"""
API operations on remote files.
"""
import logging
from typing import (
List,
Optional,
)
from fastapi import (
Body,
Response,
)
from fastapi.param_functions import Query
from typing_extensions import Annotated
from galaxy.files.sources import PluginKind
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.remote_files import RemoteFilesManager
from galaxy.schema.remote_files import (
AnyRemoteFilesListResponse,
CreatedEntryResponse,
CreateEntryPayload,
FilesSourcePluginList,
RemoteFilesDisableMode,
RemoteFilesFormat,
RemoteFilesTarget,
)
from . import (
depends,
DependsOnTrans,
Router,
)
log = logging.getLogger(__name__)
router = Router(tags=["remote files"])
TargetQueryParam: str = Query(
title="Target source",
description=("The source to load datasets from. Possible values: ftpdir, userdir, importdir"),
)
FormatQueryParam: Optional[RemoteFilesFormat] = Query(
title="Response format",
description=(
"The requested format of returned data. Either `flat` to simply list all the files"
", `jstree` to get a tree representation of the files, or the default `uri` to list "
"files and directories by their URI."
),
)
RecursiveQueryParam: Optional[bool] = Query(
title="Recursive",
description=(
"Whether to recursively lists all sub-directories. This will be `True` by default depending on the `target`."
),
)
DisableModeQueryParam: Optional[RemoteFilesDisableMode] = Query(
title="Disable mode",
description=(
"(This only applies when `format` is `jstree`)"
" The value can be either `folders` or `files` and it will disable the"
" corresponding nodes of the tree."
),
)
WriteableQueryParam: Optional[bool] = Query(
title="Writeable",
description=(
"Whether the query is made with the intention of writing to the source."
" If set to True, only entries that can be written to will be returned."
),
)
BrowsableQueryParam: Optional[bool] = Query(
title="Browsable filesources only",
description=(
"Whether to return browsable filesources only. The default is `True`, which will omit filesources"
"like `http` and `base64` that do not implement a list method."
),
)
IncludeKindQueryParam = Query(
title="Include kind",
description=(
"Whether to return **only** filesources of the specified kind. The default is `None`, which will return"
" all filesources. Multiple values can be specified by repeating the parameter."
),
)
ExcludeKindQueryParam = Query(
title="Exclude kind",
description=(
"Whether to exclude filesources of the specified kind from the list. The default is `None`, which will return"
" all filesources. Multiple values can be specified by repeating the parameter."
),
)
LimitQueryParam = Query(title="Limit", description="Maximum number of entries to return.")
OffsetQueryParam = Query(title="Offset", description="Number of entries to skip.")
SearchQueryParam = Query(
title="Query",
description="Search query to filter entries by. The syntax could be different depending on the target source.",
)
SortByQueryParam = Query(
title="Sort by",
description="Sort the entries by the specified field.",
)
[docs]@router.cbv
class FastAPIRemoteFiles:
manager: RemoteFilesManager = depends(RemoteFilesManager)
[docs] @router.get(
"/api/remote_files",
summary="Displays remote files available to the user.",
response_description="A list with details about the remote files available to the user.",
)
@router.get(
"/api/ftp_files",
deprecated=True,
summary="Displays remote files available to the user. Please use /api/remote_files instead.",
)
async def index(
self,
response: Response,
user_ctx: ProvidesUserContext = DependsOnTrans,
target: Annotated[str, TargetQueryParam] = RemoteFilesTarget.ftpdir,
format: Annotated[Optional[RemoteFilesFormat], FormatQueryParam] = RemoteFilesFormat.uri,
recursive: Annotated[Optional[bool], RecursiveQueryParam] = None,
disable: Annotated[Optional[RemoteFilesDisableMode], DisableModeQueryParam] = None,
writeable: Annotated[Optional[bool], WriteableQueryParam] = None,
limit: Annotated[Optional[int], LimitQueryParam] = None,
offset: Annotated[Optional[int], OffsetQueryParam] = None,
query: Annotated[Optional[str], SearchQueryParam] = None,
sort_by: Annotated[Optional[str], SortByQueryParam] = None,
) -> AnyRemoteFilesListResponse:
"""Lists all remote files available to the user from different sources.
The total count of files and directories is returned in the 'total_matches' header.
"""
result, count = self.manager.index(
user_ctx, target, format, recursive, disable, writeable, limit, offset, query, sort_by
)
response.headers["total_matches"] = str(count)
return result
[docs] @router.get(
"/api/remote_files/plugins",
summary="Display plugin information for each of the gxfiles:// URI targets available.",
response_description="A list with details about each plugin.",
)
async def plugins(
self,
user_ctx: ProvidesUserContext = DependsOnTrans,
browsable_only: Annotated[Optional[bool], BrowsableQueryParam] = True,
include_kind: Annotated[Optional[List[PluginKind]], IncludeKindQueryParam] = None,
exclude_kind: Annotated[Optional[List[PluginKind]], ExcludeKindQueryParam] = None,
) -> FilesSourcePluginList:
"""Display plugin information for each of the gxfiles:// URI targets available."""
return self.manager.get_files_source_plugins(
user_ctx,
browsable_only,
set(include_kind) if include_kind else None,
set(exclude_kind) if exclude_kind else None,
)
[docs] @router.post(
"/api/remote_files",
summary="Creates a new entry (directory/record) on the remote files source.",
)
async def create_entry(
self,
user_ctx: ProvidesUserContext = DependsOnTrans,
payload: CreateEntryPayload = Body(
...,
title="Entry Data",
description="Information about the entry to create. Depends on the target file source.",
),
) -> CreatedEntryResponse:
"""Creates a new entry on the remote files source."""
return self.manager.create_entry(user_ctx, payload)