Merge pull request #13552 from mvdbeek/fix_tag_creation_metadata_stra…

…tegy_extended

[21.09] Fix creating tags within sessionless context

lib/galaxy/model/store/discover.py

@@ -134,7 +134,8 @@ def create_dataset(
             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 @@ def __init__(self, object_store, export_store, working_directory):
         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 collect_elements_for_history(elements):
                 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 collect_elements_for_history(elements):
                     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

@@ -248,8 +248,10 @@ def _get_tag(self, tag_name):
 
     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 @@ def _get_tag(self, tag_name):
         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

@@ -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)