refactor create and write sql for foreign key and primary key

R/createFkFromFile.R

@@ -16,31 +16,23 @@
 
 #' Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.
 
-#' @param cdmVersionNum The version of the CDM you are creating
+#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
-#'
-#' @param cdmFieldCsvLoc The location of the csv file with the CDM field information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv".
-#'                        If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".
-#' @param outputFile  The name of the output foreign key file. This is defaulted to a location in the inst/sql/sql server folder and named with today's date and CDM version.
 #' @export
 
-createFkFromFile <- function(cdmVersionNum = cdmVersion,
+createFkFromFile <- function(cdmVersion = cdmVersion){
-                             cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv",
+  cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
-                             outputFile = paste0("inst/sql/sql_server/OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql")){
-
   cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
 
-  fks <- subset(cdmSpecs, isForeignKey == "Yes")
+  foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
-  fks$key <- paste0(fks$cdmTableName,"_",fks$cdmFieldName)
+  foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
 
-  s <- c()
+  sql_result <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
-  s <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ",cdmVersionNum, "\n"))
+  for (foreignKey in foreignKeys$key){
-  for (t in fks$key){
 
-      q <- subset(fks, fks$key==t)
+      subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
 
-      s <- c(s, paste0("\nALTER TABLE @cdmDatabaseSchema.", q$cdmTableName, " ADD CONSTRAINT fpk_", q$cdmTableName, "_", q$cdmFieldName, " FOREIGN KEY (", q$cdmFieldName ,") REFERENCES @cdmDatabaseSchema.", q$fkTableName, " (", q$fkFieldName, ");\n"))
+      sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT fpk_", subquery$cdmTableName, "_", subquery$cdmFieldName, " FOREIGN KEY (", subquery$cdmFieldName , ") REFERENCES @cdmDatabaseSchema.", subquery$fkTableName, " (", subquery$fkFieldName, ");\n"))
 
   }
-  SqlRender::writeSql(s, targetFile = outputFile)
+  return(paste0(sql_result, collapse = ""))
-  return(s)
 }

R/createPkFromFile.R

@@ -16,32 +16,23 @@
 
 #' Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.
 
-#' @param cdmVersionNum The version of the CDM you are creating
+#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
-#'
-#' @param cdmFieldCsvLoc The location of the csv file with the CDM field information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv".
-#'                        If a new version of this file was committed to the CDM repository the package automatically will grab it and place it in "inst/csv/".
-#' @param outputFile  The name of the output primary key sql file. This is defaulted to a location in the inst/sql/sql server folder and named with today's date and CDM Version.
 #' @export
 
-createPkFromFile <- function(cdmVersionNum = cdmVersion,
+createPkFromFile <- function(cdmVersion = cdmVersion){
-                              cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv",
+  cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
-                              outputFile = paste0("inst/sql/sql_server/OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql")){
-
   cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
 
-  pks <- subset(cdmSpecs, isPrimaryKey == "Yes")
+  primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
+  pkFields <- primaryKeys$cdmFieldName
 
-  pkFields <- pks$cdmFieldName
+  sql_result <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  for (pkField in pkFields){
 
-  s <- c()
+    subquery <- subset(primaryKeys, cdmFieldName==pkField)
-  s <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ",cdmVersionNum, "\n"))
-  for (f in pkFields){
 
-    q <- subset(pks, cdmFieldName==f)
+    sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
-
-    s <- c(s, paste0("\nALTER TABLE @cdmDatabaseSchema.", q$cdmTableName, " ADD CONSTRAINT xpk_", q$cdmTableName, " PRIMARY KEY NONCLUSTERED (", q$cdmFieldName ,");\n"))
 
   }
-  SqlRender::writeSql(s, targetFile = outputFile)
+  return(paste0(sql_result, collapse = ""))
-  return(s)
 }

R/writeConstraints.R

@@ -18,27 +18,20 @@
 #'
 #' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
 #' @param cdmVersion The version of the CDM that you are creating the primary keys for
-#' @param cdmDatabaseSchema The name of the schema where the cdm sits.
+#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
-#' @param sqlFilename The name of the file that should be rendered and translated to a different dbms.
 #'
 #' @export
 
-writeConstraints <- function(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFileName) {
+writeConstraints <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
-if(!dir.exists("output")){
+  outputpath <- file.path("ddl", cdmVersion, targetdialect)
-  dir.create("output")
+  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
-}
+
-
+  sql <- createFkFromFile(cdmVersion)
-if(!dir.exists(paste0("output/",targetdialect))){
+  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
-  dir.create(paste0("output/",targetdialect))
+  sql <- SqlRender::translate(sql, targetDialect = targetdialect)
-}
+
-
+  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "constraints.sql", sep = " ")
-sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFileName,
+  SqlRender::writeSql(sql = sql,
-                                         packageName = "CdmDdlBase",
+                      targetFile = file.path(outputpath, filename)
-                                         dbms = targetdialect,
+  )
-                                         targetdialect = targetdialect,
-                                         cdmDatabaseSchema = cdmDatabaseSchema)
-
-SqlRender::writeSql(sql = sql,
-                    targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," ", cdmVersion, " constraints.sql"))
-
 }

