Consolidate 'create' functions into one file.
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Adam Black
parent
9508b28c51
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02260fb855
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of CdmDdlBase
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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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#' Create a DDL script from a two csv files that detail the OMOP CDM Specifications. These files also form the basis of the CDM documentation and the Data Quality
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#' Dashboard.
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#'
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#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
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#'
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#' @param cdmTableCsvLoc The location of the csv file with the high-level CDM table information. This is defaulted to "inst/csv/OMOP_CDMv5.3.1_Table_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 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 ddl sql file. This is defaulted to a location in the inst/sql/sql server folder and named with today's date and the CDM version.
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#' @export
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createDdl <- function(cdmVersion = cdmVersion){
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cdmTableCsvLoc = paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Table_Level.csv")
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cdmFieldCsvLoc = paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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tableList <- tableSpecs$cdmTableName
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sql_result <- c()
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sql_result <- c(paste0("--@targetdialect CDM DDL Specification for OMOP Common Data Model ", cdmVersion))
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for (tableName in tableList){
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fields <- subset(cdmSpecs, cdmTableName == tableName)
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fieldNames <- fields$cdmFieldName
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if ('person_id' %in% fieldNames){
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query <- "\n\n--HINT DISTRIBUTE ON KEY (person_id)\n"
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} else {
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query <- "\n\n--HINT DISTRIBUTE ON RANDOM\n"
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}
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sql_result <- c(sql_result, query, paste0("CREATE TABLE @cdmDatabaseSchema.", tableName, " ("))
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n_fields <- length(fieldNames)
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for(fieldName in fieldNames) {
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if (subset(fields, cdmFieldName == fieldName, isRequired) == "Yes") {
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nullable_sql <- (" NOT NULL")
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} else {
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nullable_sql <- (" NULL")
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}
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if (fieldName == fieldNames[[n_fields]]) {
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closing_sql <- (" );")
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} else {
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closing_sql <- (",")
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}
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if (fieldName=="offset") {
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field <- paste0('"',fieldName,'"')
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} else {
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field <- fieldName
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}
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fieldSql <- paste0("\n\t\t\t",
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field," ",
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subset(fields, cdmFieldName == fieldName, cdmDatatype),
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nullable_sql,
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closing_sql)
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sql_result <- c(sql_result, fieldSql)
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}
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sql_result <- c(sql_result, "")
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}
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return(paste0(sql_result, collapse = ""))
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}
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@ -1,38 +0,0 @@
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of CdmDdlBase
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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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#' 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, e.g. 5.3.1
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#' @export
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createForeignKeys <- 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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foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
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foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
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sql_result <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
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for (foreignKey in foreignKeys$key){
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subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
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sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$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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return(paste0(sql_result, collapse = ""))
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}
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@ -1,38 +0,0 @@
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of CdmDdlBase
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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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#' 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, e.g. 5.3
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#' @export
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createPrimaryKeys <- 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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primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
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pkFields <- primaryKeys$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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subquery <- subset(primaryKeys, cdmFieldName==pkField)
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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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return(paste0(sql_result, collapse = ""))
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}
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@ -0,0 +1,141 @@
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# Copyright 2019 Observational Health Data Sciences and Informatics
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#
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# This file is part of CdmDdlBase
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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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#' Create the OHDSI-SQL Common Data Model DDL code
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#'
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#' The createDdl, createForeignKeys, and createPrimaryKeys functions each return a character string
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#' containing their respective DDL SQL code in OHDSQL dialect for a specific CDM version.
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#' The SQL they generate needs to be rendered and translated before it can be executed.
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#'
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#' The DDL SQL code is created from a two csv files that detail the OMOP CDM Specifications.
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#' These files also form the basis of the CDM documentation and the Data Quality
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#' Dashboard.
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#'
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#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
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#' @return A character string containing the OHDSQL DDL
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#' @export
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#' @examples
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#' ddl <- createDdl("5.4")
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#' pk <- createPrimaryKeys("5.4")
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#' fk <- createForeignKeys("5.4")
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createDdl <- function(cdmVersion){
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# argument checks
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stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
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cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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tableList <- tableSpecs$cdmTableName
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sql_result <- c()
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sql_result <- c(paste0("--@targetdialect CDM DDL Specification for OMOP Common Data Model ", cdmVersion))
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for (tableName in tableList){
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fields <- subset(cdmSpecs, cdmTableName == tableName)
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fieldNames <- fields$cdmFieldName
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if ('person_id' %in% fieldNames){
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query <- "\n\n--HINT DISTRIBUTE ON KEY (person_id)\n"
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} else {
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query <- "\n\n--HINT DISTRIBUTE ON RANDOM\n"
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}
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sql_result <- c(sql_result, query, paste0("CREATE TABLE @cdmDatabaseSchema.", tableName, " ("))
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n_fields <- length(fieldNames)
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for(fieldName in fieldNames) {
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if (subset(fields, cdmFieldName == fieldName, isRequired) == "Yes") {
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nullable_sql <- (" NOT NULL")
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} else {
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nullable_sql <- (" NULL")
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}
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if (fieldName == fieldNames[[n_fields]]) {
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closing_sql <- (" );")
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} else {
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closing_sql <- (",")
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}
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if (fieldName=="offset") {
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field <- paste0('"',fieldName,'"')
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} else {
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field <- fieldName
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}
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fieldSql <- paste0("\n\t\t\t",
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field," ",
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subset(fields, cdmFieldName == fieldName, cdmDatatype),
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nullable_sql,
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closing_sql)
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sql_result <- c(sql_result, fieldSql)
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}
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sql_result <- c(sql_result, "")
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}
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return(paste0(sql_result, collapse = ""))
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}
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#' @describeIn createDdl
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#' @export
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createPrimaryKeys <- function(cdmVersion){
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# argument checks
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stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
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cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
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pkFields <- primaryKeys$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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subquery <- subset(primaryKeys, cdmFieldName==pkField)
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sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
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}
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return(paste0(sql_result, collapse = ""))
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}
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#' @describeIn createDdl
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#' @export
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createForeignKeys <- function(cdmVersion){
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# argument checks
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stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
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cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
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cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
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foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
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foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
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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$key){
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subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
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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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return(paste0(sql_result, collapse = ""))
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}
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