Unverified Commit 5c38cae7 authored by mvdbeek's avatar mvdbeek
Browse files

Merge branch 'release_23.0' into release_23.1

parents f4d52d7d cdba4a09

lib/galaxy/app.py

+2 −2
Original line number Diff line number Diff line
@@ -582,8 +582,6 @@ class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication): 


        self._configure_tool_shed_registry()

        self._register_singleton(tool_shed_registry.Registry, self.tool_shed_registry)

        # Tool Data Tables

        self._configure_tool_data_tables(from_shed_config=False)



    def _configure_tool_shed_registry(self) -> None:

        # Set up the tool sheds registry
@@ -638,6 +636,8 @@ class UniverseApplication(StructuredApp, GalaxyManagerApplication): 
        )

        self.api_keys_manager = self._register_singleton(ApiKeyManager)



        # Tool Data Tables

        self._configure_tool_data_tables(from_shed_config=False)

        # Load dbkey / genome build manager

        self._configure_genome_builds(data_table_name="__dbkeys__", load_old_style=True)

lib/galaxy/celery/tasks.py

+10 −0
Original line number Diff line number Diff line
@@ -38,6 +38,7 @@ from galaxy.model.base import transaction 
from galaxy.model.scoped_session import galaxy_scoped_session

from galaxy.objectstore import BaseObjectStore

from galaxy.objectstore.caching import check_caches

from galaxy.queue_worker import GalaxyQueueWorker

from galaxy.schema.tasks import (

    ComputeDatasetHashTaskRequest,

    GenerateHistoryContentDownload,
@@ -63,6 +64,11 @@ from galaxy.web.short_term_storage import ShortTermStorageMonitor 
log = get_logger(__name__)





@lru_cache()

def setup_data_table_manager(app):

    app._configure_tool_data_tables(from_shed_config=False)





@lru_cache()

def cached_create_tool_from_representation(app, raw_tool_source):

    return create_tool_from_representation(
@@ -381,6 +387,7 @@ def compute_dataset_hash( 


@galaxy_task(action="import a data bundle")

def import_data_bundle(

    app: MinimalManagerApp,

    hda_manager: HDAManager,

    ldda_manager: LDDAManager,

    tool_data_import_manager: ToolDataImportManager,
@@ -390,6 +397,7 @@ def import_data_bundle( 
    id: Optional[int] = None,

    tool_data_file_path: Optional[str] = None,

):

    setup_data_table_manager(app)

    if src == "uri":

        assert uri

        tool_data_import_manager.import_data_bundle_by_uri(config, uri, tool_data_file_path=tool_data_file_path)
@@ -401,6 +409,8 @@ def import_data_bundle( 
        else:

            dataset = ldda_manager.by_id(id)

        tool_data_import_manager.import_data_bundle_by_dataset(config, dataset, tool_data_file_path=tool_data_file_path)

    queue_worker = GalaxyQueueWorker(app)

    queue_worker.send_control_task("reload_tool_data_tables")





@galaxy_task(action="pruning history audit table")

test/integration/test_tool_data_delete.py

+2 −0
Original line number Diff line number Diff line
@@ -45,6 +45,8 @@ class DataManagerIntegrationTestCase(integration_util.IntegrationTestCase): 
        return show_response.json()["fields"]



    def _testbeta_field_count(self) -> int:

        # We need to wait for the reload message to reach the control message consumer

        time.sleep(1)

        return len(self._testbase_fields())