Tests and tidy up

OHDSI · May 12, 2023 · 6d287df · 6d287df
1 parent de53edf
commit 6d287df
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Showing 3 changed files with 31 additions and 6 deletions.
diff --git a/R/Module.R b/R/Module.R
@@ -22,7 +22,7 @@
 #' Returns a list of module info for a given module
 #'
 loadModule <- function(moduleName = null, version = NULL, folder = NULL, instantiate = FALSE) {
-  available <- listAvailableModules()
+  available <- getAvailableModules()
   module <- list(
 
   )
@@ -60,7 +60,7 @@ moduleExec <- function(module, code, substituteVars = list(), useLocalStrategusL
                              tempScriptFile = tempfile(fileext = ".R"),
                              useLocalStrategusLibrary = useLocalStrategusLibrary,
                              job = job,
-                             processName = paste(moduleFolder, "_renv_run"))
+                             processName = paste(module$moduleFolder, "_renv_run"))
 
   unlink(tempFile)
 }
diff --git a/R/ModuleInstaller.R b/R/ModuleInstaller.R
@@ -34,8 +34,7 @@ checkModuleDependencies <- function(dependencies, moduleSet) {
 #' This returns the set of currently installed in the specifed system path
 #'
 #' @export
-getAvailableModules <- function(installedModulesPath = Sys.getenv("STRATEGUS_INSTALLED_MODULES"),
-                                refreshCache = FALSE) {
+getAvailableModules <- function(installedModulesPath = Sys.getenv("STRATEGUS_INSTALLED_MODULES")) {
 
   if (installedModulesPath == "") {
     warning("No system module path set, set STRATEGUS_INSTALLED_MODULES in your .renviron to enable global modules")
@@ -74,6 +73,10 @@ installLocalModule <- function(pathToModule,
   )
 
   checkmate::assertFileExists(file.path(pathToModule, requiredFiles))
+
+  if (!dir.exists(installedModulesPath)) {
+    dir.create(installedModulesPath)
+  }
   # lock rds object
   installLockFile <- file.path(installedModulesPath, "install_module.lock")
   if (file.exists(installLockFile)) {
@@ -82,7 +85,7 @@ installLocalModule <- function(pathToModule,
   }
 
   # Save a timestamp inside a file to inform when last lock was
-  a <- writeLines(timestamp(), con = installLockFile)
+  writeLines(timestamp(quiet = TRUE), con = installLockFile)
   on.exit(unlink(installLockFile, force = TRUE))
   currentModules <- getAvailableModules(installedModulesPath = installedModulesPath)
   metaData <- getModuleMetaData(pathToModule)
@@ -119,7 +122,7 @@ installLocalModule <- function(pathToModule,
   # Write to install path
   modulesRdsFile <- file.path(installedModulesPath, "installedModules.rds")
   # save rds
-  saveRDS(currentModules, modulesRdsFile)
+  saveRDS(currentModules %>% dplyr::distinct(), modulesRdsFile)
 
   message(paste("Module", iRow$moduleName, "Installed"))
   invisible(NULL)

diff --git a/tests/testthat/test-ModuleInstaller.R b/tests/testthat/test-ModuleInstaller.R
@@ -0,0 +1,22 @@
+test_that("Modules install from github", {
+  installedModulesPath <- tempfile()
+  unlink(installedModulesPath, recursive = TRUE)
+  on.exit(unlink(installedModulesPath, recursive = TRUE))
+
+  installGithubModule("OHDSI/CohortGeneratorModule", installedModulesPath = installedModulesPath)
+  checkmate::expect_directory_exists(file.path(installedModulesPath, "/CohortGeneratorModule"))
+  expect_error(installGithubModule("OHDSI/CohortGeneratorModule", installedModulesPath = installedModulesPath))
+
+  checkmate::expect_data_frame(getAvailableModules(installedModulesPath))
+
+  installGithubModule("OHDSI/CohortGeneratorModule", installedModulesPath = installedModulesPath, overwrite = TRUE)
+  installGithubModule("OHDSI/CohortMethodModule", installedModulesPath = installedModulesPath)
+  checkmate::expect_directory_exists(file.path(installedModulesPath, "CohortGeneratorModule"))
+
+  # Should not be able to install if lock file is present
+  installLockFile <- file.path(installedModulesPath, "install_module.lock")
+  writeLines(timestamp(quiet = TRUE), con = installLockFile)
+
+  expect_error(installGithubModule("OHDSI/CohortGeneratorModule", installedModulesPath = installedModulesPath, overwrite = TRUE))
+  unlink(installLockFile)
+})