Drop legacy_eager_objectstore_initialization option.

Reduce branching/complexity around when/where objectstore is getting set for downstream work.

doc/source/admin/galaxy_options.rst

@@ -630,27 +630,6 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``legacy_eager_objectstore_initialization``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    As of 18.09, Galaxy defaults to setting up the object store
-    configuration for output datasets during the job queue step in job
-    handlers. This should generally provide for more robust job
-    submission, more configurability, and a better user experience but
-    may in some cases slightly slow down the job handler job setup
-    process. On the off chance that an admin would like to or need to
-    optimize job handlers at the expense of user experience and web
-    handling this option will remain for some time by setting this
-    option to true. This behavior however should be considered
-    deprecated and this option will likely be removed in future
-    versions of Galaxy. For more information see
-    https://github.com/galaxyproject/galaxy/issues/6513.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``file_sources_config_file``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/config/config_manage.py

@@ -316,6 +316,7 @@ OPTION_ACTIONS = {
     'communication_server_host': _DeprecatedAndDroppedAction(),
     'communication_server_port': _DeprecatedAndDroppedAction(),
     'persistent_communication_rooms': _DeprecatedAndDroppedAction(),
+    'legacy_eager_objectstore_initialization': _DeprecatedAndDroppedAction(),
 }
 
 

lib/galaxy/config/sample/galaxy.yml.sample

@@ -412,20 +412,6 @@ galaxy:
   # option.
   #watch_tours: 'false'
 
-  # As of 18.09, Galaxy defaults to setting up the object store
-  # configuration for output datasets during the job queue step in job
-  # handlers. This should generally provide for more robust job
-  # submission, more configurability, and a better user experience but
-  # may in some cases slightly slow down the job handler job setup
-  # process. On the off chance that an admin would like to or need to
-  # optimize job handlers at the expense of user experience and web
-  # handling this option will remain for some time by setting this
-  # option to true. This behavior however should be considered
-  # deprecated and this option will likely be removed in future versions
-  # of Galaxy. For more information see
-  # https://github.com/galaxyproject/galaxy/issues/6513.
-  #legacy_eager_objectstore_initialization: false
-
   # Configured FileSource plugins.
   # The value of this option will be resolved with respect to
   # <config_dir>.

lib/galaxy/tools/actions/__init__.py

@@ -12,7 +12,6 @@ from galaxy.jobs.actions.post import ActionBox
 from galaxy.model import LibraryDatasetDatasetAssociation, WorkflowRequestInputParameter
 from galaxy.model.dataset_collections.builder import CollectionBuilder
 from galaxy.model.none_like import NoneDataset
-from galaxy.objectstore import ObjectStorePopulator
 from galaxy.tools.parameters import update_dataset_ids
 from galaxy.tools.parameters.basic import DataCollectionToolParameter, DataToolParameter, RuntimeValue
 from galaxy.tools.parameters.wrapped import WrappedParameters
@@ -363,7 +362,6 @@ class DefaultToolAction:
         # datasets first, then create the associations
         parent_to_child_pairs = []
         child_dataset_names = set()
-        object_store_populator = ObjectStorePopulator(app, trans.user)
         async_tool = tool.tool_type == 'data_source_async'
 
         def handle_output(name, output, hidden=None):
@@ -415,11 +413,6 @@ class DefaultToolAction:
                     trans.app.security_agent.set_all_dataset_permissions(data.dataset, output_permissions, new=True, flush=False)
             data.copy_tags_to(preserved_tags.values())
 
-            if not completed_job and trans.app.config.legacy_eager_objectstore_initialization:
-                # Must flush before setting object store id currently.
-                trans.sa_session.flush()
-                object_store_populator.set_object_store_id(data)
-
             # This may not be neccesary with the new parent/child associations
             data.designation = name
             # Copy metadata from one of the inputs if requested.
@@ -543,7 +536,6 @@ class DefaultToolAction:
         job, galaxy_session = self._new_job_for_session(trans, tool, history)
         self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections)
         self._record_outputs(job, out_data, output_collections)
-        job.object_store_id = object_store_populator.object_store_id
         if job_params:
             job.params = dumps(job_params)
         if completed_job:

lib/galaxy/tools/actions/upload_common.py

@@ -14,7 +14,6 @@ from webob.compat import cgi_FieldStorage
 from galaxy import datatypes, util
 from galaxy.exceptions import (
     ConfigDoesNotAllowException,
-    ObjectInvalid,
     RequestParameterInvalidException,
 )
 from galaxy.model import tags
@@ -430,14 +429,6 @@ def create_job(trans, params, tool, json_file_path, outputs, folder=None, histor
                 job.add_output_library_dataset(output_name, dataset)
             else:
                 job.add_output_dataset(output_name, dataset)
-            # Create an empty file immediately
-            if not dataset.dataset.external_filename and trans.app.config.legacy_eager_objectstore_initialization:
-                dataset.dataset.object_store_id = object_store_id
-                try:
-                    trans.app.object_store.create(dataset.dataset)
-                except ObjectInvalid:
-                    raise Exception('Unable to create output dataset: object store is full')
-                object_store_id = dataset.dataset.object_store_id
 
         trans.sa_session.add(output_object)
 

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -471,21 +471,6 @@ mapping:
           changes are found, modified tours are automatically reloaded. Takes the same values as the
           'watch_tools' option.
 
-      legacy_eager_objectstore_initialization:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          As of 18.09, Galaxy defaults to setting up the object store configuration
-          for output datasets during the job queue step in job handlers. This should generally
-          provide for more robust job submission, more configurability, and a better
-          user experience but may in some cases slightly slow down the job handler job
-          setup process. On the off chance that an admin would like to or need to optimize job
-          handlers at the expense of user experience and web handling this option will remain
-          for some time by setting this option to true. This behavior however should be
-          considered deprecated and this option will likely be removed in future versions of
-          Galaxy. For more information see https://github.com/galaxyproject/galaxy/issues/6513.
-
       file_sources_config_file:
         type: str
         default: file_sources_conf.yml        

test/unit/unittest_utils/galaxy_mock.py

@@ -164,7 +164,6 @@ class MockAppConfig(Bunch):
         self.shed_tool_config_file_set = False
         self.preserve_python_environment = "always"
         self.enable_beta_gdpr = False
-        self.legacy_eager_objectstore_initialization = True
 
         self.version_major = "19.09"