WIP add config schema & generate HTML docs #107
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| # Before we validate the config against the schema, check to see if we've failed to provide one | ||
| if not len(config.keys()): | ||
| print("-"*80 + "\nNo config loaded!", file=sys.stderr) | ||
| print("Avian-flu is indented to be run from the snakefile inside a subdir " |
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| print("Avian-flu is indented to be run from the snakefile inside a subdir " | |
| print("Avian-flu is intended to be run from the Snakefile inside a subdir " |
| oneOf: | ||
| - type: object | ||
| patternProperties: | ||
| "^[^_/]+/[^_/]+/[^_/]+$": |
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Maybe a nit? I'm not sure if it matters too much, but I think the intent of your wildcarding approach is that *, when it appears as an element, should appear alone, and that is not enforced by this regex — you'd need to replace the [^_/]+ bits with something more like (*|[^_/]+), I think?
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@tsibley & I discussed a little bit what these docs might look like in an ideal world. TL;DR it wouldn't be the auto-generated ones here, although the schema's a good start. If we imagine people will run workflows either with no adjustments or with config overlays (YAML and/or
If this were served locally (as HTML) you could imagine one day generating config overlays from it. |
Generate docs using json-schema-for-humans: ``` generate-schema-doc --config template_name=js config/schema.yaml public/schema.html ```
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| # prototype based on <https://github.com/nextstrain/augur/blob/master/augur/validate.py> | ||
| from importlib import metadata | ||
| # <https://github.com/nextstrain/augur/issues/1358> | ||
| assert str(metadata.version("jsonschema")).startswith('3.'), "jsonschema must be version 3" |
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Need to change this since Augur 27.0.0 no longer supports v3
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@victorlin why was this closed? Oh, I think it was automatically closed after you (correctly) deleted the branch from the already-closed #106, and that branch was the base branch for this PR. |
Very much an experimental PR.
I think checking configs against this schema (within Snakemake) is useful by itself. I find JSON schemas painful to write but they work. Writing them indentified a few omissions from #104 which was immediate positive feedback.
I'm less certain about the generated HTML docs, but they are essentially free given the investment in the schema. I've committed the HTML in this PR to make it easier to review / try out, but you can generate docs using json-schema-for-humans via: