Add workflow test schema #17128
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Add workflow test schema #17128
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jmchilton
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Dec 8, 2023
lib/galaxy/tool_util/xsd/galaxy.xsd
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| <xs:enumeration value="yes"/> | ||
| <xs:enumeration value="no"/> | ||
| </xs:restriction> | ||
| <xs:union> |
To generate dataclasses in generated/galaxy from xsd: ``` pip install 'xsdata[cli]' cd lib/galaxy/tool_util/schemas xsdata ../xsd/galaxy.xsd --unnest-classes --kw-only --docstring-style Accessible --ignore-patterns --max-line-length 10000 ``` Fix up tool test schema for workflow particularities (and xsdata odditites) ``` python postprocess_schema.py ``` To generate json schema (requires pydantic 2.0 to deal with recursive data classes): ``` python test_file_from_xsd.py > test_file_schema.json ``` To validate a workflow test file with check-jsonschema ``` check-jsonschema --traceback-mode full --schemafile test_file_schema.json sra-manifest-to-concatenated-fastqs-tests.yml ``` TODO: - jobs is not modeled - element / element_tests needs work - special handling for primitive workflow parameter output values - de-RST-ify description fields
Pydantic's dataclass does not complain about optional attributes before required attributes, so we can drop `--kw-only` from the `xsdata` call (which is now `xsdata ../xsd/galaxy.xsd --unnest-classes --output pydantic --docstring-style Accessible --ignore-patterns --max-line-length 10000 && python postprocess_schema.py && python test_file_from_xsd.py > test_file_schema.json && cd ~/src/galaxy && make format && cd -`)
…Collection.elements instead
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9 tasks
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Much improved in #18884 |
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To generate dataclasses in generated/galaxy from xsd:
Fix up tool test schema for workflow particularities (and xsdata
odditites)
To generate json schema (requires pydantic 2.0 to deal with recursive
data classes):
To validate a workflow test file with check-jsonschema
TODO:
How to test the changes?
(Select all options that apply)
License