Update for lint errors

OHDSI · Jan 2, 2024 · 939d59f · 939d59f
1 parent d2cf2d0
commit 939d59f
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Showing 13 changed files with 150 additions and 135 deletions.
diff --git a/R/CreateCDMTables.r b/R/CreateCDMTables.r
@@ -26,41 +26,41 @@ CreateCDMTables <-
            cdmSchema,
            cdmVersion,
            outputFolder = NULL,
-		   createIndices = FALSE,
+           createIndices = FALSE,
            sqlOnly = FALSE)
   {
     if (!sqlOnly) {
-
-		print("Creating CDM Tables....")
-
-		CommonDataModel::executeDdl(
-			connectionDetails = connectionDetails,
-			cdmVersion        = cdmVersion,
-			cdmDatabaseSchema = cdmSchema,
-			executeDdl        = TRUE,
-			executePrimaryKey = TRUE,
-			executeForeignKey = FALSE
-		) # False for now due to bug: https://github.com/OHDSI/CommonDataModel/issues/452
+      print("Creating CDM Tables....")
 
-		print("CDM Tables Created.")
-
-		if (createIndices) {
-
-			print("Creating Indices on CDM Tables....")
+      CommonDataModel::executeDdl(
+        connectionDetails = connectionDetails,
+        cdmVersion        = cdmVersion,
+        cdmDatabaseSchema = cdmSchema,
+        executeDdl        = TRUE,
+        executePrimaryKey = TRUE,
+        executeForeignKey = FALSE
+      ) # False for now due to bug: https://github.com/OHDSI/CommonDataModel/issues/452
+
+      print("CDM Tables Created.")
+
+      if (createIndices) {
+        print("Creating Indices on CDM Tables....")
 
-			indexSQLFile <- CommonDataModel::writeIndex(
-				targetDialect     = connectionDetails$dbms,
-				cdmVersion        = cdmVersion,
-				cdmDatabaseSchema = cdmSchema,
-				outputfolder      = tempdir())
+        indexSQLFile <- CommonDataModel::writeIndex(
+          targetDialect     = connectionDetails$dbms,
+          cdmVersion        = cdmVersion,
+          cdmDatabaseSchema = cdmSchema,
+          outputfolder      = tempdir()
+        )
+
+        indexDDL <-
+          SqlRender::readSql(paste0(tempdir(), "/", indexSQLFile))
+        conn <- DatabaseConnector::connect(connectionDetails)
+        DatabaseConnector::executeSql(conn, indexDDL)
+        DatabaseConnector::disconnect(conn)
+        print("Index Creation Complete.")
+      }
 
-			indexDDL <- SqlRender::readSql(paste0(tempdir(),"/",indexSQLFile))
-			conn <- DatabaseConnector::connect(connectionDetails)
-			DatabaseConnector::executeSql(conn,indexDDL)
-			DatabaseConnector::disconnect(conn)
-			print("Index Creation Complete.")
-		}
-
     } else {
       if (is.null(outputFolder)) {
         stop("Must specify an outputFolder location when using sqlOnly = TRUE")

diff --git a/R/CreateMapAndRollupTables.r b/R/CreateMapAndRollupTables.r
@@ -30,30 +30,28 @@
 
 
 CreateMapAndRollupTables <- function(connectionDetails,
-                            cdmSchema,
-                            syntheaSchema,
-                            cdmVersion,
-                            syntheaVersion = "2.7.0",
-                            cdmSourceName = "Synthea synthetic health database",
-                            cdmSourceAbbreviation = "Synthea",
-                            cdmHolder = "OHDSI",
-                            cdmSourceDescription = "SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.",
-                            sqlOnly = FALSE)
+                                     cdmSchema,
+                                     syntheaSchema,
+                                     cdmVersion,
+                                     syntheaVersion = "2.7.0",
+                                     cdmSourceName = "Synthea synthetic health database",
+                                     cdmSourceAbbreviation = "Synthea",
+                                     cdmHolder = "OHDSI",
+                                     cdmSourceDescription = "SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.",
+                                     sqlOnly = FALSE)
 {
-  # Determine which sql scripts to run based on the given version.
-  # The path is relative to inst/sql/sql_server.
-  if (cdmVersion == "5.3") {
-    sqlFilePath <- "cdm_version/v531"
-  } else if (cdmVersion == "5.4") {
-    sqlFilePath <- "cdm_version/v540"
-  } else {
+  supportedCDMVersions <- c("5.3", "5.4")
+
+  if (!(cdmVersion %in% supportedCDMVersions)) {
     stop("Unsupported CDM specified. Supported CDM versions are \"5.3\" and \"5.4\".")
   }
 
