129 lines
5.9 KiB
R
129 lines
5.9 KiB
R
# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of DDLGeneratr
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#' Write DDL script
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#'
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#' Write the DDL to a SQL file. The SQL will be rendered (parameters replaced) and translated to the target SQL
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#' dialect. By default the @cdmDatabaseSchema parameter is kept in the SQL file and needs to be replaced before
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#' execution.
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#'
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#' @param targetDialect The dialect of the target database. Support dialects are specified by SqlRender::listSupportedDialects
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#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
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#' @param outputfolder The directory or folder where the SQL file should be saved.
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#' @param cdmDatabaseSchema The schema of the CDM instance where the DDL will be run. For example, this would be "ohdsi.dbo" when testing on sql server.
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#' Defaults to "@cdmDatabaseSchema"
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#' @return Writes SQL file with the OMOP CDM DDL for the specified CDM version and target dialect in the output folder.
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#'
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#' @export
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writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
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# argument checks
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stopifnot(targetDialect %in% listSupportedDialects())
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stopifnot(cdmVersion %in% listSupportedVersions())
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stopifnot(is.character(cdmDatabaseSchema))
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if(missing(outputfolder)) {
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outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
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}
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if(!dir.exists(outputfolder)) dir.create(outputfolder, showWarnings = FALSE, recursive = TRUE)
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sql <- createDdl(cdmVersion)
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
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sql <- SqlRender::translate(sql, targetDialect = targetDialect)
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filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "ddl.sql", sep = "_")
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SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, filename))
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invisible(filename)
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}
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#' @describeIn writeDdl writePrimaryKeys Write the SQL code that creates the primary keys to a file.
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#' @return Writes a SQL file with the primary keys for the OMOP CDM based on the specified target dialect and CDM version.
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#' @export
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#'
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writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
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# argument checks
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stopifnot(targetDialect %in% listSupportedDialects())
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stopifnot(cdmVersion %in% listSupportedVersions())
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stopifnot(is.character(cdmDatabaseSchema))
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if(missing(outputfolder)) {
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outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
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}
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if(!dir.exists(outputfolder)) dir.create(outputfolder, showWarnings = FALSE, recursive = TRUE)
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sql <- createPrimaryKeys(cdmVersion)
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
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sql <- SqlRender::translate(sql, targetDialect = targetDialect)
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filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "primary", "keys.sql", sep = "_")
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SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, filename))
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invisible(filename)
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}
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#' @describeIn writeDdl writeForeignKeys Write the SQL code that creates the foreign keys to a file.
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#' @return Writes a SQL file with the foreign keys for the OMOP CDM based on the specified target dialect and CDM version.
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#' @export
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writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
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# argument checks
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stopifnot(targetDialect %in% listSupportedDialects())
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stopifnot(cdmVersion %in% listSupportedVersions())
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stopifnot(is.character(cdmDatabaseSchema))
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if(missing(outputfolder)) {
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outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
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}
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if(!dir.exists(outputfolder)) dir.create(outputfolder, showWarnings = FALSE, recursive = TRUE)
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sql <- createForeignKeys(cdmVersion)
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sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
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sql <- SqlRender::translate(sql, targetDialect = targetDialect)
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filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "constraints.sql", sep = "_")
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SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, filename))
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invisible(filename)
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}
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#' @describeIn writeDdl writeIndex Write the rendered and translated sql that creates recommended indexes to a file.
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#' @return Writes a SQL file with the indices for the OMOP CDM based on the specified target dialect and CDM version.
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#' @export
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writeIndex <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
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# argument checks
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stopifnot(targetDialect %in% listSupportedDialects())
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stopifnot(cdmVersion %in% listSupportedVersions())
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stopifnot(is.character(cdmDatabaseSchema))
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if(missing(outputfolder)) {
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outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
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}
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if(!dir.exists(outputfolder)) dir.create(outputfolder, showWarnings = FALSE, recursive = TRUE)
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sqlFilename <- paste0("OMOP_CDM_indices_v", cdmVersion, ".sql")
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sql <- readr::read_file(system.file(file.path("sql", "sql_server", sqlFilename), package = "CommonDataModel"))
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sql <- SqlRender::render(sql, targetDialect = targetDialect, cdmDatabaseSchema = cdmDatabaseSchema)
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sql <- SqlRender::translate(sql, targetDialect = targetDialect)
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filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "indices.sql", sep = "_")
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SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, filename))
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invisible(filename)
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}
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