Merge pull request #437 from OHDSI/v5.4_unittest

Add more unit tests

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 .github/*
+extras/*

.github/workflows/R_CMD_check.yaml

@@ -33,6 +33,18 @@ jobs:
       CDMDDLBASE_POSTGRESQL_PASSWORD: ${{ secrets.CDMDDLBASE_POSTGRESQL_PASSWORD }}
       CDMDDLBASE_POSTGRESQL_SERVER: ${{ secrets.CDMDDLBASE_POSTGRESQL_SERVER }}
       CDMDDLBASE_POSTGRESQL_SCHEMA: ${{ secrets.CDMDDLBASE_POSTGRESQL_SCHEMA }}
+      CDMDDLBASE_REDSHIFT_USER: ${{ secrets.CDMDDLBASE_REDSHIFT_USER }}
+      CDMDDLBASE_REDSHIFT_PASSWORD: ${{ secrets.CDMDDLBASE_REDSHIFT_PASSWORD }}
+      CDMDDLBASE_REDSHIFT_SERVER: ${{ secrets.CDMDDLBASE_REDSHIFT_SERVER }}
+      CDMDDLBASE_REDSHIFT_SCHEMA: ${{ secrets.CDMDDLBASE_REDSHIFT_SCHEMA }}
+      CDMDDLBASE_SQL_SERVER_USER: ${{ secrets.CDMDDLBASE_SQL_SERVER_USER }}
+      CDMDDLBASE_SQL_SERVER_PASSWORD: ${{ secrets.CDMDDLBASE_SQL_SERVER_PASSWORD }}
+      CDMDDLBASE_SQL_SERVER_SERVER: ${{ secrets.CDMDDLBASE_SQL_SERVER_SERVER }}
+      CDMDDLBASE_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_SQL_SERVER_CDM_SCHEMA }}
+      CDMDDLBASE_ORACLE_USER: ${{ secrets.CDMDDLBASE_ORACLE_USER }}
+      CDMDDLBASE_ORACLE_PASSWORD: ${{ secrets.CDMDDLBASE_ORACLE_PASSWORD }}
+      CDMDDLBASE_ORACLE_SERVER: ${{ secrets.CDMDDLBASE_ORACLE_SERVER }}
+      CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }}
 
     steps:
       - uses: actions/checkout@v2

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(buildRelease)
 export(buildReleaseZip)
 export(createDdl)
 export(createForeignKeys)
@@ -13,3 +14,6 @@ export(writeDdl)
 export(writeForeignKeys)
 export(writeIndex)
 export(writePrimaryKeys)
+importFrom(utils,download.file)
+importFrom(utils,read.csv)
+importFrom(utils,write.csv)

R/WikiParser.R

@@ -23,7 +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.
-#'
+#' @importFrom utils write.csv
 #' @export
 parseWiki <- function(mdFilesLocation, output_file) {
   # mdFilesLocation <- "../CommonDataModel.wiki"

R/buildRelease.R

@@ -19,25 +19,36 @@
 #' 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.
+#' @param cdmVersions The versions 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) {
+#' @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.
+#' @export
+buildRelease <- function(cdmVersions = listSupportedVersions(),
+                         targetDialects = listSupportedDialects(),
+                         outputfolder = file.path(getwd(), "inst", "ddl")){
+  basefolder <- outputfolder
+  for (cdmVersion in cdmVersions) {
+    for (targetDialect in targetDialects) {
+      outputfolder <- file.path(basefolder, cdmVersion, gsub(" ", "_", targetDialect))
+
       writeDdl(targetDialect = targetDialect,
-               cdmVersion = cdmVersion)
+               cdmVersion = cdmVersion,
+               outputfolder = outputfolder)
 
       writePrimaryKeys(targetDialect = targetDialect,
-                       cdmVersion = cdmVersion)
+                       cdmVersion = cdmVersion,
+                       outputfolder = outputfolder)
 
       writeForeignKeys(targetDialect = targetDialect,
-                       cdmVersion = cdmVersion)
+                       cdmVersion = cdmVersion,
+                       outputfolder = outputfolder)
 
       writeIndex(targetDialect = targetDialect,
-                 cdmVersion = cdmVersion)
+                 cdmVersion = cdmVersion,
+                 outputfolder = outputfolder)
     }
   }
 }
@@ -62,7 +73,7 @@ buildRelease <- function(cdmVersion = listSupportedVersions(),
 #'
 buildReleaseZip <- function(cdmVersion,
                             targetDialect = listSupportedDialects(),
-                            outputfolder = "output"){
+                            outputfolder = file.path(getwd(), "inst", "ddl")){
   # argument checks
   stopifnot(is.character(cdmVersion), length(cdmVersion) == 1, cdmVersion %in% listSupportedVersions())
 
