sssom invert chokes on `UnboundLocalError`
Closed this issue · 4 comments
matentzn commented
Eventually we will deprecated sssom invert, but for now we need it to work:
sssom invert mondo_exactmatch_omim.sssom.tsv -o test.sssom.tsv
results in:
/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/sssom/util.py:156: 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 "/Users/matentzn/.pyenv/versions/3.11.7/bin/sssom", line 8, in <module>
sys.exit(main())
^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/matentzn/.pyenv/versions/3.11.7/lib/python3.11/site-packages/sssom/cli.py", line 758, in invert
inverse_dictionary["inverse_predicate_map"],
^^^^^^^^^^^^^^^^^^
UnboundLocalError: cannot access local variable 'inverse_dictionary' where it is not associated with a value
Testfile:
# comment: The latest OMIM is integrated with every Mondo release.
# curie_map:
# MONDO: http://purl.obolibrary.org/obo/MONDO_
# OMIM: https://omim.org/entry/
# owl: http://www.w3.org/2002/07/owl#
# rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
# rdfs: http://www.w3.org/2000/01/rdf-schema#
# semapv: https://w3id.org/semapv/vocab/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_date: '2022-02-11'
# mapping_set_id: http://purl.obolibrary.org/obo/mondo/mappings/mondo_exactmatch_omim.sssom.tsv
# mapping_set_version: http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mappings/mondo_exactmatch_omim.sssom.tsv
# object_source: https://www.omim.org/
# object_source_version: http://www.orphadata.org/data/ORDO/ordo_orphanet_3.1.owl
# subject_source: http://purl.obolibrary.org/obo/mondo.owl
subject_id subject_label predicate_id object_id object_label mapping_justification
MONDO:0000208 microcephaly, short stature, and impaired glucose metabolism 1 skos:exactMatch OMIM:616033 microcephaly, short stature, and impaired glucose metabolism 1 semapv:ManualMappingCuration
MONDO:0000902 agenesis of the corpus callosum with peripheral neuropathy skos:exactMatch OMIM:218000 agenesis of the corpus callosum with peripheral neuropathy semapv:ManualMappingCuration
Problem 2: Inversion does not do anything
sssom invert mondo_exactmatch_omim.sssom.tsv -o test.sssom.tsv --inverse-map inverse-predicates.yaml
Does not throw an error, but no inversion occurs (input and output file are the same). By default, inversion should invert everything.
hrshdhgd commented
What does inverse-predicates.yaml look like?
matentzn commented