Add tests, github actions, and executeDdl function (#425)

* Add github actions workflow to build package and run tests.

* update Description file

* rename .Rproj file.

* Consolidate 'create' functions into one file.

* Add tests for create functions.

* update description

* removed spaces in file and folder names. Regenerated ddl output. Tried to fix Field_Level.csv file.

* consolidate write functions into one file. Add execute function.

* update docs

* add tests for write and execute functions

* update documentation

* Add windows and linux runners in github actions.

* update github actions

* download drivers before running tests

* fix small error in setup test file.

* debug github actions

* debug github actions

* debug github actions

* debug github actions

* fix tiny bug

* comment out execute ddl test

* fix bug in test

* Add execute test back in

* revert accidental change in description

* add print statement for debugging schema error on github actions.

* Fix schema environment variable name

* Add comment to github actions workflow file.

* remove placeholder text in function documentation.

* Rename createdDdl.R to createDdl.R

Co-authored-by: Adam Black <adam.black@odysseusinc.com>

.Rbuildignore

@@ -1,2 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+.github/*

.github/workflows/R_CMD_check.yaml

@@ -0,0 +1,117 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      # Test create and drop tables in a database so they cannot be executed in parallel
+      max-parallel: 1
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CDMDDLBASE_POSTGRESQL_USER: ${{ secrets.CDMDDLBASE_POSTGRESQL_USER }}
+      CDMDDLBASE_POSTGRESQL_PASSWORD: ${{ secrets.CDMDDLBASE_POSTGRESQL_PASSWORD }}
+      CDMDDLBASE_POSTGRESQL_SERVER: ${{ secrets.CDMDDLBASE_POSTGRESQL_SERVER }}
+      CDMDDLBASE_POSTGRESQL_SCHEMA: ${{ secrets.CDMDDLBASE_POSTGRESQL_SCHEMA }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libssh-dev
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
+

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: CdmDdlBase
+Package: CommonDataModel
 Type: Package
 Title: OMOP CDM DDL and Documentation Generator
 Version: 0.1.0
@@ -14,6 +14,15 @@ Imports:
   rmarkdown,
   stringr,
   readxl,
-  dplyr
+  DatabaseConnector,
+  DBI,
+  dplyr,
+  readr
+Suggests:
+    knitr,
+    testthat (>= 3.0.0),
+    RSQLite,
+    withr
 NeedsCompilation: no
 RoxygenNote: 7.1.1
+Config/testthat/edition: 3

NAMESPACE

@@ -4,9 +4,10 @@ export(createDdl)
 export(createForeignKeys)
 export(createPrimaryKeys)
 export(downloadCurrentDdl)
+export(executeDdl)
 export(listSupportedVersions)
 export(parseWiki)
-export(writeDDL)
+export(writeDdl)
 export(writeForeignKeys)
 export(writeIndex)
 export(writePrimaryKeys)

R/createDdl.R

@@ -1,4 +1,3 @@
-
 # Copyright 2019 Observational Health Data Sciences and Informatics
 #
 # This file is part of CdmDdlBase
@@ -15,21 +14,30 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-#' 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
+#' Create the OHDSI-SQL Common Data Model DDL code
+#'
+#' The createDdl, createForeignKeys, and createPrimaryKeys functions each return a character string
+#' containing their respective DDL SQL code in OHDSQL dialect for a specific CDM version.
+#' The SQL they generate needs to be rendered and translated before it can be executed.
+#'
+#' The DDL SQL code is created 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
 #' Dashboard.
 #'
-#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
-#'
+#' @return A character string containing the OHDSQL DDL
-#' @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".
-#'                        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 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 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.
 #' @export
+#' @examples
+#' ddl <- createDdl("5.4")
+#' pk <- createPrimaryKeys("5.4")
+#' fk <- createForeignKeys("5.4")
+createDdl <- function(cdmVersion){
 
