chanzuckerberg / cellxgene-ontology-guide

MIT License
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feat: update ontology_info.json for 5.1 #207

Closed Bento007 closed 2 months ago

Bento007 commented 2 months ago

Reason for Change

Bento007 commented 2 months ago
  "EFO:0022503": {
    "ancestors": {
      "EFO:0002888": 1,
      "EFO:0001639": 2,
      "EFO:0000001": 6
    },
    "label": "92-1",
    "description": "Human uveal melanoma",
    "synonyms": [
      92.1
    ],
    "deprecated": false
  }

It looks like something that could easily be a typo. 92.1 could be converted to a string and then it will work fine.

brianraymor commented 2 months ago

Not commenting on the typing, but it looks like EFO is adding cell lines?

Human uveal melanoma

brianraymor commented 2 months ago

Typed as decimal?

<oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">92.1</oboInOwl:hasExactSynonym>

Bento007 commented 2 months ago

It's being parsed into a float in python

nayib-jose-gloria commented 2 months ago
  "EFO:0022503": {
    "ancestors": {
      "EFO:0002888": 1,
      "EFO:0001639": 2,
      "EFO:0000001": 6
    },
    "label": "92-1",
    "description": "Human uveal melanoma",
    "synonyms": [
      92.1
    ],
    "deprecated": false
  }

It looks like something that could easily be a typo. 92.1 could be converted to a string and then it work work fine.

I think its probably safe to add a str cast in the builder for anything in synonym, label, description

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 0% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 85.26%. Comparing base (1ba810e) to head (6c11b71).

:exclamation: Current head 6c11b71 differs from pull request most recent head f11690e. Consider uploading reports for the commit f11690e to get more accurate results

Files Patch % Lines
...ols/ontology-builder/src/all_ontology_generator.py 0.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #207 +/- ## ======================================= Coverage 85.26% 85.26% ======================================= Files 18 18 Lines 1106 1106 Branches 214 215 +1 ======================================= Hits 943 943 Misses 153 153 Partials 10 10 ``` | [Flag](https://app.codecov.io/gh/chanzuckerberg/cellxgene-ontology-guide/pull/207/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/chanzuckerberg/cellxgene-ontology-guide/pull/207/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg) | `85.26% <0.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=chanzuckerberg#carryforward-flags-in-the-pull-request-comment) to find out more.

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