diff --git a/doc/source/admin/file_source_templates.png b/doc/source/admin/file_source_templates.png index 0e57efd51048..8e3c3fabe39e 100644 Binary files a/doc/source/admin/file_source_templates.png and b/doc/source/admin/file_source_templates.png differ diff --git a/doc/source/admin/file_source_webdav_configuration.png b/doc/source/admin/file_source_webdav_configuration.png index 95c7fd0576af..26ec57bd246d 100644 Binary files a/doc/source/admin/file_source_webdav_configuration.png and b/doc/source/admin/file_source_webdav_configuration.png differ diff --git a/doc/source/admin/file_source_webdav_configuration_template.png b/doc/source/admin/file_source_webdav_configuration_template.png index 2898c14849d8..4684e8f05b8a 100644 Binary files a/doc/source/admin/file_source_webdav_configuration_template.png and b/doc/source/admin/file_source_webdav_configuration_template.png differ diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py index 80d57ab04bf6..64b9a64b68e4 100644 --- a/lib/galaxy/config/__init__.py +++ b/lib/galaxy/config/__init__.py @@ -741,6 +741,7 @@ 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) diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index d6718cf176e7..f062754d6fed 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/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 # . diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml index 4b8519a6624f..3ed0c7455e74 100644 --- a/lib/galaxy/config/schemas/config_schema.yml +++ b/lib/galaxy/config/schemas/config_schema.yml @@ -3746,7 +3746,7 @@ mapping: Workflows launched with URI/URL inputs that are not marked as 'deferred' are "materialized" (or undeferred) by the workflow scheduler. This might be a lengthy process. Setting this to 'True' will place the invocation back in - the queue after materialization before scheduling the workflow so it is less + the queue after materialization before scheduling the workflow so it is less likely to starve other workflow scheduling. Ideally, Galaxy would allow more fine grain control of handlers but until then, this provides a way to tip the balance between "doing more work" and "being more fair". The default here is @@ -4110,7 +4110,7 @@ mapping: required: false desc: | Directory to store temporary files for file sources. This defaults to new_file_path if not set. - + file_source_webdav_use_temp_files: type: bool default: true diff --git a/lib/galaxy/files/sources/webdav.py b/lib/galaxy/files/sources/webdav.py index 9aec17fdbdc4..6e8faacae6a4 100644 --- a/lib/galaxy/files/sources/webdav.py +++ b/lib/galaxy/files/sources/webdav.py @@ -3,7 +3,6 @@ except ImportError: WebDAVFS = None -import tempfile from typing import ( cast, Optional, @@ -12,6 +11,8 @@ from typing_extensions import NotRequired +from typing_extensions import NotRequired + from . import ( FilesSourceOptions, FilesSourceProperties, diff --git a/lib/galaxy/files/templates/examples/production_webdav.yml b/lib/galaxy/files/templates/examples/production_webdav.yml index eb98ea28ef39..0767dc550867 100644 --- a/lib/galaxy/files/templates/examples/production_webdav.yml +++ b/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 diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py index 16c3a0490824..a849ee8d24f8 100644 --- a/lib/galaxy/files/templates/models.py +++ b/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[