Merge branch 'main' into doc-tooling-support

.Rbuildignore

@@ -3,3 +3,7 @@
 ^LICENSE\.md$
 .github/*
 extras/*
+docs/*
+rmd/*
+^CRAN-SUBMISSION$
+^cran-comments\.md$

.github/workflows/R_CMD_check.yaml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches:
       - '**'
+  schedule:
+    - cron: '0 19 * * 0' # every Sunday at 7pm UTC
 
 name: R-CMD-check
 
@@ -47,15 +49,14 @@ jobs:
       CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }}
 
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-tinytex@v1
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -66,7 +67,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v2
+        uses: actions/cache@v3.3.1
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

.gitignore

@@ -15,4 +15,3 @@ ehthumbs.db
 Thumbs.db
 extras/codeToRun.R
 output/
-ddl/

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.2.0
+Date: 2024-02-06 20:13:33 UTC
+SHA: d152472484fb2bedd2596e2279a24afbd0084f0b

DESCRIPTION

@@ -1,20 +1,20 @@
 Package: CommonDataModel
 Type: Package
 Title: OMOP CDM DDL and Documentation Generator
-Version: 0.1.0
+Version: 0.2.0
 Author: Clair Blacketer [aut, cre]
 Maintainer: Clair Blacketer <mblacke@its.jnj.com>
-Description: This package uses an input csv file to create the OHDSql version of the DDL as well as the documentation associated. Then it leverages the SqlRender package to convert the DDL script written in OHDSql to the other supported dialects.
+Description: Generates the scripts required to create an Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) database and associated documentation for supported database platforms. Leverages the 'SqlRender' package to convert the Data Definition Language (DDL) script written in parameterized Structured Query Language (SQL) to the other supported dialects.
 License: Apache License 2.0
 Encoding: UTF-8
 LazyData: true
-VignetteBuilder: knitr
+Depends:
+  DatabaseConnector,
+  SqlRender,
+  rJava
 Imports: 
-  SqlRender, 
   rmarkdown,
   stringr,
-  readxl,
-  DatabaseConnector,
   DBI,
   dplyr,
   readr
@@ -24,5 +24,5 @@ Suggests:
     RSQLite,
     withr
 NeedsCompilation: no
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NAMESPACE

@@ -14,6 +14,9 @@ export(writeDdl)
 export(writeForeignKeys)
 export(writeIndex)
 export(writePrimaryKeys)
+import(DatabaseConnector)
+import(SqlRender)
+import(rJava)
 importFrom(utils,download.file)
 importFrom(utils,read.csv)
 importFrom(utils,write.csv)

R/CommonDataModel-package.R

@@ -0,0 +1,4 @@
+#' @import rJava
+#' @import DatabaseConnector
+#' @import SqlRender
+NULL

R/WikiParser.R

@@ -23,6 +23,7 @@
 #'
 #' @param mdFilesLocation Path to the root folder of the Wiki repository.
 #' @param output_file     Path to where the output CSV file should be written.
+#' @return CSV files with the OMOP CDM specifications.
 #' @importFrom utils write.csv
 #' @export
 parseWiki <- function(mdFilesLocation, output_file) {

R/buildRelease.R

@@ -17,18 +17,20 @@
 #' Create OMOP CDM SQL files
 #'
 #' Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion
-#' and targetDialect to the 'ddl' folder in current working directory.
+#' and targetDialect to the 'ddl' folder in specifed output folder.
 #'
 #' @param cdmVersions The versions of the CDM you are creating, e.g. 5.3, 5.4.
 #'                   Defaults to all supported CDM versions.
 #' @param targetDialects A character vector of target dialects.
 #'                      Defaults to all supported dialects.
 #' @param outputfolder The base folder where the SQL files will be written.
 #'                     Subfolders will be created for each cdmVersion and targetDialect.
+#' @return Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion
+#'         and targetDialect to the 'ddl' folder in specifed output folder.
 #' @export
 buildRelease <- function(cdmVersions = listSupportedVersions(),
                          targetDialects = listSupportedDialects(),
-                         outputfolder = file.path(getwd(), "inst", "ddl")){
+                         outputfolder = file.path(tempdir(), "inst", "ddl")){
   basefolder <- outputfolder
   for (cdmVersion in cdmVersions) {
     for (targetDialect in targetDialects) {
@@ -69,11 +71,12 @@ buildRelease <- function(cdmVersions = listSupportedVersions(),
 #' @return A character string containing the OHDSQL DDL
 #' @export
 #' @examples
+#'\dontrun{
 #' buildReleaseZip(cdmVersion='5.3', targetDialect='sql server', outputfolder='.')
-#'
+#'}
 buildReleaseZip <- function(cdmVersion,
                             targetDialect = listSupportedDialects(),
-                            outputfolder = file.path(getwd(), "output")){
+                            outputfolder = file.path(tempdir(), "output")){
   # argument checks
   stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
 

R/createDdl.R

@@ -29,10 +29,14 @@
 #' @importFrom utils read.csv
 #' @export
 #' @examples
+#'\dontrun{
 #' ddl <- createDdl("5.4")
 #' pk <- createPrimaryKeys("5.4")
 #' fk <- createForeignKeys("5.4")
+#'}
 createDdl <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  cdmTableName <- cdmFieldName <- isRequired <- cdmDatatype <- NULL
 
   # argument checks
   stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
@@ -93,8 +97,11 @@ createDdl <- function(cdmVersion){
 
 
 #' @describeIn createDdl createPrimaryKeys Returns a string containing the OHDSQL for creation of primary keys in the OMOP CDM.
+#' @return A string containing the OHDSQL for creation of primary keys in the OMOP CDM.
 #' @export
 createPrimaryKeys <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  isPrimaryKey <- cdmFieldName <- NULL
 
   # argument checks
   stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
@@ -117,8 +124,11 @@ createPrimaryKeys <- function(cdmVersion){
 }
 
 #' @describeIn createDdl createForeignKeys Returns a string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
+#' @return A string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
 #' @export
 createForeignKeys <- function(cdmVersion){
+  # prevent check NOTE from occurring due to non-standard evaluation of variables
+  isForeignKey <- NULL
 
   # argument checks
   stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())