Nicola Soranzo 1a1d7265a5 Fix `TestJobFilesIntegration` initialization ...

`input_hda_dict` and `input_hda` are initialized once for all tests
in the class, i.e. they needed to be class attributes.

Fix the following error when running all tests in the class with
`./run_tests.sh -integration test/integration/test_job_files.py`:

```
self = <integration.test_job_files.TestJobFilesIntegration object at 0x73c52a002260>

    def test_read_fails_if_input_file_purged(self):
        job, _, _ = self.create_static_job_with_state("running")
        job_id, job_key = self._api_job_keys(job)
>       input_file_path = self.input_hda.get_file_name()
E       AttributeError: 'TestJobFilesIntegration' object has no attribute 'input_hda'
```

2026-07-10 01:49:05 +01:00

..

chained_dyndest_rules

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delay_rules

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htcondor_fake

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

job_resource_rules

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mock_biotools_content/data

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objectstore

Serve download redirects from a dedicated /download route

2026-07-07 23:11:02 +05:30

objectstore_selection_rules

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oidc

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

panel_views_1

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resubmission_rules

Address review comments

2026-05-11 11:02:48 +05:30

test_visualization_plugins/jupyterlite/static

Remove currently unused param option

2026-01-27 19:43:03 +03:00

webdav

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__init__.py

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chained_dyndest_job_conf.xml

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conftest.py

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delay_job_conf.yml

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dockerized_job_conf.yml

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dummy_job_resource_parameters.xml

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embedded_pulsar_docker_job_conf.yml

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embedded_pulsar_job_conf.yml

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embedded_pulsar_metadata_extended_job_conf.yml

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embedded_pulsar_metadata_job_conf.yml

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embedded_pulsar_none_job_conf.yml

Test Pulsar integration with default_file_action: none

2026-01-13 20:00:56 +01:00

embedded_pulsar_singularity_job_conf.yml

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embedded_pulsar_tpv_job_conf.yml

Update integration test job_conf syntax for TPV 3.2.0

2026-04-09 12:29:45 +01:00

fallback_container_resolver.yml

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file_sources_conf_remote_files.yml

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file_sources_conf_vault.yml

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file_sources_conf.yml

simplify webdav endpoint config

2026-04-22 18:15:26 +10:00

handler_template_job_conf.xml

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io_injection_job_conf.yml

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job_resource_error_recovery_job_conf.yml

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refgenie.yml

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resubmission_default_job_conf.yml

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resubmission_dynamic_job_conf.xml

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resubmission_dynamic_multiple_job_conf.yml

Convert chained-resubmission job conf fixture to YAML

2026-05-19 16:09:11 +05:30

resubmission_job_conf.yml

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resubmission_job_resource_parameters_conf.xml

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resubmission_pulsar_job_conf.xml

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resubmission_runners.py

replace more imports, lets go all in

2026-05-19 19:19:02 +02:00

resubmission_small_memory_job_conf.xml

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resubmission_small_memory_resubmission_to_large_job_conf.xml

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resubmission_tool_detected_always_error_job_conf.xml

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resubmission_tool_detected_resubmit_job_conf.xml

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sets_tmp_dir_expression_job_conf.xml

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sets_tmp_dir_to_true_job_conf.xml

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simple_job_conf.xml

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singularity_job_conf.yml

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test_agents.py

Unify page rendered-content stripping; drop edit_source param

2026-06-14 15:03:54 -04:00

test_apache_nginx_sendfile.py

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test_async_downloads.py

Use requires_new_history decorator instead of unregistered marker

2026-04-15 09:33:10 +02:00

test_celery_fetch_quota.py

Enforce storage quota for Celery-based data fetch jobs

2026-02-26 15:29:33 +01:00

test_celery_tasks.py

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test_celery_user_concurrency_limit.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_celery_user_rate_limit.py

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test_chained_dynamic_destinations.py

…

test_cli_runners.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_coexecution.py

Move more setup code into handle_galaxy_config_kwds which has test_driver configured

2026-01-01 15:08:26 +01:00

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_container_resolvers.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_containerized_jobs.py

Merge branch 'release_25.1' into release_26.0

2026-02-24 13:12:42 +00:00

test_credentials.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_data_manager_refgenie.py

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test_data_manager_workflow_bundle.py

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test_data_manager.py

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test_dataset_copy_metadata_files.py

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test_dataset_hashing.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_datatype_upload.py

Rename test helper classes that pytest tries to collect

2026-04-14 15:51:19 +02:00

test_default_permissions.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_drs_compact_identifiers.py

Add DRS compact identifier support

2026-01-27 08:46:10 -05:00

test_dynamic_edam_loading.py

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test_edam_toolbox.py

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test_entry_point_sse.py

Add shared id-decode helpers to IntegrationInstance

2026-04-28 18:07:48 +02:00

test_error_report.py

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test_event_loop_blocking.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_extended_metadata_mapping.py

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test_extended_metadata_outputs_to_working_directory.py

