdentifierTypeSystem());
             LOG.info("Adding Identifier: Type Display - {}, Value - {}",
                     coding.getDisplay(), identifier.getValue());
 
@@ -166,7 +166,7 @@ private static void populateOrganizationAddress(Organization organization, QeAdm
     }
 
     private static void populateIsActive(Organization organization, QeAdminData qrAdminData) {
-        if (StringUtils.isNotEmpty("TRUE")) {  //Static_Value
+        if (StringUtils.isNotEmpty("TRUE")) {  //TODO : remove static reference
             organization.setActive(Boolean.parseBoolean("TRUE"));
         }
     }

diff --git a/hub-prime/src/main/java/org/techbd/service/converters/shinny/PatientConverter.java b/hub-prime/src/main/java/org/techbd/service/converters/shinny/PatientConverter.java
@@ -9,6 +9,7 @@
 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.CodeType;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.ContactPoint;
@@ -17,8 +18,6 @@
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Identifier;
 import org.hl7.fhir.r4.model.Meta;
-import org.hl7.fhir.r4.model.Narrative;
-import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Patient.PatientCommunicationComponent;
 import org.hl7.fhir.r4.model.Reference;
@@ -92,9 +91,6 @@ public List<BundleEntryComponent> convert(Bundle bundle, DemographicData demogra
         populatePreferredLanguage(patient, demographicData);
         populatePatientRelationContact(patient, demographicData);
 
-        Narrative text = new Narrative();
-        text.setStatus(NarrativeStatus.GENERATED);
-        patient.setText(text);
         // populatePatientText(patient, demographicData);
         BundleEntryComponent bundleEntryComponent = new BundleEntryComponent();
         bundleEntryComponent.setFullUrl(fullUrl);
@@ -139,14 +135,14 @@ public static void populatePatientWithExtensions(Patient patient,DemographicData
 
         if (demographicData.getExtensionSexAtBirthCodeValue() != null) {
             Extension birthSexExtension = new Extension("http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex");
-            birthSexExtension.setValue(new StringType(demographicData.getExtensionSexAtBirthCodeValue()));
+            birthSexExtension.setValue(new CodeType(demographicData.getExtensionSexAtBirthCodeValue())); // Use CodeType for valueCode
             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")
+                    .setSystem(demographicData.getExtensionPersonalPronounsSystem())
                     .setCode(demographicData.getExtensionPersonalPronounsCode())
                     .setDisplay(demographicData.getExtensionPersonalPronounsDisplay())));
             patient.addExtension(pronounsExtension);
@@ -155,7 +151,7 @@ public static void populatePatientWithExtensions(Patient patient,DemographicData
         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")
+                    .setSystem(demographicData.getExtensionGenderIdentitySystem())
                     .setCode(demographicData.getExtensionGenderIdentityCode())
                     .setDisplay(demographicData.getExtensionGenderIdentityDisplay())));
             patient.addExtension(genderIdentityExtension);
@@ -310,7 +306,7 @@ private void populatePreferredLanguage(Patient patient, DemographicData data) {
                 .filter(StringUtils::isNotEmpty)
                 .ifPresent(languageCode -> {
                     Coding coding = new Coding();
-                    coding.setSystem("urn:ietf:bcp:47");
+                    coding.setSystem(data.getPreferredLanguageCodeSystemName());
                     coding.setCode(languageCode);
                     CodeableConcept language = new CodeableConcept();
                     language.addCoding(coding);

