Fix error caused by sssom convert command
Running:
run.bat bash
pip install sssom --upgrade
make refresh-imports
results in this error message:
sssom convert tmp/mappings.owl-merged.sssom.tsv --output tmp/mappings.owl-converted.sssom.owl &&\
robot --catalog catalog-v001.xml merge -i tmp/mappings.owl-converted.sssom.owl \
annotate --ontology-iri https://w3id.org/cpont/ontology/components/mappings.owl annotate -V https://w3id.org/cpont/ontology/releases/2023-08-01/components/mappings.owl --annotation owl:versionInfo 2023-08-01 convert -f ofn --output components/mappings.owl.tmp.owl && mv components/mappings.owl.tmp.owl components/mappings.owl; fi nfo 2023-08-01 convert -f ofn --output comp
INVALID ONTOLOGY FILE ERROR Could not load a valid ontology from file: mappings.owl-converted.sssom.owl
For details see: http://robot.obolibrary.org/errors#invalid-ontology-file-error
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make[1]: *** [Makefile:416: components/mappings.owl] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [Makefile:356: refresh-imports] Error 2
The error is the result of a change made to sssom-py where the sssom convert
command now requires the output format to be specified in order to work.