Ahmed Awan a739f88aa6 Restore deprecated ToolsApi and create new api route for new panel structure ...

- restore `api/tools` that had the older (list of tool sections
  with `.elems`) structure
- but use the new `api/tool_panel` structure in the client

2023-10-17 13:58:43 -05:00

..

chained_dyndest_rules

Apply black formatting.

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

cloudauthz

Format Python code with black 23.1.0

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

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

Switch to trailing underscore

2023-07-31 18:51:40 +02:00

objectstore_selection_rules

Apply black formatting.

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

panel_views_1

Fix short ids in tool panel views.

2023-10-06 12:38:06 -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

…

chained_dyndest_job_conf.xml

…

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

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.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

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

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

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

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.

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

resubmission_small_memory_job_conf.xml

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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_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

Fix SA2.0 syntax (query->select) in integration tests

2023-07-21 13:04:23 -04:00

test_celery_user_rate_limit.py

Pass user id to celery tasks to enable new user rate limiting functionality.

2023-07-12 10:35:54 -04:00

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

Rename class which is not derived from `TestCase`

2022-11-07 15:44:03 +00:00

test_cli_runners.py

Update and apply ruff refactorings

2023-08-09 17:14:07 +02:00

test_coexecution.py

Fixes for Pulsar 0.15.0.

2023-02-09 09:51:27 -05:00

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

Apply suggestions from code review

2023-06-20 10:30:19 +02:00

test_containerized_jobs.py

follow-up restucture integration tests

2023-06-14 15:32:18 +01:00

test_data_manager_refgenie.py

Even more typing

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

test_data_manager.py

Even more typing

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

test_datatype_upload.py

Fix test_objectstore_datatype_upload.py . More type annotations

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

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

Restore deprecated ToolsApi and create new api route for new panel structure

2023-10-17 13:58:43 -05:00

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

Fix and extend extended metadata outputs to working directory tests

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

test_extended_metadata.py

Fix and extend extended metadata outputs to working directory tests

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

test_fail_job_tool_unavailable.py

use history_id fixture instead of instance variable with the same name

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

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

Format Python code with black 23.1.0

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

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

Format Python code with black 23.1.0

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

test_history_archiving.py

Increase test coverage + fixes

2023-06-19 09:44:17 +02:00

test_history_import_export.py

Refactor history archival testing related actions

2023-06-19 09:39:55 +02:00

test_interactivetools_api.py

Merge branch 'release_22.05' into dev

2023-01-03 13:13:53 -08:00

test_job_environments.py

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

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

test_job_files.py

Fix SA2.0 syntax (query->select) in integration tests

2023-07-21 13:04:23 -04:00

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

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

Format Python code with black 23.1.0

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

test_kubernetes_runner.py

Fix SA2.0 syntax (query->select) in integration tests

2023-07-21 13:04:23 -04:00

test_local_job_cancellation.py

Fix SA20 syntax in test_local_job_cancel., refactor

2023-07-21 13:04:23 -04:00

test_materialize_dataset_instance_tasks.py

Fix test failures

2023-02-09 18:14:18 +05:30

test_max_discovered_files.py

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

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

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

remove notification favorite field from backend and update schema, migration and tests

2023-06-14 14:16:11 +02:00

test_page_revision_json_encoding.py

Fix new errors from ruff 0.0.279

2023-07-23 16:25:27 +01:00

test_panel_views.py

Restore deprecated ToolsApi and create new api route for new panel structure

2023-10-17 13:58:43 -05:00

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

Fix tool stdio on pulsar and implement job stdio

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

test_pulsar_embedded_mq.py

Extend pulsar test cases with composite_output_tests

2023-08-24 10:44:40 +02:00

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

Extend pulsar test cases with composite_output_tests

2023-08-24 10:44:40 +02:00

test_purge_datasets.py

Attempt to fix typing issues in integration tests.

2023-05-24 13:20:21 -04:00

test_quota.py

Implement quota tracking options per ObjectStore.

2023-02-19 10:33:21 -05:00

test_recalculate_user_disk_usage.py

Extend test to reproduce disk usage recalculation wrongly dropping to 0 when no quota source is defined

2023-07-07 22:09:49 +10:00

test_remote_files_histories.py

Format Python code with black 23.1.0

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

test_remote_files_posix.py

Relax file source access requirements in tests

2022-12-08 13:33:08 +01:00

test_remote_files.py

Manually compute hash in test of drs fetch

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

test_repository_operations.py

Merge branch 'release_23.1' into dev

2023-10-06 16:17:22 -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

Fix SA2.0 syntax (query->select) in integration tests

2023-07-21 13:04:23 -04:00

test_scripts.py

Drop test for help display in deleted scripts

2023-02-08 00:39:42 -05:00

test_shed_tool_tests.py

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

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

test_storage_cleaner.py

Add missing API endpoints to deal with archived cleanup

2023-07-27 13:23:35 +02:00

test_structured_dataset.py

Attempt to fix typing issues in integration tests.

2023-05-24 13:20:21 -04:00

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

Send reload message after data bundle import is complete

2023-09-03 18:24:28 +02:00

test_upload_configuration_options.py

Format Python code with black 23.1.0

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

test_user_preferences.py

Refactor get_user_by_username, get_user_by_email; use across code base

2023-09-25 09:23:08 -04:00

test_vault_extra_prefs.py

Refactor get_user_by_username, get_user_by_email; use across code base

2023-09-25 09:23:08 -04:00

test_vault_file_source.py

Refactor get_user_by_username, get_user_by_email; use across code base

2023-09-25 09:23:08 -04:00

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

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

Fix SA2.0 syntax (query->select) in integration tests

2023-07-21 13:04:23 -04:00

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

Merge branch 'release_23.1' into dev

2023-08-09 16:06:08 +02:00

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

Format Python code with black 23.1.0

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

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

workflow_handler_configuration_job_conf.xml

…