"""
API operations on remote files.
"""
import logging
from typing import (
List,
Optional,
)
from fastapi import Body
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(
default=RemoteFilesTarget.ftpdir,
title="Target source",
description=("The source to load datasets from." " Possible values: ftpdir, userdir, importdir"),
)
FormatQueryParam: Optional[RemoteFilesFormat] = Query(
default=RemoteFilesFormat.uri,
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(
default=None,
title="Recursive",
description=(
"Whether to recursively lists all sub-directories." " This will be `True` by default depending on the `target`."
),
)
DisableModeQueryParam: Optional[RemoteFilesDisableMode] = Query(
default=None,
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(
default=None,
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(
default=True,
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."
),
)
[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,
user_ctx: ProvidesUserContext = DependsOnTrans,
target: str = TargetQueryParam,
format: Optional[RemoteFilesFormat] = FormatQueryParam,
recursive: Optional[bool] = RecursiveQueryParam,
disable: Optional[RemoteFilesDisableMode] = DisableModeQueryParam,
writeable: Optional[bool] = WriteableQueryParam,
) -> AnyRemoteFilesListResponse:
"""Lists all remote files available to the user from different sources."""
return self.manager.index(user_ctx, target, format, recursive, disable, writeable)
[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: Optional[bool] = BrowsableQueryParam,
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)