48 lines
2.1 KiB
R
48 lines
2.1 KiB
R
# Copyright 2019 Observational Health Data Sciences and Informatics
|
|
#
|
|
# This file is part of CdmDdlBase
|
|
#
|
|
# Licensed under the Apache License, Version 2.0 (the "License");
|
|
# you may not use this file except in compliance with the License.
|
|
# You may obtain a copy of the License at
|
|
#
|
|
# http://www.apache.org/licenses/LICENSE-2.0
|
|
#
|
|
# Unless required by applicable law or agreed to in writing, software
|
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
# See the License for the specific language governing permissions and
|
|
# limitations under the License.
|
|
|
|
#' Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.
|
|
|
|
#' @param cdmVersionNum The version of the CDM you are creating
|
|
#'
|
|
#' @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".
|
|
#' 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/".
|
|
#' @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.
|
|
#' @export
|
|
|
|
createPkFromFile <- function(cdmVersionNum = cdmVersion,
|
|
cdmFieldCsvLoc = "inst/csv/OMOP_CDMv5.3.1_Field_Level.csv",
|
|
outputFile = paste0("inst/sql/sql_server/OMOP CDM pk ", cdmVersion, " ", Sys.Date(), ".sql")){
|
|
|
|
cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
|
|
|
|
pks <- subset(cdmSpecs, isPrimaryKey == "Yes")
|
|
|
|
pkFields <- pks$cdmFieldName
|
|
|
|
s <- c()
|
|
s <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ",cdmVersionNum, "\n"))
|
|
for (f in pkFields){
|
|
|
|
q <- subset(pks, cdmFieldName==f)
|
|
|
|
s <- c(s, paste0("\nALTER TABLE @cdmDatabaseSchema.", q$cdmTableName, " ADD CONSTRAINT xpk_", q$cdmTableName, " PRIMARY KEY NONCLUSTERED (", q$cdmFieldName ,");\n"))
|
|
|
|
}
|
|
SqlRender::writeSql(s, targetFile = outputFile)
|
|
return(s)
|
|
}
|