Fix importing a directory from user_library_import_dir

Fix the following traceback:
```
Traceback (most recent call last):
  File "/galaxy/lib/galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "/galaxy/lib/galaxy/webapps/galaxy/api/library_contents.py", line 250, in create
    status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload)
  File "/galaxy/lib/galaxy/webapps/galaxy/api/library_contents.py", line 337, in _upload_library_dataset
    **kwd)
  File "/galaxy/lib/galaxy/actions/library.py", line 91, in _upload_dataset
    full_dir, import_dir_desc = validate_server_directory_upload(trans, server_dir)
  File "/galaxy/lib/galaxy/actions/library.py", line 48, in validate_server_directory_upload
    if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist, username=username):
TypeError: safe_contains() got an unexpected keyword argument 'username'
```

Also add a test case to reproduce the fixed issue, which was introduced in
commit f4442ff .

Reported by @jhl667 .

lib/galaxy/actions/library.py

@@ -45,8 +45,8 @@ def validate_server_directory_upload(trans, server_dir):
     unsafe = None
     if safe_relpath(server_dir):
         username = trans.user.username if trans.app.config.user_library_import_check_permissions else None
-        if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist, username=username):
-            for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist):
+        if import_dir_desc == 'user_library_import_dir' and safe_contains(import_dir, full_dir, whitelist=trans.app.config.user_library_import_symlink_whitelist):
+            for unsafe in unsafe_walk(full_dir, whitelist=[import_dir] + trans.app.config.user_library_import_symlink_whitelist, username=username):
                 log.error('User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', unsafe, os.path.realpath(unsafe))
     else:
         log.error('User attempted to import a directory path that resolves to a path outside of their import dir: %s -> %s', server_dir, os.path.realpath(full_dir))

test/integration/test_upload_configuration_options.py

@@ -705,7 +705,7 @@ def server_dir(cls):
         return cls.temp_config_dir("server")
 
 
-class ServerDirectoryRestrictedToAdminsUsageTestCase(BaseUploadContentConfigurationTestCase):
+class UserServerDirectoryOffByDefaultTestCase(BaseUploadContentConfigurationTestCase):
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -719,6 +719,36 @@ def test_library_import_dir_not_available_to_non_admins(self):
         assert response.status_code == 403, response.json()
 
 
+class UserServerDirectoryValidUsageTestCase(BaseUploadContentConfigurationTestCase):
+
+    @classmethod
+    def user_server_dir(cls):
+        return cls.temp_config_dir("user_library_import_dir")
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        user_server_dir = cls.user_server_dir()
+        os.makedirs(user_server_dir)
+        config["user_library_import_dir"] = os.path.join(user_server_dir)
+
+    def test_valid_user_server_dir_uploads_okay(self):
+        dir_to_import = 'library'
+        full_dir_path = os.path.join(self.user_server_dir(), TEST_USER, dir_to_import)
+        os.makedirs(full_dir_path)
+        file_content = "hello world\n"
+        with tempfile.NamedTemporaryFile(mode='w', dir=full_dir_path, delete=False) as fh:
+            fh.write(file_content)
+            file_to_import = fh.name
+
+        library_dataset = self.library_populator.new_library_dataset("serverdirupload", upload_option="upload_directory", server_dir=dir_to_import)
+        # Check the file is still there and was not modified
+        with open(file_to_import, 'r') as fh:
+            read_content = fh.read()
+        assert read_content == file_content
+
+        assert library_dataset["file_size"] == 12, library_dataset
+
+
 class FetchByPathTestCase(BaseUploadContentConfigurationTestCase):
 
     require_admin_user = True