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galaxy/test/integration
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Nicola Soranzo 6a6abf37ef Split run_tool_raw() out of BaseDatasetPopulator.run_tool() 
so that the former always returns a `Response` object while the latter
returns the response content.

Also:
- In `CwlPopulator.run_cwl_job()` wait for the run only if `assert_ok`
  is True; if the `wait()` call fails, summarize history also for
  workflow runs.
2021-11-27 03:14:52 +00:00
..
chained_dyndest_rules
fix chained dynamic destinations integration test
2021-02-25 13:49:19 +01:00
cloudauthz
Minor test cleanup
2020-09-18 12:28:33 +02:00
delay_rules
Integration test for job recovery (before and after handler has picked it up).
2018-08-21 15:17:12 -04:00
mock_biotools_content/data
Parse edam operation and topic data from bio.tools if available.
2021-09-07 14:29:38 -04:00
objectstore
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
objectstore_selection_rules
Allow configuring object stores on a per-job-destination basis.
2018-08-06 11:29:08 -04:00
panel_views_1
Allow static panel views without explicit "items" - just start with integrated panel and apply filters.
2021-09-15 10:50:57 -04:00
resubmission_rules
Allow YAML configuration of job_conf.xml.
2019-05-07 08:23:30 -04:00
webdav
Pluggable URI handling across upload components.
2020-07-14 10:09:50 -04:00
__init__.py
…
chained_dyndest_job_conf.xml
Cleanup integration test configuration code.
2019-05-02 08:45:11 -04:00
conftest.py
Shut down driver instance after collection
2021-10-19 13:27:15 +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
Support setting per-job-environment container resolvers using the container_resolvers key in the environment config.
2021-08-17 10:28:51 -04:00
embedded_pulsar_docker_job_conf.yml
Use remote_metadata: true when using extended metadata
2021-10-26 17:59:05 +02:00
embedded_pulsar_job_conf.xml
Use remote_metadata: true when using extended metadata
2021-10-26 17:59:05 +02:00
embedded_pulsar_metadata_extended_job_conf.yml
Allow specifying useful classes of tools for mapping in job conf.
2021-07-14 13:46:56 -04:00
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
Allow specifying useful classes of tools for mapping in job conf.
2021-07-14 13:46:56 -04:00
file_sources_conf.yml
Pluggable URI handling across upload components.
2020-07-14 10:09:50 -04:00
handler_template_job_conf.xml
Integration tests for handler assignment methods
2019-01-04 16:46:29 -05:00
io_injection_job_conf.yml
Allow YAML configuration of job_conf.xml.
2019-05-07 08:23:30 -04:00
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
Allow YAML configuration of job_conf.xml.
2019-05-07 08:23:30 -04:00
resubmission_pulsar_job_conf.xml
Allow specifying useful classes of tools for mapping in job conf.
2021-07-14 13:46:56 -04:00
resubmission_runners.py
mypy for test/
2020-12-25 17:38:51 -05:00
resubmission_small_memory_job_conf.xml
Allow YAML configuration of job_conf.xml.
2019-05-07 08:23:30 -04:00
resubmission_small_memory_resubmission_to_large_job_conf.xml
Tool-centric annotation of out of memory errors.
2017-12-22 09:08:18 -05:00
resubmission_tool_detected_always_error_job_conf.xml
Fix resubmission on tool error detection.
2018-11-23 14:32:04 +01:00
resubmission_tool_detected_resubmit_job_conf.xml
Fix resubmission on tool error detection.
2018-11-23 14:32:04 +01:00
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
Cleanup integration test configuration code.
2019-05-02 08:45:11 -04:00
simple_job_conf.xml
Fix failing integration test.
2019-05-03 08:38:33 -04:00
singularity_job_conf.yml
Support setting per-job-environment container resolvers using the container_resolvers key in the environment config.
2021-08-17 10:28:51 -04:00
test_celery_tasks.py
Allow passing Pydantic models as arguments to Celery tasks.
2021-10-13 22:32:36 -04:00
test_chained_dynamic_destinations.py
Move galaxy testing utilities into more sane package structure.
2019-11-12 09:03:06 -05:00
test_change_datatype_with_store_by_id.py
Move test_assign_column_pja to own class
2020-08-11 14:53:53 +02:00
test_cli_runners.py
Move ssh_util from galaxy_test.base to galaxy.security
2021-11-09 14:37:48 +01:00
test_config_defaults.py
Merge branch 'release_21.09' into dev
2021-10-28 11:40:04 +02:00
test_config_options_users.py
Move galaxy testing utilities into more sane package structure.
2019-11-12 09:03:06 -05:00
test_config_schema.py
Move schema loading/validating code out of config
2020-03-02 15:55:29 -05:00
test_configuration_decode.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
test_containerized_jobs.py
Support setting per-job-environment container resolvers using the container_resolvers key in the environment config.
2021-08-17 10:28:51 -04:00
test_data_manager_refgenie.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_data_manager.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_datatype_upload.py
Rev mypy.
2021-04-23 14:49:53 -04:00
test_default_permissions.py
Test cases and fix for config option new_user_dataset_access_role_default_private.
2020-12-01 09:05:57 -05:00
test_dynamic_edam_loading.py
Parse edam operation and topic data from bio.tools if available.
