add testthat tests on IRIS

.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}
-

CommonDataModel.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 54514637-59b4-4d43-83cf-67c54a4f8941
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

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)