239 lines
9.7 KiB
R
239 lines
9.7 KiB
R
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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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cdmVersion <- "v6_0"
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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(cdmTableCsvLoc = "inst/csv/OMOP_CDMv6.0_Table_Level.csv",
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cdmFieldCsvLoc = "inst/csv/OMOP_CDMv6.0_Field_Level.csv")
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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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# 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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# 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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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 = "@cdmDatabaseSchema",
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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 = "@cdmDatabaseSchema",
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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 = "@cdmDatabaseSchema",
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cleanUpScript = F) #This needs to be updated manually right now
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writeDDL(targetdialect = "bigquery",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema",
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cleanUpScript = F)
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writeDDL(targetdialect = "impala",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema",
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cleanUpScript = F)
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writeDDL(targetdialect = "netezza",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema",
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cleanUpScript = F)
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writeDDL(targetdialect = "pdw",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema",
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cleanUpScript = F)
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writeDDL(targetdialect = "redshift",
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cdmVersion = cdmVersion,
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sqlFilename = paste0("OMOP CDM ddl ", cdmVersion, " ", Sys.Date(), ".sql"),
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cdmDatabaseSchema = "@cdmDatabaseSchema",
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cleanUpScript = F)
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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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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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# step 9: Run the following code to create the pdf documentation. It will be written to the reports folder. Use knit with pagedown
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pagedown::chrome_print("rmd/cdm531.Rmd") # create a comprehensive rmd with background, conventions, etc like https://stackoverflow.com/questions/25824795/how-to-combine-two-rmarkdown-rmd-files-into-a-single-output
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# Step 10: After updating any of the .Rmd files, rendering the site following directions in SiteMaintenance.R, then move the files to the CommonDataModel directory
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newdir <- "C:/Git/Github/CommonDataModel/docs"
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currentdir <- paste0(getwd(),"/docs/")
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file.copy(currentdir, newdir, recursive = TRUE, overwrite = TRUE)
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