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geo2r now returns a CAPTCHA page to scripted requests, which broke CI on master. The test stubs the metadata call, and _create_metadata raises a clear error when the response is not JSON.
NHANES_2010, NHANES_2012 and FHS have no samples field, so the data table step of doc/generate.py raised KeyError and broke make html.
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What
doc/generate.pycrashes on master while writinggenerated/data_table.csv:The NHANES_2010, NHANES_2012 and FHS entries added in #203 have no
samplesfield, and the generator indexed it directly.make htmlruns this script first, so the docs build fails.How
samplesis only read by the doc generator and nothing in the loader requires it, so it is treated as optional: missing counts render asN/A, the same placeholder the model table uses. Sample counts were not added tolibrary.yamlbecause the clinical cohorts don't have one fixed number that would be accurate to publish.Verification
python doc/generate.pyexits 1 on master and 0 here.data_table.csvhas all 48 library entries.make check-formatclean.make test: 202 passed, 5 skipped, 0 failed.Depends on #218
This branch is stacked on #218, which fixes the CI failure every PR currently hits. Merge #218 first and this diff reduces to the one-line change in
doc/generate.py.Follow-up (not in this PR)
The new NHANES and FHS rows show
Age Present: NoandSex Present: No. That is wrong: both loaders provide age and sex (biolearn/load.py). The generator only looks at GEO-styleparser.metadata, which clinical entries don't use. Fixing that needs a way for non-GEO entries to declare their metadata and is better as its own change.