CNDIT-1729 Update liquibase and transformation

liquibase-service/src/main/resources/db/changelog/db.odse.changelog-16.1.yaml

@@ -160,3 +160,10 @@ databaseChangeLog:
         - sqlFile:
             path: 020-sp_notification_event-002.sql
             splitStatements: false
+  - changeSet:
+      id: 23
+      author: liquibase
+      changes:
+        - sqlFile:
+            path: 021_sp_observation_event-001.sql
+            splitStatements: false

liquibase-service/src/main/resources/db/changelog/db.rdb.changelog-16.1.yaml

@@ -258,3 +258,10 @@ databaseChangeLog:
         - sqlFile:
             path: 015-sp_nrt_ldf_postprocessing-001.sql
             splitStatements: false
+  - changeSet:
+      id: 37
+      author: liquibase
+      changes:
+        - sqlFile:
+            path: 017-create_nrt_observation-003.sql
+            splitStatements: false

liquibase-service/src/main/resources/db/rdb/tables/017-create_nrt_observation-003.sql

@@ -0,0 +1,248 @@
+IF EXISTS (SELECT 1 FROM sysobjects WHERE name = 'nrt_observation' and xtype = 'U')
+    BEGIN
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'ctrl_cd_display_form' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD ctrl_cd_display_form varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'obs_domain_cd_st_1' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD obs_domain_cd_st_1 varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'processing_decision_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD processing_decision_cd varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD cd varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'shared_ind' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD shared_ind char(1);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'status_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD status_cd char(1);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'cd_system_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD cd_system_cd varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'cd_system_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD cd_system_desc_txt varchar(1000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'ctrl_cd_user_defined_1' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD ctrl_cd_user_defined_1 varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD alt_cd varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD alt_cd_desc_txt varchar(1000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd_system_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+            ALTER TABLE nrt_observation
+                ADD alt_cd_system_cd varchar(1000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd_system_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD alt_cd_system_desc_txt varchar(100);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'method_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD method_cd varchar(2000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'method_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD method_desc_txt varchar(2000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'target_site_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD target_site_cd varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'target_site_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD target_site_desc_txt varchar(100);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD txt varchar(1000);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'interpretation_cd' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD interpretation_cd varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'interpretation_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD interpretation_desc_txt varchar(100);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'report_observation_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_observation_id bigint;
+            END;
+
+        IF EXISTS(SELECT 1 FROM sys.columns WHERE name = N'result_observation_id' AND  DATA_TYPE = 'bigint' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                ALTER COLUMN result_observation_id nvarchar(max);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'followup_observation_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD followup_observation_id nvarchar(max);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'report_refr_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_refr_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'report_sprt_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_sprt_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'morb_physician_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD morb_physician_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'morb_reporter_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD morb_reporter_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'transcriptionist_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD transcriptionist_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'transcriptionist_val' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD transcriptionist_val varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'transcriptionist_first_nm' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD transcriptionist_first_nm varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'transcriptionist_last_nm' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD transcriptionist_last_nm varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'assistant_interpreter_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD assistant_interpreter_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'assistant_interpreter_val' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD assistant_interpreter_val varchar(20);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'assistant_interpreter_first_nm' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD assistant_interpreter_first_nm varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'assistant_interpreter_last_nm' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD transcriptionist_last_nm varchar(50);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'result_interpreter_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD result_interpreter_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'specimen_collector_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD specimen_collector_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'copy_to_provider_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD copy_to_provider_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'lab_test_technician_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD lab_test_technician_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'health_care_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD health_care_id bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'morb_hosp_reporter_id' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD morb_hosp_reporter_id bigint;
+            END;
+    END;

observation-service/src/main/java/gov/cdc/etldatapipeline/observation/repository/model/dto/ObservationTransformed.java

@@ -11,6 +11,9 @@ public class ObservationTransformed {
     private Long authorOrganizationId;
     private Long orderingOrganizationId;
     private Long materialId;
-    private String resultObservationUid;
-    private String followUpObservationUid;
+    private String resultObservationId;
+    private String followUpObservationId;
+    private Long reportObservationId;
+    private Long reportSprtId;
+    private Long reportRefrId;
 }

observation-service/src/main/java/gov/cdc/etldatapipeline/observation/repository/model/reporting/ObservationReporting.java

@@ -52,19 +52,21 @@ public class ObservationReporting {
     private Long reportObservationId;
     private Long reportRefrId;
     private Long reportSprtId;
-    private String resultObservationUid;
-    private String followupObservationUid;
+    private String resultObservationId;
+    private String followupObservationId;
 
     private Long patientId;
     private Long orderingPersonId;
     private Long morbPhysicianId;
     private Long morbReporterId;
     private Long transcriptionistId;
     private String transcriptionistVal;
-    private String transcriptionistName;
+    private String transcriptionistFirstNm;
+    private String transcriptionistLastNm;
     private Long assistantInterpreterId;
     private String assistantInterpreterVal;
-    private String assistantInterpreterName;
+    private String assistantInterpreterFirstNm;
+    private String assistantInterpreterLastNm;
     private Long resultInterpreterId;
     private Long specimenCollectorId;
     private Long copyToProviderId;

observation-service/src/main/java/gov/cdc/etldatapipeline/observation/service/ObservationService.java

@@ -122,7 +122,11 @@ protected void buildReportingModelForTransformedData(ObservationReporting report
         reportingModel.setAuthorOrganizationId(observationTransformed.getAuthorOrganizationId());
         reportingModel.setOrderingOrganizationId(observationTransformed.getOrderingOrganizationId());
         reportingModel.setMaterialId(observationTransformed.getMaterialId());
-        reportingModel.setResultObservationUid(observationTransformed.getResultObservationUid());
-        reportingModel.setFollowupObservationUid(observationTransformed.getFollowUpObservationUid());
+        reportingModel.setResultObservationId(observationTransformed.getResultObservationId());
+        reportingModel.setFollowupObservationId(observationTransformed.getFollowUpObservationId());
+        reportingModel.setReportObservationId(Optional.ofNullable(observationTransformed.getReportObservationId())
+                .orElse(reportingModel.getObservationUid()));
+        reportingModel.setReportRefrId(observationTransformed.getReportRefrId());
+        reportingModel.setReportSprtId(observationTransformed.getReportSprtId());
     }
 }