Unverified Commit a7af3526 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #18083 from davelopez/23.2_backport_18052 

[23.2] Fix history export with missing dataset hids
parents ecef3ef5 419e4954

lib/galaxy/model/store/__init__.py

+8 −10
Original line number Diff line number Diff line
@@ -1961,8 +1961,6 @@ class DirectoryModelExportStore(ModelExportStore): 


        dir_name = "datasets"

        dir_path = os.path.join(export_directory, dir_name)

        dataset_hid = as_dict["hid"]

        assert dataset_hid, as_dict



        if dataset.dataset.id in self.dataset_id_to_path:

            file_name, extra_files_path = self.dataset_id_to_path[dataset.dataset.id]
@@ -1981,7 +1979,7 @@ class DirectoryModelExportStore(ModelExportStore): 
                self.serialization_options.get_identifier(self.security, conversion) if conversion else None

            )

            target_filename = get_export_dataset_filename(

                as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key

                as_dict["name"], as_dict["extension"], as_dict["encoded_id"], conversion_key=conversion_key

            )

            arcname = os.path.join(dir_name, target_filename)

            src = file_name
@@ -1997,7 +1995,7 @@ class DirectoryModelExportStore(ModelExportStore): 


            if len(file_list):

                extra_files_target_filename = get_export_dataset_extra_files_dir_name(

                    as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key

                    as_dict["encoded_id"], conversion_key=conversion_key

                )

                arcname = os.path.join(dir_name, extra_files_target_filename)

                add(extra_files_path, os.path.join(export_directory, arcname))
@@ -2967,22 +2965,22 @@ def tar_export_directory(export_directory: StrPath, out_file: StrPath, gzip: boo 
            store_archive.add(os.path.join(export_directory, export_path), arcname=export_path)





def get_export_dataset_filename(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:

def get_export_dataset_filename(name: str, ext: str, encoded_id: str, conversion_key: Optional[str]) -> str:

    """

    Builds a filename for a dataset using its name an extension.

    """

    base = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in name)

    if not conversion_key:

        return f"{base}_{hid}.{ext}"

        return f"{base}_{encoded_id}.{ext}"

    else:

        return f"{base}_{hid}_conversion_{conversion_key}.{ext}"

        return f"{base}_{encoded_id}_conversion_{conversion_key}.{ext}"





def get_export_dataset_extra_files_dir_name(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:

def get_export_dataset_extra_files_dir_name(encoded_id: str, conversion_key: Optional[str]) -> str:

    if not conversion_key:

        return f"extra_files_path_{hid}"

        return f"extra_files_path_{encoded_id}"

    else:

        return f"extra_files_path_{hid}_conversion_{conversion_key}"

        return f"extra_files_path_{encoded_id}_conversion_{conversion_key}"





def imported_store_for_metadata(

test/unit/data/model/test_model_store.py

+15 −0
Original line number Diff line number Diff line
@@ -544,6 +544,21 @@ def validate_invocation_collection_crate_directory(crate_directory): 
        assert dataset in root["hasPart"]





def test_export_history_with_missing_hid():

    # The dataset's hid was used to compose the file name during the export but it

    # can be missing sometimes. We now use the dataset's encoded id instead.

    app = _mock_app()

    u, history, d1, d2, j = _setup_simple_cat_job(app)



    # Remove hid from d1

    d1.hid = None

    app.commit()



    temp_directory = mkdtemp()

    with store.DirectoryModelExportStore(temp_directory, app=app, export_files="copy") as export_store:

        export_store.export_history(history)





def test_export_history_to_ro_crate(tmp_path):

    app = _mock_app()

    u, history, d1, d2, j = _setup_simple_cat_job(app)