2021-09-07 14:29:38 -04:00
test_edam_toolbox.py
Implement tool panel views - config, toolbox, search, client.
2021-08-11 10:14:43 -04:00
test_extended_metadata_mapping.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
test_extended_metadata_outputs_to_working_directory.py
Run extended_metadata integration tests with outputs_to_working_directory as well
2019-11-14 12:20:48 +01:00
test_extended_metadata.py
Tighten test
2021-10-23 21:32:18 +02:00
test_fail_job_tool_unavailable.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
test_fluent_metrics.py
Replace API test with integration test
2021-03-10 12:54:41 +01:00
test_flush_per_n_datasets.py
Add test for paired discovery and fix paired discovery
2021-03-23 10:29:34 +01:00
test_galaxy_interactor.py
Merge API GalaxyInteractorTestCase into integration test
2021-09-23 19:05:30 +02:00
test_genomes.py
Add tests for sequences and indexes endpoints
2021-02-10 15:55:21 -05:00
test_handler_assignment_methods.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
test_history_import_export.py
Type fixes: integration_setup.py
2021-10-11 16:32:29 -04:00
test_interactivetools_api.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_job_environments.py
Fix isolated job home dir on pulsar
2021-05-21 21:01:58 +02:00
test_job_outputs_to_working_directory.py
Update test class docstring
2021-01-07 17:53:29 +01:00
test_job_recovery.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_job_resubmission.py
fix mutable arguments in tests
2021-01-02 18:48:31 +00:00
test_kubernetes_runner.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_kubernetes_staging.py
Run kubernetes staging test against uvicorn
2021-04-13 10:13:42 +02:00
test_local_job_cancellation.py
Split run_tool_raw() out of BaseDatasetPopulator.run_tool()
2021-11-27 03:14:52 +00:00
test_mules_as_job_handlers.py
Move galaxy testing utilities into more sane package structure.
2019-11-12 09:03:06 -05:00
test_page_revision_json_encoding.py
Fix pages integration test
2021-02-11 16:01:34 +01:00
test_panel_views.py
Allow static panel views without explicit "items" - just start with integrated panel and apply filters.
2021-09-15 10:50:57 -04:00
test_pulsar_embedded_containers.py
try something else
2021-03-31 13:42:17 +02:00
test_pulsar_embedded_copy_working.py
test a tool with from_working_dir and pulsar
2019-12-13 22:58:32 +01:00
test_pulsar_embedded_extended_metadata.py
Fix from work dir glob with extended metadata
2021-10-31 13:06:41 +01:00
test_pulsar_embedded_mq.py
Use remote_metadata in pulsar_embedded_mq test
2021-10-26 17:59:07 +02:00
test_pulsar_embedded_remote_metadata.py
Separate tests for "remote" and "remote + extended" metadata.
2021-04-14 13:21:15 -04:00
test_pulsar_embedded.py
Fix Pulsar's ability to read tool provided metadata when path is overridden.
2021-07-21 15:21:26 -04:00
test_quota.py
Adapt quotas tests to use JSON payload
2021-09-08 18:34:37 +02:00
test_remote_files_histories.py
Allow history export to galaxy.files plugins.
2020-12-26 08:36:48 -05:00
test_remote_files_posix.py
Type fixes: integration_setup.py
2021-10-11 16:32:29 -04:00
test_remote_files.py
Typing fixes for integration tests around galaxy.files stuff.
2021-10-11 16:32:30 -04:00
test_repository_operations.py
Merge branch 'release_21.01' into release_21.05
2021-07-30 16:34:18 +02:00
test_resolvers.py
Make conda test methods self-contained
2021-10-18 08:50:13 +02:00
test_save_job_id_on_datasets.py
Make sure test driver shuts down on failure
2021-10-26 17:59:04 +02:00
test_scripts.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
test_shed_tool_tests.py
Fix installation of tools with biotools id
2021-11-15 10:14:56 +01:00
test_tool_data_delete.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
test_upload_configuration_options.py
improve type hints for test/integration/test_upload_configuration_options.py.
2021-11-12 19:00:33 +01:00
test_web_framework_config.py
FastAPI/ASGI CORS handling.
2021-01-27 19:55:48 -05:00
test_webdav.py
More comments for rapid testing optional galaxy.files stuff.
2020-10-22 09:30:50 -04:00
test_work_queue_put_failure.py
Replace usage of mkstemp with NamedTemporaryFile
2020-12-07 22:31:53 +01:00
test_workflow_handler_configuration.py
Don't start workflow scheduler for handler in job pool
2021-06-15 18:23:49 +02:00
test_workflow_refactoring.py
Merge remote-tracking branch 'upstream/release_21.01' into dev
2021-03-01 16:52:02 -05:00
test_workflow_scheduling_options.py
New pyupgrade fixes
2021-10-24 12:10:34 +01:00
test_workflow_sync.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
tool_sheds_conf.xml
py3: fix installing and running data managers
2018-08-14 14:56:06 +02:00
uses_shed.py
typing fixes for integration testing framework stuff...
2021-10-14 00:51:59 -04:00
workflow_handler_configuration_job_conf.xml
[17.01] Restrict workflow scheduling within a history to a fixed, random handler.
2017-03-29 22:20:41 -04:00