mvdbeek 7af0f056cd LazyToolBox: reload must read the index the inline populator just wrote ...

The populator writes through its own store instances, so after the
inline backfill the toolbox's store still served its cached pre-populate
index. Single-instance that cache is merely stale-but-identical; on a
shared database (the CI integration shards share one postgres DB, and
any multi-server deployment shares one in production) the cached index
is another instance's view and the eager walk drops every tool missing
from it — the post-reload 'no index entry for upload.xml' cascade.

Reload integration tests drive galaxy.queue_worker.reload_toolbox
directly and reproduce the failure with a foreign index row; the earlier
send_control_task-based attempts passed vacuously because the control
message never executes in this harness.

2026-07-28 17:27:23 +02:00

..

chained_dyndest_rules

Add type annotations to job handling code

2025-10-25 13:52:24 +01:00

delay_rules

…

htcondor_fake

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

job_resource_rules

Add integration test for ignoring invalid resource request in tool state

2023-08-22 15:29:03 +02:00

mock_biotools_content/data

…

objectstore

Serve download redirects from a dedicated /download route

2026-07-07 23:11:02 +05:30

objectstore_selection_rules

Add type annotations to job handling code

2025-10-25 13:52:24 +01:00

oidc

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

panel_views_1

Exclude multiple_versions from test_global_filters_on_integrated_panel

2023-11-16 15:08:21 +01:00

resubmission_rules

Address review comments

2026-05-11 11:02:48 +05:30

test_visualization_plugins/jupyterlite/static

Remove currently unused param option

2026-01-27 19:43:03 +03:00

webdav

…

__init__.py

…

chained_dyndest_job_conf.xml

…

conftest.py

Share mulled resolution cache across integration tests

2026-07-19 11:59:45 +02:00

delay_job_conf.yml

…

dockerized_job_conf.yml

Test that tmp_dir gets mounted correctly

2023-08-09 15:34:39 +02:00

dummy_job_resource_parameters.xml

Add integration test for ignoring invalid resource request in tool state

2023-08-22 15:29:03 +02:00

embedded_pulsar_docker_job_conf.yml

…

embedded_pulsar_job_conf.yml

Add test for proposed prod-like deployment

2025-09-21 17:03:17 +02:00

embedded_pulsar_metadata_extended_job_conf.yml

Disable conda_auto_init in embedded_pulsar_metadata_extended_job_conf.yml

2023-11-21 17:44:37 +01:00

embedded_pulsar_metadata_job_conf.yml

…

embedded_pulsar_none_job_conf.yml

Test Pulsar integration with default_file_action: none

2026-01-13 20:00:56 +01:00

embedded_pulsar_singularity_job_conf.yml

Add `--no-mount tmp` for singularity destination in tests

2023-02-28 18:49:30 +00:00

embedded_pulsar_tpv_job_conf.yml

Update integration test job_conf syntax for TPV 3.2.0

2026-04-09 12:29:45 +01:00

fallback_container_resolver.yml

add test for loading a per destination container resolver config

2023-04-02 10:39:44 +02:00

file_sources_conf_remote_files.yml

Add url_regex matching for DRS filesources and add integration test

2023-06-14 19:27:31 +05:30

file_sources_conf_vault.yml

…

file_sources_conf.yml

simplify webdav endpoint config

2026-04-22 18:15:26 +10:00

handler_template_job_conf.xml

…

io_injection_job_conf.yml

…

job_resource_error_recovery_job_conf.yml

Add integration test for ignoring invalid resource request in tool state

2023-08-22 15:29:03 +02:00

refgenie.yml

…

resubmission_default_job_conf.yml

…

resubmission_dynamic_job_conf.xml

…

resubmission_dynamic_multiple_job_conf.yml

Convert chained-resubmission job conf fixture to YAML

2026-05-19 16:09:11 +05:30

resubmission_job_conf.yml

…

resubmission_job_resource_parameters_conf.xml

…

resubmission_pulsar_job_conf.xml

Lower pulsar transport_timeout param instead of extending wait

2025-03-17 10:21:43 +01:00

resubmission_runners.py

replace more imports, lets go all in

2026-05-19 19:19:02 +02:00

resubmission_small_memory_job_conf.xml

…

resubmission_small_memory_resubmission_to_large_job_conf.xml

…

resubmission_tool_detected_always_error_job_conf.xml

…

resubmission_tool_detected_resubmit_job_conf.xml

…

sets_tmp_dir_expression_job_conf.xml

…

sets_tmp_dir_to_true_job_conf.xml

…

simple_job_conf.xml

…

singularity_job_conf.yml

require_container in tests

2023-06-20 10:28:21 +02:00

test_agents.py

Type the agents stack for the context it actually receives

2026-07-20 15:04:46 +02:00

test_apache_nginx_sendfile.py

…

test_async_downloads.py

Use requires_new_history decorator instead of unregistered marker

2026-04-15 09:33:10 +02:00

test_celery_fetch_quota.py

Enforce storage quota for Celery-based data fetch jobs

2026-02-26 15:29:33 +01:00

test_celery_tasks.py

Merge branch 'release_23.2' into dev

2024-01-18 12:23:00 +01:00

test_celery_user_concurrency_limit.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_celery_user_rate_limit.py

