Remove PL for module install; test RS on Ubuntu

OHDSI · Dec 19, 2023 · 4805086 · 4805086
1 parent 28bacf4
commit 4805086
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diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
@@ -20,12 +20,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          #- {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          #- {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
+          #- {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           #- {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          #- {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}

diff --git a/R/ModuleInstantiation.R b/R/ModuleInstantiation.R
@@ -418,12 +418,6 @@ instantiateModule <- function(module, version, remoteRepo, remoteUsername, modul
 
   withModuleRenv(
     code = {
-      ParallelLogger::addDefaultFileLogger(
-        fileName = file.path(moduleFolder, "moduleInitLog.txt")
-      )
-      ParallelLogger::addDefaultErrorReportLogger(
-        fileName = file.path(moduleFolder, "moduleInitErrorReport.txt")
-      )
       renv::restore(prompt = FALSE)
     },
     moduleFolder = moduleFolder,

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -76,102 +76,102 @@ connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
   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")
+# # 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 = "redshift",
-#       user = Sys.getenv("CDM5_REDSHIFT_USER"),
-#       password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
-#       server = Sys.getenv("CDM5_REDSHIFT_SERVER"),
-#       port = 5439,
+#       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_REDSHIFT_CDM_SCHEMA"),
-#     workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
-#     vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
+#     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")
+#   )
+# }
 
-# 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")
+# 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 = "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,
+      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_SQL_SERVER_CDM_SCHEMA"),
-    workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
-    vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
+    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
 keyringName <- "strategus"