Skip registration for files and ignore files with insufficient rights (…

…#15)

Currently the registration fails silently if the dataset to register
is not wrapped in a directory.

Also, the dataset registration fails, when the application has not sufficient rights to execute and write to the dataset folder (e.g. wrong access group, etc).


# Co-authored-by: KochTobi <tobias.koch@qbic.uni-tuebingen.de>

src/main/java/life/qbic/data/processing/scanner/Scanner.java

@@ -102,16 +102,36 @@ public void run() {
   private List<RegistrationRequest> detectDataForRegistration() {
     return userProcessDirectories.parallelStream()
         .map(Path::toFile)
+        .filter(this::matchesAccessRightsCriteria)
+        .filter(this::matchesRegistrationCriteria)
         .map(file -> createRequests(file.listFiles(), file.toPath())).flatMap(
             Collection::stream).toList();
   }
 
+  private boolean matchesAccessRightsCriteria(File file) {
+    if (!file.canWrite()) {
+      log.error("Cannot write to file '{}'", file);
+      return false;
+    }
+    if (!file.canExecute()) {
+      log.error("Cannot execute file '{}'", file);
+      return false;
+    }
+    return true;
+  }
+
+  private boolean matchesRegistrationCriteria(File file) {
+    if (file.isHidden()) {
+      return false;
+    }
+    return file.isDirectory();
+  }
+
   private List<RegistrationRequest> createRequests(File[] files, Path userDirectory) {
     if (files == null || files.length == 0) {
       return new ArrayList<>();
     }
-    return Arrays.stream(files).filter(file -> !file.isHidden())
-        .map(file -> createRequest(file, userDirectory)).toList();
+    return Arrays.stream(files).map(file -> createRequest(file, userDirectory)).toList();
   }
 
   private RegistrationRequest createRequest(File file, Path userDirectory) {