consolidate write functions into one file. Add execute function.

R/createdDdl.R

@@ -1,4 +1,3 @@
-
 # Copyright 2019 Observational Health Data Sciences and Informatics
 #
 # This file is part of CdmDdlBase
@@ -46,7 +45,7 @@ createDdl <- function(cdmVersion){
   tableList <- tableSpecs$cdmTableName
 
   sql_result <- c()
-  sql_result <- c(paste0("--@targetdialect CDM DDL Specification for OMOP Common Data Model ", cdmVersion))
+  sql_result <- c(paste0("--@targetDialect CDM DDL Specification for OMOP Common Data Model ", cdmVersion))
   for (tableName in tableList){
     fields <- subset(cdmSpecs, cdmTableName == tableName)
     fieldNames <- fields$cdmFieldName
@@ -92,7 +91,7 @@ createDdl <- function(cdmVersion){
 }
 
 
-#' @describeIn createDdl
+#' @describeIn createDdl createPrimaryKeys asdfladsfj
 #' @export
 createPrimaryKeys <- function(cdmVersion){
 
@@ -105,7 +104,7 @@ createPrimaryKeys <- function(cdmVersion){
   primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
   pkFields <- primaryKeys$cdmFieldName
 
-  sql_result <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  sql_result <- c(paste0("--@targetDialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
   for (pkField in pkFields){
 
     subquery <- subset(primaryKeys, cdmFieldName==pkField)
@@ -116,7 +115,7 @@ createPrimaryKeys <- function(cdmVersion){
   return(paste0(sql_result, collapse = ""))
 }
 
-#' @describeIn createDdl
+#' @describeIn createDdl createForeignKeys asdfladsf
 #' @export
 createForeignKeys <- function(cdmVersion){
 
@@ -129,7 +128,7 @@ createForeignKeys <- function(cdmVersion){
   foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
   foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
 
-  sql_result <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  sql_result <- c(paste0("--@targetDialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
   for (foreignKey in foreignKeys$key){
 
     subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)

R/downloadCurrentDdl.R

@@ -11,7 +11,8 @@
 #'
 #' @examples
 #' \dontrun{
-#' downloadCurrentDdl("OHDSI/CommonDataModel", pathToCsv="Sql%20Server/OMOP%20CDM%20sql%20server%20ddl.txt")
+#' downloadCurrentDdl("OHDSI/CommonDataModel",
+#'  pathToCsv="Sql%20Server/OMOP%20CDM%20sql%20server%20ddl.txt")
 #' }
 #'
 #' @export

R/executeDdl.R

@@ -0,0 +1,86 @@
+# 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.
+
+#' Generate and execute the DDL on a database
+#'
+#' This function will generate the DDL for a specific dbms and CDM version and
+#' then execute the DDL on a database.
+#'
+#' @param connectionDetails An object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails function.
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
+#' @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.
+#' @param executeDdl Should the DDL be executed? TRUE or FALSE
+#' @param executePrimaryKey Should the primary keys be added? TRUE or FALSE
+#' @param executeForeignKey Should the foreign keys be added? TRUE or FALSE
+#' @param ... Other arguments passed on to DatabaseConnector::executeSql. (This allows the user to set the path to errorReportFile.)
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' executeDdl(connectionDetails = connectionDetails,
+#'            cdmVersion = "5.4",
+#'            cdmDatabaseSchema = "myCdm")
+#'}
+executeDdl <- function(connectionDetails,
+                       cdmVersion,
+                       cdmDatabaseSchema,
+                       executeDdl = TRUE,
+                       executePrimaryKey = TRUE,
+                       executeForeignKey = TRUE,
+                       ...) {
+
+  outputpath <- tempdir(check = TRUE)
+
+
+  if(executeDdl) {
+    filename <- writeDdl(targetDialect = connectionDetails$dbms,
+                         cdmVersion = cdmVersion,
+                         cdmDatabaseSchema = cdmDatabaseSchema,
+                         outputpath = outputpath)
+
+    sql <- readr::read_file(file.path(outputpath, filename))
+  } else {
+    sql <- ""
+  }
+
+  if(executePrimaryKey) {
+    filename <- writePrimaryKeys(targetDialect = connectionDetails$dbms,
+                                 cdmVersion = cdmVersion,
+                                 cdmDatabaseSchema = cdmDatabaseSchema,
+                                 outputpath = outputpath)
+
+    sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n")
+  }
+
+  if(executeForeignKey) {
+    filename <- writeForeignKeys(targetDialect = connectionDetails$dbms,
+                                 cdmVersion = cdmVersion,
+                                 cdmDatabaseSchema = cdmDatabaseSchema,
+                                 outputpath = outputpath)
+
+    sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n")
+  }
+
+  con <- DatabaseConnector::connect(connectionDetails = connectionDetails)
+
+  DatabaseConnector::executeSql(con, sql = sql, ...)
+
+  DatabaseConnector::disconnect(con)
+}
+
+
+
+

