mvdbeek 7b94e4b1d5 Test tool source storage: extend integration coverage and add unit tests ...

Round out the test suite that exercises LazyToolBox end-to-end against
a real boot:

- Extend ``BaseToolSourceStorageIntegrationTestCase`` helpers to hit
  ``/api/tools?in_panel=False`` (the index-backed listing) and to
  reach the lazy ``tools_by_id`` map directly when the resolver path
  isn't what's being asserted.
- New unit tests under ``test/unit/tool_source_store/`` pin the index's
  version handling: default-version selection, sibling-version
  discovery, and ``packaging.version`` ordering.

Tests that bind specific behaviours to specific LazyToolBox commits
land alongside the code commits that introduced them; this commit
collects the cross-cutting helpers and pure-unit coverage.

2026-07-28 17:26:57 +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

Parse edam operation and topic data from bio.tools if available.

2021-09-07 14:29:38 -04:00

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

Allow specifying useful classes of tools for mapping in job conf.

2021-07-14 13:46:56 -04:00

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

Drop more uWSGI legacy things

2022-03-15 21:32:00 +01:00

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

Allow specifying useful classes of tools for mapping in job conf.

2021-07-14 13:46:56 -04:00

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

Add new secret type to user preferences that is not sent to client

2021-12-01 10:48:36 +05:30

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

add more tests

2021-03-25 14:01:17 +01:00

resubmission_default_job_conf.yml

Allow specifying useful classes of tools for mapping in job conf.

2021-07-14 13:46:56 -04:00

resubmission_dynamic_job_conf.xml

Allow specifying useful classes of tools for mapping in job conf.

2021-07-14 13:46:56 -04:00

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

Allow specifying useful classes of tools for mapping in job conf.

2021-07-14 13:46:56 -04:00

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

Fix another integration test

2021-02-25 13:49:58 +01:00

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

Merge remote-tracking branch 'upstream/release_22.05' into dev

2022-11-16 12:07:04 +01:00

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

Fix Integeration typo

2022-11-23 01:20:00 +00:00

test_config_schema.py

Replace `unittest.TestCase` with pytest-based partial re-implementation

2022-09-27 03:34:58 +01:00

test_configuration_decode.py

Replace `unittest.TestCase` with pytest-based partial re-implementation

2022-09-27 03:34:58 +01:00

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

Replace `unittest.TestCase` with pytest-based partial re-implementation

2022-09-27 03:34:58 +01:00

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

Even more typing

2022-11-28 04:50:00 +00:00

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

Replace `unittest.TestCase` with pytest-based partial re-implementation

2022-09-27 03:34:58 +01:00

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

Use `history_id` fixture instead of instance attribute. More type annotations

2022-11-23 04:04:51 +00:00

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

Test tool source storage: extend integration coverage and add unit tests

2026-07-28 17:26:57 +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

use history_id fixture instead of instance variable with the same name

2022-11-23 01:19:59 +00:00

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

…