├── .coveragerc ├── .gitattributes ├── .github ├── dependabot.yml └── workflows │ ├── ci.yml │ └── docker.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yml ├── LICENSE ├── MANIFEST.in ├── README.rst ├── docs ├── CHANGELOG.rst ├── api.rst ├── composer.rst ├── conf.py ├── contributing.rst ├── example │ └── example │ │ └── processes │ │ ├── all_fields.yml │ │ ├── example.py │ │ ├── example.yml │ │ ├── example_basic.py │ │ ├── minimal.py │ │ └── template_py_process.py ├── flow.rst ├── images │ ├── proc_01.png │ ├── proc_02_flow.png │ ├── proc_03_types.png │ ├── resolwe_01_context.png │ ├── resolwe_02_internals.png │ ├── resolwe_03_workflow.png │ └── resolwe_04_workers.png ├── index.rst ├── intro.rst ├── overview.rst ├── proc.rst ├── ref.rst └── storage.rst ├── pyproject.toml ├── resolwe ├── __init__.py ├── api_urls.py ├── auditlog │ ├── __init__.py │ ├── apps.py │ ├── auditmanager.py │ ├── logger.py │ ├── middleware.py │ └── models.py ├── composer.py ├── db │ ├── __init__.py │ └── postgresql │ │ ├── __init__.py │ │ └── base.py ├── flow │ ├── __init__.py │ ├── admin.py │ ├── apps.py │ ├── docker_images │ │ ├── Dockerfile.communication │ │ └── Readme.md │ ├── engine.py │ ├── exceptions.py │ ├── execution_engines │ │ ├── __init__.py │ │ ├── base.py │ │ ├── bash │ │ │ └── __init__.py │ │ ├── exceptions.py │ │ ├── python │ │ │ └── __init__.py │ │ └── workflow │ │ │ └── __init__.py │ ├── executors │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── constants.py │ │ ├── docker │ │ │ ├── __init__.py │ │ │ ├── prepare.py │ │ │ └── run.py │ │ ├── global_settings.py │ │ ├── init_container.py │ │ ├── local │ │ │ ├── __init__.py │ │ │ ├── prepare.py │ │ │ └── run.py │ │ ├── logger.py │ │ ├── null │ │ │ ├── __init__.py │ │ │ ├── prepare.py │ │ │ └── run.py │ │ ├── prepare.py │ │ ├── protocol.py │ │ ├── requirements.txt │ │ ├── run.py │ │ ├── socket_utils.py │ │ ├── startup_communication_container.py │ │ ├── startup_processing_container.py │ │ ├── transfer.py │ │ └── zeromq_utils.py │ ├── expression_engines │ │ ├── __init__.py │ │ ├── base.py │ │ ├── exceptions.py │ │ └── jinja │ │ │ ├── __init__.py │ │ │ └── filters.py │ ├── filters.py │ ├── finders.py │ ├── management │ │ ├── __init__.py │ │ └── commands │ │ │ ├── __init__.py │ │ │ ├── cleantestdir.py │ │ │ ├── clear_redis_cache.py │ │ │ ├── collecttools.py │ │ │ ├── collecttools_kubernetes.py │ │ │ ├── list_docker_images.py │ │ │ ├── migrate_annotations.py │ │ │ ├── prepare_runtime.py │ │ │ ├── register.py │ │ │ ├── runlistener.py │ │ │ └── test_data_output.py │ ├── managers │ │ ├── __init__.py │ │ ├── consumer.py │ │ ├── dispatcher.py │ │ ├── listener │ │ │ ├── __init__.py │ │ │ ├── authenticator.py │ │ │ ├── basic_commands_plugin.py │ │ │ ├── bootstrap_plugin.py │ │ │ ├── listener.py │ │ │ ├── metrics.py │ │ │ ├── permission_plugin.py │ │ │ ├── plugin.py │ │ │ ├── plugin_interface.py │ │ │ ├── python_process_plugin.py │ │ │ └── redis_cache.py │ │ ├── protocol.py │ │ ├── state.py │ │ ├── utils.py │ │ └── workload_connectors │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── celery.py │ │ │ ├── kubernetes.py │ │ │ ├── local.py │ │ │ └── slurm.py │ ├── migration_ops.py │ ├── migrations │ │ ├── 0001_squashed_0043_full_text_search.py │ │ ├── 0002_squashed_0049_json_field.py │ │ ├── 0003_add_permission_group.py │ │ ├── 0004_data_process_resources.py │ │ ├── 0005_duplicate_data_dependency.py │ │ ├── 0006_add_descriptor_to_relation.py │ │ ├── 0007_alter_data_process_rc.py │ │ ├── 0008_annotations.py │ │ ├── 0009_preset_base_model.py │ │ ├── 0010_annotationfield_required.py │ │ ├── 0011_annotationpreset_contributor_correct_user.py │ │ ├── 0012_alter_relation_category.py │ │ ├── 0013_alter_annotationpreset_permission_group_and_more.py │ │ ├── 0014_alter_annotationfield_validator_regex.py │ │ ├── 0015_alter_annotationfield_vocabulary.py │ │ ├── 0016_annotationvalue_uniquetogether_entity_field.py │ │ ├── 0017_collectionhistory_datahistory_sizechange_and_more.py │ │ ├── 0018_add_annotationvalue_default_order.py │ │ ├── 0019_alter_annotationpreset_modified_and_more.py │ │ ├── 0020_alter_annotationvalue_field.py │ │ ├── 0021_annotationvalue_modified.py │ │ ├── 0022_fix_group_by.py │ │ ├── 0023_remove_entity_descriptor_and_more.py │ │ ├── 0024_update_sql_entity_methods.py │ │ ├── 0025_add_unaccent_extension.py │ │ ├── 0026_create_unaccent_full_text_search_config.py │ │ ├── 0027_worker_private_key_worker_public_key.py │ │ ├── 0028_update_all_sql_entity_methods.py │ │ ├── 0029_remove_annotationfield_uniquetogether_name_group_and_more.py │ │ ├── 0030_annotationvalue_contributor.py │ │ ├── 0031_remove_annotationvalue_uniquetogether_entity_field_and_more.py │ │ ├── 0032_alter_process_managers.py │ │ ├── 0033_data_idx_data_status_priority.py │ │ ├── 0034_remove_data_idx_data_status_priority_and_more.py │ │ ├── 0035_move_version_field_to_resolwe.py │ │ ├── 0036_annotationvalue_deleted.py │ │ ├── 0037_annotation_value_data_migrate.py │ │ ├── __init__.py │ │ ├── triggers_collection.sql │ │ ├── triggers_data.sql │ │ ├── triggers_entity.sql │ │ └── utils.sql │ ├── models │ │ ├── __init__.py │ │ ├── annotations.py │ │ ├── base.py │ │ ├── collection.py │ │ ├── data.py │ │ ├── descriptor.py │ │ ├── entity.py │ │ ├── fields.py │ │ ├── functions.py │ │ ├── history.py │ │ ├── history_manager.py │ │ ├── migrations.py │ │ ├── process.py │ │ ├── secret.py │ │ ├── storage.py │ │ ├── utils │ │ │ ├── __init__.py │ │ │ ├── duplicate.py │ │ │ ├── hydrate.py │ │ │ ├── reference.py │ │ │ ├── render.py │ │ │ └── validation.py │ │ └── worker.py │ ├── routing.py │ ├── serializers │ │ ├── __init__.py │ │ ├── annotations.py │ │ ├── base.py │ │ ├── collection.py │ │ ├── contributor.py │ │ ├── data.py │ │ ├── descriptor.py │ │ ├── entity.py │ │ ├── fields.py │ │ ├── process.py │ │ ├── relation.py │ │ └── storage.py │ ├── signals.py │ ├── static │ │ └── flow │ │ │ ├── descriptorSchema.json │ │ │ ├── fieldSchema.json │ │ │ ├── processSchema.json │ │ │ ├── resourcesSchema.json │ │ │ └── typeSchema.json │ ├── tasks.py │ ├── tests │ │ ├── __init__.py │ │ ├── descriptors │ │ │ └── tests.yml │ │ ├── expression_filters.py │ │ ├── fields_test_app │ │ │ ├── __init__.py │ │ │ ├── migrations │ │ │ │ ├── 0001_initial.py │ │ │ │ └── __init__.py │ │ │ └── models.py │ │ ├── files │ │ │ ├── conf.py │ │ │ ├── contents.rst │ │ │ ├── errors.txt │ │ │ └── processes │ │ │ │ ├── test.yaml │ │ │ │ └── test_python.py │ │ ├── fixtures │ │ │ └── relationtypes.yaml │ │ ├── processes │ │ │ ├── first_version │ │ │ │ └── tests.yml │ │ │ ├── second_version │ │ │ │ └── tests.yml │ │ │ ├── secrets.yml │ │ │ ├── spawned.yml │ │ │ ├── tests.yml │ │ │ ├── workflow.yml │ │ │ └── wrong_defaults │ │ │ │ └── tests.yml │ │ ├── test_annotations.py │ │ ├── test_api.py │ │ ├── test_commands.py │ │ ├── test_descriptors.py │ │ ├── test_docs.py │ │ ├── test_env_vars.py │ │ ├── test_executors.py │ │ ├── test_expression_filters.py │ │ ├── test_fields.py │ │ ├── test_filtering.py │ │ ├── test_history.py │ │ ├── test_manager.py │ │ ├── test_models.py │ │ ├── test_ordering.py │ │ ├── test_purge.py │ │ ├── test_redis_cache.py │ │ ├── test_relations.py │ │ ├── test_resources.py │ │ ├── test_runtime.py │ │ ├── test_secrets.py │ │ ├── test_serializers.py │ │ ├── test_stats.py │ │ ├── test_tool.py │ │ ├── test_transfer.py │ │ ├── test_utils.py │ │ └── test_validation.py │ ├── utils │ │ ├── __init__.py │ │ ├── decorators.py │ │ ├── docs │ │ │ ├── __init__.py │ │ │ └── autoprocess.py │ │ ├── exceptions.py │ │ ├── iterators.py │ │ ├── singleton.py │ │ └── stats.py │ └── views │ │ ├── __init__.py │ │ ├── annotations.py │ │ ├── collection.py │ │ ├── data.py │ │ ├── descriptor.py │ │ ├── entity.py │ │ ├── mixins.py │ │ ├── process.py │ │ ├── relation.py │ │ ├── storage.py │ │ └── utils.py ├── observers │ ├── __init__.py │ ├── apps.py │ ├── consumers.py │ ├── decorators.py │ ├── management │ │ ├── __init__.py │ │ └── commands │ │ │ ├── __init__.py │ │ │ └── clean_observers.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0002_backgroundtask.py │ │ ├── 0003_alter_observer_object_id.py │ │ ├── 0004_alter_backgroundtask_permission_group.py │ │ └── __init__.py │ ├── mixins.py │ ├── models.py │ ├── protocol.py │ ├── routing.py │ ├── signals.py │ ├── tests.py │ ├── utils.py │ └── views.py ├── permissions │ ├── __init__.py │ ├── filters.py │ ├── fixtures │ │ ├── collections.yaml │ │ ├── data.yaml │ │ ├── permissions.yaml │ │ ├── processes.yaml │ │ ├── readme.txt │ │ └── users.yaml │ ├── loader.py │ ├── management │ │ ├── __init__.py │ │ └── commands │ │ │ ├── __init__.py │ │ │ └── validate_permission_hierarchy.py │ ├── migrations │ │ ├── 0001_initial.py │ │ ├── 0003_change_default_manager_on_permission_model.py │ │ ├── 0004_create_anonymous_user.py │ │ └── __init__.py │ ├── mixins.py │ ├── models.py │ ├── permissions.py │ ├── shortcuts.py │ ├── tests │ │ ├── __init__.py │ │ ├── test_collection.py │ │ ├── test_data.py │ │ ├── test_permissions.py │ │ ├── test_shortcuts.py │ │ ├── test_tool.py │ │ └── test_utils.py │ └── utils.py ├── process │ ├── __init__.py │ ├── bootstrap_python_runtime.py │ ├── communicator.py │ ├── descriptor.py │ ├── fields.py │ ├── models.py │ ├── parser.py │ ├── resources.py │ ├── runtime.py │ ├── runtimes.py │ ├── socket_utils.py │ └── tests │ │ ├── __init__.py │ │ ├── descriptors │ │ └── tests.yml │ │ ├── files │ │ ├── testfile.txt │ │ └── testfile2.txt │ │ ├── processes │ │ ├── python_data_by_slug.py │ │ ├── python_json.py │ │ ├── python_test.py │ │ └── tests.yml │ │ ├── test_python_process.py │ │ └── workflows │ │ └── test_workflow.yml ├── rest │ ├── __init__.py │ ├── fields.py │ ├── projection.py │ ├── serializers.py │ └── tests.py ├── storage │ ├── __init__.py │ ├── apps.py │ ├── cleanup.py │ ├── connectors │ │ ├── __init__.py │ │ ├── baseconnector.py │ │ ├── circular_buffer.py │ │ ├── exceptions.py │ │ ├── googleconnector.py │ │ ├── hasher.py │ │ ├── localconnector.py │ │ ├── registry.py │ │ ├── s3connector.py │ │ ├── transfer.py │ │ └── utils.py │ ├── consumers.py │ ├── fixtures │ │ ├── storage_data.yaml │ │ ├── storage_processes.yaml │ │ └── storage_users.yaml │ ├── management │ │ ├── __init__.py │ │ └── commands │ │ │ ├── __init__.py │ │ │ ├── compare_models_and_csv.py │ │ │ ├── runstoragecleanup.py │ │ │ └── runstoragemanager.py │ ├── manager.py │ ├── migrations │ │ ├── 0001_squashed_0009_referencedpath_chunk_size.py │ │ ├── 0010_add_directory_references.py │ │ └── __init__.py │ ├── models.py │ ├── protocol.py │ ├── settings.py │ ├── signals.py │ ├── tests │ │ ├── __init__.py │ │ ├── files │ │ │ └── compare_models_and_csv.csv │ │ ├── storage_credentials_test_connectors.py │ │ ├── storage_credentials_test_transfer.py │ │ ├── test_circular_buffer.py │ │ ├── test_cleanup.py │ │ ├── test_listener.py │ │ ├── test_management.py │ │ ├── test_manager.py │ │ ├── test_models.py │ │ ├── test_streamhasher.py │ │ ├── test_transfer.py │ │ ├── test_utils.py │ │ └── test_views.py │ └── views.py ├── test │ ├── __init__.py │ ├── testcases │ │ ├── __init__.py │ │ ├── api.py │ │ ├── process.py │ │ └── setting_overrides.py │ ├── tests │ │ ├── files │ │ │ └── example_file.txt │ │ ├── processes │ │ │ └── tests.yml │ │ └── test_testing_framework.py │ └── utils.py ├── test_helpers │ ├── __init__.py │ ├── management │ │ ├── __init__.py │ │ └── commands │ │ │ ├── __init__.py │ │ │ └── show_profile.py │ └── test_runner.py ├── toolkit │ ├── __init__.py │ ├── docker_images │ │ └── base │ │ │ ├── Dockerfile.fedora-40 │ │ │ ├── Dockerfile.ubuntu-24.04 │ │ │ ├── README.md │ │ │ ├── curlprogress.py │ │ │ └── re-import.sh │ ├── processes │ │ ├── dirs.yml │ │ └── files.py │ └── tests │ │ ├── __init__.py │ │ ├── files │ │ ├── bt_index.tar.gz │ │ ├── compressed dir.tar.gz │ │ ├── dir bad format.tar.gz │ │ ├── dir sym link.tar.gz │ │ ├── file binary │ │ ├── input_file.txt.gz │ │ ├── input_file.txt.zip │ │ └── upload_file │ │ │ ├── input_file.txt │ │ │ └── input_file.txt.gz │ │ ├── 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