Source code for galaxy.webapps.galaxy.api.tool_data

from typing import Optional

from fastapi import (
    Body,
    Path,
)
from pydantic import (
    BaseModel,
    Field,
)

from galaxy.celery.tasks import import_data_bundle
from galaxy.managers.tool_data import ToolDataManager
from galaxy.schema.schema import (
    AsyncTaskResultSummary,
    ImportToolDataBundleSource,
)
from galaxy.tool_util.data._schema import (
    ToolDataDetails,
    ToolDataEntryList,
    ToolDataField,
    ToolDataItem,
)
from galaxy.webapps.base.api import GalaxyFileResponse
from galaxy.webapps.galaxy.services.base import async_task_summary
from . import (
    depends,
    Router,
)

router = Router(tags=["tool data tables"])

ToolDataTableName = Path(
    ...,  # Mark this field as required
    title="Data table name",
    description="The name of the tool data table",
    examples=["all_fasta"],
)

ToolDataTableFieldName = Path(
    ...,  # Mark this field as required
    title="Field name",
    description="The name of the tool data table field",
)


[docs]class ImportToolDataBundle(BaseModel): source: ImportToolDataBundleSource = Field(..., discriminator="src")
[docs]@router.cbv class FastAPIToolData: tool_data_manager: ToolDataManager = depends(ToolDataManager)
[docs] @router.get( "/api/tool_data", summary="Lists all available data tables", response_description="A list with details on individual data tables.", public=True, ) async def index(self) -> ToolDataEntryList: """Get the list of all available data tables.""" return self.tool_data_manager.index()
[docs] @router.post( "/api/tool_data", summary="Import a data manager bundle", require_admin=True, ) def create( self, tool_data_file_path: Optional[str] = None, import_bundle_model: ImportToolDataBundle = Body(...) ) -> AsyncTaskResultSummary: source = import_bundle_model.source result = import_data_bundle.delay(tool_data_file_path=tool_data_file_path, **source.model_dump()) summary = async_task_summary(result) return summary
[docs] @router.get( "/api/tool_data/{table_name}", summary="Get details of a given data table", response_description="A description of the given data table and its content", require_admin=True, ) async def show(self, table_name: str = ToolDataTableName) -> ToolDataDetails: """Get details of a given tool data table.""" return self.tool_data_manager.show(table_name)
[docs] @router.get( "/api/tool_data/{table_name}/reload", summary="Reloads a tool data table", response_description="A description of the reloaded data table and its content", require_admin=True, ) def reload(self, table_name: str = ToolDataTableName) -> ToolDataDetails: """Reloads a data table and return its details.""" return self.tool_data_manager.reload(table_name)
[docs] @router.get( "/api/tool_data/{table_name}/fields/{field_name}", summary="Get information about a particular field in a tool data table", response_description="Information about a data table field", require_admin=True, ) async def show_field( self, table_name: str = ToolDataTableName, field_name: str = ToolDataTableFieldName, ) -> ToolDataField: """Reloads a data table and return its details.""" return self.tool_data_manager.show_field(table_name, field_name)
[docs] @router.get( "/api/tool_data/{table_name}/fields/{field_name}/files/{file_name}", summary="Get information about a particular field in a tool data table", response_description="Information about a data table field", response_class=GalaxyFileResponse, require_admin=True, ) def download_field_file( self, table_name: str = ToolDataTableName, field_name: str = ToolDataTableFieldName, file_name: str = Path( ..., # Mark this field as required title="File name", description="The name of a file associated with this data table field", ), ): """Download a file associated with the data table field.""" path = self.tool_data_manager.get_field_file_path(table_name, field_name, file_name) return GalaxyFileResponse(str(path))
[docs] @router.delete( "/api/tool_data/{table_name}", summary="Removes an item from a data table", response_description="A description of the affected data table and its content", require_admin=True, ) def delete( self, payload: ToolDataItem, table_name: str = ToolDataTableName, ) -> ToolDataDetails: """Removes an item from a data table and reloads it to return its updated details.""" return self.tool_data_manager.delete(table_name, payload.values)