Release 2.4.0 fixes (#400)

* Fixed Healthcare Visit reports mapping
* PostgreSQL Flyway script fix
* Bump circe-be to 1.5.0
* Evidence_job increment fix
* Rollup to ancestor visit concept IDs for analysis 4020, 4021
* Update webapi.version to 2.4.0
* Revert column name change in drug_reports CTE.

Author: chrisknoll

pom.xml

@@ -9,7 +9,7 @@
   <version>1.0.0-SNAPSHOT</version>
   <name>WebAPI</name>
   <properties>
-    <webapi.version>2.3.0</webapi.version>
+    <webapi.version>2.4.0</webapi.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <jersey.version>2.14</jersey.version>
     <!-- Spring Boot manages spring.version as well -->
@@ -549,7 +549,7 @@
     <dependency>
       <groupId>org.ohdsi</groupId>
       <artifactId>circe</artifactId>
-      <version>1.4.0</version>
+      <version>1.5.0</version>
     </dependency>
     <dependency>
       <groupId>org.json</groupId>

src/main/java/org/ohdsi/webapi/cohortresults/CohortResultsAnalysisRunner.java

@@ -1676,8 +1676,8 @@ public HealthcareVisitUtilizationReport getHealthcareVisitReport(JdbcTemplate jd
 			s.chargedPmPm = rs.getString("charged_pmpm") == null ? null : new BigDecimal(rs.getDouble("charged_pmpm")).setScale(2, BigDecimal.ROUND_HALF_UP);
 			s.paid = rs.getString("paid") == null ? null : new BigDecimal(rs.getDouble("paid")).setScale(2, BigDecimal.ROUND_HALF_UP);
 			s.paidPmPm = rs.getString("paid_pmpm") == null ? null : new BigDecimal(rs.getDouble("paid_pmpm")).setScale(2, BigDecimal.ROUND_HALF_UP);
-			s.allowedChargedRatio = rs.getString("allowed_charged") == null ? null : new BigDecimal(rs.getDouble("paid_pmpm")).setScale(2, BigDecimal.ROUND_HALF_UP);
-			s.paidAllowedRatio = rs.getString("paid_allowed") == null ? null : new BigDecimal(rs.getDouble("paid_pmpm")).setScale(2, BigDecimal.ROUND_HALF_UP);
+			s.allowedChargedRatio = rs.getString("allowed_charged") == null ? null : new BigDecimal(rs.getDouble("allowed_charged")).setScale(2, BigDecimal.ROUND_HALF_UP);
+			s.paidAllowedRatio = rs.getString("paid_allowed") == null ? null : new BigDecimal(rs.getDouble("paid_allowed")).setScale(2, BigDecimal.ROUND_HALF_UP);
 
 			return s;
 		});

src/main/resources/db/migration/postgresql/V1.0.11.1__schema-executions.sql

@@ -42,10 +42,10 @@ INSERT INTO ${ohdsiSchema}.analysis_execution (analysis_id, analysis_type, durat
                          AND sec_user_id = cca.sec_user_id
                          AND source_id = cca.source_id
   )
-ON CONFLICT DO NOTHING;
+;
 
 ALTER TABLE ${ohdsiSchema}.input_files
-  ADD COLUMN IF NOT EXISTS execution_id INTEGER;
+  ADD COLUMN execution_id INTEGER;
 
 UPDATE ${ohdsiSchema}.input_files f
 SET execution_id =
@@ -57,7 +57,7 @@ SET execution_id =
  LIMIT 1);
 
 ALTER TABLE ${ohdsiSchema}.output_files
-  ADD COLUMN IF NOT EXISTS execution_id INTEGER;
+  ADD COLUMN execution_id INTEGER;
 
 UPDATE ${ohdsiSchema}.output_files f
 SET execution_id =

src/main/resources/resources/cohortanalysis/sql/runHeraclesAnalyses.sql

@@ -11166,7 +11166,7 @@ DROP TABLE #raw_de_p_4019;
 select c1.cohort_definition_id,
 	c1.subject_id,
   vo1.visit_occurrence_id,
-  vo1.visit_concept_id,
+  vca.ancestor_concept_id visit_concept_id,
   vo1.visit_type_concept_id,
 	cst1.cost_concept_id,
   cst1.cost_type_concept_id,
@@ -11179,6 +11179,7 @@ join @CDM_schema.visit_occurrence vo1 on c1.subject_id = vo1.person_id
 join @CDM_schema.cost cst1 on c1.subject_id = cst1.person_id
   and cst1.person_id = vo1.person_id
   and vo1.visit_occurrence_id = cst1.cost_event_id
+join @CDM_schema.concept_ancestor vca on vca.descendant_concept_id = vo1.visit_concept_id
 where cost >= 0
     and currency_concept_id = 44818668
 ;
@@ -11376,7 +11377,7 @@ DROP TABLE #raw_period_4020;
 select c1.cohort_definition_id,
 	c1.subject_id,
   vo1.visit_occurrence_id,
-  vo1.visit_concept_id,
+  vca.ancestor_concept_id visit_concept_id,
   vo1.visit_type_concept_id,
 	cst1.cost_concept_id,
   cst1.cost_type_concept_id,
@@ -11388,6 +11389,7 @@ join @CDM_schema.visit_occurrence vo1 on c1.subject_id = vo1.person_id
     and vo1.visit_start_date >= c1.cohort_start_date and vo1.visit_start_date <= c1.cohort_end_date
 join @CDM_schema.cost cst1 on c1.subject_id = cst1.person_id
     and vo1.visit_occurrence_id = cst1.cost_event_id
+join @CDM_schema.concept_ancestor vca on vca.descendant_concept_id = vo1.visit_concept_id
 where cost >= 0
     and currency_concept_id = 44818668
 ;

src/main/resources/resources/evidence/sql/negativecontrols/getJobId.sql

@@ -1 +1 @@
-INSERT INTO @evidenceSchema.evidence_job SELECT MAX(id) + 1 from @evidenceSchema.evidence_job;
+INSERT INTO @evidenceSchema.evidence_job SELECT ISNULL(MAX(id), 0) + 1 from @evidenceSchema.evidence_job;