Only run execution test on Eunomia

OHDSI · Jan 16, 2024 · b6b6bb6 · b6b6bb6
1 parent 90bb5e4
commit b6b6bb6
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Showing 4 changed files with 453 additions and 453 deletions.
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -79,102 +79,102 @@ connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
   cohortTable = "cohort",
   tempEmulationSchema = NULL
 )
-
-# PostgreSQL
-if (!(Sys.getenv("CDM5_POSTGRESQL_USER") == "" &
-  Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" &
-  Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" &
-  Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" &
-  Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "")) {
-  DatabaseConnector::downloadJdbcDrivers("postgresql")
-  connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
-    connectionDetails = DatabaseConnector::createConnectionDetails(
-      dbms = "postgresql",
-      user = Sys.getenv("CDM5_POSTGRESQL_USER"),
-      password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
-      server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
-      port = 5432,
-      pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
-    ),
-    cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
-    workDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
-    vocabularyDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
-    cohortTable = "cohort",
-    tempEmulationSchema = NULL
-  )
-}
-
-# Oracle
-if (!(Sys.getenv("CDM5_ORACLE_USER") == "" &
-  Sys.getenv("CDM5_ORACLE_PASSWORD") == "" &
-  Sys.getenv("CDM5_ORACLE_SERVER") == "" &
-  Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" &
-  Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "")) {
-  DatabaseConnector::downloadJdbcDrivers("oracle")
-  connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
-    connectionDetails = DatabaseConnector::createConnectionDetails(
-      dbms = "oracle",
-      user = Sys.getenv("CDM5_ORACLE_USER"),
-      password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
-      server = Sys.getenv("CDM5_ORACLE_SERVER"),
-      port = 1521,
-      pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
-    ),
-    cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
-    workDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
-    vocabularyDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
-    cohortTable = "cohort",
-    tempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA")
-  )
-}
-
-# RedShift
-if (!(Sys.getenv("CDM5_REDSHIFT_USER") == "" &
-  Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" &
-  Sys.getenv("CDM5_REDSHIFT_SERVER") == "" &
-  Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" &
-  Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")) {
-  DatabaseConnector::downloadJdbcDrivers("redshift")
-  connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
-    connectionDetails = DatabaseConnector::createConnectionDetails(
-      dbms = "redshift",
-      user = Sys.getenv("CDM5_REDSHIFT_USER"),
-      password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
-      server = Sys.getenv("CDM5_REDSHIFT_SERVER"),
-      port = 5439,
-      pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
-    ),
-    cdmDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
-    workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
-    vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
-    cohortTable = "cohort",
-    tempEmulationSchema = NULL
-  )
-}
-
-# SQL Server
-if (!(Sys.getenv("CDM5_SQL_SERVER_USER") == "" &
-  Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" &
-  Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" &
-  Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" &
-  Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "")) {
-  DatabaseConnector::downloadJdbcDrivers("sql server")
-  connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
-    connectionDetails = DatabaseConnector::createConnectionDetails(
-      dbms = "sql server",
-      user = Sys.getenv("CDM5_SQL_SERVER_USER"),
-      password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
-      server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
-      port = 1433,
-      pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
-    ),
-    cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
-    workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
-    vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
-    cohortTable = "cohort",
-    tempEmulationSchema = NULL
-  )
-}
+#
+# # PostgreSQL
+# if (!(Sys.getenv("CDM5_POSTGRESQL_USER") == "" &
+#   Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" &
+#   Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" &
+#   Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" &
+#   Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "")) {
+#   DatabaseConnector::downloadJdbcDrivers("postgresql")
+#   connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
+#     connectionDetails = DatabaseConnector::createConnectionDetails(
+#       dbms = "postgresql",
+#       user = Sys.getenv("CDM5_POSTGRESQL_USER"),
+#       password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
+#       server = Sys.getenv("CDM5_POSTGRESQL_SERVER"),
+#       port = 5432,
+#       pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
+#     ),
+#     cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
+#     workDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
+#     vocabularyDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
+#     cohortTable = "cohort",
+#     tempEmulationSchema = NULL
+#   )
+# }
+#
+# # Oracle
+# if (!(Sys.getenv("CDM5_ORACLE_USER") == "" &
+#   Sys.getenv("CDM5_ORACLE_PASSWORD") == "" &
+#   Sys.getenv("CDM5_ORACLE_SERVER") == "" &
+#   Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" &
+#   Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "")) {
+#   DatabaseConnector::downloadJdbcDrivers("oracle")
+#   connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
+#     connectionDetails = DatabaseConnector::createConnectionDetails(
+#       dbms = "oracle",
+#       user = Sys.getenv("CDM5_ORACLE_USER"),
+#       password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
+#       server = Sys.getenv("CDM5_ORACLE_SERVER"),
+#       port = 1521,
+#       pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
+#     ),
+#     cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
+#     workDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
+#     vocabularyDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
+#     cohortTable = "cohort",
+#     tempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA")
+#   )
+# }
+#
+# # RedShift
+# if (!(Sys.getenv("CDM5_REDSHIFT_USER") == "" &
+#   Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" &
+#   Sys.getenv("CDM5_REDSHIFT_SERVER") == "" &
+#   Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" &
+#   Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "")) {
+#   DatabaseConnector::downloadJdbcDrivers("redshift")
+#   connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
+#     connectionDetails = DatabaseConnector::createConnectionDetails(
+#       dbms = "redshift",
+#       user = Sys.getenv("CDM5_REDSHIFT_USER"),
+#       password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
+#       server = Sys.getenv("CDM5_REDSHIFT_SERVER"),
+#       port = 5439,
+#       pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
+#     ),
+#     cdmDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
+#     workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
+#     vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
+#     cohortTable = "cohort",
+#     tempEmulationSchema = NULL
+#   )
+# }
+#
+# # SQL Server
+# if (!(Sys.getenv("CDM5_SQL_SERVER_USER") == "" &
+#   Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" &
+#   Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" &
+#   Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" &
+#   Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "")) {
+#   DatabaseConnector::downloadJdbcDrivers("sql server")
+#   connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
+#     connectionDetails = DatabaseConnector::createConnectionDetails(
+#       dbms = "sql server",
+#       user = Sys.getenv("CDM5_SQL_SERVER_USER"),
+#       password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),
+#       server = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
+#       port = 1433,
+#       pathToDriver = Sys.getenv("DATABASECONNECTOR_JAR_FOLDER")
+#     ),
+#     cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
+#     workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
+#     vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
+#     cohortTable = "cohort",
+#     tempEmulationSchema = NULL
+#   )
+# }
 
 # Keyring helpers --------------
 # Set the keyring name & password for testing