R/writeDDL.R

@@ -16,22 +16,108 @@
 
 #' Write DDL script
 #'
-#' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
+#' Write the DDL to a SQL file. The SQL will be rendered (parameters replaced) and translated to the target SQL
-#' @param cdmVersion The version of the CDM for which you are creating the DDL. e.g. 5.3.1
+#' dialect. By default the @cdmDatabaseSchema parameter is kept in the SQL file and needs to be replaced before
+#' execution.
+#'
+#' @param targetDialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
+#' @param outputpath The directory or folder where the SQL file should be saved.
 #' @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.
 #'                          Defaults to "@cdmDatabaseSchema"
 #'
 #' @export
-writeDDL <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
+writeDdl <- function(targetDialect, cdmVersion, outputpath, cdmDatabaseSchema = "@cdmDatabaseSchema") {
-  outputpath <- file.path("ddl", cdmVersion, targetdialect)
+
-  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+  # argument checks
+  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
+  stopifnot(cdmVersion %in% listSupportedVersions())
+  stopifnot(is.character(cdmDatabaseSchema))
+
+  if(missing(outputpath)) {
+    outputpath <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
+  }
+
+  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
 
   sql <- createDdl(cdmVersion)
-  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetdialect = targetdialect)
+  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
-  sql <- SqlRender::translate(sql, targetDialect = targetdialect)
+  sql <- SqlRender::translate(sql, targetDialect = targetDialect)
 
-  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "ddl.sql", sep = "_")
+  filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "ddl.sql", sep = "_")
-  SqlRender::writeSql(sql = sql,
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputpath, filename))
-                      targetFile = file.path(outputpath, filename)
+  invisible(filename)
-  )
+}
+
+#' @describeIn writeDdl writePrimaryKeys Write the SQL code that creates the primary keys to a file.
+#' @export
+writePrimaryKeys <- function(targetDialect, cdmVersion, outputpath, cdmDatabaseSchema = "@cdmDatabaseSchema") {
+
+  # argument checks
+  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
+  stopifnot(cdmVersion %in% listSupportedVersions())
+  stopifnot(is.character(cdmDatabaseSchema))
+
+  if(missing(outputpath)) {
+    outputpath <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
+  }
+
+  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+
+  sql <- createPrimaryKeys(cdmVersion)
+  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
+  sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+
+  filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "primary", "keys.sql", sep = "_")
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputpath, filename))
+  invisible(filename)
+}
+
+#' @describeIn writeDdl writeForeignKeys Write the SQL code that creates the foreign keys to a file.
+#' @export
+writeForeignKeys <- function(targetDialect, cdmVersion, outputpath, cdmDatabaseSchema = "@cdmDatabaseSchema") {
+
+  # argument checks
+  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
+  stopifnot(cdmVersion %in% listSupportedVersions())
+  stopifnot(is.character(cdmDatabaseSchema))
+
+  if(missing(outputpath)) {
+    outputpath <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
+  }
+
+  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+
+  sql <- createForeignKeys(cdmVersion)
+  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
+  sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+
+  filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "constraints.sql", sep = "_")
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputpath, filename))
+  invisible(filename)
+}
+
+#' @describeIn writeDdl writeIndex Write the rendered and translated sql that creates recommended indexes to a file.
+#' @export
+writeIndex <- function(targetDialect, cdmVersion, outputpath, cdmDatabaseSchema  = "@cdmDatabaseSchema") {
+
+  # argument checks
+  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"))
+  stopifnot(cdmVersion %in% listSupportedVersions())
+  stopifnot(is.character(cdmDatabaseSchema))
+
+  if(missing(outputpath)) {
+    outputpath <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
+  }
+
+  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+
+  sqlFilename <- paste0("OMOP_CDM_indices_v", cdmVersion, ".sql")
+  sql <- readr::read_file(system.file(file.path("sql", "sql_server", sqlFilename), package = "CommonDataModel"))
+  sql <- SqlRender::render(sql, targetDialect = targetDialect, cdmDatabaseSchema = cdmDatabaseSchema)
+  sql <- SqlRender::translate(sql, targetDialect = targetDialect)
+
+  filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "indices.sql", sep = "_")
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputpath, filename))
+  invisible(filename)
 }