-createDdl <- function(cdmVersion = cdmVersion){
+  # argument checks
-  cdmTableCsvLoc = paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Table_Level.csv")
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
-  cdmFieldCsvLoc = paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
+
+  cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
 
   tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)
   cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
@@ -37,7 +45,7 @@ createDdl <- function(cdmVersion = 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$cdmFieldName
@@ -81,3 +89,52 @@ createDdl <- function(cdmVersion = cdmVersion){
   }
   return(paste0(sql_result, collapse = ""))
 }
+
+
+#' @describeIn createDdl createPrimaryKeys Returns a string containing the OHDSQL for creation of primary keys in the OMOP CDM.
+#' @export
+createPrimaryKeys <- function(cdmVersion){
+
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
+
+  primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
+  pkFields <- primaryKeys$cdmFieldName
+
+  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)
+
+    sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
+
+  }
+  return(paste0(sql_result, collapse = ""))
+}
+
+#' @describeIn createDdl createForeignKeys Returns a string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
+#' @export
+createForeignKeys <- function(cdmVersion){
+
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  cdmFieldCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Field_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
+
+  foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
+  foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
+
+  sql_result <- c(paste0("--@targetDialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
+  for (foreignKey in foreignKeys$key){
+
+    subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
+
+    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"))
+
+  }
+  return(paste0(sql_result, collapse = ""))
+}

R/createForeignKeys.R

@@ -1,38 +0,0 @@
-# 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 foreign key sql script from two csv files that detail the OMOP CDM Specifications.
-
-#' @param cdmVersionNum The version of the CDM you are creating, e.g. 5.3.1
-#' @export
-
-createForeignKeys <- function(cdmVersion = cdmVersion){
-  cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
-  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
-
-  foreignKeys <- subset(cdmSpecs, isForeignKey == "Yes")
-  foreignKeys$key <- paste0(foreignKeys$cdmTableName, "_", foreignKeys$cdmFieldName)
-
-  sql_result <- c(paste0("--@targetdialect CDM Foreign Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
-  for (foreignKey in foreignKeys$key){
-
-      subquery <- subset(foreignKeys, foreignKeys$key==foreignKey)
-
-      sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT fpk_", subquery$cdmTableName, "_", subquery$cdmFieldName, " FOREIGN KEY (", subquery$cdmFieldName , ") REFERENCES @cdmDatabaseSchema.", subquery$fkTableName, " (", subquery$fkFieldName, ");\n"))
-
-  }
-  return(paste0(sql_result, collapse = ""))
-}

R/createPrimaryKeys.R

@@ -1,38 +0,0 @@
-# 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, e.g. 5.3
-#' @export
-
-createPrimaryKeys <- function(cdmVersion = cdmVersion){
-  cdmFieldCsvLoc <- paste0("inst/csv/OMOP_CDMv", cdmVersion, "_Field_Level.csv")
-  cdmSpecs <- read.csv(cdmFieldCsvLoc, stringsAsFactors = FALSE)
-
-  primaryKeys <- subset(cdmSpecs, isPrimaryKey == "Yes")
-  pkFields <- primaryKeys$cdmFieldName
-
-  sql_result <- c(paste0("--@targetdialect CDM Primary Key Constraints for OMOP Common Data Model ", cdmVersion, "\n"))
-  for (pkField in pkFields){
-
-    subquery <- subset(primaryKeys, cdmFieldName==pkField)
-
-    sql_result <- c(sql_result, paste0("\nALTER TABLE @cdmDatabaseSchema.", subquery$cdmTableName, " ADD CONSTRAINT xpk_", subquery$cdmTableName, " PRIMARY KEY NONCLUSTERED (", subquery$cdmFieldName , ");\n"))
-
-  }
-  return(paste0(sql_result, collapse = ""))
-}

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)
-  )
-}

errorReport.txt

@@ -1,26 +0,0 @@
-DBMS:
-sql server
-
-Error:
-com.microsoft.sqlserver.jdbc.SQLServerException: 'fpk_NOTE_person_id' is not a constraint.
-
-SQL:
-ALTER TABLE ohdsi.dbo.NOTE DROP CONSTRAINT fpk_NOTE_person_id 
-
-R version:
-R version 3.4.2 (2017-09-28)
-
-Platform:
-x86_64-w64-mingw32
-
-Attached base packages:
-- stats
-- graphics
-- grDevices
-- utils
-- datasets
-- methods
-- base
-
-Other attached packages:
-- CdmDdlBase (0.1.0)

extras/codeToRun.R

@@ -7,17 +7,17 @@ cdmVersion <- "5.3"
 supportedVersions <- listSupportedVersions()
 
 for (cdmVersion in supportedVersions) {
-  for (targetdialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
+  for (targetDialect in c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")) {
-    writeDDL(targetdialect = targetdialect,
+    writeDdl(targetDialect = targetDialect,
              cdmVersion = cdmVersion)
 
