[stevevanhooser]

Fixes item 1 of #11. Items 2–4 stay open there.

Summary

MATLAB's ndi.ontology.lookup sets three of its outputs itself, after the provider returns, so every ontology answers the same way. Python left all three to each provider, and the providers disagreed. lookup() now sets them as MATLAB does:

Field	Now (as MATLAB)	Before
short_name	name2variableName(name) (ontology.m:332)	OLS-backed providers returned OLS's short_form (CL_0000540); NDIC, NCIm, NCBITaxon, RRID, PubChem, WormBase, EDAM, IAO and schema returned ''
prefix	The prefix as typed, trimmed (:295): ndic:8 → ndic, taxonomy:9606 → taxonomy	Several providers returned a canonical prefix: NDIC, NCBITaxon, EDAM, …
synonyms	Flattened, with empty entries dropped (:316-327)	Passed through as the provider returned them

Why it matters

NDI-python's subject tables (ndi/fun/doc_table.py) name treatment columns from lookup(...).short_name, following MATLAB's treatment.m. Before this change, the same dataset got different column names in each language. A CHEBI treatment became CHEBI_15377 in Python but Water in MATLAB. An NDIC treatment got '' from the lookup, so Python fell back to the treatment's own name.

Callers comparing prefix will see the prefix they typed (ndic, taxonomy, format) rather than the canonical one, which is what MATLAB has always returned.

Tests

• TestLookupSetsMatlabFields (offline) checks five things:
  • an OLS short_form is replaced by name2variableName(name)
  • a blank short_name gets filled in
  • the prefix comes back as typed
  • an alias prefix is kept
  • synonyms are flattened, with empty entries dropped
• The shared-case runner now also asserts prefix and short_name for every success case.
• On the old code, 6 of the 7 new unit tests and 2 offline shared cases fail; with the fix all pass.
• black, ruff and the offline suite pass: 153 passed, 3 skipped.

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