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galaxy/test/integration
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Marius van den Beek 6f6aac1a67 Merge pull request #21515 from mvdbeek/fix-collection-discovery-directory 
Restrict collection of dynamic working dir output to specified directory in pulsar
2026-01-13 18:14:17 +01:00
..
chained_dyndest_rules
Add type annotations to job handling code
2025-10-25 13:52:24 +01:00
delay_rules
…
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
Pulsar relay implementation
2025-11-28 11:12:12 +01:00
objectstore_selection_rules
Add type annotations to job handling code
2025-10-25 13:52:24 +01:00
oidc
Fix regex pattern for failing tests
2025-12-13 23:44:32 +05:30
panel_views_1
Exclude multiple_versions from test_global_filters_on_integrated_panel
2023-11-16 15:08:21 +01:00
resubmission_rules
Add type annotations to job handling code
2025-10-25 13:52:24 +01:00
test_visualization_plugins/jupyterlite/static
Replace get_plugin mock with test viz plugin fixture
2026-01-06 10:25:09 -05:00
webdav
…
__init__.py
…
chained_dyndest_job_conf.xml
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conftest.py
Replace pytest-celery with `celery.contrib.pytest` plugin loading
2024-04-16 17:16:52 +01:00
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_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
Match last version of https://github.com/galaxyproject/total-perspective-vortex/pull/166
2025-09-30 21:09:33 +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
Restore original filename for file_source_conf_webdav.yml
2023-06-14 19:27:31 +05:30
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_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
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
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
Clean up code with pyupgrade
2026-01-06 22:25:34 +00:00
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
Replace `unittest.TestCase` in API, framework, performance, Selenium and ToolShed tests
2022-11-07 15:44:01 +00:00
test_celery_tasks.py
Merge branch 'release_23.2' into dev
2024-01-18 12:23:00 +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
Move more setup code into handle_galaxy_config_kwds which has test_driver configured
2026-01-01 15:08:26 +01:00
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
Use test_driver.mkdtemp systematically
2026-01-01 15:08:26 +01:00
test_containerized_jobs.py
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
test_credentials.py
Updates API routes to use plural 'groups' for credential group endpoints
2025-10-07 16:07:59 +02:00
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
Add data manager bundle workflow integration test
2024-02-16 15:53:16 +01:00
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
Calculate hash for new non-deferred datasets when finishing a job
2024-11-21 15:55:14 +00:00
test_datatype_upload.py
Merge pull request #17106 from tuncK/tarxz
2024-03-01 11:03:36 -05:00
test_default_permissions.py
Use `history_id` fixture instead of instance attribute. More type annotations
2022-11-23 04:04:51 +00:00
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_error_report.py
tool error integration test
2024-04-11 10:09:05 -04:00
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
Test `from_work_dir="dir"` feature
2025-10-01 09:01:31 +02:00
test_fail_job_tool_unavailable.py
YamlToolSource parser fixes
2025-05-12 10:54:24 +02:00
test_fluent_metrics.py
Replace `unittest.TestCase` with pytest-based partial re-implementation
2022-09-27 03:34:58 +01:00
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_history_archiving.py
Deduplicate history archive test additions
2025-12-18 12:38:55 -05:00
test_history_import_export.py
Type annotation fixes for mypy 1.16.0
2025-06-10 02:22:18 +01:00
test_interactivetools_api.py
Move more setup code into handle_galaxy_config_kwds which has test_driver configured
2026-01-01 15:08:26 +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
Code cleanups from pyupgrade
2025-07-31 11:17:22 +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
fix test
2025-03-26 18:07:57 +01:00
test_kubernetes_runner.py
Move more setup code into handle_galaxy_config_kwds which has test_driver configured
2026-01-01 15:08:26 +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_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
Calculate hash for new non-deferred datasets when finishing a job
2024-11-21 15:55:14 +00:00
test_max_discovered_files.py
Fix up integration test for max discovered files
2024-03-01 22:45:39 -05:00
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_notifications.py
Adjust API tests
2025-09-23 22:16:20 +02:00
test_page_revision_json_encoding.py
Type annotation improvements
2025-02-21 15:46:14 +00:00
test_panel_views.py
Merge branch 'release_23.1' into dev
2023-11-21 09:36:51 +01:00
test_plugins.py
Lint test
2026-01-08 15:39:31 +03:00
test_prefix_handling.py
Various fixes to path prefix handling
2023-05-05 16:38:17 +02:00
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_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
Attempt to fix typing issues in integration tests.
2023-05-24 13:20:21 -04:00
test_quota.py
remove assert
2024-09-19 09:39:08 +02:00
test_recalculate_user_disk_usage.py
Fix new linting errors from flake8 6.1.0
2023-10-19 12:53:59 +01:00
test_remote_files_histories.py
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
test_remote_files_posix.py
Type annotation fixes for mypy 1.16.0
2025-06-10 02:22:18 +01:00
test_remote_files.py
Use test_driver.mkdtemp systematically
2026-01-01 15:08:26 +01:00
test_repository_operations.py
Remove transaction helper from test.integration
2025-01-23 11:39:24 -05:00
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
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
test_scripts.py
Format code with black 25.1.0
2025-02-16 18:07:51 +00:00
test_shed_tool_tests.py
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
test_storage_cleaner.py
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
test_structured_dataset.py
Fix new UP031 errors from ruff 0.4.2
2024-04-29 00:09:38 +01:00
test_tool_data_bundles.py
Push extra files from object store cache to object store
2023-08-26 08:30:16 +02:00
test_tool_data_delete.py
Use test_driver.mkdtemp systematically
2026-01-01 15:08:26 +01:00
test_tool_submission_errors.py
Serialize message exceptions on execution error
2025-01-30 09:43:55 +01:00
test_upload_configuration_options.py
Tests for preserving column definitions in different metadata collection strategies.
2025-08-14 09:57:45 -04:00
test_user_defined_tool_job_conf.py
Uncomment basic test assrtions
2025-09-30 21:09:34 +01:00
test_user_preferences.py
Add first user data access tests
2024-06-10 15:48:10 -04:00
test_users.py
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
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
Restore original filename for file_source_conf_webdav.yml
2023-06-14 19:27:31 +05:30
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_handler_configuration.py
Type annotation improvements
2025-02-21 15:46:14 +00:00
test_workflow_invocation.py
Add test for keeping picked dataset's extension in place
2024-09-10 18:50:12 +02:00
test_workflow_refactoring.py
Code cleanups from pyupgrade
2025-07-31 11:17:22 +01:00
test_workflow_scheduling_options.py
Merge branch 'release_23.2' into dev
2024-03-04 13:02:17 -05:00
test_workflow_sync.py
Format Python code with black 23.1.0
2023-02-01 23:51:03 +00:00
test_workflow_tasks.py
Merge branch 'release_25.0' into release_25.1
2025-10-31 11:58:58 +00:00
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
…