Make codebase compatible w/ latest ODK

[joeflack4]

Overview

As of now, I'm getting errors if I run on obolibrary/odkfull: latest or dev. Right now we are stuck to v1.4.3.

Sub-tasks

• 1. Get working on latest
• 2. Find out what version that container is, and update the GH action to use that version label rather than latest
  • Update the reference in the GitHub action
  • Update the reference in run.sh, or perhaps there it might indeed be best to use dev or latest

Error details

Err: KeyError: "['subject_label'] not in index"
Happens when: creating mondo_exactmatch_omimps.sssom.owl

Details

sh run.sh make mondo_genes.robot.tsv; beep
sssom convert mondo_exactmatch_omimps.sssom.tsv -O owl -o mondo_exactmatch_omimps.sssom.owl
/usr/local/lib/python3.10/dist-packages/sssom/util.py:168: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`
  df.replace("", np.nan, inplace=True)
Traceback (most recent call last):
  File "/usr/local/bin/sssom", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/sssom/cli.py", line 161, in convert
    convert_file(input_path=input, output=output, output_format=output_format)
  File "/usr/local/lib/python3.10/dist-packages/sssom/io.py", line 50, in convert_file
    write_func(doc, output, serialisation=fileformat)  # type:ignore
  File "/usr/local/lib/python3.10/dist-packages/sssom/writers.py", line 162, in write_owl
    graph = to_owl_graph(msdf)
  File "/usr/local/lib/python3.10/dist-packages/sssom/writers.py", line 173, in to_owl_graph
    msdf.df = invert_mappings(
  File "/usr/local/lib/python3.10/dist-packages/sssom/util.py", line 1462, in invert_mappings
    inverted_df = inverted_df[df.columns]
  File "/usr/local/lib/python3.10/dist-packages/pandas/core/frame.py", line 4108, in __getitem__
    indexer = self.columns._get_indexer_strict(key, "columns")[1]
  File "/usr/local/lib/python3.10/dist-packages/pandas/core/indexes/base.py", line 6200, in _get_indexer_strict
    self._raise_if_missing(keyarr, indexer, axis_name)
  File "/usr/local/lib/python3.10/dist-packages/pandas/core/indexes/base.py", line 6252, in _raise_if_missing
    raise KeyError(f"{not_found} not in index")
KeyError: "['subject_label'] not in index"
make: *** [makefile:23: mondo_exactmatch_omimps.sssom.owl] Error 1

[joeflack4]

@matentzn @twhetzel FYI

Set this to low priority, though perhaps it should be medium.

[matentzn]

If this happens in the latest ODK this is a high priority issue.

[joeflack4]

It does. High it is~