Function to Build Release Zips (#429)

* buildRelease and buildReleaseZip

* add buildRelease

CommonDataModel.Rproj

@@ -1,21 +1,21 @@
-Version: 1.0
+Version: 1.0
-
+
-RestoreWorkspace: Default
+RestoreWorkspace: Default
-SaveWorkspace: Default
+SaveWorkspace: Default
-AlwaysSaveHistory: Default
+AlwaysSaveHistory: Default
-
+
-EnableCodeIndexing: Yes
+EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
+UseSpacesForTab: Yes
-NumSpacesForTab: 2
+NumSpacesForTab: 2
-Encoding: UTF-8
+Encoding: UTF-8
-
+
-RnwWeave: Sweave
+RnwWeave: Sweave
-LaTeX: XeLaTeX
+LaTeX: XeLaTeX
-
+
-AutoAppendNewline: Yes
+AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
+StripTrailingWhitespace: Yes
-
+
-BuildType: Package
+BuildType: Package
-PackageUseDevtools: Yes
+PackageUseDevtools: Yes
-PackageInstallArgs: --no-multiarch --with-keep.source
+PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+export(buildReleaseZip)
 export(createDdl)
 export(createForeignKeys)
 export(createPrimaryKeys)
 export(downloadCurrentDdl)
 export(executeDdl)
+export(listSupportedDialects)
 export(listSupportedVersions)
 export(parseWiki)
 export(writeDdl)

R/buildRelease.R

@@ -0,0 +1,88 @@
+# 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 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.
+#'
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4.
+#'                   Defaults to all supported CDM versions.
+#' @param targetDialect The target dialect
+#'
+buildRelease <- function(cdmVersion = listSupportedVersions(),
+                         targetDialect = listSupportedDialects()){
+  for (cdmVersion in cdmVersion) {
+    for (targetDialect in targetDialect) {
+      writeDdl(targetDialect = targetDialect,
+               cdmVersion = cdmVersion)
+
+      writePrimaryKeys(targetDialect = targetDialect,
+                       cdmVersion = cdmVersion)
+
+      writeForeignKeys(targetDialect = targetDialect,
+                       cdmVersion = cdmVersion)
+
+      writeIndex(targetDialect = targetDialect,
+                 cdmVersion = cdmVersion)
+    }
+  }
+}
+
+#' Create OMOP CDM release zip
+#'
+#' First calls \code{buildReleaseZips} for given cdmVersions and targetDialects.
+#' This writes the ddl sql files to the ddl folder.
+#' Then zips all written ddl files into a release zip to given output folder.
+#'
+#' If no (or multiple) targetDialect is given,
+#' then one zip is written with the files of all supported dialects.
+#'
+#' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4.
+#'                   Defaults to all supported CDM versions.
+#' @param targetDialect The target dialect. Defaults to all supported dialects.
+#' @param outputfolder The output folder. Defaults to "output"
+#' @return A character string containing the OHDSQL DDL
+#' @export
+#' @examples
+#' buildReleaseZip(cdmVersion='5.3', targetDialect='sql server', outputfolder='.')
+#'
+buildReleaseZip <- function(cdmVersion,
+                            targetDialect = listSupportedDialects(),
+                            outputfolder = "output"){
+  # argument checks
+  stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
+
+  if (!dir.exists(outputfolder)) {
+    dir.create(outputfolder)
+  }
+
+  files <- c()
+  for (dialect in targetDialect) {
+    buildRelease(cdmVersion, dialect)
+    files <- c(files, list.files(file.path('ddl', cdmVersion, gsub(" ", "_", dialect)),
+                                 pattern = ".*\\.sql$",
+                                 full.names = TRUE))
+  }
+
+  if (length(targetDialect) == 1) {
+    zipName <- file.path(outputfolder, paste0("OMOPCDM", "_", gsub(" ", "_", targetDialect), "_", cdmVersion, '.zip'))
+  } else {
+    zipName <- file.path(outputfolder, paste0("OMOPCDM", "_", cdmVersion, '.zip'))
+  }
+
+  DatabaseConnector::createZipFile(zipFile = zipName, files = files)
+}

