CNDIT-1729: Update observation services for Montana reports (#37)

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

@@ -167,3 +167,10 @@ databaseChangeLog:
         - sqlFile:
             path: 010-sp_investigation_event-002.sql
             splitStatements: false
+  - changeSet:
+      id: 24
+      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 +1,249 @@
+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(100);
+            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(300);
+            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_uid' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_observation_uid bigint;
+            END;
+
+        IF EXISTS(SELECT 1 FROM sys.columns col JOIN sys.types t on col.user_type_id = t.user_type_id
+                           WHERE col.name = N'result_observation_uid' AND t.name = 'bigint' AND col.object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ALTER COLUMN result_observation_uid nvarchar(max);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'followup_observation_uid' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD followup_observation_uid nvarchar(max);
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'report_refr_uid' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_refr_uid bigint;
+            END;
+
+        IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'report_sprt_uid' AND object_id = Object_ID(N'nrt_observation'))
+            BEGIN
+                ALTER TABLE nrt_observation
+                    ADD report_sprt_uid 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/Observation.java

@@ -20,6 +20,12 @@ public class Observation {
     @Column(name = "mood_cd")
     private String moodCd;
 
+    @Column(name = "interpretation_cd")
+    private String interpretationCd;
+
+    @Column(name = "interpretation_desc_txt")
+    private String interpretationDescTxt;
+
     @Id
     @Column(name = "observation_uid")
     private Long observationUid;
@@ -60,6 +66,9 @@ public class Observation {
     @Column(name = "electronic_ind")
     private Character electronicInd;
 
+    @Column(name = "version_ctrl_nbr")
+    private Short versionCtrlNbr;
+
     @Column(name = "ctrl_cd_display_form")
     private String ctrlCdDisplayForm;
 
@@ -72,8 +81,44 @@ public class Observation {
     @Column(name = "shared_ind")
     private Character sharedInd;
 
-    @Column(name = "version_ctrl_nbr")
-    private Short versionCtrlNbr;
+    @Column(name = "status_cd")
+    private String statusCd;
+
+    @Column(name = "cd_system_cd")
+    private String cdSystemCd;
+
+    @Column(name = "cd_system_desc_txt")
+    private String cdSystemDescTxt;
+
+    @Column(name = "ctrl_cd_user_defined_1")
+    private String ctrlCdUserDefined1;
+
+    @Column(name = "alt_cd")
+    private String altCd;
+
+    @Column(name = "alt_cd_desc_txt")
+    private String altCdDescTxt;
+
+    @Column(name = "alt_cd_system_cd")
+    private String altCdSystemCd;
+
+    @Column(name = "alt_cd_system_desc_txt")
+    private String altCdSystemDescTxt;
+
+    @Column(name = "method_cd")
+    private String methodCd;
+
+    @Column(name = "method_desc_txt")
+    private String methodDescTxt;
+
+    @Column(name = "target_site_cd")
+    private String targetSiteCd;
+
+    @Column(name = "target_site_desc_txt")
+    private String targetSiteDescTxt;
+
+    @Column(name = "txt")
+    private String txt;
 
     @Column(name = "add_user_id")
     private Long addUserId;
@@ -105,7 +150,27 @@ public class Observation {
     @Column(name = "followup_observations")
     private String followupObservations;
 
+    @Column(name = "parent_observations")
+    private String parentObservations;
+
     @Column(name = "act_ids")
     private String actIds;
 
+    @Column(name = "edx_ids")
+    private String edxIds;
+
+    @Column(name = "obs_reason")
+    private String obsReason;
+
+    @Column(name = "obs_txt")
+    private String obsTxt;
+
+    @Column(name = "obs_code")
+    private String obsCode;
+
+    @Column(name = "obs_date")
+    private String obsDate;
+
+    @Column(name = "obs_num")
+    private String obsNum;
 }

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

@@ -11,5 +11,9 @@ public class ObservationTransformed {
     private Long authorOrganizationId;
     private Long orderingOrganizationId;
     private Long materialId;
-    private Long resultObservationUid;
+    private String resultObservationUid;
+    private String followUpObservationUid;
+    private Long reportObservationUid;
+    private Long reportSprtUid;
+    private Long reportRefrUid;
 }