-  supportedSyntheaVersions <- c("2.7.0", "3.0.0","3.1.0","3.2.0")
+  supportedSyntheaVersions <- c("2.7.0", "3.0.0", "3.1.0", "3.2.0")
 
   if (!(syntheaVersion %in% supportedSyntheaVersions))
-    stop("Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported.")
+    stop(
+      "Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported."
+    )
 
   # Create Vocabulary mapping tables
   CreateVocabMapTables(connectionDetails, cdmSchema, cdmVersion, sqlOnly)
@@ -66,5 +64,3 @@ CreateMapAndRollupTables <- function(connectionDetails,
                           sqlOnly)
 
 }
-
-
diff --git a/R/CreateSyntheaTables.r b/R/CreateSyntheaTables.r
@@ -17,9 +17,9 @@
 
 
 CreateSyntheaTables <-
-  function (connectionDetails,
-            syntheaSchema,
-            syntheaVersion = "2.7.0")
+  function(connectionDetails,
+           syntheaSchema,
+           syntheaVersion = "2.7.0")
   {
     if (syntheaVersion == "2.7.0")
       sqlFilePath <- "synthea_version/v270"
@@ -30,9 +30,12 @@ CreateSyntheaTables <-
     else if (syntheaVersion == "3.2.0")
       sqlFilePath <- "synthea_version/v320"
     else
-      stop("Invalid synthea version specified. Currently \"2.7.0\", \"3.0.0\", \"3.1.0\" and \"3.2.0\" are supported.")
+      stop(
+        "Invalid synthea version specified. Currently \"2.7.0\", \"3.0.0\", \"3.1.0\" and \"3.2.0\" are supported."
+      )
 
-    sqlFilename <-  paste0(sqlFilePath, "/", "create_synthea_tables.sql")
+    sqlFilename <-
+      paste0(sqlFilePath, "/", "create_synthea_tables.sql")
 
     translatedSql <- SqlRender::loadRenderTranslateSql(
       sqlFilename     = sqlFilename,

diff --git a/R/DropSyntheaTables.r b/R/DropSyntheaTables.r
@@ -19,8 +19,8 @@ DropSyntheaTables <- function(connectionDetails, syntheaSchema)
   syntheaTables <- c(
     "ALLERGIES",
     "CAREPLANS",
-	"CLAIMS",
-	"CLAIMS_TRANSACTIONS",
+    "CLAIMS",
+    "CLAIMS_TRANSACTIONS",
     "CONDITIONS",
     "DEVICES",
     "ENCOUNTERS",
@@ -30,32 +30,33 @@ DropSyntheaTables <- function(connectionDetails, syntheaSchema)
     "OBSERVATIONS",
     "ORGANIZATIONS",
     "PATIENTS",
-	"PAYERS",
-	"PAYER_TRANSITIONS",
+    "PAYERS",
+    "PAYER_TRANSITIONS",
     "PROCEDURES",
     "PROVIDERS",
-	"SUPPLIES"
+    "SUPPLIES"
   )
 
   conn <- DatabaseConnector::connect(connectionDetails)
   allTables <- DatabaseConnector::getTableNames(conn, syntheaSchema)
   tablesToDrop <- allTables[which(allTables %in% syntheaTables)]
 
   if (length(tablesToDrop) > 0) {
-      writeLines("Dropping Synthea tables...")
-	  sql <-
-		paste(
-		  "drop table @synthea_schema.",
-		  tablesToDrop,
-		  ";",
-		  collapse = "\n",
-		  sep = ""
-		)
-	  sql <- SqlRender::render(sql, synthea_schema = syntheaSchema)
-	  sql <- SqlRender::translate(sql, targetDialect = connectionDetails$dbms)
-	  DatabaseConnector::executeSql(conn, sql)
+    writeLines("Dropping Synthea tables...")
+    sql <-
+      paste(
+        "drop table @synthea_schema.",
+        tablesToDrop,
+        ";",
+        collapse = "\n",
+        sep = ""
+      )
+    sql <- SqlRender::render(sql, synthea_schema = syntheaSchema)
+    sql <-
+      SqlRender::translate(sql, targetDialect = connectionDetails$dbms)
+    DatabaseConnector::executeSql(conn, sql)
   } else {
-	print(sprintf("No synthea tables to drop in schema %s",syntheaSchema))
+    print(sprintf("No synthea tables to drop in schema %s", syntheaSchema))
   }
 
   on.exit(DatabaseConnector::disconnect(conn))

diff --git a/R/LoadEventTables.r b/R/LoadEventTables.r
@@ -39,7 +39,7 @@ LoadEventTables <- function(connectionDetails,
                             cdmHolder = "OHDSI",
                             cdmSourceDescription = "SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.",
                             createIndices = FALSE,
-							sqlOnly = FALSE)
+                            sqlOnly = FALSE)
 {
   # Determine which sql scripts to run based on the given version.
   # The path is relative to inst/sql/sql_server.
@@ -51,25 +51,28 @@ LoadEventTables <- function(connectionDetails,
     stop("Unsupported CDM specified. Supported CDM versions are \"5.3\" and \"5.4\".")
   }
 
