From 1bcb2236e890854173aebf1ea498998eeaadd5a2 Mon Sep 17 00:00:00 2001 From: Frank DeFalco Date: Thu, 7 Sep 2023 13:52:20 -0400 Subject: [PATCH] resolved issues with CHECK and tests. --- .Rbuildignore | 2 + DESCRIPTION | 3 +- LICENSE | 201 ------------------------------- R/buildRelease.R | 3 +- R/createDdl.R | 8 ++ R/executeDdl.R | 2 +- R/utils.R | 8 ++ extras/testthat.R | 45 ++++--- man/buildReleaseZip.Rd | 3 +- man/createDdl.Rd | 2 + tests/testthat/setup.R | 52 +++----- tests/testthat/test-executeDdl.R | 8 +- 12 files changed, 76 insertions(+), 261 deletions(-) delete mode 100644 LICENSE create mode 100644 R/utils.R diff --git a/.Rbuildignore b/.Rbuildignore index 070fca2..2ad0a0c 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -3,3 +3,5 @@ ^LICENSE\.md$ .github/* extras/* +docs/* +rmd/* diff --git a/DESCRIPTION b/DESCRIPTION index ea98f9a..4aa0591 100644 --- a/DESCRIPTION +++ b/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 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, diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 261eeb9..0000000 --- a/LICENSE +++ /dev/null @@ -1,201 +0,0 @@ - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. 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We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - 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. diff --git a/R/buildRelease.R b/R/buildRelease.R index 4c3dbd1..733e106 100644 --- a/R/buildRelease.R +++ b/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")){ diff --git a/R/createDdl.R b/R/createDdl.R index 06bbca6..018b73a 100644 --- a/R/createDdl.R +++ b/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()) diff --git a/R/executeDdl.R b/R/executeDdl.R index 3c1d3ff..98fad37 100644 --- a/R/executeDdl.R +++ b/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) } diff --git a/R/utils.R b/R/utils.R new file mode 100644 index 0000000..213b47f --- /dev/null +++ b/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 +} diff --git a/extras/testthat.R b/extras/testthat.R index 0d8ff7e..01e7f34 100644 --- a/extras/testthat.R +++ b/extras/testthat.R @@ -14,7 +14,8 @@ sql <- SqlRender::readSql(paste0("output/oracle/OMOP CDM oracle ", cdmVersion," DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run oracle primary keys @@ -22,7 +23,8 @@ sql <- SqlRender::readSql(paste0("output/oracle/OMOP CDM oracle ", cdmVersion," DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run oracle constraints @@ -30,7 +32,8 @@ sql <- SqlRender::readSql(paste0("output/oracle/OMOP CDM oracle ", cdmVersion," DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run oracle indices @@ -38,7 +41,8 @@ sql <- SqlRender::readSql(paste0("output/oracle/OMOP CDM oracle ", cdmVersion," DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Remove oracle tables @@ -46,7 +50,8 @@ sql <- SqlRender::readSql(paste0("output/oracle/oracle testCleanUp ", "v5_3_1"," DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) @@ -67,7 +72,8 @@ sql <- SqlRender::readSql(paste0("output/postgresql/OMOP CDM postgresql ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run postgres primary keys @@ -75,7 +81,8 @@ sql <- SqlRender::readSql(paste0("output/postgresql/OMOP CDM postgresql", cdmVer DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run postgres constraints @@ -83,7 +90,8 @@ sql <- SqlRender::readSql(paste0("output/postgresql/OMOP CDM postgresql ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run postgres indices @@ -91,7 +99,8 @@ sql <- SqlRender::readSql(paste0("output/postgresql/OMOP CDM postgresql ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Remove postgres tables @@ -99,7 +108,8 @@ sql <- SqlRender::readSql(paste0("output/postgresql/postgresql testCleanUp ", "v DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) @@ -119,7 +129,8 @@ sql <- SqlRender::readSql(paste0("output/sql server/OMOP CDM sql server ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run sql server primary keys and indices @@ -127,7 +138,8 @@ sql <- SqlRender::readSql(paste0("output/sql server/OMOP CDM sql server ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run sql server constraints @@ -135,7 +147,8 @@ sql <- SqlRender::readSql(paste0("output/sql server/OMOP CDM sql server ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Run sql server indices @@ -143,7 +156,8 @@ sql <- SqlRender::readSql(paste0("output/sql server/OMOP CDM sql server ", cdmVe DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) ## Remove sql server tables @@ -151,7 +165,8 @@ sql <- SqlRender::readSql(paste0("output/sql server/sql server testCleanUp ", "v DatabaseConnector::executeSql(connection = conn, sql = sql, - progressBar = TRUE + progressBar = FALSE, + reportOverallTime = FALSE ) diff --git a/man/buildReleaseZip.Rd b/man/buildReleaseZip.Rd index 61ae6ea..7489f45 100644 --- a/man/buildReleaseZip.Rd +++ b/man/buildReleaseZip.Rd @@ -31,6 +31,7 @@ If no (or multiple) targetDialect is given, then one zip is written with the files of all supported dialects. } \examples{ +\dontrun{ buildReleaseZip(cdmVersion='5.3', targetDialect='sql server', outputfolder='.') - +} } diff --git a/man/createDdl.Rd b/man/createDdl.Rd index dfd8612..b7866fa 100644 --- a/man/createDdl.Rd +++ b/man/createDdl.Rd @@ -36,7 +36,9 @@ Dashboard. }} \examples{ +\dontrun{ ddl <- createDdl("5.4") pk <- createPrimaryKeys("5.4") fk <- createForeignKeys("5.4") } +} diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 60ea953..85be35e 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,15 +1,15 @@ # Download the JDBC drivers used in the tests library(DatabaseConnector) -driverPath <- file.path(Sys.getenv("HOME"), "drivers") -if(!dir.exists(driverPath)) dir.create(driverPath) - -if(Sys.getenv("LOCAL_TEST") != "TRUE") { +if (is.na(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))) { + driverPath <- tempdir() cat("\ndownloading drivers\n") downloadJdbcDrivers("redshift", pathToDriver = driverPath) downloadJdbcDrivers("postgresql", pathToDriver = driverPath) downloadJdbcDrivers("oracle", pathToDriver = driverPath) downloadJdbcDrivers("sql server", pathToDriver = driverPath) +} else { + driverPath <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER") } # Helper functions used in tests ----------------------------------------------- @@ -20,28 +20,28 @@ getConnectionDetails <- function(dbms) { 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") + pathToDriver = driverPath ), "redshift" = createConnectionDetails( dbms = "redshift", user = Sys.getenv("CDMDDLBASE_REDSHIFT_USER"), password = Sys.getenv("CDMDDLBASE_REDSHIFT_PASSWORD"), server = Sys.getenv("CDMDDLBASE_REDSHIFT_SERVER"), - pathToDriver = file.path(Sys.getenv("HOME"), "drivers") + pathToDriver = driverPath ), "sql server" = createConnectionDetails( dbms = "sql server", user = Sys.getenv("CDMDDLBASE_SQL_SERVER_USER"), password = Sys.getenv("CDMDDLBASE_SQL_SERVER_PASSWORD"), server = Sys.getenv("CDMDDLBASE_SQL_SERVER_SERVER"), - pathToDriver = file.path(Sys.getenv("HOME"), "drivers") + pathToDriver = driverPath ), "oracle" = createConnectionDetails( dbms = "oracle", user = Sys.getenv("CDMDDLBASE_ORACLE_USER"), password = Sys.getenv("CDMDDLBASE_ORACLE_PASSWORD"), server = Sys.getenv("CDMDDLBASE_ORACLE_SERVER"), - pathToDriver = file.path(Sys.getenv("HOME"), "drivers") + pathToDriver = driverPath ) ) } @@ -56,7 +56,7 @@ getSchema <- function(dbms) { } listTablesInSchema <- function(connectionDetails, schema) { - stopifnot(class(connectionDetails) == "connectionDetails", class(schema) == "character", length(schema) == 1) + stopifnot("ConnectionDetails" %in% class(connectionDetails), class(schema) == "character", length(schema) == 1) stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle")) con <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(con)) @@ -71,43 +71,21 @@ listTablesInSchema <- function(connectionDetails, schema) { } dropAllTablesFromSchema <- function(connectionDetails, schema) { - stopifnot(class(connectionDetails) == "connectionDetails", class(schema) == "character", length(schema) == 1) + stopifnot("ConnectionDetails" %in% class(connectionDetails), class(schema) == "character", length(schema) == 1) stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle")) - tables <- listTablesInSchema(connectionDetails, schema) + tableNames <- listTablesInSchema(connectionDetails, schema) con <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(con)) dbms <- connectionDetails$dbms if(dbms %in% c("redshift", "postgresql", "sql server")) { - for(table in tables) { - DBI::dbRemoveTable(con, name = DBI::SQL(paste(schema, table, sep = "."))) + for(tableName in tableNames) { + DBI::dbExecute(con, paste("DROP TABLE IF EXISTS",paste(schema, tableName, sep = "."),"CASCADE")) } } else if(dbms == "oracle") { - for(table in tables) { - DBI::dbRemoveTable(con, name = table) + for(tableName in tableNames) { + DBI::dbExecute(con, paste("DROP TABLE IF EXISTS",tableName,"CASCADE")) } } } - -# .removeConstraintsPostgresql <- function(connectionDetails, schema) { -# # the order of removal of constraints matters! -# con <- DatabaseConnector::connect(connectionDetails) -# constraints <- DBI::dbGetQuery(con, -# "SELECT con.conname, rel.relname as relname -# FROM pg_catalog.pg_constraint con -# INNER JOIN pg_catalog.pg_class rel -# ON rel.oid = con.conrelid -# INNER JOIN pg_catalog.pg_namespace nsp -# ON nsp.oid = connamespace -# WHERE nsp.nspname = 'cdmddlbase';") -# -# -# constraints <- dplyr::mutate(constraints, sql = paste0("alter table ", schema, ".", relname, " drop constraint if exists ", conname, ";\n" )) -# -# sql <- paste(rev(constraints$sql), collapse = "") -# executeSql(con, sql) -# -# disconnect(con) -# -# } diff --git a/tests/testthat/test-executeDdl.R b/tests/testthat/test-executeDdl.R index 4f77cb2..30f0fe6 100644 --- a/tests/testthat/test-executeDdl.R +++ b/tests/testthat/test-executeDdl.R @@ -1,12 +1,14 @@ # To run tests for one dbms and one cdmVersion use the variables below -# dbms <- "postgresql"; cdmVersion <- "5.4" +dbms <- "postgresql" +cdmVersion <- "5.4" +testDatabases <- c(dbms) -testDatabases <- c("oracle", "postgresql", "sql server", "redshift") +# testDatabases <- c("oracle", "postgresql", "sql server", "redshift") # testDatabases <- c("redshift") test_that("getConnectionDetails works", { for(dbms in testDatabases) { - expect_s3_class(getConnectionDetails(dbms), "connectionDetails") + expect_s3_class(getConnectionDetails(dbms), "ConnectionDetails") } })