Use of cohort table unified

OHDSI · Oct 4, 2023 · 65f1c3a · 65f1c3a
1 parent 5e34dd6
commit 65f1c3a
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Showing 3 changed files with 8 additions and 20 deletions.
diff --git a/R/cohort-diagnostics-compareCharacterization.R b/R/cohort-diagnostics-compareCharacterization.R
@@ -480,20 +480,6 @@ compareCohortCharacterizationView <- function(id, title = "Compare cohort charac
   )
 }
 
-# Returns data from cohort table of Cohort Diagnostics results data model
-getResultsCohort <- function(dataSource, cohortIds = NULL) {
-  data <- dataSource$connectionHandler$queryDb(
-    sql = "SELECT * FROM @schema.@table_name
-                                          {@cohort_id != \"\"} ? { WHERE cohort_id IN (@cohort_id)};",
-    schema = dataSource$schema,
-    cohort_id = cohortIds,
-    table_name = paste0(dataSource$cgTablePrefix,dataSource$cgTable),
-    snakeCaseToCamelCase = TRUE
-  )
-  return(data)
-}
-
-
 # Returns cohort as feature characterization
 getCohortRelationshipCharacterizationResults <-
   function(dataSource,
@@ -505,7 +491,8 @@ getCohortRelationshipCharacterizationResults <-
         cohortIds = cohortIds,
         databaseIds = databaseIds
       )
-    cohort <- getResultsCohort(dataSource = dataSource)
+    cohort <- getCdCohortRows(dataSource = dataSource,
+                              cohortIds = cohortIds)
 
     cohortRelationships <-
       getResultsCohortRelationships(
@@ -577,6 +564,7 @@ getCohortRelationshipCharacterizationResults <-
                             dplyr::distinct(),
                           by = c("analysisId")
         )
+
     covariateRef <- tidyr::crossing(
       cohort,
       analysisRef %>%

diff --git a/R/cohort-diagnostics-definition.R b/R/cohort-diagnostics-definition.R
@@ -209,8 +209,8 @@ getConceptSetDetailsFromCohortDefinition <-
   }
 
 
-getCohortJsonSql <- function(dataSource, cohortIds) {
-  sql <- "SELECT * FROM @schema.@cohort_table
+getCdCohortRows <- function(dataSource, cohortIds) {
+  sql <- "SELECT {@use_cg_table} ? {cohort_definition_id as cohort_id,} * FROM @schema.@cohort_table
     WHERE {@use_cg_table} ? {cohort_definition_id} : {cohort_id} IN (@cohort_ids)"
   dataSource$connectionHandler$queryDb(
     sql = sql,
@@ -574,7 +574,7 @@ cohortDefinitionsModule <- function(
           return(NULL)
         }
         row <- subset[idx[1],]
-        return(getCohortJsonSql(dataSource, row$cohortId))
+        return(getCdCohortRows(dataSource, row$cohortId))
       }
     })
 
@@ -1095,7 +1095,7 @@ cohortDefinitionsModule <- function(
         shiny::withProgress(
           message = "Export is in progress",
         {
-          definitions <- getCohortJsonSql(dataSource, cohortTable$cohortId)
+          definitions <- getCdCohortRows(dataSource, cohortTable$cohortId)
           exportCohortDefinitionsZip(definitions, zipFile = file)
         },
           detail = "Please Wait"

diff --git a/tests/testthat/test-cohort-diagnostics-definition.R b/tests/testthat/test-cohort-diagnostics-definition.R
@@ -7,7 +7,7 @@ shiny::testServer(cohortDefinitionsModule, args = list(
 ), {
   getCohortDefinitionResolvedConceptsReactive()
   checkmate::expect_data_frame(cohortDefinitionTableData())
-  defs <- getCohortJsonSql(dataSourceCd, dataSourceCd$cohortTable$cohortId)
+  defs <- getCdCohortRows(dataSourceCd, dataSourceCd$cohortTable$cohortId)
   def <- defs$json[1] %>% RJSONIO::fromJSON(digits = 23)
   checkmate::expect_list(getCirceRenderedExpression(def))