212 lines
9.0 KiB
R
212 lines
9.0 KiB
R
# 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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#' @importFrom utils read.csv
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#' @export
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#' @examples
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#'\dontrun{
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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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#'}
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createDdl <- function(cdmVersion){
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# prevent check NOTE from occurring due to non-standard evaluation of variables
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cdmTableName <- cdmFieldName <- isRequired <- cdmDatatype <- NULL
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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 createPrimaryKeys Returns a string containing the OHDSQL for creation of primary keys in the OMOP CDM.
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#' @return A string containing the OHDSQL for creation of primary keys in the OMOP CDM.
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#' @export
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createPrimaryKeys <- function(cdmVersion){
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# prevent check NOTE from occurring due to non-standard evaluation of variables
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isPrimaryKey <- cdmFieldName <- NULL
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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 createForeignKeys Returns a string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
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#' @return A string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
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#' @export
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createForeignKeys <- function(cdmVersion){
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# prevent check NOTE from occurring due to non-standard evaluation of variables
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isForeignKey <- NULL
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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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# A helper function that will return a character string with the omop ascii art given a major and minor cdm version
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# example: cat(createAsciiHeader(5, 3))
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createAsciiHeader <- function(major, minor) {
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stopifnot(is.numeric(major), is.numeric(minor), length(major) == 1, length(minor) == 1)
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stopifnot(major %in% 0:99, minor %in% 0:99)
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# An inner function that returns an ascii art matrix for any number between 0 and 99
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numberMatrix <- function(num){
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stopifnot(is.numeric(num), num %in% 0:99)
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# An inner function that returns a 7x7 matrix of number ascii art for the number 0 through 9
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# for the number 1 a 7x5 matrix is returned because 1 is narrower than other numbers.
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singleDigit <- function(num) {
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nums <- c(' ### # ##### ##### # ####### ##### ####### ##### ##### # # ## # ## ## # # # ## # # ## ## # # # # ## # # # # # ## ## # # ##### ##### # # ###### ###### # ##### ####### # # # ######## ## # # # # # # # # # # # # # ## # # # ## # ### ##### ####### ##### # ##### ##### # ##### ##### ')
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numsMatrix <- matrix(data = strsplit(nums, character(0))[[1]], nrow = 7, byrow = T)
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cols <- seq(num*7+1, num*7+7, by = 1)
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out <- numsMatrix[1:7, cols]
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# the number 1 is narrower than the other numbers
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if(num == 1) out<- out[1:7, 2:6]
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out
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}
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if(num < 10){
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return(singleDigit(num))
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} else {
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space <- matrix(rep(" ", 7), nrow = 7)
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return(cbind(singleDigit(floor(num/10)), space, singleDigit(num %% 10)))
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}
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}
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omop <- c('.
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####### # # ####### ###### ##### ###### # # .
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# # ## ## # # # # # # # # ## ## # #.
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# # # # # # # # # # # # # # # # # # #.
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# # # # # # # ###### # # # # # # # #.
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# # # # # # # # # # # # # #.
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# # # # # # # # # # # # # # # .
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####### # # ####### # ##### ###### # # ## ')
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# convert to matrix and remove first column
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omop <- matrix(strsplit(omop, character(0))[[1]], nrow = 7, byrow = TRUE)
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omop <- omop[,c(-1, -2)]
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dot <- matrix(c(rep(" ", 3*4), rep("#", 3*3)), nrow = 7, byrow = TRUE)
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space <- matrix(rep(" ", 7), nrow = 7)
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newline <- matrix(rep("\n", 7, nrow = 7))
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header <- character(0)
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headerMatrix <- cbind(omop, space, numberMatrix(major), space, dot, space, numberMatrix(minor), newline)
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for(i in 1:7) {
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header <- c(header, as.character(headerMatrix[i,]))
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}
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header <- paste(header, collapse = "")
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return(header)
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}
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