-    writePrimaryKeys(targetdialect = targetdialect,
+    writePrimaryKeys(targetDialect = targetDialect,
                      cdmVersion = cdmVersion)
 
-    writeForeignKeys(targetdialect = targetdialect,
+    writeForeignKeys(targetDialect = targetDialect,
                      cdmVersion = cdmVersion)
 
-    writeIndex(targetdialect = targetdialect,
+    writeIndex(targetDialect = targetDialect,
                cdmVersion = cdmVersion)
   }
 }

inst/csv/OMOP_CDMv5.3_Field_Level.csv

@@ -514,20 +514,4 @@ ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,,
 ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,,
 ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
 ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,,
-=======
+
-1-Jan-1970.",,No,No,,,,,
-DRUG_STRENGTH,valid_end_date,Yes,date,The date when then Concept became invalid.,,No,No,,,,,
-DRUG_STRENGTH,invalid_reason,No,varchar(1),"Reason the concept was invalidated. Possible values are D (deleted), U (replaced with an update) or NULL when valid_end_date has the default value.",,No,No,,,,,
-COHORT_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,,,,,
-COHORT_DEFINITION,cohort_definition_name,Yes,varchar(255),A short description of the cohort,,No,No,,,,,
-COHORT_DEFINITION,cohort_definition_description,No,varchar(MAX),A complete description of the cohort.,,No,No,,,,,
-COHORT_DEFINITION,definition_type_concept_id,Yes,integer,Type defining what kind of Cohort Definition the record represents and how the syntax may be executed.,,No,Yes,CONCEPT,CONCEPT_ID,,,
-COHORT_DEFINITION,cohort_definition_syntax,No,varchar(MAX),Syntax or code to operationalize the Cohort Definition.,,No,No,,,,,
-COHORT_DEFINITION,subject_concept_id,Yes,integer,"This field contains a Concept that represents the domain of the subjects that are members of the cohort (e.g., Person, Provider, Visit).",,No,Yes,CONCEPT,CONCEPT_ID,,,
-COHORT_DEFINITION,cohort_initiation_date,No,date,A date to indicate when the Cohort was initiated in the COHORT table.,,No,No,,,,,
-ATTRIBUTE_DEFINITION,attribute_definition_id,Yes,integer,,,No,No,,,,,
-ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,,
-ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,,
-ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
-ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,,
->>>>>>> v5.4:inst/csv/OMOP_CDMv5.3.1_Field_Level.csv

inst/sql/sql_server/OMOP_CDM_indices_v5.3.sql

@@ -1,4 +1,4 @@
-/*@targetdialect OMOP CDM Indices
+/*@targetDialect OMOP CDM Indices
 
   There are no unique indices created because it is assumed that the primary key constraints have been run prior to
   implementing indices.

inst/sql/sql_server/OMOP_CDM_indices_v5.4.sql

@@ -1,4 +1,4 @@
-/*@targetdialect OMOP CDM Indices
+/*@targetDialect OMOP CDM Indices
 
   There are no unique indices created because it is assumed that the primary key constraints have been run prior to
   implementing indices.

inst/sql/sql_server/OMOP_CDM_indices_v6.0.sql

@@ -1,4 +1,4 @@
-/*@targetdialect OMOP CDM Indices*/
+/*@targetDialect OMOP CDM Indices*/
 
 
 /************************

man/createDdl.Rd

@@ -1,24 +1,42 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createDdl.R
+% Please edit documentation in R/createdDdl.R
 \name{createDdl}
 \alias{createDdl}
-\title{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
+\alias{createPrimaryKeys}
-Dashboard.}
+\alias{createForeignKeys}
+\title{Create the OHDSI-SQL Common Data Model DDL code}
 \usage{
-createDdl(cdmVersion = cdmVersion)
+createDdl(cdmVersion)
+
+createPrimaryKeys(cdmVersion)
+
+createForeignKeys(cdmVersion)
 }
 \arguments{
-\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3.1}
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4}
-
+}
-\item{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".
+\value{
-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/".}
+A character string containing the OHDSQL DDL
-
-\item{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/".}
-
-\item{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.}
 }
 \description{
-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
+The createDdl, createForeignKeys, and createPrimaryKeys functions each return a character string
+containing their respective DDL SQL code in OHDSQL dialect for a specific CDM version.
+The SQL they generate needs to be rendered and translated before it can be executed.
+}
+\details{
+The DDL SQL code is created 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
 Dashboard.
 }
+\section{Functions}{
+\itemize{
+\item \code{createPrimaryKeys}: createPrimaryKeys asdfladsfj
+
+\item \code{createForeignKeys}: createForeignKeys asdfladsf
+}}
+
+\examples{
+ddl <- createDdl("5.4")
+pk <- createPrimaryKeys("5.4")
+fk <- createForeignKeys("5.4")
+}