diff --git a/...main/java/org/techbd/service/converters/shinny/ScreeningResponseObservationConverter.java b/...main/java/org/techbd/service/converters/shinny/ScreeningResponseObservationConverter.java
@@ -11,8 +11,6 @@
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.DateTimeType;
 import org.hl7.fhir.r4.model.Meta;
-import org.hl7.fhir.r4.model.Narrative;
-import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Reference;
 import org.hl7.fhir.r4.model.ResourceType;
@@ -53,21 +51,40 @@ 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 observationId = CsvConversionUtil.sha256(data.getQuestionCodeDisplay().replace(" ", "")+ data.getQuestionCode()); 
             observation.setId(observationId);
-            String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/%s%s"
-            .formatted(data.getQuestionCodeDisplay().replace(" ", ""), data.getQuestionCode());
+            String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/"+observationId;
             setMeta(observation);
             Meta meta = observation.getMeta();
             meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated())); // max date available in all
                                                                                               // screening records
             observation.setLanguage("en");
-            Narrative narrative = new Narrative();
-            narrative.setStatus(NarrativeStatus.GENERATED);
-            observation.setText(narrative);
-            observation.setStatus(Observation.ObservationStatus.FINAL);
-            observation.addCategory(createCategory("http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/SDOHCC-CodeSystemTemporaryCodes",
-                    "housing-instability", "Housing Instability"));
+            observation.setStatus(Observation.ObservationStatus.fromCode(screeningProfileData.getScreeningStatusCode()));
+            if (data.getObservationCategorySdohCode() != null && !data.getObservationCategorySnomedCode().equals("sdoh-category-unspecified")) {
+                observation.addCategory(createCategory("http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/SDOHCC-CodeSystemTemporaryCodes",
+                    data.getObservationCategorySdohCode(), data.getObservationCategorySdohDisplay()));
+            } else {
+                observation.addCategory(createCategory("http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/SDOHCC-CodeSystemTemporaryCodes",
+                    "sdoh-category-unspecified", "SDOH Category Unspecified"));
+
+                if (data.getObservationCategorySnomedCode() != null) {
+                    observation.addCategory(createCategory("http://snomed.info/sct",
+                        data.getObservationCategorySnomedCode(), data.getObservationCategorySnomedDisplay()));
+                }
+            }
+            if(data.getDataAbsentReasonCode() != null) {
+                CodeableConcept dataAbsentReason = new CodeableConcept();
+
+                dataAbsentReason.addCoding(
+                    new Coding()
+                        .setSystem("http://terminology.hl7.org/CodeSystem/data-absent-reason")
+                        .setCode(data.getDataAbsentReasonCode())
+                        .setDisplay(data.getDataAbsentReasonDisplay())
+                );
+                dataAbsentReason.setText(data.getDataAbsentReasonText());
+
+                observation.setDataAbsentReason(dataAbsentReason);
+            }
             observation.addCategory(createCategory("http://terminology.hl7.org/CodeSystem/observation-category",
                     "social-history", null));
             observation.addCategory(createCategory("http://terminology.hl7.org/CodeSystem/observation-category",

diff --git a/...main/java/org/techbd/service/converters/shinny/SexualOrientationObservationConverter.java b/...main/java/org/techbd/service/converters/shinny/SexualOrientationObservationConverter.java
@@ -47,7 +47,7 @@ public List<BundleEntryComponent>   convert(Bundle bundle,DemographicData demogr
         LOG.info("SexualOrientationObservationConverter:: convert BEGIN for interaction id :{} ", interactionId);
         Observation observation = new Observation();
         setMeta(observation);
-        observation.setId("SexualOrientation-" +CsvConversionUtil.sha256(screeningProfileData.getEncounterId()));
+        observation.setId(CsvConversionUtil.sha256(screeningProfileData.getPatientMrIdValue()+screeningProfileData.getEncounterId()));
         Meta meta = observation.getMeta();
         String fullUrl = "http://shinny.org/us/ny/hrsn/Observation/" + observation.getId();
         meta.setLastUpdated(DateUtil.parseDate(demographicData.getPatientLastUpdated()));

diff --git a/hub-prime/src/main/resources/shinny/shinny-artifacts/profile.yml b/hub-prime/src/main/resources/shinny/shinny-artifacts/profile.yml
@@ -7,4 +7,4 @@ observation: http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-observation
 questionnaire: http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-questionnaire
 practitioner: http://shinny.org/us/ny/hrsn/StructureDefinition/shin-ny-practitioner
 questionnaireResponse: http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-questionnaire
-observationSexualOrientation: http://shinny.org/us/ny/hrsn/StructureDefinition/shin-ny-observation-sexual-orientation
+observationSexualOrientation: http://shinny.org/us/ny/hrsn/StructureDefinition/shinny-observation-sexual-orientation
diff --git a/udi-prime/src/main/postgres/ingestion-center/001_idempotent_interaction.psql b/udi-prime/src/main/postgres/ingestion-center/001_idempotent_interaction.psql
@@ -139,7 +139,14 @@ AS SELECT hub_interaction_id AS interaction_id,
         WHEN 'Condition' = ANY(string_to_array(resource_type_set, ', '))
             THEN 'Assessment'
         ELSE NULL
-    END AS bundle_resource_type
+    END AS bundle_resource_type,
+    CASE 
+    	WHEN (source_type = 'CSV') then 'CSV'
+    	WHEN (source_type = 'fhir') then 'FHIR'
+    	WHEN (source_type = 'FHIR') then 'FHIR'
+    	ELSE 'FHIR'
+    END as source_type,   
+    source_hub_interaction_id    
    FROM techbd_udi_ingress.sat_interaction_fhir_request htt_req
    WHERE uri != '/api/expect/fhir/bundle'; 
 
@@ -3772,28 +3779,44 @@ $$ LANGUAGE plpgsql;
 
