refactor index creation and cleanup codeToRun

R/writeIndex.R

@@ -17,27 +17,22 @@
 #' Write Index script
 #'
 #' @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 cdmVersion The version of the CDM that you are creating the indices for. e.g. 5.3.1
-#' @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. This is either "OMOP CDM indices v5_3_1.sql" or "OMOP CDM indices v6_0.sql".
 #'
 #' @export
-writeIndex <- function(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFilename) {
+writeIndex <- 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))){
-  dir.create(paste0("output/",targetdialect))
-}
 
+  sqlFilename <- paste0("OMOP CDM indices v", cdmVersion, ".sql")
   sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFilename,
                                            packageName = "CdmDdlBase",
                                            dbms = targetdialect,
                                            targetdialect = targetdialect,
                                            cdmDatabaseSchema = cdmDatabaseSchema)
 
+  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "indices.sql", sep = " ")
   SqlRender::writeSql(sql = sql,
-                    targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," ", cdmVersion, " indices.sql"))
+                      targetFile = file.path(outputpath, filename))
-
 }

extras/codeToRun.R

@@ -1,106 +1,9 @@
 # This script is meant to create the OMOP Common Data Model DDLs for each dialect as well as the pdf of the documentation.
 
-# Step 1-2 from README: Create new csv files "..._Field_Level.csv" and "..._Table_Level.csv" in inst/csv for the new version and make changes to the files reflecting
+# For a given cdmVersion, create all ddl sql files for every sql dialect
-# the new CDM versions. Set the below variable to indicate the version of the cdm you are creating. This will be used for the name of the pdf so, for
+# Results are written to ddl/cdm_version/dialect.
-# example, write v5.3 as v5_3.
-
 cdmVersion <- "5.3.1"
 
-# Step 3: After creating the csv files for the new version, create the sql server DDL from the file
-
-    ddl <- CdmDdlBase::createDdlFromFile(cdmVersion)
-
-  # Step 3.1: Create the primary key constraints for the new version
-
-    primaryKeys <- CdmDdlBase::createPkFromFile(cdmVersion)
-
-  # Step 3.2: Create the foreign key constraints for the new version
-
-    foreignKeys <- CdmDdlBase::createFkFromFile(cdmVersion)
-# 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.
-
-writeDDL(targetdialect = "oracle",
-         cdmVersion = cdmVersion,
-         sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
-         cdmDatabaseSchema = "OHDSI",
-         cleanUpScript = F) #oracle syntax for removing tables is weird, set this to F and make any changes to the raw file
-
-writeDDL(targetdialect = "postgresql",
-         cdmVersion = cdmVersion,
-         sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
-         cdmDatabaseSchema = "ohdsi",
-         cleanUpScript = F) #This needs to be updated manually right now
-
-writeDDL(targetdialect = "sql server",
-         cdmVersion = cdmVersion,
-         sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
-         cdmDatabaseSchema = "ohdsi.dbo",
-         cleanUpScript = F) #This needs to be updated manually right now
-
-# Step 5: Run the following code to render the primary key constraints for Oracle, Postgres, and Sql Server
-
-writePrimaryKeys(targetdialect = "oracle",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "OHDSI")
-
-
-writePrimaryKeys(targetdialect = "postgresql",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "ohdsi")
-
-
-writePrimaryKeys(targetdialect = "sql server",
-                 cdmVersion = cdmVersion,
-                 sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 cdmDatabaseSchema = "ohdsi.dbo")
-
-# Step 6: Run the following code to render the foreign key constraints for Oracle, Postgres, and Sql Server
-
-writeConstraints("oracle",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "OHDSI")
-
-writeConstraints("postgresql",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "ohdsi")
-
-writeConstraints("sql server",
-                 cdmVersion,
-                 sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
-                 "ohdsi.dbo")
-
-# Step 7: Run the following code to render the indices for Oracle, Postgres, and Sql Server
-
-writeIndex("oracle", ### NOTE: ORACLE CREATES AUTO INDEXING AND NEED TO UPDATE INST/INDEX FILE TO REPRESENT IT
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v6_0.sql",
-           "OHDSI")
-
-writeIndex("postgresql",
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v6_0.sql",
-           "ohdsi")
-
-writeIndex("sql server",
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v6_0.sql",
-           "ohdsi.dbo")
-
-
-##############################
-# RUN THE TESTTHAT.R TO TEST ORACLE, POSTGRES, AND SQLSERVER
-
-
-# Step 8: After testing the files for Oracle, Postgres, and Sql Server run the following to create the files for all dialects. Oracle
-# Postgres and Sql Server are rewritten to overwrite the cdmDatabaseSchema with a token.
-
-
 for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
   writeDDL(targetdialect = targetdialect,
            cdmVersion = cdmVersion)
@@ -110,32 +13,12 @@ for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "ne
 
   writeConstraints(targetdialect = targetdialect,
                    cdmVersion = cdmVersion)
+
+  writeIndex(targetdialect = targetdialect,
+             cdmVersion = cdmVersion)
 }
 
 
-## write all indices
-
-writeIndex("oracle", ### NOTE: ORACLE CREATES AUTO INDEXING AND NEED TO UPDATE INST/INDEX FILE TO REPRESENT IT
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v5_3_1.sql",
-           "@cdmDatabaseSchema")
-
-writeIndex("postgresql",
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v5_3_1.sql",
-           "@cdmDatabaseSchema")
-
-writeIndex("sql server",
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v5_3_1.sql",
-           "@cdmDatabaseSchema")
-
-writeIndex("pdw",
-           cdmVersion,
-           sqlFilename = "OMOP CDM indices v5_3_1.sql",
-           "@cdmDatabaseSchema")
-
-
 #############
 # BE SURE TO RUN THE EXTRAS/SITEMAINTENANCE.R BEFORE CREATING THE PDF
 

man/writeIndex.Rd

@@ -13,7 +13,7 @@ writeIndex(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFilename)
 
 \item{cdmDatabaseSchema}{The name of the schema where the cdm sits.}
 
-\item{sqlFilename}{The name of the file that should be rendered and translated to a different dbms. This is either "OMOP CDM indices v5_3_1.sql" or "OMOP CDM indices v6_0.sql".}
+\item{sqlFilename}{The name of the file that should be rendered and translated to a different dbms. This is either "OMOP CDM indices v5.3.1.sql" or "OMOP CDM indices v6.0.sql".}
 }
 \description{
 Write Index script