Unverified Commit 0441b456 authored by mvdbeek's avatar mvdbeek
Browse files

Fix dataset controller ``get_metadata_file`` 

We need to keep the metadata_name argument, this broke in
https://github.com/galaxyproject/galaxy/pull/13348.

Also uses the API service code.
parent 5b0360e6

lib/galaxy/webapps/galaxy/controllers/dataset.py

+10 −12
Original line number Diff line number Diff line
@@ -47,6 +47,7 @@ from galaxy.webapps.base.controller import ( 
    url_for,

    UsesExtendedMetadataMixin,

)

from galaxy.webapps.galaxy.services.datasets import DatasetsService

from ..api import depends



log = logging.getLogger(__name__)
@@ -65,6 +66,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
    history_manager: HistoryManager = depends(HistoryManager)

    hda_manager: HDAManager = depends(HDAManager)

    hda_deserializer: HDADeserializer = depends(HDADeserializer)

    service: DatasetsService = depends(DatasetsService)



    def __init__(self, app: StructuredApp):

        super().__init__(app)
@@ -134,19 +136,15 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
    def default(self, trans, dataset_id=None, **kwd):

        return "This link may not be followed from within Galaxy."



    @web.expose

    def get_metadata_file(self, trans, hda_id, metadata_file):

    @web.expose_api_raw_anonymous_and_sessionless

    def get_metadata_file(self, trans, hda_id, metadata_name):

        """Allows the downloading of metadata files associated with datasets (eg. bai index for bam files)"""

        data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(self.decode_id(hda_id))

        if not data or not self._can_access_dataset(trans, data):

            return trans.show_error_message("You are not allowed to access this dataset")



        fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in data.name)[0:150]



        file_ext = data.metadata.spec.get(metadata_file).get("file_ext", metadata_file)

        trans.response.headers["Content-Type"] = "application/octet-stream"

        trans.response.headers["Content-Disposition"] = f'attachment; filename="Galaxy{data.hid}-[{fname}].{file_ext}"'

        return open(data.metadata.get(metadata_file).file_name, "rb")

        # Backward compatibility with legacy links, should use `/api/datasets/{hda_id}/get_metadata_file` instead

        fh, headers = self.service.get_metadata_file(

            trans, history_content_id=hda_id, metadata_file=metadata_name, open_file=True

        )

        trans.response.headers.update(headers)

        return fh



    def _check_dataset(self, trans, hda_id):

        # DEPRECATION: We still support unencoded ids for backward compatibility