Fix bug where visible but non-editable files were missing in run/grading

src/main/kotlin/ch/uzh/ifi/access/service/CourseLifecycle.kt

@@ -123,6 +123,19 @@ class CourseLifecycle(
                 task.files.forEach { file ->
                     file.enabled = false
                 }
+                // TODO: maybe do this in a less convoluted fashion
+                // reset all file attributes to false
+                taskDTO.files?.let {
+                    (it.instruction + it.visible + it.grading + it.editable + it.solution).forEach { filePath ->
+                        val file = createOrUpdateTaskFile(task, taskPath, filePath)
+                        file.instruction = false
+                        file.visible = false
+                        file.grading = false
+                        file.editable = false
+                        file.solution = false
+                    }
+                }
+                // set desired file attributes
                 taskDTO.files?.instruction?.forEach { filePath ->
                     createOrUpdateTaskFile(task, taskPath, filePath).instruction = true
                 }

src/main/kotlin/ch/uzh/ifi/access/service/CourseService.kt

@@ -287,6 +287,12 @@ class CourseService(
             .toList()
     }
 
+    fun getVisibleNonEditableFiles(taskId: Long?): List<TaskFile> {
+        return taskFileRepository.findByTask_IdAndEnabledTrue(taskId)
+            .filter { file: TaskFile -> file.visible && !file.editable }
+            .toList()
+    }
+
     private fun readLogsFile(path: Path): String {
         val logsFile = path.resolve("logs.txt").toFile()
 
@@ -362,6 +368,31 @@ class CourseService(
                 }
                 dockerClient.createContainerCmd(it).use { containerCmd ->
                     val submissionDir = workingDir.resolve("submissions").resolve(submission.id.toString())
+                    // add submission files (supplied by the frontend)
+                    submission.files.forEach { file ->
+                        file.taskFile?.path?.let { it1 -> // TODO: cleanup
+                            file.content?.let { it2 ->
+                                createLocalFile(
+                                    submissionDir,
+                                    it1,
+                                    it2
+                                )
+                            }
+                        }
+                    }
+                    // add visible but not editable files (because these are not part of the submission files)
+                    getVisibleNonEditableFiles(task.id)
+                        .forEach(Consumer { file: TaskFile ->
+                            file.path?.let { it1 -> // TODO: cleanup
+                                file.template?.let { it2 ->
+                                    createLocalFile(
+                                        submissionDir,
+                                        it1, it2
+                                    )
+                                }
+                            }
+                        })
+                    // add grading files if submission is graded
                     if (submission.isGraded) {
                         getGradingFiles(task.id)
                             .forEach(Consumer { file: TaskFile ->
@@ -383,18 +414,6 @@ class CourseService(
                             }
                         }
                     }
-                    submission.files.forEach { file ->
-                        file.taskFile?.path?.let { it1 -> // TODO: cleanup
-                            file.content?.let { it2 ->
-                                createLocalFile(
-                                    submissionDir,
-                                    it1,
-                                    it2
-                                )
-                            }
-                        }
-                    }
-
                     // The student code is run on the tmpfs.
                     // Main reason for this is that we have no other way of enforcing a disk quota.
                     // TODO: make this size configurable in task config.toml?
@@ -543,6 +562,12 @@ fi
         return courseLifecycle.updateFromRepository(existingCourse)
     }
 
+    @Transactional
+    fun updateCourseFromDirectory(courseSlug: String, directory: Path): Course {
+        val existingCourse = getCourseBySlug(courseSlug)
+        return courseLifecycle.updateFromDirectory(existingCourse, directory )
+    }
+
     @Transactional
     fun deleteCourse(courseSlug: String): Course {
         val existingCourse = getCourseBySlug(courseSlug)

src/test/kotlin/ch/uzh/ifi/access/service/CourseLifecycleTests.kt

@@ -51,6 +51,14 @@ class CourseLifecycleTests(
         courseService.getCourseBySlug("access-mock-course")
     }
 
+    @Test
+    @WithMockUser(username="[email protected]", authorities = ["supervisor"])
+    @Order(0)
+    fun `Course update succeeds`() {
+        val absolutePath = Paths.get(File("Mock-Course-Re").absolutePath)
+        courseService.updateCourseFromDirectory("access-mock-course", absolutePath)
+    }
+
     fun getCourse(): CourseWorkspace {
         return courseService.getCourseWorkspaceBySlug("access-mock-course")
     }