Merge pull request #5138 from scholtalbers/feature/auto_create_userfolder

Add option to auto create user_library_import_dir directories upon user login

config/galaxy.yml.sample

@@ -1050,6 +1050,11 @@ galaxy:
   # in their directory.
   #user_library_import_dir: null
 
+  # If user_library_import_dir is set, this option will auto create a
+  # library import directory for every user (based on their email) upon
+  # login.
+  #user_library_import_dir_auto_creation: false
+
   # For security reasons, users may not import any files that actually
   # lie outside of their `user_library_import_dir` (e.g. using symbolic
   # links). A list of directories can be allowed by setting the

doc/source/admin/galaxy_options.rst

@@ -2188,6 +2188,18 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``user_library_import_dir_auto_creation``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    If user_library_import_dir is set, this option will auto create a
+    library import directory for every user (based on their email)
+    upon login.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``user_library_import_symlink_whitelist``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config.py

@@ -431,6 +431,7 @@ class Configuration(object):
         self.user_library_import_dir = kwargs.get('user_library_import_dir', None)
         self.user_library_import_symlink_whitelist = listify(kwargs.get('user_library_import_symlink_whitelist', []), do_strip=True)
         self.user_library_import_check_permissions = string_as_bool(kwargs.get('user_library_import_check_permissions', False))
+        self.user_library_import_dir_auto_creation = string_as_bool(kwargs.get('user_library_import_dir_auto_creation', False)) if self.user_library_import_dir else False
         # Searching data libraries
         self.ftp_upload_dir = kwargs.get('ftp_upload_dir', None)
         self.ftp_upload_dir_identifier = kwargs.get('ftp_upload_dir_identifier', 'email')  # attribute on user - email, username, id, etc...

lib/galaxy/web/framework/webapp.py

@@ -24,10 +24,11 @@ from sqlalchemy.orm import joinedload
 from sqlalchemy.orm.exc import NoResultFound
 
 from galaxy import util
-from galaxy.exceptions import MessageException
+from galaxy.exceptions import ConfigurationError, MessageException
 from galaxy.managers import context
 from galaxy.util import (
     asbool,
+    safe_makedirs,
     safe_str_cmp
 )
 from galaxy.util.sanitize_html import sanitize_html
@@ -630,16 +631,31 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
         self.set_cookie(self.security.encode_guid(self.galaxy_session.session_key),
                         name=name, path=self.app.config.cookie_path)
 
+    def check_user_library_import_dir(self, user):
+        if getattr(self.app.config, "user_library_import_dir_auto_creation", False):
+            # try to create a user library import directory
+            try:
+                safe_makedirs(os.path.join(self.app.config.user_library_import_dir, user.email))
+            except ConfigurationError as e:
+                self.log_event(str(e))
+
+    def user_checks(self, user):
+        """
+        This could contain more checks around a user upon login
+        """
+        self.check_user_library_import_dir(user)
+
     def handle_user_login(self, user):
         """
         Login a new user (possibly newly created)
-
+           - do some 'system' checks (if any) for this user
            - create a new session
            - associate new session with user
            - if old session had a history and it was not associated with a user, associate it with the new session,
              otherwise associate the current session's history with the user
            - add the disk usage of the current session to the user's total disk usage
         """
+        self.user_checks(user)
         # Set the previous session
         prev_galaxy_session = self.galaxy_session
         prev_galaxy_session.is_valid = False

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -1629,6 +1629,14 @@ mapping:
           must contain sub-directories named the same as the non-admin user's Galaxy
           login ( email ).  The non-admin user is restricted to uploading files or
           sub-directories of files contained in their directory.
+
+      user_library_import_dir_auto_creation:
+        type: bool
+        default: false
+        required: false
+        desc: |
+          If user_library_import_dir is set, this option will auto create a library
+          import directory for every user (based on their email) upon login.
          
       user_library_import_symlink_whitelist:
         type: str