"""
API operations allowing clients to determine datatype supported by Galaxy.
"""
import logging
from typing import (
Dict,
List,
Optional,
Union,
)
from fastapi import Query
from galaxy.datatypes.registry import Registry
from galaxy.managers.datatypes import (
DatatypeConverterList,
DatatypeDetails,
DatatypesCombinedMap,
DatatypesMap,
view_converters,
view_index,
view_mapping,
view_sniffers,
)
from . import (
depends,
Router,
)
log = logging.getLogger(__name__)
router = Router(tags=["datatypes"])
ExtensionOnlyQueryParam: Optional[bool] = Query(
default=True,
title="Extension only",
description="Whether to return only the datatype's extension rather than the datatype's details",
)
UploadOnlyQueryParam: Optional[bool] = Query(
default=True,
title="Upload only",
description="Whether to return only datatypes which can be uploaded",
)
[docs]@router.cbv
class FastAPIDatatypes:
datatypes_registry: Registry = depends(Registry)
[docs] @router.get(
"/api/datatypes",
summary="Lists all available data types",
response_description="List of data types",
)
async def index(
self,
extension_only: Optional[bool] = ExtensionOnlyQueryParam,
upload_only: Optional[bool] = UploadOnlyQueryParam,
) -> Union[List[DatatypeDetails], List[str]]:
"""Gets the list of all available data types."""
return view_index(self.datatypes_registry, extension_only, upload_only)
[docs] @router.get(
"/api/datatypes/mapping",
summary="Returns mappings for data types and their implementing classes",
response_description="Dictionary to map data types with their classes",
)
async def mapping(self) -> DatatypesMap:
"""Gets mappings for data types."""
return view_mapping(self.datatypes_registry)
[docs] @router.get(
"/api/datatypes/types_and_mapping",
summary="Returns all the data types extensions and their mappings",
response_description="Dictionary to map data types with their classes",
)
async def types_and_mapping(
self,
extension_only: Optional[bool] = ExtensionOnlyQueryParam,
upload_only: Optional[bool] = UploadOnlyQueryParam,
) -> DatatypesCombinedMap:
"""Combines the datatype information from (/api/datatypes) and the
mapping information from (/api/datatypes/mapping) into a single
response."""
return DatatypesCombinedMap(
datatypes=view_index(self.datatypes_registry, extension_only, upload_only),
datatypes_mapping=view_mapping(self.datatypes_registry),
)
[docs] @router.get(
"/api/datatypes/sniffers",
summary="Returns the list of all installed sniffers",
response_description="List of datatype sniffers",
)
async def sniffers(self) -> List[str]:
"""Gets the list of all installed data type sniffers."""
return view_sniffers(self.datatypes_registry)
[docs] @router.get(
"/api/datatypes/converters",
summary="Returns the list of all installed converters",
response_description="List of all datatype converters",
)
async def converters(self) -> DatatypeConverterList:
"""Gets the list of all installed converters."""
return view_converters(self.datatypes_registry)
[docs] @router.get(
"/api/datatypes/edam_data",
summary="Returns a dictionary/map of datatypes and EDAM data",
response_description="Dictionary/map of datatypes and EDAM data",
)
async def edam_data(self) -> Dict[str, str]:
"""Gets a map of datatypes and their corresponding EDAM data."""
return self.datatypes_registry.edam_data