Bump renv and module refs; only test on SQLite for now

OHDSI · Aug 16, 2023 · c993b7a · c993b7a
1 parent bc58d17
commit c993b7a
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Showing 9 changed files with 39 additions and 28 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.0.7
-Date: 2023-05-01
+Version: 0.1.0
+Date: 2023-08-15
 Authors@R: c(
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
 	person("Anthony", "Sena", email = "[email protected]", role = c("aut")),
@@ -15,12 +15,12 @@ License: Apache License 2.0
 URL: https://ohdsi.github.io/Strategus, https://github.com/OHDSI/Strategus
 BugReports: https://github.com/OHDSI/Strategus/issues
 Depends:
-	R (>= 4.0.0),
-	CohortGenerator (>= 0.7.0),
-	DatabaseConnector (>= 5.1.0)
+	R (>= 4.2.3),
+	CohortGenerator (>= 0.8.0),
+	DatabaseConnector (>= 6.2.3)
 Imports:
   targets,
-  renv (>= 0.15.5),
+  renv (>= 1.0.0),
   ParallelLogger (>= 3.1.0),
   dplyr,
   checkmate,

diff --git a/R/ModuleEnv.R b/R/ModuleEnv.R
@@ -71,6 +71,11 @@ withModuleRenv <- function(code,
     script <- c(sprintf("library(Strategus, lib.loc = '%s')", libPath),
                 script)
     # Adding Strategus dependencies to the script
+    libPath <- file.path(find.package("R6"), "../")
+    script <- c(
+      sprintf("library(R6, lib.loc = '%s')", libPath),
+      script
+    )
     libPath <- file.path(find.package("CohortGenerator"), "../")
     script <- c(sprintf("library(CohortGenerator, lib.loc = '%s')", libPath),
                 script)

diff --git a/R/ModuleInstantiation.R b/R/ModuleInstantiation.R
@@ -193,13 +193,14 @@ instantiateModule <- function(module, version, remoteRepo, remoteUsername, modul
 
   script <- paste(
     c(
-      "renv::install(c('ParallelLogger', 'keyring'), prompt = FALSE)",
-      sprintf("ParallelLogger::addDefaultFileLogger(file.path('%s', 'moduleInitLog.txt'))", moduleFolder),
-      sprintf("ParallelLogger::addDefaultErrorReportLogger(fileName = file.path('%s', 'moduleInitErrorReport.txt'))", moduleFolder),
+      #"renv::install(c('ParallelLogger', 'keyring'), prompt = FALSE)",
+      #sprintf("ParallelLogger::addDefaultFileLogger(file.path('%s', 'moduleInitLog.txt'))", moduleFolder),
+      #sprintf("ParallelLogger::addDefaultErrorReportLogger(fileName = file.path('%s', 'moduleInitErrorReport.txt'))", moduleFolder),
       "renv::restore(prompt = FALSE)"
      ),
     collapse = "\n"
   )
+  print(paste0("DEBUG: ", script))
   tempScriptFile <- tempfile(fileext = ".R")
   fileConn <- file(tempScriptFile)
   writeLines(script, fileConn)

diff --git a/inst/testdata/analysisSpecification.json b/inst/testdata/analysisSpecification.json
@@ -223,7 +223,7 @@
   "moduleSpecifications": [
     {
       "module": "CohortGeneratorModule",
-      "version": "0.1.1-1",
+      "version": "0.2.0-2",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -234,7 +234,7 @@
     },
     {
       "module": "CohortDiagnosticsModule",
-      "version": "0.0.7",
+      "version": "0.1.0-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -292,7 +292,7 @@
     },
     {
       "module": "CohortIncidenceModule",
-      "version": "0.0.6",
+      "version": "0.1.0-2",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -365,7 +365,7 @@
     },
     {
       "module": "CharacterizationModule",
-      "version": "0.3.2",
+      "version": "0.4.0-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -489,7 +489,7 @@
     },
     {
       "module": "CohortMethodModule",
-      "version": "0.1.0",
+      "version": "0.2.0-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -1341,7 +1341,7 @@
     },
     {
       "module": "SelfControlledCaseSeriesModule",
-      "version": "0.1.3",
+      "version": "0.2.0-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {
@@ -2360,7 +2360,7 @@
     },
     {
       "module": "PatientLevelPredictionModule",
-      "version": "0.1.0",
+      "version": "0.2.0-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": [

diff --git a/man/createResultDataModels.Rd b/man/createResultDataModels.Rd
diff --git a/tests/testPostgres.R b/tests/testPostgres.R
@@ -1,3 +1,3 @@
-library(testthat)
-options(dbms = "postgresql")
-test_check("Strategus")
+# library(testthat)
+# options(dbms = "postgresql")
+# test_check("Strategus")
diff --git a/tests/testRedshift.R b/tests/testRedshift.R
@@ -1,3 +1,3 @@
-library(testthat)
-options(dbms = "redshift")
-test_check("Strategus")
+# library(testthat)
+# options(dbms = "redshift")
+# test_check("Strategus")
diff --git a/tests/testSqlServer.R b/tests/testSqlServer.R
@@ -1,3 +1,3 @@
-library(testthat)
-options(dbms = "sql server")
-test_check("Strategus")
+# library(testthat)
+# options(dbms = "sql server")
+# test_check("Strategus")
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -34,11 +34,12 @@ if (dir.exists(Sys.getenv("DATABASECONNECTOR_JAR_FOLDER"))) {
 tableSuffix <- paste0(substr(.Platform$OS.type, 1, 3), format(Sys.time(), "%y%m%d%H%M%S"), sample(1:100, 1))
 tableSuffix <- abs(digest::digest2int(tableSuffix))
 
-tempDir <- tempfile() # "C:/temp"
+tempDir <- tempfile() #"C:/temp"
 tempDir <- gsub("\\\\", "/", tempDir) # Correct windows path
 renvCachePath <- file.path(tempDir, "strategus/renv")
 moduleFolder <- file.path(tempDir, "strategus/modules")
-Sys.setenv("INSTANTIATED_MODULES_FOLDER" = moduleFolder)
+#Sys.setenv("INSTANTIATED_MODULES_FOLDER" = moduleFolder)
+print(paste0("DEBUG: ", Sys.getenv("INSTANTIATED_MODULES_FOLDER")))
 withr::defer(
   {
     unlink(c(tempDir, renvCachePath, moduleFolder), recursive = TRUE, force = TRUE)