John Chilton 821b31c3b2 More structured indexing for user data objects. ...

I think I clung to the idea of having two ways to do this too long. I did a bunch of testing with the old way (exposing integer references based on numeric database primary keys). Having a config option that if changed would break everything exisiting is also a symptom of maybe me clinging too hard for too long.

The result of dropping this option is a much cleaner API schema, simpler API objects, and better typing throughout. We can also be more certain of how things entering the Vault are stored - I think being more strucutured about this is good.

Ultimately, the future facing stuff (e.g. OAuth 2.0) is going to require UUIDs so that I can store things like refresh tokens in the store before the object has been fully created.

2024-06-07 19:20:11 -04:00

..

chained_dyndest_rules

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

cloudauthz

Format Python code with black 23.1.0

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

delay_rules

Integration test for job recovery (before and after handler has picked it up).

2018-08-21 15:17:12 -04:00

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

More structured indexing for user data objects.

2024-06-07 19:20:11 -04:00

objectstore_selection_rules

Apply black formatting.

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

oidc

Create wrapper for requests with default user agent

2024-04-16 17:54:29 +02:00

panel_views_1

Exclude multiple_versions from test_global_filters_on_integrated_panel

2023-11-16 15:08:21 +01:00

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

Fix things found by @mvdbeek

2016-04-05 14:59:09 -04:00

chained_dyndest_job_conf.xml

Cleanup integration test configuration code.

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

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

Disable conda_auto_init in embedded_pulsar_metadata_extended_job_conf.yml

2023-11-21 17:44:37 +01:00

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

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

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

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

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.

2022-02-03 07:42:20 -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

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

Merge branch 'release_23.2' into dev

2024-01-18 12:23:00 +01:00

test_celery_user_rate_limit.py

Fix integration tests for Celery 5.4.0

2024-04-25 18:16:39 +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_cli_runners.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_coexecution.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_containerized_jobs.py

follow-up restucture integration tests

2023-06-14 15:32:18 +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

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_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_display_applications.py

Update to black 2024 stable style

2024-01-30 18:09:51 +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

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

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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

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

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

Revert some requests import changes

2024-05-23 15:55:56 +01:00

test_job_environments.py

Disable conda_auto_init in embedded_pulsar_metadata_extended_job_conf.yml

2023-11-21 17:44:37 +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

Raise appropriate exception if accessing deleted input file

2024-05-24 18:26:18 +02:00

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

Enable flake8-comprehensions ruff rules

2024-03-09 19:11:20 +00:00

test_kubernetes_runner.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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

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

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

Adapt notification integration tests to work w/o tasks

2024-04-16 17:31:53 +02:00

test_page_revision_json_encoding.py

Fix `test_page_encoding` test

2024-03-04 14:40:11 +00:00

test_panel_views.py

Merge branch 'release_23.1' into dev

2023-11-21 09:36:51 +01:00

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 a tool with from_working_dir and pulsar

2019-12-13 22:58:32 +01:00

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

Disable conda_auto_init in embedded_pulsar_metadata_extended_job_conf.yml

2023-11-21 17:44:37 +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

Change wrong quota_source value from KeyError to ValueError

2024-04-22 19:44:31 +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

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

Fix new UP031 errors from ruff 0.4.2

2024-04-29 00:09:38 +01:00

test_resolvers.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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_pgcleanup.py

Augment pgcleanup to allow periodically deleting old datasets.

2023-09-25 15:10:13 -04:00

test_scripts.py

Augment pgcleanup to allow periodically deleting old datasets.

2023-09-25 15:10:13 -04:00

test_shed_tool_tests.py

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

test_storage_cleaner.py

Merge branch 'release_23.1' into dev

2023-10-29 09:05:09 +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

Send reload message after data bundle import is complete

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

test_upload_configuration_options.py

Rename classes derived from `IntegrationInstance` which are not test cases

2024-02-16 10:53:04 +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_users.py

Fix linting unnecessary list literal

2024-06-07 11:51:26 +02:00

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

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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

Add json keyword in tests calling invoke endpoint

2024-02-26 18:06:48 +01:00

test_workflow_invocation.py

Access the error message of invoke endpoint correctly

2024-02-26 18:06:49 +01:00

test_workflow_refactoring.py

Adjust integration test for additional conditional

2024-04-09 11:50:52 +02:00

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

Update to black 2024 stable style

2024-01-30 18:09:51 +00:00

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

[17.01] Restrict workflow scheduling within a history to a fixed, random handler.

2017-03-29 22:20:41 -04:00