John Chilton 5a3069d283 Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes. ...

Updating the Pulsar job runner/client for https://github.com/galaxyproject/pulsar/pull/302 and as described in the new docs at https://pulsar.readthedocs.io/en/latest/containers.html.

2022-10-16 09:56:58 +02:00

..

chained_dyndest_rules

Apply black formatting.

2022-02-03 07:42:20 -05:00

cloudauthz

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

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

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

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

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

objectstore_selection_rules

Apply black formatting.

2022-02-03 07:42:20 -05:00

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

Apply black formatting.

2022-02-03 07:42:20 -05:00

webdav

Pluggable URI handling across upload components.

2020-07-14 10:09:50 -04:00

__init__.py

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chained_dyndest_job_conf.xml

Cleanup integration test configuration code.

2019-05-02 08:45:11 -04:00

conftest.py

Enable celery in API, Selenium, Integration tests

2022-05-25 19:46:47 +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

Drop more uWSGI legacy things

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

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.

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embedded_pulsar_metadata_job_conf.yml

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

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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_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

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.

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resubmission_dynamic_job_conf.xml

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

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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

Apply black formatting.

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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_async_downloads.py

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

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

test_celery_tasks.py

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

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

test_chained_dynamic_destinations.py

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

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

test_change_datatype_with_store_by_id.py

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

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

test_cli_runners.py

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

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

test_coexecution.py

Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes.

2022-10-16 09:56:58 +02:00

test_config_options_users.py

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

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

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_containerized_jobs.py

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

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

test_data_manager_refgenie.py

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

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

test_data_manager.py

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

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

test_datatype_upload.py

Misc test fixes

2022-09-27 03:34:55 +01:00

test_default_permissions.py

Misc test fixes

2022-09-27 03:34:55 +01:00

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

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

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

test_extended_metadata_mapping.py

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

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

test_extended_metadata_outputs_to_working_directory.py

Apply black formatting.

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test_extended_metadata.py

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

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

test_fail_job_tool_unavailable.py

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

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

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

Use celery in more integration tests

2022-05-26 12:48:44 +02:00

test_galaxy_interactor.py

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

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

test_genomes.py

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

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

test_handler_assignment_methods.py

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

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

test_history_import_export.py

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

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

test_interactivetools_api.py

Pulsar infrastructure improvements for TES execution and MQ-less Kubernetes.

2022-10-16 09:56:58 +02:00

test_job_environments.py

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

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

test_job_files.py

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

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

test_job_outputs_to_working_directory.py

Use celery in more integration tests

2022-05-26 12:48:44 +02:00

test_job_recovery.py

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

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

test_job_resubmission.py

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

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

test_kubernetes_runner.py

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

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

test_local_job_cancellation.py

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

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

test_materialize_dataset_instance_tasks.py

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

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

test_max_discovered_files.py

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

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

test_model_store_scripts.py

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

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

test_page_revision_json_encoding.py

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

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

test_panel_views.py

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

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

test_pulsar_embedded_containers.py

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

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

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

Apply black formatting.

2022-02-03 07:42:20 -05:00

test_pulsar_embedded_mq.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

test_pulsar_embedded_remote_metadata.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

test_pulsar_embedded.py

Use celery in more integration tests

2022-05-26 12:48:44 +02:00

test_quota.py

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

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

test_remote_files_histories.py

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

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

test_remote_files_posix.py

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

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

test_remote_files.py

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

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

test_repository_operations.py

Extend tool shed install testing to include index API.

2022-10-10 11:19:18 -04:00

test_resolvers.py

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

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

test_save_job_id_on_datasets.py

Apply black formatting.

2022-02-03 07:42:20 -05:00

test_scripts.py

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

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

test_shed_tool_tests.py

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

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

test_tool_data_delete.py

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

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

test_upload_configuration_options.py

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

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

test_vault_extra_prefs.py

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

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

test_vault_file_source.py

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

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

test_web_framework_config.py

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

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

test_webdav.py

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

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

test_work_queue_put_failure.py

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

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

test_workflow_handler_configuration.py

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

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

test_workflow_invocation.py

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

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

test_workflow_refactoring.py

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

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

test_workflow_scheduling_options.py

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

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

test_workflow_sync.py

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

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

test_workflow_tasks.py

Validate BioCompute Objects against schema in tests

2022-10-14 12:20:24 +02:00

user_preferences_extra_conf.yml

Change vault api test case to integration test case and add missing conditional requirements

2021-12-20 18:23:00 +05:30

vault_conf.yml

Make sure filesources can access user level and app level vaults

2021-11-28 06:56:35 +05:30

workflow_handler_configuration_job_conf.xml

…