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John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
2022-05-23 19:48:47 -04:00
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chained_dyndest_rules
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cloudauthz
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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
Add DEFERRED datasets to Galaxy
2022-05-23 19:48:47 -04:00
objectstore_selection_rules
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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
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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
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2022-02-03 07:42:20 -05:00
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.
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_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.
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
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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
Implement asynchronous download APIs using STS.
2022-04-13 09:53:56 -04:00
test_celery_tasks.py
Add DEFERRED datasets to Galaxy
2022-05-23 19:48:47 -04:00
test_chained_dynamic_destinations.py
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2022-02-03 07:42:20 -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
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2022-02-03 07:42:20 -05:00
test_config_defaults.py
Apply URI access checks more uniformly.
2022-05-21 17:22:41 -04:00
test_config_options_users.py
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test_config_schema.py
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test_configuration_decode.py
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test_containerized_jobs.py
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test_data_manager_refgenie.py
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test_data_manager.py
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test_datatype_upload.py
Switch most tests to use `__DATA_FETCH__ instead of upload1`
2022-04-23 12:05:54 +02:00
test_default_permissions.py
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2022-02-03 07:42:20 -05:00
test_dynamic_edam_loading.py
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2022-02-03 07:42:20 -05:00
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
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test_extended_metadata_outputs_to_working_directory.py
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2022-02-03 07:42:20 -05:00
test_extended_metadata.py
Improved typing of Galaxy model store related stuff.
2022-05-04 12:11:17 -04:00
test_fail_job_tool_unavailable.py
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test_fluent_metrics.py
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test_flush_per_n_datasets.py
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test_galaxy_interactor.py
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test_genomes.py
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test_handler_assignment_methods.py
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test_history_import_export.py
Add DEFERRED datasets to Galaxy
2022-05-23 19:48:47 -04:00
test_interactivetools_api.py
Raise exception when waiting for entry point
2022-03-15 21:32:00 +01:00
test_job_environments.py
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test_job_outputs_to_working_directory.py
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test_job_recovery.py
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test_job_resubmission.py
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2022-02-03 07:42:20 -05:00
test_kubernetes_runner.py
Switch most tests to use `__DATA_FETCH__ instead of upload1`
2022-04-23 12:05:54 +02:00
test_kubernetes_staging.py
Switch most tests to use `__DATA_FETCH__ instead of upload1`
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test_local_job_cancellation.py
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test_materialize_dataset_instance_tasks.py
Add DEFERRED datasets to Galaxy
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test_max_discovered_files.py
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test_model_store_scripts.py
Add DEFERRED datasets to Galaxy
2022-05-23 19:48:47 -04:00
test_page_revision_json_encoding.py
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test_panel_views.py
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test_pulsar_embedded_containers.py
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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
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test_pulsar_embedded_mq.py
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test_pulsar_embedded_remote_metadata.py
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test_pulsar_embedded.py
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test_quota.py
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test_remote_files_histories.py
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test_remote_files_posix.py
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test_remote_files.py
Don't do extra json.dumps of targets
2022-04-25 18:28:01 +02:00
test_repository_operations.py
Add FastAPI route for tools/fetch
2022-04-23 12:01:32 +02:00
test_resolvers.py
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2022-02-03 07:42:20 -05:00
test_save_job_id_on_datasets.py
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2022-02-03 07:42:20 -05:00
test_scripts.py
Add create/migrate scripts for Alembic dbs (squashed)
2022-03-09 18:41:02 -05:00
test_shed_tool_tests.py
Fix tool id not getting updated on tool update
2022-01-19 14:46:31 +01:00
test_tool_data_delete.py
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2022-02-03 07:42:20 -05:00
test_upload_configuration_options.py
Wait for datasets / collections
2022-04-26 11:12:37 +02:00
test_vault_extra_prefs.py
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test_vault_file_source.py
Don't do extra json.dumps of targets
2022-04-25 18:28:01 +02:00
test_web_framework_config.py
First pass in dropping uwsgi specific things
2022-03-15 21:31:59 +01:00
test_webdav.py
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test_work_queue_put_failure.py
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test_workflow_handler_configuration.py
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test_workflow_invocation.py
More structured and typed workflow test helpers.
2022-03-31 17:22:46 -04:00
test_workflow_refactoring.py
modify update_step_position refactor action to make change relative to previous position
2022-03-31 14:08:57 +02:00
test_workflow_scheduling_options.py
Switch most tests to use `__DATA_FETCH__ instead of upload1`
2022-04-23 12:05:54 +02:00
test_workflow_sync.py
Drop support for retired Python 3.5
2020-10-07 11:52:13 +01:00
test_workflow_tasks.py
Add DEFERRED datasets to Galaxy
2022-05-23 19:48:47 -04:00
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
[17.01] Restrict workflow scheduling within a history to a fixed, random handler.
2017-03-29 22:20:41 -04:00