Create .zip with test module for testing

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,8 +20,8 @@ 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: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}

R/ModuleInstantiation.R

@@ -144,44 +144,33 @@ instantiateModule <- function(module, version, remoteRepo, remoteUsername, modul
   dir.create(moduleFolder)
   success <- FALSE
   on.exit(if (!success) unlink(moduleFolder, recursive = TRUE))
+  moduleFile <- file.path(moduleFolder, sprintf("%s_%s.zip", module, version))
   if (module == "TestModule1") {
-    # For test purposes only: get module from extras folder
-    files <- list.files(
-      system.file(
-        "testdata/TestModules/TestModule1",
-        package = "Strategus"
+    # For unit testing purposes only: get module from inst/testdata folder
+    file.copy(
+      from = system.file(
+        file.path("testdata", basename(moduleFile)),
+        package = utils::packageName()
       ),
-      full.names = TRUE,
-      include.dirs = TRUE,
-      all.files = TRUE
+      to = moduleFolder
     )
-    files <- c(files, list.files("extras/TestModules/TestModule1/renv", full.names = TRUE, include.dirs = FALSE, all.files = TRUE))
-    print(paste0("DEBUG 1: ", files))
-    #files <- files[!grepl("extras/TestModules/TestModule1/renv/library", files)]
-    files <- files[!grepl("\\.$", files)]
-    files <- files[!grepl(".Rhistory$", files)]
-    print(paste0("DEBUG 2: ", files))
-    file.copy(files, moduleFolder, recursive = TRUE)
-    #dir.create(file.path(moduleFolder, "renv"))
-    #file.copy("extras/TestModules/TestModule1/renv/activate.R", file.path(moduleFolder, "renv"), recursive = TRUE)
   } else {
-    moduleFile <- file.path(moduleFolder, sprintf("%s_%s.zip", module, version))
     moduleUrl <- sprintf("https://%s/%s/%s/archive/refs/tags/v%s.zip", remoteRepo, remoteUsername, module, version)
     utils::download.file(url = moduleUrl, destfile = moduleFile)
-    utils::unzip(zipfile = moduleFile, exdir = moduleFolder)
-    unlink(moduleFile)
-    # At this point, the unzipped folders will likely exist in a sub folder.
-    # Move all files from that sub folder to the main module folder
-    subFolders <- list.dirs(path = moduleFolder, recursive = FALSE)
-    if (length(subFolders) > 0) {
-      for (i in 1:length(subFolders)) {
-        R.utils::copyDirectory(
-          from = subFolders[i],
-          to = moduleFolder,
-          recursive = TRUE
-        )
-        unlink(subFolders[i], recursive = TRUE)
-      }
+  }
+  utils::unzip(zipfile = moduleFile, exdir = moduleFolder)
+  unlink(moduleFile)
+  # At this point, the unzipped folders will likely exist in a sub folder.
+  # Move all files from that sub folder to the main module folder
+  subFolders <- list.dirs(path = moduleFolder, recursive = FALSE)
+  if (length(subFolders) > 0) {
+    for (i in 1:length(subFolders)) {
+      R.utils::copyDirectory(
+        from = subFolders[i],
+        to = moduleFolder,
+        recursive = TRUE
+      )
+      unlink(subFolders[i], recursive = TRUE)
     }
   }
 

extras/PackageMaintenance.R

@@ -115,6 +115,32 @@ unlink("inst/doc/IntroductionToStrategus.tex")
 pkgdown::build_site()
 OhdsiRTools::fixHadesLogo()
 
+# Repackage the test module for unit testing
+# NOTE: This is only necessary when the TestModule
+# has been updated
+testModuleRootFolder <- "extras/TestModule1-0.0.1"
+targetModuleZipFile <- "TestModule1_0.0.1.zip"
+testModuleFilesToRemove <- c(
+  file.path(testModuleRootFolder, ".RData"),
+  file.path(testModuleRootFolder, ".Rhistory")
+)
+testModuleDirToRemove <- c(
+  file.path(testModuleRootFolder, ".Rproj.user"),
+  file.path(testModuleRootFolder, "renv/library")
+)
+unlink(testModuleFilesToRemove)
+unlink(testModuleDirToRemove, recursive = TRUE)
 
-
-
+oldwd <- getwd()
+setwd("extras")
+zip::zip(
+  zipfile = targetModuleZipFile,
+  files = list.files("TestModule1-0.0.1", all.files = TRUE, recursive = TRUE, include.dirs = TRUE, full.names = TRUE)
+)
+file.copy(
+  from = targetModuleZipFile,
+  to = file.path("../inst/testdata", targetModuleZipFile),
+  overwrite = TRUE
+)
+file.remove(targetModuleZipFile)
+setwd(oldwd)

tests/testthat/test-Strategus.R

@@ -15,7 +15,7 @@ test_that("Run Eunomia study", {
   )
 
   analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
-    fileName = system.file("testdata/testModuleAnalysisSpecification.json",
+    fileName = system.file("testdata/unitTestAnalysisSpecification.json",
       package = "Strategus"
     )
   )