man/createForeignKeys.Rd

@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createForeignKeys.R
-\name{createForeignKeys}
-\alias{createForeignKeys}
-\title{Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.}
-\usage{
-createForeignKeys(cdmVersion = cdmVersion)
-}
-\arguments{
-\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3.1}
-}
-\description{
-Create a foreign key sql script from two csv files that detail the OMOP CDM Specifications.
-}

man/createPrimaryKeys.Rd

@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createPrimaryKeys.R
-\name{createPrimaryKeys}
-\alias{createPrimaryKeys}
-\title{Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.}
-\usage{
-createPrimaryKeys(cdmVersion = cdmVersion)
-}
-\arguments{
-\item{cdmVersionNum}{The version of the CDM you are creating, e.g. 5.3}
-}
-\description{
-Create a primary key sql script from two csv files that detail the OMOP CDM Specifications.
-}

man/downloadCurrentDdl.Rd

@@ -27,7 +27,8 @@ The default location is
 }
 \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")
 }
 
 }

man/executeDdl.Rd

@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/executeDdl.R
+\name{executeDdl}
+\alias{executeDdl}
+\title{Generate and execute the DDL on a database}
+\usage{
+executeDdl(
+  connectionDetails,
+  cdmVersion,
+  cdmDatabaseSchema,
+  executeDdl = TRUE,
+  executePrimaryKey = TRUE,
+  executeForeignKey = TRUE,
+  ...
+)
+}
+\arguments{
+\item{connectionDetails}{An object of class connectionDetails as created by the DatabaseConnector::createConnectionDetails function.}
+
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4}
+
+\item{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.}
+
+\item{executeDdl}{Should the DDL be executed? TRUE or FALSE}
+
+\item{executePrimaryKey}{Should the primary keys be added? TRUE or FALSE}
+
+\item{executeForeignKey}{Should the foreign keys be added? TRUE or FALSE}
+
+\item{...}{Other arguments passed on to DatabaseConnector::executeSql. (This allows the user to set the path to errorReportFile.)}
+}
+\description{
+This function will generate the DDL for a specific dbms and CDM version and
+then execute the DDL on a database.
+}
+\examples{
+\dontrun{
+executeDdl(connectionDetails = connectionDetails,
+           cdmVersion = "5.4",
+           cdmDatabaseSchema = "myCdm")
+}
+}

man/writeDDL.Rd

@@ -1,19 +1,61 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeDDL.R
+% Please edit documentation in R/writeDdl.R
-\name{writeDDL}
+\name{writeDdl}
-\alias{writeDDL}
+\alias{writeDdl}
+\alias{writePrimaryKeys}
+\alias{writeForeignKeys}
+\alias{writeIndex}
 \title{Write DDL script}
 \usage{
-writeDDL(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema")
+writeDdl(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writePrimaryKeys(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writeForeignKeys(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
+
+writeIndex(
+  targetDialect,
+  cdmVersion,
+  outputpath,
+  cdmDatabaseSchema = "@cdmDatabaseSchema"
+)
 }
 \arguments{
-\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
+\item{targetDialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
 
-\item{cdmVersion}{The version of the CDM for which you are creating the DDL. e.g. 5.3.1}
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4}
+
+\item{outputpath}{The directory or folder where the SQL file should be saved.}
 
