#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
# 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
# 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.
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
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
# step 9: Run the following code to create the pdf documentation. It will be written to the reports folder. Use knit with pagedown
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
# 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