refactor index creation and cleanup codeToRun
This commit is contained in:
Maxim Moinat
parent
5d9887a356
commit
8d29222563
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@ -17,27 +17,22 @@
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#' Write Index script
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#'
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#' @param targetdialect The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
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#' @param cdmVersion The version of the CDM that you are creating the primary keys for
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#' @param cdmDatabaseSchema The name of the schema where the cdm sits.
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#' @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".
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#' @param cdmVersion The version of the CDM that you are creating the indices for. e.g. 5.3.1
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#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
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#'
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#' @export
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writeIndex <- function(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFilename) {
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if(!dir.exists("output")){
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dir.create("output")
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}
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if(!dir.exists(paste0("output/",targetdialect))){
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dir.create(paste0("output/",targetdialect))
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}
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writeIndex <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
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outputpath <- file.path("ddl", cdmVersion, targetdialect)
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dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
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sqlFilename <- paste0("OMOP CDM indices v", cdmVersion, ".sql")
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sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFilename,
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packageName = "CdmDdlBase",
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dbms = targetdialect,
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targetdialect = targetdialect,
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cdmDatabaseSchema = cdmDatabaseSchema)
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filename <- paste("OMOPCDM", targetdialect, cdmVersion, "indices.sql", sep = " ")
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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," ", cdmVersion, " indices.sql"))
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targetFile = file.path(outputpath, filename))
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}
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@ -1,106 +1,9 @@
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# This script is meant to create the OMOP Common Data Model DDLs for each dialect as well as the pdf of the documentation.
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# 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
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# 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
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# example, write v5.3 as v5_3.
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# For a given cdmVersion, create all ddl sql files for every sql dialect
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# Results are written to ddl/cdm_version/dialect.
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cdmVersion <- "5.3.1"
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# Step 3: After creating the csv files for the new version, create the sql server DDL from the file
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ddl <- CdmDdlBase::createDdlFromFile(cdmVersion)
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# Step 3.1: Create the primary key constraints for the new version
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primaryKeys <- CdmDdlBase::createPkFromFile(cdmVersion)
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# Step 3.2: Create the foreign key constraints for the new version
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foreignKeys <- CdmDdlBase::createFkFromFile(cdmVersion)
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# At this point you should rebuild the package
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# 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.
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writeDDL(targetdialect = "oracle",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "OHDSI",
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cleanUpScript = F) #oracle syntax for removing tables is weird, set this to F and make any changes to the raw file
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writeDDL(targetdialect = "postgresql",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "ohdsi",
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cleanUpScript = F) #This needs to be updated manually right now
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writeDDL(targetdialect = "sql server",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "ohdsi.dbo",
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cleanUpScript = F) #This needs to be updated manually right now
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# Step 5: Run the following code to render the primary key constraints for Oracle, Postgres, and Sql Server
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writePrimaryKeys(targetdialect = "oracle",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "OHDSI")
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writePrimaryKeys(targetdialect = "postgresql",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "ohdsi")
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writePrimaryKeys(targetdialect = "sql server",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "ohdsi.dbo")
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# Step 6: Run the following code to render the foreign key constraints for Oracle, Postgres, and Sql Server
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writeConstraints("oracle",
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cdmVersion,
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sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
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"OHDSI")
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writeConstraints("postgresql",
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cdmVersion,
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sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
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"ohdsi")
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writeConstraints("sql server",
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cdmVersion,
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sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
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"ohdsi.dbo")
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# Step 7: Run the following code to render the indices for Oracle, Postgres, and Sql Server
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writeIndex("oracle", ### NOTE: ORACLE CREATES AUTO INDEXING AND NEED TO UPDATE INST/INDEX FILE TO REPRESENT IT
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cdmVersion,
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sqlFilename = "OMOP CDM indices v6_0.sql",
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"OHDSI")
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writeIndex("postgresql",
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cdmVersion,
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sqlFilename = "OMOP CDM indices v6_0.sql",
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"ohdsi")
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writeIndex("sql server",
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cdmVersion,
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sqlFilename = "OMOP CDM indices v6_0.sql",
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"ohdsi.dbo")
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##############################
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# RUN THE TESTTHAT.R TO TEST ORACLE, POSTGRES, AND SQLSERVER
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# Step 8: After testing the files for Oracle, Postgres, and Sql Server run the following to create the files for all dialects. Oracle
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# Postgres and Sql Server are rewritten to overwrite the cdmDatabaseSchema with a token.
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for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
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writeDDL(targetdialect = targetdialect,
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cdmVersion = cdmVersion)
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@ -110,32 +13,12 @@ for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "ne
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writeConstraints(targetdialect = targetdialect,
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cdmVersion = cdmVersion)
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writeIndex(targetdialect = targetdialect,
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cdmVersion = cdmVersion)
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}
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## write all indices
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writeIndex("oracle", ### NOTE: ORACLE CREATES AUTO INDEXING AND NEED TO UPDATE INST/INDEX FILE TO REPRESENT IT
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cdmVersion,
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sqlFilename = "OMOP CDM indices v5_3_1.sql",
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"@cdmDatabaseSchema")
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writeIndex("postgresql",
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cdmVersion,
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sqlFilename = "OMOP CDM indices v5_3_1.sql",
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"@cdmDatabaseSchema")
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writeIndex("sql server",
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cdmVersion,
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sqlFilename = "OMOP CDM indices v5_3_1.sql",
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"@cdmDatabaseSchema")
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writeIndex("pdw",
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cdmVersion,
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sqlFilename = "OMOP CDM indices v5_3_1.sql",
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"@cdmDatabaseSchema")
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#############
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# BE SURE TO RUN THE EXTRAS/SITEMAINTENANCE.R BEFORE CREATING THE PDF
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@ -13,7 +13,7 @@ writeIndex(targetdialect, cdmVersion, cdmDatabaseSchema, sqlFilename)
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\item{cdmDatabaseSchema}{The name of the schema where the cdm sits.}
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\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".}
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\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".}
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}
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\description{
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Write Index script
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