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)
@@ -1200,6 +1201,9 @@ 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
@@ -1310,6 +1314,7 @@ 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

@@ -4075,3 +4075,9 @@ 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

@@ -111,7 +111,6 @@ 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
 
@@ -123,7 +122,6 @@ class WebdavFileSourceConfiguration(StrictModel):
     login: str
     password: str
     writable: bool = False
-    temp_path: Optional[str] = None
 
 
 FileSourceTemplateConfiguration = Union[