Add new config parameter for file sources temp dir and update the web…

…dav file source

lib/galaxy/config/__init__.py

@@ -740,6 +740,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
  user_tool_section_filters: List[str]
  visualization_plugins_directory: str
  workflow_resource_params_mapper: str
+ file_source_temp_dir: str
 
  def __init__(self, **kwargs):
  super().__init__(**kwargs)
@@ -1236,6 +1237,9 @@ def _load_theme(path: str, theme_dict: dict):
  else:
  _load_theme(self.themes_config_file, self.themes)
 
+ if self.file_source_temp_dir:
+ self.file_source_temp_dir = os.path.abspath(self.file_source_temp_dir)
+
  def _process_celery_config(self):
  if self.celery_conf and self.celery_conf.get("result_backend") is None:
  # If the result_backend is not set, use a SQLite database in the data directory
@@ -1348,6 +1352,7 @@ def check(self):
  self.template_cache_path,
  self.tool_data_path,
  self.user_library_import_dir,
+ self.file_source_temp_dir,
  ]
  for path in paths_to_check:
  self._ensure_directory(path)

lib/galaxy/config/sample/galaxy.yml.sample

@@ -697,6 +697,11 @@ galaxy:
  # cleaned up in default Celery task configuration.
  #short_term_storage_cleanup_interval: 3600
 
+ # The file_source_temp_dir is a temporary directory used by file sources
+ # that require temporary storage for file operations.
+ # Defaults to new_file_path.
+ #file_source_temp_dir: null
+
  # Configured FileSource plugins.
  # The value of this option will be resolved with respect to
  # <config_dir>.

lib/galaxy/config/schemas/config_schema.yml

@@ -4089,3 +4089,9 @@ mapping:
  per_host: true
  desc: |
  Enable the integration of the Galaxy Help Forum in the tool panel. This requires the help_forum_api_url to be set.
+
+ file_source_temp_dir:
+ type: str
+ required: false
+ desc: |
+ Directory to store temporary files for file sources. This defaults to new_file_path if not set.

lib/galaxy/files/sources/webdav.py

@@ -3,12 +3,12 @@
 except ImportError:
  WebDAVFS = None
 
-import tempfile
 from typing import (
  Optional,
  Union,
 )
 
+from galaxy import config
 from . import (
  FilesSourceOptions,
  FilesSourceProperties,
@@ -23,11 +23,17 @@ class WebDavFilesSource(PyFilesystem2FilesSource):
 
  def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
  props = self._serialization_props(user_context)
- use_temp_files = props.pop("use_temp_files", None)
- if use_temp_files is None:
- # Default to True to avoid memory issues with large files.
- props["use_temp_files"] = True
- props["temp_path"] = props.get("temp_path", tempfile.TemporaryDirectory(prefix="webdav_"))
+
+ # Check if 'use_temp_files' and 'temp_path' are set in the config, otherwise fallback
+ props["use_temp_files"] = getattr(config, 'webdav_use_temp_files', True)
+ temp_path = getattr(config, 'file_source_temp_dir', None)
+
+ if temp_path is None:
+ # Fallback to props value or use new_file_path from config
+ new_file_path = getattr(config, 'new_file_path')
+ temp_path = props.get("temp_path", new_file_path)
+ props["temp_path"] = temp_path
+
  extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
  handle = WebDAVFS(**{**props, **extra_props})
  return handle

lib/galaxy/files/templates/examples/production_webdav.yml

@@ -40,4 +40,3 @@
  login: '{{ variables.login }}'
  writable: '{{ variables.writable }}'
  password: '{{ secrets.password }}'
- temp_path: null # Uses /tmp as default, configure it if needed

lib/galaxy/files/templates/models.py

@@ -128,7 +128,6 @@ class WebdavFileSourceTemplateConfiguration(StrictModel):
  login: Union[str, TemplateExpansion]
  password: Union[str, TemplateExpansion]
  writable: Union[bool, TemplateExpansion] = False
- temp_path: Optional[Union[str, TemplateExpansion]] = None
  template_start: Optional[str] = None
  template_end: Optional[str] = None
 
@@ -140,7 +139,6 @@ class WebdavFileSourceConfiguration(StrictModel):
  login: str
  password: str
  writable: bool = False
- temp_path: Optional[str] = None
 
 
 FileSourceTemplateConfiguration = Union[