R/writeDDL.R

@@ -30,7 +30,7 @@ writeDDL <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabas
   sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
   sql <- SqlRender::translate(sql, targetDialect = targetdialect)
 
-  filename <- paste0("OMOPCDM_", targetdialect, "_", cdmVersion, "_ddl.sql")
+  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "ddl.sql", sep = " ")
   SqlRender::writeSql(sql = sql,
                       targetFile = file.path(outputpath, filename)
   )

R/writePrimaryKeys.R

@@ -18,27 +18,20 @@
 #'
 #' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
 #' @param cdmVersion The version of the CDM that you are creating the primary keys for
-#' @param cdmDatabaseSchema The name of the schema where the cdm sits.
+#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
-#' @param sqlFilename The name of the file that should be rendered and translated to a different dbms.
 #'
 #' @export
 
-writePrimaryKeys <- function(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFilename) {
+writePrimaryKeys <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
-  if(!dir.exists("output")){
+  outputpath <- file.path("ddl", cdmVersion, targetdialect)
-    dir.create("output")
+  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
-  }
 
-  if(!dir.exists(paste0("output/",targetdialect))){
+  sql <- createFkFromFile(cdmVersion)
-    dir.create(paste0("output/",targetdialect))
+  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
-  }
+  sql <- SqlRender::translate(sql, targetDialect = targetdialect)
-
-  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFilename,
-                                           packageName = "CdmDdlBase",
-                                           dbms = targetdialect,
-                                           targetdialect = targetdialect,
-                                           cdmDatabaseSchema = cdmDatabaseSchema)
 
+  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "primary", "keys.sql", sep = " ")
   SqlRender::writeSql(sql = sql,
-                      targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect, " ", cdmVersion, " primary keys.sql" ))
+                      targetFile = file.path(outputpath, filename)
-
+  )
 }

extras/codeToRun.R

@@ -8,17 +8,15 @@
 
 # Step 3: After creating the csv files for the new version, create the sql server DDL from the file
 
-    s <- CdmDdlBase::createDdlFromFile(cdmVersion)
+    ddl <- CdmDdlBase::createDdlFromFile(cdmVersion)
 
   # Step 3.1: Create the primary key constraints for the new version
 
-    p <- CdmDdlBase::createPkFromFile(cdmVersionNum = cdmVersion,
+    primaryKeys <- CdmDdlBase::createPkFromFile(cdmVersion)
-                                      cdmFieldCsvLoc = "inst/csv/OMOP_CDMv6.0_Field_Level.csv")
 
   # Step 3.2: Create the foreign key constraints for the new version
 
-    f <- CdmDdlBase::createFkFromFile(cdmVersionNum = cdmVersion,
+    foreignKeys <- CdmDdlBase::createFkFromFile(cdmVersion)
-                                      cdmFieldCsvLoc = "inst/csv/OMOP_CDMv6.0_Field_Level.csv")
 # At this point you should rebuild the package
 
 # Step 4: Run the following code to render the DDLs for each dialect. These will be used for testing on the ohdsi servers which is why the cdmDatabaseSchema is specified.
@@ -106,55 +104,15 @@ writeIndex("sql server",
 for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
   writeDDL(targetdialect = targetdialect,
            cdmVersion = cdmVersion)
+
+  writePrimaryKeys(targetdialect = targetdialect,
+                   cdmVersion = cdmVersion)
+
+  writeConstraints(targetdialect = targetdialect,
+                   cdmVersion = cdmVersion)
 }
 
 
-## Write all primary keys
-
-writePrimaryKeys(targetdialect = "oracle",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "@cdmDatabaseSchema")
-
-
-writePrimaryKeys(targetdialect = "postgresql",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "@cdmDatabaseSchema")
-
-
-writePrimaryKeys(targetdialect = "sql server",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "@cdmDatabaseSchema")
-
-writePrimaryKeys(targetdialect = "netezza",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "@cdmDatabaseSchema")
-
-## write all foreign key constraints
-
-writeConstraints("oracle",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "@cdmDatabaseSchema")
-
-writeConstraints("postgresql",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "@cdmDatabaseSchema")
-
-writeConstraints("sql server",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "@cdmDatabaseSchema")
-
-writeConstraints("pdw",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "@cdmDatabaseSchema")
-
 ## write all indices
 
 writeIndex("oracle", ### NOTE: ORACLE CREATES AUTO INDEXING AND NEED TO UPDATE INST/INDEX FILE TO REPRESENT IT