R/listSupportedVersions.R

@@ -6,3 +6,12 @@ listSupportedVersions <- function() {
   supportedVersions <- c("5.3", "5.4")
   return(supportedVersions)
 }
+
+#' List RDBMS dialects supported by this package
+#'
+#' @export
+
+listSupportedDialects <- function() {
+  supportedDialects <- c("oracle", "postgresql", "pdw", "redshift", "impala", "netezza", "bigquery", "sql server")
+  return(supportedDialects)
+}

extras/codeToRun.R

@@ -22,6 +22,14 @@ for (cdmVersion in supportedVersions) {
   }
 }
 
+#############
+# Zipping release
+# All dialects
+buildReleaseZip(cdmVersion="5.3", outputfolder="output")
+
+# One dialect
+buildReleaseZip(cdmVersion="5.4", targetDialect="postgresql", outputfolder="output")
+
 #############
 # BE SURE TO RUN THE EXTRAS/SITEMAINTENANCE.R BEFORE CREATING THE PDF
 

man/buildRelease.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildRelease.R
+\name{buildRelease}
+\alias{buildRelease}
+\title{Create OMOP CDM SQL files}
+\usage{
+buildRelease(
+  cdmVersion = listSupportedVersions(),
+  targetDialect = listSupportedDialects()
+)
+}
+\arguments{
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4.
+Defaults to all supported CDM versions.}
+
+\item{targetDialect}{The target dialect}
+}
+\description{
+Writes DDL, ForeignKey, PrimaryKey and index SQL files for given cdmVersion
+and targetDialect to the 'ddl' folder in current working directory.
+}

man/buildReleaseZip.Rd

@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/buildRelease.R
+\name{buildReleaseZip}
+\alias{buildReleaseZip}
+\title{Create OMOP CDM release zip}
+\usage{
+buildReleaseZip(
+  cdmVersion,
+  targetDialect = listSupportedDialects(),
+  outputfolder = "output"
+)
+}
+\arguments{
+\item{cdmVersion}{The version of the CDM you are creating, e.g. 5.3, 5.4.
+Defaults to all supported CDM versions.}
+
+\item{targetDialect}{The target dialect. Defaults to all supported dialects.}
+
+\item{outputfolder}{The output folder. Defaults to "output"}
+}
+\value{
+A character string containing the OHDSQL DDL
+}
+\description{
+First calls \code{buildReleaseZips} for given cdmVersions and targetDialects.
+This writes the ddl sql files to the ddl folder.
+Then zips all written ddl files into a release zip to given output folder.
+}
+\details{
+If no (or multiple) targetDialect is given,
+then one zip is written with the files of all supported dialects.
+}
+\examples{
+buildReleaseZip(cdmVersion='5.3', targetDialect='sql server', outputfolder='.')
+
+}

man/createDdl.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/createdDdl.R
+% Please edit documentation in R/createDdl.R
 \name{createDdl}
 \alias{createDdl}
 \alias{createPrimaryKeys}
@@ -30,9 +30,9 @@ Dashboard.
 }
 \section{Functions}{
 \itemize{
-\item \code{createPrimaryKeys}: createPrimaryKeys asdfladsfj
+\item \code{createPrimaryKeys}: createPrimaryKeys Returns a string containing the OHDSQL for creation of primary keys in the OMOP CDM.
 
-\item \code{createForeignKeys}: createForeignKeys asdfladsf
+\item \code{createForeignKeys}: createForeignKeys Returns a string containing the OHDSQL for creation of foreign keys in the OMOP CDM.
 }}
 
 \examples{

man/listSupportedDialects.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/listSupportedVersions.R
+\name{listSupportedDialects}
+\alias{listSupportedDialects}
+\title{List RDBMS dialects supported by this package}
+\usage{
+listSupportedDialects()
+}
+\description{
+List RDBMS dialects supported by this package
+}

man/writeDDL.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/writeDdl.R
+% Please edit documentation in R/writeDDL.R
 \name{writeDdl}
 \alias{writeDdl}
 \alias{writePrimaryKeys}