Code cleanups from pyupgrade

2025-07-31 11:17:22 +01:00

test_chained_dynamic_destinations.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_cli_runners.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_coexecution.py

Move more setup code into handle_galaxy_config_kwds which has test_driver configured

2026-01-01 15:08:26 +01:00

test_config_options_users.py

…

test_config_schema.py

…

test_configuration_decode.py

…

test_container_resolvers.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_containerized_jobs.py

Merge branch 'release_25.1' into release_26.0

2026-02-24 13:12:42 +00:00

test_credentials.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_data_manager_refgenie.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_data_manager_workflow_bundle.py

Allow longer workflow invocation waits

2026-07-19 11:59:49 +02:00

test_data_manager.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_dataset_copy_metadata_files.py

Fix copying metadata to copied job outputs

2023-11-10 18:03:45 +01:00

test_dataset_hashing.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_datatype_upload.py

Rename test helper classes that pytest tries to collect

2026-04-14 15:51:19 +02:00

test_default_permissions.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_drs_compact_identifiers.py

Add DRS compact identifier support

2026-01-27 08:46:10 -05:00

test_dynamic_edam_loading.py

…

test_edam_toolbox.py

change api/tool_panels from dict of views to dict containing

2023-10-26 12:50:31 -05:00

test_entry_point_sse.py

Add shared id-decode helpers to IntegrationInstance

2026-04-28 18:07:48 +02:00

test_error_report.py

tool error integration test

2024-04-11 10:09:05 -04:00

test_event_loop_blocking.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_extended_metadata_mapping.py

Numerous fixes for tool input format "21.01" parameters.

2024-10-30 10:52:08 -04:00

test_extended_metadata_outputs_to_working_directory.py

Fix and extend extended metadata outputs to working directory tests

2023-09-12 13:07:10 +02:00

test_extended_metadata.py

Move tests into TestExtendedMetadataIntegration

2026-03-18 16:29:41 +01:00

test_fail_job_tool_unavailable.py

Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow

2026-03-24 12:17:06 -04:00

test_flush_per_n_datasets.py

Rename classes derived from `IntegrationInstance` which are not test cases

2024-02-16 10:53:04 +00:00

test_galaxy_interactor.py

Format Python code with black 23.1.0

2023-02-01 23:51:03 +00:00

test_genomes.py

Drop support for Python 3.8

2025-02-25 19:20:46 +00:00

test_handler_assignment_methods.py

Format Python code with black 23.1.0

2023-02-01 23:51:03 +00:00

test_hashicorp_vault.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_history_archiving.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_history_import_export.py

Type annotation fixes for mypy 1.16.0

2025-06-10 02:22:18 +01:00

test_history_sse.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_htcondor_runner.py

attempt to fix the infrastructure tests

2026-05-09 18:44:18 +02:00

test_interactivetools_api.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_job_cache.py

Refactor to decrease duplication

2026-01-09 11:44:41 +01:00

test_job_environments.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_job_files_tus.py

Allow job files to consume TUS uploads

2024-01-16 10:03:02 -05:00

test_job_files.py

Fix `TestJobFilesIntegration` initialization

2026-07-10 01:49:05 +01:00

test_job_outputs_to_working_directory.py

Test `from_work_dir="dir"` feature

2025-10-01 09:01:31 +02:00

test_job_recovery.py

…

test_job_resource_error_recovery.py

Add integration test for ignoring invalid resource request in tool state

2023-08-22 15:29:03 +02:00

test_job_resubmission.py

Convert chained-resubmission job conf fixture to YAML

2026-05-19 16:09:11 +05:30

test_kubernetes_runner.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_landing_requests.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_legacy_store_by.py

Rename classes derived from `IntegrationInstance` which are not test cases

2024-02-16 10:53:04 +00:00

test_live_evals.py

Drop the dead lgtm comments.

2026-05-20 11:08:33 -04:00

test_local_job_cancellation.py

Use model classes from `galaxy.model instead of app.model` object

2025-02-26 12:41:40 +00:00

test_materialize_dataset_instance_tasks.py

Use requires_new_history decorator instead of unregistered marker

2026-04-15 09:33:10 +02:00

test_max_discovered_files.py

Handle MaxDiscoveredFilesExceededError gracefully for dynamic collections

2026-04-07 11:23:23 +02:00

test_metadata_strategy.py

Test case to demonstrate disk usage update for work dir outputs is broken with celery_extended.

