updated truncate functions to use DatabaseConnector since object_id i…

…sn't translated to PG by SqlRender
OHDSI · May 22, 2019 · 5c277a9 · 5c277a9
1 parent eba743e
commit 5c277a9
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Showing 2 changed files with 22 additions and 26 deletions.
diff --git a/R/TruncateEventTables.r b/R/TruncateEventTables.r
@@ -18,23 +18,22 @@
 TruncateEventTables <- function (connectionDetails, cdmDatabaseSchema)
 {
 
+    eventTables <- c( 'care_site', 'cdm_source', 'cohort', 'cohort_attribute', 'condition_era', 'condition_occurrence', 'cost',
+                      'death', 'device_exposure', 'dose_era', 'drug_era', 'drug_exposure', 'fact_relationship', 'location',
+                      'measurement', 'metadata', 'note', 'note_nlp', 'observation', 'observation_period', 'payer_plan_period',
+                      'person', 'procedure_occurrence', 'provider', 'specimen', 'visit_detail', 'visit_occurrence' )
 
-    pathToSql <- base::system.file("sql/sql_server", package = "ETLSyntheaBuilder")
+    conn <- DatabaseConnector::connect(connectionDetails) 
 
-    sqlFile <- base::paste0(pathToSql, "/", "truncate_event_tables.sql")
-
-    sqlQuery <- base::readChar(sqlFile, base::file.info(sqlFile)$size)
-
-    renderedSql <- SqlRender::render(sqlQuery, cdm_schema = cdmDatabaseSchema)
-
-    translatedSql <- SqlRender::translate(renderedSql, targetDialect = connectionDetails$dbms)
-
-    writeLines("Running truncate_event_tables.sql")
+    writeLines("Truncating event tables...")
 
-	conn <- DatabaseConnector::connect(connectionDetails) 
+    for (tableName in eventTables) {
+	  if (DatabaseConnector::dbExistsTable(conn = conn, name = tableName, schema = cdmDatabaseSchema)) { 
+	    writeLines(paste0("Truncating ",tableName))
+        DatabaseConnector::dbExecute(conn, paste0("truncate table ",cdmDatabaseSchema,".",tableName,";"))
+      }
+	}
 
-    DatabaseConnector::dbExecute(conn, translatedSql, progressBar = TRUE, reportOverallTime = TRUE)
-
     on.exit(DatabaseConnector::disconnect(conn)) 
 
 }
diff --git a/R/TruncateVocabTables.r b/R/TruncateVocabTables.r
@@ -18,23 +18,20 @@
 TruncateVocabTables <- function (connectionDetails, vocabDatabaseSchema)
 {
 
+  vocabTables <- c( 'attribute_definition', 'cohort_definition', 'concept', 'concept_ancestor', 'concept_class', 'concept_relationship', 
+                    'concept_synonym', 'domain', 'drug_strength', 'relationship', 'source_to_concept_map', 'vocabulary' )
 
-    pathToSql <- base::system.file("sql/sql_server", package = "ETLSyntheaBuilder")
+  conn <- DatabaseConnector::connect(connectionDetails) 
 
-    sqlFile <- base::paste0(pathToSql, "/", "truncate_vocab_tables.sql")
-
-    sqlQuery <- base::readChar(sqlFile, base::file.info(sqlFile)$size)
-
-    renderedSql <- SqlRender::render(sqlQuery, vocab_schema = vocabDatabaseSchema)
-
-    translatedSql <- SqlRender::translate(renderedSql, targetDialect = connectionDetails$dbms)
-
-    writeLines("Running truncate_vocab_tables.sql")
+  writeLines("Truncating vocabulary tables...")
 
-	conn <- DatabaseConnector::connect(connectionDetails) 
+    for (tableName in vocabTables) {
+	  if (DatabaseConnector::dbExistsTable(conn = conn, name = tableName, schema = vocabDatabaseSchema)) { 
+	    writeLines(paste0("Truncating ",tableName))
+        DatabaseConnector::dbExecute(conn, paste0("truncate table ",vocabDatabaseSchema,".",tableName,";"))
+      }
+	}
 
-    DatabaseConnector::dbExecute(conn, translatedSql, progressBar = TRUE, reportOverallTime = TRUE)
-
     on.exit(DatabaseConnector::disconnect(conn)) 
 
 }