mvdbeek 681a59b089 Relax legacy doi:-prefixed citation handling (#22795) ...

Tools declaring profile >= 24.2 with a legacy 'doi:'-prefixed citation
crashed during loading on 26.1 and were silently dropped from the toolbox.

- Normalize the legacy 'doi:' prefix to a bare DOI in the shared Citation
  model so these citations load and resolve correctly downstream.
- Only fail tool loading fatally for profile >= 26.1; older profiles skip
  the offending citation and log a warning instead of silently dropping the
  whole tool.
- Add a CitationsDoiInvalid linter so authors are told to drop the prefix.

2026-06-01 14:59:48 +02:00

..

biotools

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data

Merge & dedup data table entries on shed install (no DM gate)

2026-05-14 14:07:57 -04:00

mulled

Use `os.path.join() or pathlib.Path` instead of f-strings for filesystem paths

2026-02-27 19:48:46 +00:00

test_data/test_job_fixtures

Add strict Pydantic Job model for TestJob.job

2026-04-22 09:53:59 -04:00

tool_directories/r-tool-dir

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toolbox

Remove trackster tests

2025-10-07 07:33:38 +03:00

upgrade

Integrate tool test validation into upgrade advisor.

2024-08-24 16:12:32 -04:00

verify

Fix spellings: occurences/exacly/precence in assertion docs.

2026-04-22 22:16:46 -04:00

__init__.py

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doi_prefixed_citation.xml

Relax legacy doi:-prefixed citation handling (#22795)

2026-06-01 14:59:48 +02:00

framework_tool_checks.yml

Tool Request models.

2024-09-30 13:25:02 -04:00

invalid_citation_26.1.xml

Relax legacy doi:-prefixed citation handling (#22795)

2026-06-01 14:59:48 +02:00

invalid_citation.xml

Fix #19515 - invalid citation handling changed with 24.2.

2025-03-20 10:39:31 -04:00

parameter_specification.yml

Rename json_schema_skip → _json_schema_skip, update docstring.

2026-04-03 17:50:02 -04:00

test_assertion_models.py

Apply 2026 black style

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

test_conda_resolution.py

Apply 2026 black style

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

test_container_description.py

…

test_container_resolution.py

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test_container_shape_lint.py

Move UserToolSource container-shape check to a lint rule

2026-05-21 14:35:28 +02:00

test_credential_parsing.py

Simplify test_credential_parsing to use FunctionalTestToolTestCase

2026-03-18 12:03:33 +01:00

test_cwl_util.py

Add sample_sheet workflow runtime framework tests

2026-03-17 15:15:28 -04:00

test_cwl.py

Refactor requirement parsing in multiple files to streamline credential handling

2025-10-07 16:06:04 +02:00

test_docker_volumes.py

…

test_edam_util.py

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test_format.py

Add galaxy-tool-format CLI entry point

2026-02-23 15:22:14 -05:00

test_hash_function_names_sync.py

Add strict Pydantic Job model for TestJob.job

2026-04-22 09:53:59 -04:00

test_input_models.py

Fix unit test import

2025-05-12 12:29:43 +02:00

test_loader_directory.py

Apply 2026 black style

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

test_ontologies.py

Settle on type instead of reftyp inside xref

2025-05-05 19:07:27 +02:00

test_output_checker.py

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test_output_models.py

New packages galaxy-tool-util-models, galaxy-tool-shed-schema.

2025-04-16 12:47:37 +02:00

test_parameter_convert.py

Add tests

2026-04-23 22:54:15 +03:00

test_parameter_cwl_runtime_model.py

Add runtime model to API

2025-05-12 10:54:30 +02:00

test_parameter_specification_json_schema.py

Skip JSON Schema spec tests on Python < 3.9.

2026-04-03 17:50:02 -04:00

test_parameter_specification.py

Validate parameter_specification.yml against JSON Schema, fix generation bugs.

2026-04-03 16:44:09 -04:00

test_parameter_test_cases.py

Persist validated job tool state.

2026-02-12 15:58:16 -05:00

test_parameter_validator_models.py

Pydantic models for parameter validators.

2024-10-22 07:49:37 -04:00

test_parsed_tool_model.py

Keep ParsedTool tests within tool util

2026-05-06 09:02:18 -04:00

test_parsing.py

Relax legacy doi:-prefixed citation handling (#22795)

2026-06-01 14:59:48 +02:00

test_required_files.py

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test_resolution_cache.py

…

test_runtime.py

Fail fast on unknown collection_type instead of silent fallbacks.

2026-02-12 15:58:17 -05:00

test_singularity_util.py

fix tests for singularity

2025-05-09 09:27:53 +02:00

test_test_definition_parsing.py

Merge branch 'release_26.0' into dev

2026-04-22 03:54:23 +01:00

test_test_format_model.py

Add strict Pydantic Job model for TestJob.job

2026-04-22 09:53:59 -04:00

test_test_parsing.py

Apply 2026 black style

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

test_tool_deps.py

Apply 2026 black style

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

test_tool_linters.py

Relax legacy doi:-prefixed citation handling (#22795)

2026-06-01 14:59:48 +02:00

test_tool_loader.py

Prefix XPath expressions with './' in tool loader tests

2026-04-14 15:50:27 +02:00

test_toolbox_view_parsing.py

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test_toolbox_view_sources.py

Apply 2026 black style

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

test_user_tool_source_fixtures.py

narrow YAML tool parameter schema for UserToolSource

2026-04-15 15:36:56 -04:00

test_user_tool_source_validation.py

Stabilize validator error codes; externalize test corpus

2026-05-21 14:35:28 +02:00

test_util.py

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test_verify_function.py

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test_verify_hid.py

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test_verify_script.py

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test_verify.py

Add unit test for image_diff with bool images (failing)

2026-01-03 12:13:52 +01:00

test_version.py

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test_wait.py

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test_yaml_parameters.py

accept 'format' alias on Data/DataCollection parameter models

2026-04-15 15:36:56 -04:00

user_tool_source_validation_cases.yml

Relax legacy doi:-prefixed citation handling (#22795)

2026-06-01 14:59:48 +02:00

util.py

Tool Request models.

2024-09-30 13:25:02 -04:00