Closed matentzn closed 1 month ago
Fixed these 2 errors:
biological-attribute-child-violation OBA:2045328
biological-attribute-child-violation OBA:VT0003501
in https://github.com/obophenotype/bio-attribute-ontology/pull/328, waiting to see if it's the right fix.
Fixed these 2 errors:
biological-attribute-child-violation OBA:2045328
biological-attribute-child-violation OBA:VT0003501
in #328, waiting to see if it's the right fix.
@ar-ibrahim , I have added the two updates for OBA:2045328 and OBA:VT0003501 here, because we need them to fix the current PR. In turn, we need to fix this PR (#331), before we can deal with #328.
The remaining dosdp
workflow error seems to be somehow related tolipidmaps.owl
and some recent changes in dosdp.yml.
dosdp
github action (workflow) error at step Run ontology QC checks
:...
robot --catalog catalog-v001.xml merge -i tmp/sl_subclassof.ttl -i tmp/sl_metadata.ttl -i tmp/sl_partof.ttl -i tmp/sl_haspart.ttl -i tmp/sl_subclasslipid.ttl reason reduce convert --output mirror/swisslipids.owl
if [ false = true ] ; then robot --catalog catalog-v001.xml template \
--prefix "LM: https://bioregistry.io/lipidmaps:" \
--template ../templates/lipidmaps.tsv \
annotate --ontology-iri http://purl.obolibrary.org/obo/oba/mirror/lipidmaps.owl annotate -V http://purl.obolibrary.org/obo/oba/releases/2024-05-07/mirror/lipidmaps.owl --annotation owl:versionInfo 2024-05-07 convert -f ofn --output mirror/lipidmaps.owl.tmp.owl && mv mirror/lipidmaps.owl.tmp.owl mirror/lipidmaps.owl; fi
robot --catalog catalog-v001.xml merge -i mirror/ro.owl -i mirror/chebi.owl -i mirror/goplus.owl -i mirror/go.owl -i mirror/pato.owl -i mirror/omo.owl -i mirror/hp.owl -i mirror/mondo.owl -i mirror/ncbitaxon.owl -i mirror/uberon.owl -i mirror/cl.owl -i mirror/nbo.owl -i mirror/pr.owl -i mirror/so.owl -i mirror/po.owl -i mirror/bfo.owl -i mirror/swisslipids.owl -i mirror/lipidmaps.owl -o mirror/merged.owl
mirror/lipidmaps.owl (No such file or directory)
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make: *** [Makefile:623: mirror/merged.owl] Error 1
Error: Process completed with exit code 2.
##[debug]Finishing: Run ontology QC checks
seems like you are using IMP=false, also add MIR=false if you dont want to refresh mirrors (recent breaking change in ODK)
@ar-ibrahim can you please fix this PR? I need it for #314