galaxy/lib/tool_shed/webapp/api2/tools.py

import logging
from typing import List

from fastapi import (
    Path,
    Request,
    Response,
)

from galaxy.tool_util.parameters import (
    RequestToolState,
    to_json_schema_string,
)
from tool_shed.context import SessionRequestContext
from tool_shed.managers.tools import (
    parsed_tool_model_cached_for,
    search,
)
from tool_shed.managers.trs import (
    get_tool,
    service_info,
    tool_classes,
)
from tool_shed.structured_app import ToolShedApp
from tool_shed.util.shed_index import build_index
from tool_shed_client.schema import (
    BuildSearchIndexResponse,
    ShedParsedTool,
)
from tool_shed_client.schema.trs import (
    Tool,
    ToolClass,
    ToolVersion,
)
from tool_shed_client.schema.trs_service_info import Service
from . import (
    depends,
    DependsOnTrans,
    RepositorySearchPageSizeQueryParam,
    Router,
    ToolSearchPageQueryParam,
    ToolsIndexQueryParam,
)

log = logging.getLogger(__name__)

router = Router(tags=["tools"])

TOOL_ID_PATH_PARAM: str = Path(
    ...,
    title="GA4GH TRS Tool ID",
    description="See also https://ga4gh.github.io/tool-registry-service-schemas/DataModel/#trs-tool-and-trs-tool-version-ids",
)

TOOL_VERSION_PATH_PARAM: str = Path(
    ...,
    title="Galaxy Tool Wrapper Version",
    description="The full version string defined on the Galaxy tool wrapper.",
)


def json_schema_response(pydantic_model) -> Response:
    json_str = to_json_schema_string(pydantic_model)
    return Response(content=json_str, media_type="application/json")


@router.cbv
class FastAPITools:
    app: ToolShedApp = depends(ToolShedApp)

    @router.get(
        "/api/tools",
        operation_id="tools__index",
    )
    def index(
        self,
        q: str = ToolsIndexQueryParam,
        page: int = ToolSearchPageQueryParam,
        page_size: int = RepositorySearchPageSizeQueryParam,
        trans: SessionRequestContext = DependsOnTrans,
    ):
        search_results = search(trans, q, page, page_size)
        return search_results

    @router.put(
        "/api/tools/build_search_index",
        operation_id="tools__build_search_index",
        require_admin=True,
    )
    def build_search_index(self) -> BuildSearchIndexResponse:
        """Not part of the stable API, just something to simplify
        bootstrapping tool sheds, scripting, testing, etc...
        """
        config = self.app.config
        repos_indexed, tools_indexed = build_index(
            config.whoosh_index_dir,
            config.file_path,
            config.hgweb_config_dir,
            config.hgweb_repo_prefix,
            config.database_connection,
        )
        return BuildSearchIndexResponse(
            repositories_indexed=repos_indexed,
            tools_indexed=tools_indexed,
        )

    @router.get("/api/ga4gh/trs/v2/service-info", operation_id="tools_trs_service_info")
    def service_info(self, request: Request) -> Service:
        return service_info(self.app, request.url)

    @router.get("/api/ga4gh/trs/v2/toolClasses", operation_id="tools__trs_tool_classes")
    def tool_classes(self) -> List[ToolClass]:
        return tool_classes()

    @router.get(
        "/api/ga4gh/trs/v2/tools",
        operation_id="tools__trs_index",
    )
    def trs_index(
        self,
    ):
        # we probably want to be able to query the database at the
        # tool level and such to do this right?
        return []

    @router.get(
        "/api/ga4gh/trs/v2/tools/{tool_id}",
        operation_id="tools__trs_get",
    )
    def trs_get(
        self,
        trans: SessionRequestContext = DependsOnTrans,
        tool_id: str = TOOL_ID_PATH_PARAM,
    ) -> Tool:
        return get_tool(trans, tool_id)

    @router.get(
        "/api/ga4gh/trs/v2/tools/{tool_id}/versions",
        operation_id="tools__trs_get_versions",
    )
    def trs_get_versions(
        self,
        trans: SessionRequestContext = DependsOnTrans,
        tool_id: str = TOOL_ID_PATH_PARAM,
    ) -> List[ToolVersion]:
        return get_tool(trans, tool_id).versions

    @router.get(
        "/api/tools/{tool_id}/versions/{tool_version}",
        operation_id="tools__parameter_model",
        summary="Return Galaxy's meta model description of the tool's inputs",
    )
    def show_tool(
        self,
        trans: SessionRequestContext = DependsOnTrans,
        tool_id: str = TOOL_ID_PATH_PARAM,
        tool_version: str = TOOL_VERSION_PATH_PARAM,
    ) -> ShedParsedTool:
        return parsed_tool_model_cached_for(trans, tool_id, tool_version)

    @router.get(
        "/api/tools/{tool_id}/versions/{tool_version}/parameter_request_schema",
        operation_id="tools__parameter_request_model",
        summary="Return a JSON schema description of the tool's inputs for the tool request API that will be added to Galaxy at some point",
        description="The tool request schema includes validation of map/reduce concepts that can be consumed by the tool execution API and not just the request for a single execution.",
    )
    def tool_state(
        self,
        trans: SessionRequestContext = DependsOnTrans,
        tool_id: str = TOOL_ID_PATH_PARAM,
        tool_version: str = TOOL_VERSION_PATH_PARAM,
    ) -> Response:
        parsed_tool = parsed_tool_model_cached_for(trans, tool_id, tool_version)
        return json_schema_response(RequestToolState.parameter_model_for(parsed_tool.inputs))