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test_extended_metadata.py

Move tests into TestExtendedMetadataIntegration

2026-03-18 16:29:41 +01:00

test_fail_job_tool_unavailable.py

Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow

2026-03-24 12:17:06 -04:00

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_hashicorp_vault.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_history_archiving.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_history_import_export.py

…

test_history_sse.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_htcondor_runner.py

attempt to fix the infrastructure tests

2026-05-09 18:44:18 +02:00

test_interactivetools_api.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_job_cache.py

Refactor to decrease duplication

2026-01-09 11:44:41 +01:00

test_job_environments.py

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test_job_files_tus.py

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test_job_files.py

Fix `TestJobFilesIntegration` initialization

2026-07-10 01:49:05 +01:00

test_job_outputs_to_working_directory.py

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test_job_recovery.py

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test_job_resource_error_recovery.py

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test_job_resubmission.py

Convert chained-resubmission job conf fixture to YAML

2026-05-19 16:09:11 +05:30

test_kubernetes_runner.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_landing_requests.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_legacy_store_by.py

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test_live_evals.py

Drop the dead lgtm comments.

2026-05-20 11:08:33 -04:00

test_local_job_cancellation.py

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test_materialize_dataset_instance_tasks.py

Use requires_new_history decorator instead of unregistered marker

2026-04-15 09:33:10 +02:00

test_max_discovered_files.py

Handle MaxDiscoveredFilesExceededError gracefully for dynamic collections

2026-04-07 11:23:23 +02:00

test_metadata_strategy.py

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test_model_store_scripts.py

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test_notification_sse.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_notifications.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_page_revision_json_encoding.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_panel_views.py

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test_plugins.py

Fix invalid function schema error for tools with None parameters

2026-03-10 14:18:12 +01:00

test_prefix_handling.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_pulsar_embedded_containers.py

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test_pulsar_embedded_copy_working.py

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test_pulsar_embedded_extended_metadata.py

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test_pulsar_embedded_mq.py

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test_pulsar_embedded_none.py

Test Pulsar integration with default_file_action: none

2026-01-13 20:00:56 +01:00

test_pulsar_embedded_relay.py

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test_pulsar_embedded_remote_metadata.py

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test_pulsar_embedded.py

Add test that ensures irrelevant outputs are not copied back

2026-01-12 16:08:18 +01:00

test_purge_datasets.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_quota.py

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test_recalculate_user_disk_usage.py

Apply 2026 black style

2026-01-20 10:25:45 +00:00

test_remote_files_histories.py

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test_remote_files_posix.py

Enforce file source access during dataset materialization

2026-04-15 15:14:02 +02:00

test_remote_files.py

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test_repository_operations.py

Fix bwa loc filename in integration test (bwa_mem_index, not bwa_index)

2026-05-18 11:32:51 -04:00

test_resolvers.py

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test_save_job_id_on_datasets.py

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test_scripts_pgcleanup.py

Merge branch 'release_26.0' into release_26.1

2026-07-06 15:49:42 +02:00

test_scripts.py

Add integration tests for pgcleanup with user object stores

2026-06-08 12:41:25 +02:00

test_shed_tool_tests.py

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test_storage_cleaner.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_structured_dataset.py

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test_structured_like_unpopulated.py

Rename test tool to describe shape, not test scenario

2026-05-19 19:50:56 +02:00

test_tool_data_bundles.py

Match renamed data_manager output in bundle integration test

2026-06-17 19:29:03 +02:00

test_tool_data_delete.py

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test_tool_submission_errors.py

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test_upload_configuration_options.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_user_defined_tool_job_conf.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

test_user_preferences.py

Use (also) case-insensitive comparison for user email

2026-02-19 14:40:02 +00:00

test_users.py

Fix admin resend-activation email missing hostname

2026-04-27 10:15:55 +02:00

test_vault_extra_prefs.py

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test_vault_file_source.py

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test_web_framework_config.py

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test_webdav.py

migrate webdav to fsspec

2026-04-14 16:37:27 +10:00

test_work_queue_put_failure.py

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test_workflow_completion_hooks.py

Drop redundant completion hook test, improve remaining test

2026-01-21 14:44:55 +01:00

test_workflow_handler_configuration.py

Update test workflows to respect gxformat2 0.26.0 syntax

2026-05-05 20:44:35 +01:00

test_workflow_invocation.py

Add workflow invocation test

2026-06-02 18:02:48 +03:00

test_workflow_refactoring.py

Memoize run-form history option queries on the request context (issue #22927)

2026-06-16 18:29:49 +02:00

test_workflow_scheduling_options.py

Update test workflows to respect gxformat2 0.26.0 syntax

2026-05-05 20:44:35 +01:00

test_workflow_sync.py

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test_workflow_tasks.py

Drop support for Python 3.8

2026-06-25 15:12:05 +01:00

user_preferences_extra_conf.yml

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workflow_handler_configuration_job_conf.xml

…