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linkml / schema-automator

Automated assistance for the schema development lifecycle
https://linkml.io/schema-automator/
BSD 3-Clause "New" or "Revised" License
34 stars 12 forks source link

web based term mapping #2

Closed turbomam closed 3 years ago

turbomam commented 3 years ago

can now map any set of enums to any target ontology from bioportal examples in Makefile no live pull of tables yet (limited access Google sheets? Felix Postgres?) but Makefile does include conversion of a manually obtained TSV to YAML

turbomam commented 3 years ago

@cmungall Is that failure from something I did? I haven't been working with dates/times.

PS, I haven't written any test of my own for the BioPortal mapping yet.

turbomam commented 3 years ago

I reprioritized OLS searches over BioPortal. I think this is ready to merge into master now, but the checks are failing at this unrelated code:

  coverage erase
  pytest --cov=kgx --cov-report xml:coverage.xml tests/*
  coverage combine --append || true
  coverage report
  coverage xml
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.7.10/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.7.10/x64/lib
Coverage.py warning: Module kgx was never imported. (module-not-imported)
wdduncan commented 3 years ago

You may want to consider creating a pypi package for this, and attach command-line utils to the package. I have examples of this in nmdc-schema.