 \item{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"}
 }
 \description{
-Write DDL script
+Write the DDL to a SQL file. The SQL will be rendered (parameters replaced) and translated to the target SQL
+dialect. By default the @cdmDatabaseSchema parameter is kept in the SQL file and needs to be replaced before
+execution.
 }
+\section{Functions}{
+\itemize{
+\item \code{writePrimaryKeys}: writePrimaryKeys Write the SQL code that creates the primary keys to a file.
+
+\item \code{writeForeignKeys}: writeForeignKeys Write the SQL code that creates the foreign keys to a file.
+
+\item \code{writeIndex}: writeIndex Write the rendered and translated sql that creates recommended indexes to a file.
+}}
+

man/writeForeignKeys.Rd

@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeForeignKeys.R
-\name{writeForeignKeys}
-\alias{writeForeignKeys}
-\title{Write constraint script}
-\usage{
-writeForeignKeys(
-  targetdialect,
-  cdmVersion,
-  cdmDatabaseSchema = "@cdmDatabaseSchema"
-)
-}
-\arguments{
-\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
-
-\item{cdmVersion}{The version of the CDM that you are creating the primary keys for}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write constraint script
-}

man/writeIndex.Rd

@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeIndex.R
-\name{writeIndex}
-\alias{writeIndex}
-\title{Write Index script}
-\usage{
-writeIndex(targetdialect, cdmVersion, cdmDatabaseSchema = "@cdmDatabaseSchema")
-}
-\arguments{
-\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
-
-\item{cdmVersion}{The version of the CDM that you are creating the indices for. e.g. 5.3.1}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write Index script
-}

man/writePrimaryKeys.Rd

@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writePrimaryKeys.R
-\name{writePrimaryKeys}
-\alias{writePrimaryKeys}
-\title{Write primary key script}
-\usage{
-writePrimaryKeys(
-  targetdialect,
-  cdmVersion,
-  cdmDatabaseSchema = "@cdmDatabaseSchema"
-)
-}
-\arguments{
-\item{targetdialect}{The dialect of the target database. Choices are "oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server"}
-
-\item{cdmVersion}{The version of the CDM that you are creating the primary keys for}
-
-\item{cdmDatabaseSchema}{The name of the schema where the cdm sits. Defaults to "@cdmDatabaseSchema"}
-}
-\description{
-Write primary key script
-}

tests/setup.R

@@ -0,0 +1,21 @@
+# Download the JDBC drivers used in the tests
+
+# oldJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
+
+driverPath <- file.path(Sys.getenv("HOME"), "drivers")
+if(!dir.exists(driverPath)) dir.create(driverPath)
+Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = driverPath)
+DatabaseConnector::downloadJdbcDrivers("postgresql", pathToDriver = driverPath)
+
+print(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))
+print(list.files(driverPath))
+# if(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER") == "") {
+  # driverPath <- file.path(Sys.getenv("HOME"), "drivers")
+# }
+# downloadJdbcDrivers("sql server")
+# downloadJdbcDrivers("oracle")
+
+# withr::defer({
+#   unlink(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"), recursive = TRUE, force = TRUE)
+#   Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = oldJarFolder)
+# }, testthat::teardown_env())

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(CommonDataModel)
+
+test_check("CommonDataModel")

tests/testthat/test-createDdl.R

@@ -0,0 +1,38 @@
+test_that("createDdl works", {
+  # for(cdmVersion in listSupportedVersions()) { # 5.3 ddl csv control file is currently messed up.
+    cdmVersion <- "5.4"
+    sql <- createDdl(cdmVersion)
+    expect_type(sql, "character")
+    expect_gt(nchar(sql), 10)
+  # }
+
+  expect_error(createDdl(5.4))
+  expect_error(createDdl("blah"))
+
+})
+
+test_that("createPrimaryKeys works", {
+  # for(cdmVersion in listSupportedVersions()) {
+  cdmVersion <- "5.4"
+  sql <- createPrimaryKeys(cdmVersion)
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+  # }
+
+  expect_error(createPrimaryKeys(5.4))
+  expect_error(createPrimaryKeys("blah"))
+})
+
+test_that("createForeignKeys works", {
+  # for(cdmVersion in listSupportedVersions()) {
+  cdmVersion <- "5.4"
+  sql <- createForeignKeys(cdmVersion)
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+  # }
+
+  expect_error(createForeignKeys(5.4))
+  expect_error(createForeignKeys("blah"))
+})
+
+

