Fix subset conceptset analysis (#1132)

* Fix subset conceptset analysis * Handle empty index event breakdown results * Fix tests failure when postgres is not configured --------- Co-authored-by: Gennadiy Anisimov <gennadiy.anisimov@softwarecountry.com>
OHDSI · Sep 10, 2024 · aceff29 · aceff29
1 parent deb2d20
commit aceff29
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Showing 2 changed files with 15 additions and 2 deletions.
diff --git a/R/ConceptSets.R b/R/ConceptSets.R
@@ -157,9 +157,9 @@ combineConceptSetsFromCohorts <- function(cohorts) {
     }
 
     sqlCs <-
-      extractConceptSetsSqlFromCohortSql(cohortSql = cohort$sql)
+      extractConceptSetsSqlFromCohortSql(cohortSql = cohortSql)
     jsonCs <-
-      extractConceptSetsJsonFromCohortJson(cohortJson = cohort$json)
+      extractConceptSetsJsonFromCohortJson(cohortJson = cohortJson)
 
     if (nrow(sqlCs) == 0 || nrow(jsonCs) == 0) {
       ParallelLogger::logInfo(
@@ -833,6 +833,18 @@ runConceptSetDiagnostics <- function(connection,
         }
       }
 
+      if (nrow(data) == 0 && ncol(data) == 0) {
+        data <- dplyr::tibble(
+          conceptId = numeric(),
+          conceptCount = numeric(),
+          subjectCount = numeric(),
+          cohortId = numeric(),
+          databaseId = character(),
+          domainField = character(),
+          domainTable = character()
+        )
+      }
+
       data <- makeDataExportable(
         x = data,
         tableName = "index_event_breakdown",

diff --git a/tests/testthat/test-7-DatabaseMigrations.R b/tests/testthat/test-7-DatabaseMigrations.R
@@ -24,6 +24,7 @@ if (dbms == "postgresql") {
 
 test_that("Database Migrations execute without error", {
   skip_if_not(dbms %in% c("sqlite", "postgresql"))
+  skip_if(skipCdmTests, "cdm settings not configured")
 
   connection <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))