Merge branch 'release_23.1' into release_23.2

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

@@ -12,6 +12,12 @@
   root: ${user.preferences['owncloud|root']}
   login: ${user.preferences['owncloud|username']}
   password: ${user.preferences['owncloud|password']}
+  # By default, the plugin will use temp files to avoid loading entire files into memory. 
+  # You can change the directory here or omit to use the default temp directory.
+  temp_path: /your/temp/path
+  # Set writable to true if you have write access to this source
+  # and want to allow exporting files to it, by default is read only.
+  writable: false
 
 - type: posix
   root: '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/'

lib/galaxy/dependencies/pinned-requirements.txt

@@ -157,7 +157,7 @@ pysam==0.22.0 ; python_version >= "3.7" and python_version < "3.12"
 python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12"
 python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12"
 python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12"
-python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12"
+python-multipart==0.0.7 ; python_version >= "3.7" and python_version < "3.12"
 python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12"
 pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12"

lib/galaxy/files/sources/webdav.py

@@ -3,6 +3,7 @@
 except ImportError:
     WebDAVFS = None
 
+import tempfile
 from typing import (
     Optional,
     Union,
@@ -22,6 +23,11 @@ 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_"))
         extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
         handle = WebDAVFS(**{**props, **extra_props})
         return handle

packages/util/test-requirements.txt

@@ -1,3 +1,4 @@
 pytest
 pytest-httpserver
 responses
+Werkzeug

pyproject.toml

@@ -164,6 +164,7 @@ testfixtures = "*"
 tuspy = "*"
 twill = "*"
 watchdog = "*"
+Werkzeug = "*"
 
 [tool.poetry.group.typecheck.dependencies]
 mypy = "*"