refactor create and write sql for foreign key and primary key
This commit is contained in:
Maxim Moinat
parent
f8cd93d159
commit
5d9887a356
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@ -16,31 +16,23 @@
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#' Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.
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#' @param cdmVersionNum The version of the CDM you are creating
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#'
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#' @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".
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#' 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/".
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#' @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.
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#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
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#' @export
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createFkFromFile <- function(cdmVersionNum = cdmVersion,
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv",
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outputFile = paste0("inst/sql/sql_server/OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql")){
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createFkFromFile <- function(cdmVersion = cdmVersion){
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cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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fks <- subset(cdmSpecs, isForeignKey == "Yes")
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fks$key <- paste0(fks$cdmTableName,"_",fks$cdmFieldName)
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foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
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foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
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s <- c()
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s <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ",cdmVersionNum, "\n"))
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for (t in fks$key){
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sql_result <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
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for (foreignKey in foreignKeys$key){
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q <- subset(fks, fks$key==t)
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subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
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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"))
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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"))
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}
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SqlRender::writeSql(s, targetFile = outputFile)
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return(s)
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return(paste0(sql_result, collapse = ""))
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}
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@ -16,32 +16,23 @@
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#' Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.
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#' @param cdmVersionNum The version of the CDM you are creating
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#'
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#' @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".
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#' 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/".
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#' @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.
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#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
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#' @export
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createPkFromFile <- function(cdmVersionNum = cdmVersion,
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv",
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outputFile = paste0("inst/sql/sql_server/OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql")){
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createPkFromFile <- function(cdmVersion = cdmVersion){
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cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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pks <- subset(cdmSpecs, isPrimaryKey == "Yes")
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primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
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pkFields <- primaryKeys$cdmFieldName
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pkFields <- pks$cdmFieldName
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sql_result <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
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for (pkField in pkFields){
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s <- c()
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s <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ",cdmVersionNum, "\n"))
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for (f in pkFields){
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subquery <- subset(primaryKeys, cdmFieldName==pkField)
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q <- subset(pks, cdmFieldName==f)
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s <- c(s, paste0("\nALTER TABLE @cdmDatabaseSchema.", q$cdmTableName, " ADD CONSTRAINT xpk_", q$cdmTableName, " PRIMARY KEY NONCLUSTERED (", q$cdmFieldName ,");\n"))
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sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
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}
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SqlRender::writeSql(s, targetFile = outputFile)
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return(s)
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return(paste0(sql_result, collapse = ""))
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}
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@ -18,27 +18,20 @@
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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.
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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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writeConstraints <- 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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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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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect," ", cdmVersion, " constraints.sql"))
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writeConstraints <- 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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sql <- createFkFromFile(cdmVersion)
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
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sql <- SqlRender::translate(sql, targetDialect = targetdialect)
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filename <- paste("OMOPCDM", targetdialect, cdmVersion, "constraints.sql", sep = " ")
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SqlRender::writeSql(sql = sql,
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targetFile = file.path(outputpath, filename)
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)
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}
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@ -30,7 +30,7 @@ writeDDL <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabas
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
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sql <- SqlRender::translate(sql, targetDialect = targetdialect)
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filename <- paste0("OMOPCDM_", targetdialect, "_", cdmVersion, "_ddl.sql")
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filename <- paste("OMOPCDM", targetdialect, cdmVersion, "ddl.sql", sep = " ")
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SqlRender::writeSql(sql = sql,
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targetFile = file.path(outputpath, filename)
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)
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@ -18,27 +18,20 @@
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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.
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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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writePrimaryKeys <- 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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writePrimaryKeys <- 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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if(!dir.exists(paste0("output/",targetdialect))){
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dir.create(paste0("output/",targetdialect))
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}
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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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sql <- createFkFromFile(cdmVersion)
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema)
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sql <- SqlRender::translate(sql, targetDialect = targetdialect)
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filename <- paste("OMOPCDM", targetdialect, cdmVersion, "primary", "keys.sql", sep = " ")
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SqlRender::writeSql(sql = sql,
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targetFile = paste0("output/",targetdialect,"/OMOP CDM ",targetdialect, " ", cdmVersion, " primary keys.sql" ))
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targetFile = file.path(outputpath, filename)
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)
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}
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@ -8,17 +8,15 @@
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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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s <- CdmDdlBase::createDdlFromFile(cdmVersion)
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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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p <- CdmDdlBase::createPkFromFile(cdmVersionNum = cdmVersion,
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv6.0_Field_Level.csv")
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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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f <- CdmDdlBase::createFkFromFile(cdmVersionNum = cdmVersion,
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv6.0_Field_Level.csv")
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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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@ -106,55 +104,15 @@ writeIndex("sql server",
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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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writePrimaryKeys(targetdialect = targetdialect,
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cdmVersion = cdmVersion)
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writeConstraints(targetdialect = targetdialect,
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cdmVersion = cdmVersion)
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}
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## Write all primary keys
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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 = "@cdmDatabaseSchema")
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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 = "@cdmDatabaseSchema")
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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 = "@cdmDatabaseSchema")
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writePrimaryKeys(targetdialect = "netezza",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema")
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## write all foreign key constraints
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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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"@cdmDatabaseSchema")
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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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"@cdmDatabaseSchema")
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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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"@cdmDatabaseSchema")
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writeConstraints("pdw",
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cdmVersion,
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sqlFileName = paste0("OMOP CDM fk ", cdmVersion, " ", Sys.Date(), ".sql"),
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"@cdmDatabaseSchema")
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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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