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Source code for galaxy.webapps.galaxy.api.folder_contents
"""
API operations on the contents of a library folder.
"""
import logging
from typing import Optional
from fastapi import (
Body,
Path,
Query,
)
from typing_extensions import Annotated
from galaxy.managers.context import ProvidesUserContext
from galaxy.schema.fields import LibraryFolderDatabaseIdField
from galaxy.schema.schema import (
CreateLibraryFilePayload,
LibraryFolderContentsIndexQueryPayload,
LibraryFolderContentsIndexResult,
LibraryFolderContentsIndexSortByEnum,
)
from galaxy.webapps.galaxy.api import (
depends,
DependsOnTrans,
Router,
)
from galaxy.webapps.galaxy.services.library_folder_contents import LibraryFolderContentsService
log = logging.getLogger(__name__)
router = Router(tags=["data libraries folders"])
FolderIdPathParam = Annotated[
LibraryFolderDatabaseIdField,
Path(..., title="Folder ID", description="The encoded identifier of the library folder."),
]
LimitQueryParam: int = Query(default=10, ge=1, title="Limit", description="Maximum number of contents to return.")
OffsetQueryParam: int = Query(
default=0,
ge=0,
title="Offset",
description="Return contents from this specified position. For example, if ``limit`` is set to 100 and ``offset`` to 200, contents between position 200-299 will be returned.",
)
SearchQueryParam: Optional[str] = Query(
default=None,
title="Search Text",
description="Used to filter the contents. Only the folders and files which name contains this text will be returned.",
)
IncludeDeletedQueryParam: Optional[bool] = Query(
default=False,
title="Include Deleted",
description="Returns also deleted contents. Deleted contents can only be retrieved by Administrators or users with",
)
SortByQueryParam: LibraryFolderContentsIndexSortByEnum = Query(
default="name",
title="Sort By",
description="Sort results by specified field.",
)
SortDescQueryParam: Optional[bool] = Query(
default=False,
title="Sort Descending",
description="Sort results in descending order.",
)
[docs]@router.cbv
class FastAPILibraryFoldersContents:
service: LibraryFolderContentsService = depends(LibraryFolderContentsService)
[docs] @router.get(
"/api/folders/{folder_id}/contents",
summary="Returns a list of a folder's contents (files and sub-folders) with additional metadata about the folder.",
responses={
200: {
"description": "The contents of the folder that match the query parameters.",
"model": LibraryFolderContentsIndexResult,
},
},
)
def index(
self,
folder_id: FolderIdPathParam,
trans: ProvidesUserContext = DependsOnTrans,
limit: int = LimitQueryParam,
offset: int = OffsetQueryParam,
search_text: Optional[str] = SearchQueryParam,
include_deleted: Optional[bool] = IncludeDeletedQueryParam,
order_by: LibraryFolderContentsIndexSortByEnum = SortByQueryParam,
sort_desc: Optional[bool] = SortDescQueryParam,
):
"""Returns a list of a folder's contents (files and sub-folders).
Additional metadata for the folder is provided in the response as a separate object containing data
for breadcrumb path building, permissions and other folder's details.
*Note*: When sorting, folders always have priority (they show-up before any dataset regardless of the sorting).
**Security note**:
- Accessing a library folder or sub-folder requires only access to the parent library.
- Deleted folders can only be accessed by admins or users with `MODIFY` permission.
- Datasets may be public, private or restricted (to a group of users). Listing deleted datasets has the same requirements as folders.
"""
payload = LibraryFolderContentsIndexQueryPayload(
limit=limit,
offset=offset,
search_text=search_text,
include_deleted=include_deleted,
order_by=order_by,
sort_desc=sort_desc,
)
return self.service.index(trans, folder_id, payload)
[docs] @router.post(
"/api/folders/{folder_id}/contents",
name="add_history_datasets_to_library",
summary="Creates a new library file from an existing HDA/HDCA.",
)
def create(
self,
folder_id: FolderIdPathParam,
trans: ProvidesUserContext = DependsOnTrans,
payload: CreateLibraryFilePayload = Body(...),
):
return self.service.create(trans, folder_id, payload)