Merge pull request #590 from OHDSI/supported-dialects-update

updating for recent SqlRender supported dialects

.Rbuildignore

@@ -3,3 +3,5 @@
 ^LICENSE\.md$
 .github/*
 extras/*
+docs/*
+rmd/*

.github/workflows/R_CMD_check.yaml

@@ -47,15 +47,14 @@ 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 +65,7 @@ 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/

DESCRIPTION

@@ -1,7 +1,7 @@
 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.
@@ -13,7 +13,6 @@ Imports:
   SqlRender, 
   rmarkdown,
   stringr,
-  readxl,
   DatabaseConnector,
   DBI,
   dplyr,
@@ -24,5 +23,5 @@ Suggests:
     RSQLite,
     withr
 NeedsCompilation: no
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

R/buildRelease.R

@@ -69,8 +69,9 @@ 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")){

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())
@@ -95,6 +99,8 @@ createDdl <- function(cdmVersion){
 #' @describeIn createDdl createPrimaryKeys Returns 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())
@@ -119,6 +125,8 @@ createPrimaryKeys <- function(cdmVersion){
 #' @describeIn createDdl createForeignKeys Returns 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())

R/executeDdl.R

@@ -76,7 +76,7 @@ executeDdl <- function(connectionDetails,
 
   con <- DatabaseConnector::connect(connectionDetails = connectionDetails)
 
-  DatabaseConnector::executeSql(con, sql = sql, ...)
+  DatabaseConnector::executeSql(con, sql = sql, reportOverallTime = FALSE, progressBar = FALSE, ...)
 
   DatabaseConnector::disconnect(con)
 }

R/utils.R

@@ -0,0 +1,8 @@
+# these packages are used in utilities or functions outside of check's vision
+# this function ensures that check is satisfied and does not report the
+# packages as imported but not imported from
+checkSatisfier <- function() {
+  DBI::dbConnect
+  dplyr::sql
+  rmarkdown::draft
+}

R/writeDDL.R

@@ -20,8 +20,7 @@
 #' 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",
-#'                       "spark", "snowflake", "synapse"
+#' @param targetDialect  The dialect of the target database. Support dialects are specified by SqlRender::listSupportedDialects
 #' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
 #' @param outputfolder 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.
@@ -31,7 +30,7 @@
 writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
 
   # argument checks
-  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark", "snowflake", "synapse"))
+  stopifnot(targetDialect %in% listSupportedDialects())
   stopifnot(cdmVersion %in% listSupportedVersions())
   stopifnot(is.character(cdmDatabaseSchema))
 
@@ -55,7 +54,7 @@ writeDdl <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema
 writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
 
   # argument checks
-  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark", "snowflake", "synapse"))
+  stopifnot(targetDialect %in% listSupportedDialects())
   stopifnot(cdmVersion %in% listSupportedVersions())
   stopifnot(is.character(cdmDatabaseSchema))
 
@@ -79,7 +78,7 @@ writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
 writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema = "@cdmDatabaseSchema") {
 
   # argument checks
-  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark", "snowflake", "synapse"))
+  stopifnot(targetDialect %in% listSupportedDialects())
   stopifnot(cdmVersion %in% listSupportedVersions())
   stopifnot(is.character(cdmDatabaseSchema))
 
@@ -103,7 +102,7 @@ writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, cdmDatabas
 writeIndex <- function(targetDialect, cdmVersion, outputfolder, cdmDatabaseSchema  = "@cdmDatabaseSchema") {
 
   # argument checks
-  stopifnot(targetDialect %in% c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server", "spark", "snowflake", "synapse"))
+  stopifnot(targetDialect %in% listSupportedDialects())
   stopifnot(cdmVersion %in% listSupportedVersions())
   stopifnot(is.character(cdmDatabaseSchema))