passing sqlite and duckdb

Author: cebarboza

R/runOrphanConcepts.R

@@ -386,32 +386,27 @@ runOrphanConcepts <- function(connection,
     incremental = TRUE
   )
 
-  ParallelLogger::logTrace("Dropping temp concept set table")
-  sql <-
-    "TRUNCATE TABLE #inst_concept_sets; DROP TABLE #inst_concept_sets;"
-  DatabaseConnector::renderTranslateExecuteSql(
-    connection,
-    sql,
-    tempEmulationSchema = tempEmulationSchema,
-    progressBar = FALSE,
-    reportOverallTime = FALSE
-  )
+  # TODO eliminate inst_concept_sets after three analysis complete in executeDiagnostics
+  # if (tempTableExists(connection, "inst_concept_sets")) {
+  #   ParallelLogger::logTrace("Dropping Unique ConceptSets table")
+  #   sql <-
+  #     "TRUNCATE TABLE #inst_concept_sets; DROP TABLE #inst_concept_sets;"
+  #   DatabaseConnector::renderTranslateExecuteSql(
+  #     connection,
+  #     sql,
+  #     tempEmulationSchema = tempEmulationSchema,
+  #     progressBar = FALSE,
+  #     reportOverallTime = FALSE
+  #   )
+  # }
 
-  if  (nrow(subsetOrphans) > 0) {
-    ParallelLogger::logTrace("Dropping temp concept count table")
-    if (conceptCountsTableIsTemp) {
-      countTable <- conceptCountsTable
-    } else {
-      countTable <-
-        paste(conceptCountsDatabaseSchema, conceptCountsTable, sep = ".")
-    }
-    
+  if (conceptCountsTableIsTemp) {
     sql <- "TRUNCATE TABLE @count_table; DROP TABLE @count_table;"
     DatabaseConnector::renderTranslateExecuteSql(
       connection,
       sql,
       tempEmulationSchema = tempEmulationSchema,
-      count_table = countTable,
+      count_table = conceptCountsTable,
       progressBar = FALSE,
       reportOverallTime = FALSE
     )

tests/testthat/setup.R

@@ -1,10 +1,7 @@
-library(CohortDiagnostics)
-library(testthat)
-
 dbmsToTest <- c(
-  "sqlite"#,
+  # "sqlite"#,
   # "duckdb"#,
-  # "postgresql"#,
+  "postgresql"#,
   # "redshift",
   # "sql server",
 )

tests/testthat/test-runOrphanConcepts.R

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 for (nm in names(testServers)) {
-  nm <- "sqlite"
+  # nm <- "duckdb"
   server <- testServers[[nm]]
 
   # Params
@@ -33,17 +33,18 @@ for (nm in names(testServers)) {
   cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = server$cohortTable)
   cohortDatabaseSchema <- server$cohortDatabaseSchema
   cohortTable <- server$cohortTable
-  incremental <- FALSE
-  # incremental <- TRUE
+  # incremental <- FALSE
+  incremental <- TRUE
   conceptIdTable <- "#concept_ids"
+  recordKeepingFile <- file.path(exportFolder, "record.csv")
 
   # Tests
 
   test_that(paste("test run inclusion statistics output", nm), {
     connection <- DatabaseConnector::connect(server$connectionDetails)
-    exportFolder <- file.path(tempdir(), paste0(nm, "no_concept"))
-    dir.create(exportFolder)
+    exportFolder <- file.path(tempdir(), paste0(nm, "_no_concept"))
     recordKeepingFile <- file.path(exportFolder, "record.csv")
+    dir.create(exportFolder)
     # CreateConceptcounts table
 
     CohortDiagnostics::createConceptCountsTable(connection = connection,
@@ -125,6 +126,7 @@ for (nm in names(testServers)) {
   test_that(paste("test run inclusion statistics output", nm), {
     connection <- DatabaseConnector::connect(server$connectionDetails)
     exportFolder <- file.path(tempdir(), paste0(nm, "_no_concept"))
+    recordKeepingFile <- file.path(exportFolder, "record.csv")
     dir.create(exportFolder)
 
     # Instantiate Unique ConceptSets
@@ -178,6 +180,6 @@ for (nm in names(testServers)) {
     expect_equal(unique(recordKeeping$task), "runOrphanConcepts")
     expect_true(all(recordKeeping$cohortId %in% server$cohortDefinitionSet$cohortId))
 
-    unlink(exportFolder)
+    unlink(exportFolder, recursive = TRUE)
   })
 }