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Some terms expected to receive a label do not #161

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hlapp opened this issue Feb 2, 2021 · 0 comments · Fixed by #162
Closed

Some terms expected to receive a label do not #161

hlapp opened this issue Feb 2, 2021 · 0 comments · Fixed by #162

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@hlapp
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hlapp commented Feb 2, 2021

The test failure is this:

── Failure (test-pk.R:131:3): labels for pre-generated post-comps ──────────────
sum(is.na(subs.l$label)) is not less than 1. Difference: 1

This while testing that labels for pre-generated post-comps work. The test that's failing obtains a subsumer matrix for "femur", subsamples the resulting subsumers (many of which are expected to be post-compositions), and tests whether for every one a label can be obtained. Some, though not all, CARO terms (which are not even post-compositions) fail because there they lack their label in the database.

See phenoscape/phenoscape-kb-services#378.
hlapp added a commit that referenced this issue Feb 2, 2021
@hlapp
Filters out label-less terms from flagged ontologies
eebf92b 
Some ontologies, in particular apparently CARO, have labels for terms
in the database only inconsistently. This filters out subsumer terms
that are in those ontologies, and failed to obtain a label. What is
really being tested here are post-compositions, so this shouldn't affect
the subsumers that are post-comps (whether they fail to obtain a label
or not).

Fixes #161. See also phenoscape/phenoscape-kb-services#378.
@hlapp hlapp mentioned this issue Feb 2, 2021
Merged
@hlapp hlapp closed this as completed in #162 Feb 2, 2021
hlapp added a commit that referenced this issue Feb 2, 2021
@hlapp
Filters out label-less terms from flagged ontologies
57c5f16 
Some ontologies, in particular apparently CARO, have labels for terms
in the database only inconsistently. This filters out subsumer terms
that are in those ontologies, and failed to obtain a label. What is
really being tested here are post-compositions, so this shouldn't affect
the subsumers that are post-comps (whether they fail to obtain a label
or not).

Fixes #161. See also phenoscape/phenoscape-kb-services#378.
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Filters out label-less terms from flagged ontologies phenoscape/rphenoscape
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@hlapp