@@ -72,8 +83,8 @@ buildReleaseZip <- function(cdmVersion,
 
   files <- c()
   for (dialect in targetDialect) {
-    buildRelease(cdmVersion, dialect)
-    files <- c(files, list.files(file.path('ddl', cdmVersion, gsub(" ", "_", dialect)),
+    buildRelease(cdmVersion, dialect, outputfolder = outputfolder)
+    files <- c(files, list.files(file.path(outputfolder, cdmVersion, gsub(" ", "_", dialect)),
                                  pattern = ".*\\.sql$",
                                  full.names = TRUE))
   }

R/createDdl.R

@@ -26,6 +26,7 @@
 #'
 #' @param cdmVersion The version of the CDM you are creating, e.g. 5.3, 5.4
 #' @return A character string containing the OHDSQL DDL
+#' @importFrom utils read.csv
 #' @export
 #' @examples
 #' ddl <- createDdl("5.4")
@@ -138,3 +139,63 @@ createForeignKeys <- function(cdmVersion){
   }
   return(paste0(sql_result, collapse = ""))
 }
+
+
+
+# A helper function that will return a character string with the omop ascii art given a major and minor cdm version
+# example: cat(createAsciiHeader(5, 3))
+createAsciiHeader <- function(major, minor) {
+
+  stopifnot(is.numeric(major), is.numeric(minor), length(major) == 1, length(minor) == 1)
+  stopifnot(major %in% 0:99, minor %in% 0:99)
+
+  # An inner function that returns an ascii art matrix for any number between 0 and 99
+  numberMatrix <- function(num){
+    stopifnot(is.numeric(num), num %in% 0:99)
+
+    # An inner function that returns a 7x7 matrix of number ascii art for the number 0 through 9
+    # for the number 1 a 7x5 matrix is returned because 1 is narrower than other numbers.
+    singleDigit <- function(num) {
+      nums <- c('  ###     #    #####  ##### #      ####### ##### ####### #####  #####  #   #   ##   #     ##     ##    # #      #     ##    # #     ##     ##     # # #         #      ##    # #      #          #  #     ##     ##     #   #    #####  ##### #    # ###### ######    #    #####  #######     #   #   #            ########      ##     #  #    #     #      # #   #    #   #      #     #     # #     ##     #  #    #     ##     #  ###   ##### ####### #####      #  #####  #####   #     #####  ##### ')
+      numsMatrix <- matrix(data = strsplit(nums, character(0))[[1]], nrow = 7, byrow = T)
+      cols <- seq(num*7+1, num*7+7, by = 1)
+      out <- numsMatrix[1:7, cols]
+      # the number 1 is narrower than the other numbers
+      if(num == 1) out<- out[1:7, 2:6]
+      out
+    }
+
+    if(num < 10){
+      return(singleDigit(num))
+    } else {
+      space <- matrix(rep(" ", 7), nrow = 7)
+      return(cbind(singleDigit(floor(num/10)), space, singleDigit(num %% 10)))
+    }
+  }
+
+  omop <- c('.
+  ####### #     # ####### ######      #####  ######  #     #          .
+  #     # ##   ## #     # #     #    #     # #     # ##   ##    #    #.
+  #     # # # # # #     # #     #    #       #     # # # # #    #    #.
+  #     # #  #  # #     # ######     #       #     # #  #  #    #    #.
+  #     # #     # #     # #          #       #     # #     #    #    #.
+  #     # #     # #     # #          #     # #     # #     #     #  # .
+  ####### #     # ####### #           #####  ######  #     #      ##  ')
+
+  # convert to matrix and remove first column
+  omop <- matrix(strsplit(omop, character(0))[[1]], nrow = 7, byrow = TRUE)
+  omop <- omop[,c(-1, -2)]
+
+  dot <- matrix(c(rep(" ", 3*4), rep("#", 3*3)), nrow = 7, byrow = TRUE)
+  space <- matrix(rep(" ", 7), nrow = 7)
+  newline <- matrix(rep("\n", 7, nrow = 7))
+
+
+  header <- character(0)
+  headerMatrix <- cbind(omop, space, numberMatrix(major), space, dot, space, numberMatrix(minor), newline)
+  for(i in 1:7) {
+    header <- c(header, as.character(headerMatrix[i,]))
+  }
+  header <- paste(header, collapse = "")
+  return(header)
+}