tests/testthat/test-executeDdl.R

@@ -0,0 +1,84 @@
+library(DatabaseConnector)
+
+connectionDetails <- createConnectionDetails(
+    dbms = "postgresql",
+    user = Sys.getenv("CDMDDLBASE_POSTGRESQL_USER"),
+    password = Sys.getenv("CDMDDLBASE_POSTGRESQL_PASSWORD"),
+    server = Sys.getenv("CDMDDLBASE_POSTGRESQL_SERVER"),
+    pathToDriver = file.path(Sys.getenv("HOME"), "drivers")
+)
+
+# Helper functions used in tests
+.listTablesInSchema <- function(connectionDetails, schema) {
+  con <- DatabaseConnector::connect(connectionDetails)
+  tables <- DBI::dbListObjects(con, prefix = "cdmddlbase")
+  DatabaseConnector::disconnect(con)
+  tables <- subset(tables, is_prefix == FALSE)
+  tables <- subset(tables, grepl("table", table))$table
+  tables <- vapply(tables, function(.) .@name, FUN.VALUE = character(1))
+  return(tables)
+}
+
+.dropAllTablesFromSchema <- function(connectionDetails, schema) {
+  tables <- .listTablesInSchema(connectionDetails, schema)
+
+  con <- DatabaseConnector::connect(connectionDetails)
+  for(table in tables) {
+    DBI::dbRemoveTable(con, name = DBI::SQL(paste(schema, table, sep = ".")))
+  }
+  DatabaseConnector::disconnect(con)
+}
+
+.removeConstraintsPostgresql <- function(connectionDetails, schema) {
+  # the order of removal of constraints matters!
+  con <- DatabaseConnector::connect(connectionDetails)
+  constraints <- DBI::dbGetQuery(con,
+  "SELECT con.conname, rel.relname as relname
+    FROM pg_catalog.pg_constraint con
+  INNER JOIN pg_catalog.pg_class rel
+  ON rel.oid = con.conrelid
+  INNER JOIN pg_catalog.pg_namespace nsp
+  ON nsp.oid = connamespace
+  WHERE nsp.nspname = 'cdmddlbase';")
+
+
+  constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" ))
+
+  sql <- paste(rev(constraints$sql), collapse = "")
+  executeSql(con, sql)
+
+  disconnect(con)
+
+}
+
+test_that("Database can be connected to", {
+  expect_error(con <- connect(connectionDetails), NA)
+  disconnect(con)
+})
+
+test_that("Execute DDL on Postgres", {
+  # make sure the schema is cleared out
+  cdmDatabaseSchema <- Sys.getenv("CDMDDLBASE_POSTGRESQL_SCHEMA")
+  cdmVersion <- "5.4"
+  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
+  .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+  cat(paste("Connecting to schema", cdmDatabaseSchema, "\n"))
+  executeDdl(connectionDetails,
+             cdmVersion = cdmVersion,
+             cdmDatabaseSchema = cdmDatabaseSchema,
+             executeDdl = TRUE,
+             executePrimaryKey = FALSE,
+             executeForeignKey = FALSE)
+
+  tables <- .listTablesInSchema(connectionDetails, schema = cdmDatabaseSchema)
+
+  cdmTableCsvLoc <- system.file(file.path("csv", paste0("OMOP_CDMv", cdmVersion, "_Table_Level.csv")), package = "CommonDataModel", mustWork = TRUE)
+  tableSpecs <- read.csv(cdmTableCsvLoc, stringsAsFactors = FALSE)$cdmTableName
+
+  # check that the tables in the database match the tables in the specification
+  expect_equal(sort(tables), sort(tableSpecs))
+
+  # clear schema
+  # .removeConstraintsPostgresql(connectionDetails, cdmDatabaseSchema)
+  .dropAllTablesFromSchema(connectionDetails, cdmDatabaseSchema)
+})

tests/testthat/test-writeDdl.R

@@ -0,0 +1,51 @@
+test_that("writeDdl works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeDdl(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writePrimaryKeys works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writePrimaryKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writeForeignKeys works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeForeignKeys(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})
+
+test_that("writeIndex works", {
+
+  outputpath <- tempdir(TRUE)
+  filename <- writeIndex(targetDialect = "postgresql", cdmVersion = "5.4", outputpath = outputpath)
+
+  expect_true(file.exists(file.path(outputpath, filename)))
+  sql <- readr::read_file(file.path(outputpath, filename))
+
+  expect_type(sql, "character")
+  expect_gt(nchar(sql), 10)
+
+})