diff --git a/.github/workflows/R_CMD_check.yaml b/.github/workflows/R_CMD_check.yaml index 4773511..d165a48 100644 --- a/.github/workflows/R_CMD_check.yaml +++ b/.github/workflows/R_CMD_check.yaml @@ -47,6 +47,11 @@ jobs: CDMDDLBASE_ORACLE_PASSWORD: ${{ secrets.CDMDDLBASE_ORACLE_PASSWORD }} CDMDDLBASE_ORACLE_SERVER: ${{ secrets.CDMDDLBASE_ORACLE_SERVER }} CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }} + CDM_IRIS_CONNECTION_STRING: ${{ secrets.CDM_IRIS_CONNECTION_STRING }} + CDM_IRIS_USER: ${{ secrets.CDM_IRIS_USER }} + CDM_IRIS_PASSWORD: ${{ secrets.CDM_IRIS_PASSWORD }} + CDM_IRIS_CDM_SCHEMA: ${{ secrets.CDM_IRIS_CDM_SCHEMA }} + CDM_IRIS_OHDSI_SCHEMA: ${{ secrets.CDM_IRIS_OHDSI_SCHEMA }} steps: - uses: actions/checkout@v4 @@ -67,7 +72,7 @@ jobs: - name: Cache R packages if: runner.os != 'Windows' - uses: actions/cache@v3.3.1 + uses: actions/cache@v4 with: path: ${{ env.R_LIBS_USER }} key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} @@ -127,4 +132,3 @@ jobs: if: runner.os == 'macOS' run: covr::codecov() shell: Rscript {0} - diff --git a/CommonDataModel.Rproj b/CommonDataModel.Rproj index ce013e1..dad992d 100644 --- a/CommonDataModel.Rproj +++ b/CommonDataModel.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 54514637-59b4-4d43-83cf-67c54a4f8941 RestoreWorkspace: Default SaveWorkspace: Default diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 59c953b..cb4e307 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,4 +1,4 @@ -testDatabases <- c("postgresql") +testDatabases <- c("postgres","iris") if (Sys.getenv("CDM5_POSTGRESQL_SERVER") != "") { library(DatabaseConnector) @@ -57,9 +57,9 @@ getConnectionDetails <- function(dbms) { ), "iris" = createConnectionDetails( dbms = "iris", - user = Sys.getenv("CDMDDLBASE_IRIS_USER"), - password = Sys.getenv("CDMDDLBASE_IRIS_PASSWORD"), - connectionString = Sys.getenv("CDMDDLBASE_IRIS_URL"), + user = Sys.getenv("CDM_IRIS_USER"), + password = Sys.getenv("CDM_IRIS_PASSWORD"), + connectionString = Sys.getenv("CDM_IRIS_CONNECTION_STRING"), pathToDriver = jdbcDriverFolder ) ) @@ -72,7 +72,7 @@ getSchema <- function(dbms) { "redshift" = Sys.getenv("CDMDDLBASE_REDSHIFT_SCHEMA"), "sql server" = Sys.getenv("CDMDDLBASE_SQL_SERVER_CDM_SCHEMA"), "oracle" = Sys.getenv("CDMDDLBASE_ORACLE_CDM_SCHEMA"), - "iris" = Sys.getenv("CDMDDLBASE_IRIS_CDM_SCHEMA") + "iris" = Sys.getenv("CDM_IRIS_CDM_SCHEMA") ) } @@ -82,7 +82,7 @@ listTablesInSchema <- function(connectionDetails, schema) { class(schema) == "character", length(schema) == 1 ) - stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle", "iris")) + stopifnot(connectionDetails$dbms %in% testDatabases) con <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(con)) dbms <- connectionDetails$dbms @@ -114,7 +114,7 @@ dropAllTablesFromSchema <- function(connectionDetails, schema) { class(schema) == "character", length(schema) == 1 ) - stopifnot(connectionDetails$dbms %in% c("postgresql", "redshift", "sql server", "oracle", "iris")) + stopifnot(connectionDetails$dbms %in% testDatabases) tableNames <- listTablesInSchema(connectionDetails, schema) con <- DatabaseConnector::connect(connectionDetails)