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Fix Complex Portal search paging; correct the corrections() docs example - #60
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The Complex Portal search endpoint reports `size` as the number of elements in the page at hand and `totalNumberOfResults` as the grand total, and `first` counts records rather than pages. Reading `size` as the total ended the paging loop after the first page, so any organism with more than 100 complexes was silently truncated: S. cerevisiae (taxonomy 559292) returned 100 of its 634. Page by record offset, take the total from `totalNumberOfResults`, and warn rather than truncate silently if the page bound is ever reached. The test fixtures now use the real field semantics.
`annotate_from_model` returns names, ec_codes and sources, but `EvotuneResult.corrections()` fills sources from `result.groups` itself and has no such keyword, so the documented `result.corrections(leverage=leverage, **annotations)` raises TypeError. Spell the two keywords it does take, and say where the third one goes.
edkerk
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The Complex Portal search endpoint reports
sizeas the number of elements in the page at hand andtotalNumberOfResultsas the grand total, andfirstcounts records rather than pages.get_complex_datareadsizeas the total, so the paging loop ended after the first page and any organism with more than 100 complexes was silently truncated. S. cerevisiae (taxonomy 559292) returned 100 of its 634 complexes.This pages by record offset, takes the total from
totalNumberOfResults, and logs a warning instead of truncating silently if the page bound is ever reached. The test fixtures now use the real field semantics, andtest_search_paginateschecks the record offset and the total.Also corrects the example in
docs/evotune_kcat_tuning.md:annotate_from_modelreturnsnames,ec_codesandsources, butEvotuneResult.corrections()takes onlynamesandec_codes(it fills the sources fromresult.groups), so the documented**annotationscall raisedTypeError.