2023-05-18 16:01:14 +02:00

test_model_store_scripts.py

…

test_notification_sse.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_notifications.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_page_revision_json_encoding.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_panel_views.py

Merge branch 'release_23.1' into dev

2023-11-21 09:36:51 +01:00

test_plugins.py

Fix invalid function schema error for tools with None parameters

2026-03-10 14:18:12 +01:00

test_prefix_handling.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_pulsar_embedded_containers.py

…

test_pulsar_embedded_copy_working.py

…

test_pulsar_embedded_extended_metadata.py

Test sessionless tag creation

2025-09-19 15:44:48 +02:00

test_pulsar_embedded_mq.py

Fix uploads in pulsar embedded test case

2025-02-26 14:55:08 +01:00

test_pulsar_embedded_none.py

Test Pulsar integration with default_file_action: none

2026-01-13 20:00:56 +01:00

test_pulsar_embedded_relay.py

Pulsar relay implementation

2025-11-28 11:12:12 +01:00

test_pulsar_embedded_remote_metadata.py

Fix tool stdio on pulsar and implement job stdio

2023-04-06 17:07:00 +02:00

test_pulsar_embedded.py

Add test that ensures irrelevant outputs are not copied back

2026-01-12 16:08:18 +01:00

test_purge_datasets.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_quota.py

remove assert

2024-09-19 09:39:08 +02:00

test_recalculate_user_disk_usage.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_remote_files_histories.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_remote_files_posix.py

Enforce file source access during dataset materialization

2026-04-15 15:14:02 +02:00

test_remote_files.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_repository_operations.py

Fix bwa loc filename in integration test (bwa_mem_index, not bwa_index)

2026-05-18 11:32:51 -04:00

test_resolvers.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_save_job_id_on_datasets.py

Removed deprecated `current` attribute of scoped_session

2025-02-21 09:29:41 +00:00

test_scripts_pgcleanup.py

Merge branch 'release_26.0' into release_26.1

2026-07-06 15:49:42 +02:00

test_scripts.py

Add integration tests for pgcleanup with user object stores

2026-06-08 12:41:25 +02:00

test_shed_tool_tests.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_storage_cleaner.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_structured_dataset.py

Bound memory use in h5grove structured content endpoint

2026-07-09 19:17:31 +02:00

test_structured_like_unpopulated.py

Rename test tool to describe shape, not test scenario

2026-05-19 19:50:56 +02:00

test_tool_data_bundles.py

Match renamed data_manager output in bundle integration test

2026-06-17 19:29:03 +02:00

test_tool_data_delete.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_tool_source_storage.py

LazyToolBox: reload must read the index the inline populator just wrote

2026-07-28 17:27:23 +02:00

test_tool_submission_errors.py

Serialize message exceptions on execution error

2025-01-30 09:43:55 +01:00

test_upload_configuration_options.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_user_defined_tool_job_conf.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_user_preferences.py

Use (also) case-insensitive comparison for user email

2026-02-19 14:40:02 +00:00

test_users.py

Fix admin resend-activation email missing hostname

2026-04-27 10:15:55 +02:00

test_vault_extra_prefs.py

rename parse_requirements_and_containers to parse_requirements,

2025-10-07 16:05:13 +02:00

test_vault_file_source.py

Use test_driver.mkdtemp systematically

2026-01-01 15:08:26 +01:00

test_web_framework_config.py

Allow CORS requests to api/workflow_landings

2024-10-10 09:40:28 +02:00

test_webdav.py

migrate webdav to fsspec

2026-04-14 16:37:27 +10:00

test_work_queue_put_failure.py

…

test_workflow_completion_hooks.py

Drop redundant completion hook test, improve remaining test

2026-01-21 14:44:55 +01:00

test_workflow_handler_configuration.py

Update test workflows to respect gxformat2 0.26.0 syntax

2026-05-05 20:44:35 +01:00

test_workflow_invocation.py

Add workflow invocation test

2026-06-02 18:02:48 +03:00

test_workflow_refactoring.py

Memoize run-form history option queries on the request context (issue #22927)

2026-06-16 18:29:49 +02:00

test_workflow_scheduling_options.py

Update test workflows to respect gxformat2 0.26.0 syntax

2026-05-05 20:44:35 +01:00

test_workflow_sync.py

Format Python code with black 23.1.0

2023-02-01 23:51:03 +00:00

test_workflow_tasks.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

user_preferences_extra_conf.yml

Add integration tests for non-vault user preferences handling

2025-02-13 18:40:55 +01:00

workflow_handler_configuration_job_conf.xml

…