R/downloadCurrentDdl.R

@@ -14,7 +14,7 @@
 #' downloadCurrentDdl("OHDSI/CommonDataModel",
 #'  pathToCsv="Sql%20Server/OMOP%20CDM%20sql%20server%20ddl.txt")
 #' }
-#'
+#' @importFrom utils download.file
 #' @export
 
 downloadCurrentDdl <- function(githubPath="OHDSI/CommonDataModel",

R/executeDdl.R

@@ -42,16 +42,16 @@ executeDdl <- function(connectionDetails,
                        executeForeignKey = TRUE,
                        ...) {
 
-  outputpath <- tempdir(check = TRUE)
+  outputfolder <- tempdir(check = TRUE)
 
 
   if(executeDdl) {
     filename <- writeDdl(targetDialect = connectionDetails$dbms,
                          cdmVersion = cdmVersion,
                          cdmDatabaseSchema = cdmDatabaseSchema,
-                         outputpath = outputpath)
+                         outputfolder = outputfolder)
 
-    sql <- readr::read_file(file.path(outputpath, filename))
+    sql <- readr::read_file(file.path(outputfolder, filename))
   } else {
     sql <- ""
   }
@@ -60,18 +60,18 @@ executeDdl <- function(connectionDetails,
     filename <- writePrimaryKeys(targetDialect = connectionDetails$dbms,
                                  cdmVersion = cdmVersion,
                                  cdmDatabaseSchema = cdmDatabaseSchema,
-                                 outputpath = outputpath)
+                                 outputfolder = outputfolder)
 
-    sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n")
+    sql <- paste(sql, readr::read_file(file.path(outputfolder, filename)), sep = "\n")
   }
 
   if(executeForeignKey) {
     filename <- writeForeignKeys(targetDialect = connectionDetails$dbms,
                                  cdmVersion = cdmVersion,
                                  cdmDatabaseSchema = cdmDatabaseSchema,
-                                 outputpath = outputpath)
+                                 outputfolder = outputfolder)
 
-    sql <- paste(sql, readr::read_file(file.path(outputpath, filename)), sep = "\n")
+    sql <- paste(sql, readr::read_file(file.path(outputfolder, filename)), sep = "\n")
   }
 
   con <- DatabaseConnector::connect(connectionDetails = connectionDetails)

R/listSupportedVersions.R

@@ -1,7 +1,7 @@
 #' List CDM versions supported by this package
 #'
+#' @return A character vector containing the support CDM versions in {major}.{minor} format.
 #' @export
-
 listSupportedVersions <- function() {
   supportedVersions <- c("5.3", "5.4")
   return(supportedVersions)

R/writeDDL.R

@@ -22,102 +22,102 @@
 #'
 #' @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 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.
 #'                          Defaults to "@cdmDatabaseSchema"
 #'
 #' @export
-writeDdl <- function(targetDialect, cdmVersion, outputpath, cdmDatabaseSchema = "@cdmDatabaseSchema") {
+writeDdl <- function(targetDialect, cdmVersion, outputfolder, 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(missing(outputfolder)) {
+    outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
   }
 
-  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+  if(!dir.exists(outputfolder)) dir.create(outputfolder, showWarnings = FALSE, recursive = TRUE)
 
   sql <- createDdl(cdmVersion)
   sql <- SqlRender::render(sql = sql, cdmDatabaseSchema = cdmDatabaseSchema, targetDialect = targetDialect)
   sql <- SqlRender::translate(sql, targetDialect = targetDialect)
 
   filename <- paste("OMOPCDM", gsub(" ", "_", targetDialect), cdmVersion, "ddl.sql", sep = "_")
-  SqlRender::writeSql(sql = sql, targetFile = file.path(outputpath, filename))
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, 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") {
+writePrimaryKeys <- function(targetDialect, cdmVersion, outputfolder, 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(missing(outputfolder)) {
+    outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
   }
 
-  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+  if(!dir.exists(outputfolder)) dir.create(outputfolder, 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))
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, 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") {
+writeForeignKeys <- function(targetDialect, cdmVersion, outputfolder, 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(missing(outputfolder)) {
+    outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
   }
 
-  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+  if(!dir.exists(outputfolder)) dir.create(outputfolder, 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))
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, 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") {
+writeIndex <- function(targetDialect, cdmVersion, outputfolder, 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(missing(outputfolder)) {
+    outputfolder <- file.path("ddl", cdmVersion, gsub(" ", "_", targetDialect))
   }
 
-  if(!dir.exists(outputpath)) dir.create(outputpath, showWarnings = FALSE, recursive = TRUE)
+  if(!dir.exists(outputfolder)) dir.create(outputfolder, 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))
+  SqlRender::writeSql(sql = sql, targetFile = file.path(outputfolder, filename))
   invisible(filename)
 }