 DROP VIEW IF EXISTS techbd_udi_ingress.interaction_csv_http_stat CASCADE;
 CREATE OR REPLACE VIEW techbd_udi_ingress.interaction_csv_http_stat AS
+WITH fhir_summary AS (
+    SELECT
+        source_hub_interaction_id,
+        SUM(CASE WHEN nature = 'Forwarded HTTP Response' AND source_type = 'CSV' THEN 1 ELSE 0 END) AS fhir_count_success,
+        SUM(CASE WHEN nature = 'Forwarded HTTP Response Error' AND source_type = 'CSV' THEN 1 ELSE 0 END) AS fhir_count_failed,
+        COUNT(hub_interaction_id) AS fhir_count
+    FROM techbd_udi_ingress.sat_interaction_fhir_request
+    WHERE nature IN ('Forwarded HTTP Response', 'Forwarded HTTP Response Error')
+      AND source_type = 'CSV'
+    GROUP BY source_hub_interaction_id
+)
+
 SELECT 
-	sizfr.tenant_id_lower,
-	sizfr.hub_interaction_id,
-	sizfr.created_at,
+    sizfr.tenant_id_lower,
+    sizfr.hub_interaction_id,
+    sizfr.created_at,
     SUM(CASE WHEN siffcr.demographic_data_file_name IS NOT NULL THEN 1 ELSE 0 END) +
     SUM(CASE WHEN siffcr.qe_admin_data_file_name IS NOT NULL THEN 1 ELSE 0 END) +
     SUM(CASE WHEN siffcr.screening_observation_data_file_name IS NOT NULL THEN 1 ELSE 0 END) +
-    SUM(CASE WHEN siffcr.screening_profile_data_file_name IS NOT NULL THEN 1 ELSE 0 END) 
-    AS file_count,
-    count(sifr.hub_interaction_id) as fhir_count,
-    SUM(CASE WHEN sifr.nature = 'Forwarded HTTP Response' THEN 1 ELSE 0 END) AS fhir_count_success,
-    SUM(CASE WHEN sifr.nature = 'Forwarded HTTP Response Error' THEN 1 ELSE 0 END) AS fhir_count_failed
+    SUM(CASE WHEN siffcr.screening_profile_data_file_name IS NOT NULL THEN 1 ELSE 0 END) AS file_count,
+    COALESCE(fhir_summary.fhir_count, 0) AS fhir_count,
+    COALESCE(fhir_summary.fhir_count_success, 0) AS fhir_count_success,
+    COALESCE(fhir_summary.fhir_count_failed, 0) AS fhir_count_failed
 FROM
     techbd_udi_ingress.sat_interaction_zip_file_request sizfr
 JOIN
     techbd_udi_ingress.sat_interaction_flat_file_csv_request siffcr
-    ON sizfr.hub_interaction_id = siffcr.zip_file_hub_interaction_id
+    ON sizfr.hub_interaction_id = siffcr.zip_file_hub_interaction_id 
+    AND siffcr.nature = 'Original Flat File CSV'
 LEFT JOIN
-	techbd_udi_ingress.sat_interaction_fhir_request sifr
-	ON sizfr.hub_interaction_id = sifr.source_hub_interaction_id AND (sifr.nature ='Forwarded HTTP Response' or sifr.nature='Forwarded HTTP Response Error') AND sifr.source_type ='CSV'
+    fhir_summary
+    ON sizfr.hub_interaction_id = fhir_summary.source_hub_interaction_id
 GROUP BY 
     sizfr.hub_interaction_id,
     sizfr.created_at,
-    sizfr.tenant_id_lower
-ORDER BY  sizfr.created_at DESC;
+    sizfr.tenant_id_lower,
+    fhir_summary.fhir_count,
+    fhir_summary.fhir_count_success,
+    fhir_summary.fhir_count_failed
+ORDER BY 
+    sizfr.created_at DESC;
diff --git a/udi-prime/src/main/postgres/ingestion-center/migrations/migrate-basic-infrastructure.ts b/udi-prime/src/main/postgres/ingestion-center/migrations/migrate-basic-infrastructure.ts
@@ -1162,21 +1162,6 @@ const migrateSP = pgSQLa.storedProcedure(
       ALTER TABLE techbd_udi_ingress.sat_interaction_fhir_request 
 	      ADD COLUMN IF NOT EXISTS group_hub_interaction_id TEXT NULL;      
         
-      DO $$
-      BEGIN
-          IF NOT EXISTS (
-              SELECT 1
-              FROM information_schema.table_constraints
-              WHERE table_name = 'sat_interaction_fhir_request'
-                AND constraint_name = 'sat_interaction_fhir_request_group_interaction_id_fkey'
-                AND constraint_type = 'FOREIGN KEY'
-          ) THEN
-              ALTER TABLE techbd_udi_ingress.sat_interaction_fhir_request
-              ADD CONSTRAINT sat_interaction_fhir_request_group_interaction_id_fkey
-              FOREIGN KEY (group_hub_interaction_id)
-              REFERENCES techbd_udi_ingress.hub_interaction(hub_interaction_id);
-          END IF;
-      END $$;        
 
 
       ${dependenciesSQL}