-  supportedSyntheaVersions <- c("2.7.0", "3.0.0","3.1.0","3.2.0")
+  supportedSyntheaVersions <- c("2.7.0", "3.0.0", "3.1.0", "3.2.0")
 
   if (!(syntheaVersion %in% supportedSyntheaVersions))
-    stop("Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported.")
+    stop(
+      "Invalid Synthea version specified. Currently \"2.7.0\", \"3.0.0\",\"3.1.0\", and \"3.2.0\" are supported."
+    )
 
   if (createIndices) {
-	print("Creating Indices on CDM Tables....")
+    print("Creating Indices on CDM Tables....")
 
-	indexSQLFile <- CommonDataModel::writeIndex(
-		targetDialect     = connectionDetails$dbms,
-		cdmVersion        = cdmVersion,
-		cdmDatabaseSchema = cdmSchema,
-		outputfolder      = tempdir())
+    indexSQLFile <- CommonDataModel::writeIndex(
+      targetDialect     = connectionDetails$dbms,
+      cdmVersion        = cdmVersion,
+      cdmDatabaseSchema = cdmSchema,
+      outputfolder      = tempdir()
+    )
 
-	indexDDL <- SqlRender::readSql(paste0(tempdir(),"/",indexSQLFile))
-	conn <- DatabaseConnector::connect(connectionDetails)
-	DatabaseConnector::executeSql(conn,indexDDL)
-	DatabaseConnector::disconnect(conn)
-	print("Index Creation Complete.")
+    indexDDL <- SqlRender::readSql(paste0(tempdir(), "/", indexSQLFile))
+    conn <- DatabaseConnector::connect(connectionDetails)
+    DatabaseConnector::executeSql(conn, indexDDL)
+    DatabaseConnector::disconnect(conn)
+    print("Index Creation Complete.")
   }
 
   if (!sqlOnly) {
@@ -233,7 +236,7 @@ LoadEventTables <- function(connectionDetails,
     cdm_source_name = cdmSourceName,
     cdm_source_abbreviation = cdmSourceAbbreviation,
     cdm_holder = cdmHolder,
-    source_description = paste("Synthea version: ",syntheaVersion," ",cdmSourceDescription)
+    source_description = paste("Synthea version: ", syntheaVersion, " ", cdmSourceDescription)
   )
   runStep(sql, fileQuery)
 
@@ -267,24 +270,24 @@ LoadEventTables <- function(connectionDetails,
     dbms = connectionDetails$dbms,
     cdm_schema = cdmSchema,
     synthea_schema = syntheaSchema,
-	synthea_version = syntheaVersion
+    synthea_version = syntheaVersion
   )
   runStep(sql, fileQuery)
 
   # cost
   if (syntheaVersion == "2.7.0")
-	fileQuery <- "insert_cost_v270.sql"
-  else if (syntheaVersion %in% c("3.0.0","3.1.0","3.2.0"))
-	fileQuery <- "insert_cost_v300.sql"
+    fileQuery <- "insert_cost_v270.sql"
+  else if (syntheaVersion %in% c("3.0.0", "3.1.0", "3.2.0"))
+    fileQuery <- "insert_cost_v300.sql"
 
-    sql <- SqlRender::loadRenderTranslateSql(
-      sqlFilename = file.path(sqlFilePath, fileQuery),
-      packageName = "ETLSyntheaBuilder",
-      dbms = connectionDetails$dbms,
-      cdm_schema = cdmSchema,
-      synthea_schema = syntheaSchema
-    )
-    runStep(sql, fileQuery)
+  sql <- SqlRender::loadRenderTranslateSql(
+    sqlFilename = file.path(sqlFilePath, fileQuery),
+    packageName = "ETLSyntheaBuilder",
+    dbms = connectionDetails$dbms,
+    cdm_schema = cdmSchema,
+    synthea_schema = syntheaSchema
+  )
+  runStep(sql, fileQuery)
 
   if (!sqlOnly) {
     DatabaseConnector::disconnect(conn)