Unverified Commit 74a51d99 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #13552 from mvdbeek/fix_tag_creation_metadata_strategy_extended 

[21.09] Fix creating tags within sessionless context
parents 525f4432 7aae40d1

lib/galaxy/model/store/discover.py

+4 −2
Original line number Diff line number Diff line
@@ -134,7 +134,8 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 
            primary_data.created_from_basename = created_from_basename



        if tag_list:

            self.tag_handler.add_tags_from_list(self.job.user, primary_data, tag_list, flush=False)

            job = getattr(self, "job", None)

            self.tag_handler.add_tags_from_list(job and job.user, primary_data, tag_list, flush=False)



        # If match specified a name use otherwise generate one from

        # designation.
@@ -415,7 +416,6 @@ class SessionlessModelPersistenceContext(ModelPersistenceContext): 
        self.object_store = object_store

        self.export_store = export_store

        self.flush_per_n_datasets = None



        self.job_working_directory = working_directory  # TODO: rename...



    @property
@@ -626,6 +626,7 @@ def persist_hdas(elements, model_persistence_context, final_job_state='ok'): 
                ext = fields_match.ext

                dbkey = fields_match.dbkey

                info = element.get("info", None)

                tag_list = element.get("tags")

                link_data = discovered_file.match.link_data



                # Create new primary dataset
@@ -654,6 +655,7 @@ def persist_hdas(elements, model_persistence_context, final_job_state='ok'): 
                    filename=discovered_file.path,

                    extra_files=extra_files,

                    info=info,

                    tag_list=tag_list,

                    link_data=link_data,

                    primary_data=primary_dataset,

                    sources=sources,

lib/galaxy/model/tags.py

+4 −2
Original line number Diff line number Diff line
@@ -248,8 +248,10 @@ class TagHandler: 


    def _create_tag_instance(self, tag_name):

        # For good performance caller should first check if there's already an appropriate tag

        Session = sessionmaker(self.sa_session.bind)

        tag = galaxy.model.Tag(type=0, name=tag_name)

        if not self.sa_session:

            return tag

        Session = sessionmaker(self.sa_session.bind)

        with Session() as separate_session:

            separate_session.add(tag)

            try:
@@ -424,7 +426,7 @@ class GalaxySessionlessTagHandler(GalaxyTagHandlerSession): 
        return self.created_tags.get(tag_name)



    def get_tag_by_name(self, tag_name):

        self.created_tags.get(tag_name)

        return self.created_tags.get(tag_name)





class CommunityTagHandler(TagHandler):

test/unit/test_model_discovery.py

+5 −1
Original line number Diff line number Diff line
@@ -21,6 +21,7 @@ def test_model_create_context_persist_hdas(): 
            "dbkey": "hg19",

            "name": "my file",

            "md5": "e5d21b1ea57fc9a31f8ea0110531bf3d",

            "tags": ["name:value"]

        }],

    }

    app = _mock_app(store_by="uuid")
@@ -37,6 +38,9 @@ def test_model_create_context_persist_hdas(): 
    assert imported_hda.metadata.data_lines == 2

    assert len(imported_hda.dataset.hashes) == 1

    assert imported_hda.dataset.hashes[0].hash_value == "e5d21b1ea57fc9a31f8ea0110531bf3d"

    tags = imported_hda.tags

    assert len(tags) == 1

    assert tags[0].value == "value"



    with open(imported_hda.file_name) as f:

        assert f.read().startswith("hello world\n")
@@ -228,7 +232,7 @@ def _import_directory_to_history(app, target, work_directory): 
    assert len(import_history.datasets) == 0



    import_options = store.ImportOptions(allow_dataset_object_edit=True)

    import_model_store = store.get_import_model_store_for_directory(target, app=app, user=u, import_options=import_options)

    import_model_store = store.get_import_model_store_for_directory(target, app=app, user=u, import_options=import_options, tag_handler=app.tag_handler.create_tag_handler_session())

    with import_model_store.target_history(default_history=import_history):

        import_model_store.perform_import(import_history)