R/writeForeignKeys.R

@@ -1,36 +0,0 @@
-# Copyright 2017 Observational Health Data Sciences and Informatics
-#
-#
-# 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.
-
-#' Write constraint script
-#'
-#' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
-#' @param cdmVersion The version of the CDM that you are creating the primary keys for
-#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
-#'
-#' @export
-
-writeForeignKeys <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
-  outputpath <- file.path("ddl", cdmVersion, targetdialect)
-  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
-
-  sql <- createForeignKeys(cdmVersion)
-  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetdialect = targetdialect)
-  sql <- SqlRender::translate(sql, targetDialect = targetdialect)
-
-  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "constraints.sql", sep = "_")
-  SqlRender::writeSql(sql = sql,
-                      targetFile = file.path(outputpath, filename)
-  )
-}

R/writeIndex.R

@@ -1,38 +0,0 @@
-# Copyright 2017 Observational Health Data Sciences and Informatics
-#
-# This file is part of DDLGeneratr
-#
-# 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.
-
-#' Write Index script
-#'
-#' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
-#' @param cdmVersion The version of the CDM that you are creating the indices for. e.g. 5.3.1
-#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
-#'
-#' @export
-writeIndex <- function(targetdialect, cdmVersion, cdmDatabaseSchema  = "@cdmDatabaseSchema") {
-  outputpath <- file.path("ddl", cdmVersion, targetdialect)
-  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
-
-  sqlFilename <- paste0("OMOP CDM indices v", cdmVersion, ".sql")
-  sql <- SqlRender::loadRenderTranslateSql(sqlFilename = sqlFilename,
-                                           packageName = "CdmDdlBase",
-                                           dbms = targetdialect,
-                                           targetdialect = targetdialect,
-                                           cdmDatabaseSchema = cdmDatabaseSchema)
-
-  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "indices.sql", sep = "_")
-  SqlRender::writeSql(sql = sql,
-                      targetFile = file.path(outputpath, filename))
-}

R/writePrimaryKeys.R

@@ -1,37 +0,0 @@
-# Copyright 2017 Observational Health Data Sciences and Informatics
-#
-# This file is part of DDLGeneratr
-#
-# 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.
-
-#' Write primary key script
-#'
-#' @param targetdialect  The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"
-#' @param cdmVersion The version of the CDM that you are creating the primary keys for
-#' @param cdmDatabaseSchema The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"
-#'
-#' @export
-
-writePrimaryKeys <- function(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema") {
-  outputpath <- file.path("ddl", cdmVersion, targetdialect)
-  dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
-
-  sql <- createPrimaryKeys(cdmVersion)
-  sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetdialect = targetdialect)
-  sql <- SqlRender::translate(sql, targetDialect = targetdialect)
-
-  filename <- paste("OMOPCDM", targetdialect, cdmVersion, "primary", "keys.sql", sep = "_")
-  SqlRender::writeSql(sql = sql,
-                      targetFile = file.path(outputpath, filename)
-  )
-}