search

obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL
Creative Commons Attribution 4.0 International
11 stars 1 forks source link

[DO NOT MERGE] CHEBI import #24

Closed shawntanzk closed 2 years ago

shawntanzk commented 2 years ago

Note: this PR is int base file imports to get CHEBI pulled in and CARO dangling classes removed

-CARO import seems to cause some error so I removed it (I think) -Currently tried sh run.sh refresh_imports (thought was to get the mirrors first) - ran into error, but noticed the mirrors seem to have been downloaded, so tried sh run.sh make no-mirror-refresh-imports and ran into error with go_import:

make[1]: *** [Makefile:246: imports/go_import.owl] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [Makefile:273: no-mirror-refresh-imports] Error 2
shawntanzk commented 2 years ago 
annotate --ontology-iri http://purl.obolibrary.org/obo/pcl/imports/go_import.owl annotate -V http://purl.obolibrary.org/obo/pcl/releases/2021-12-13/imports/go_import.owl --annotation owl:versionInfo 2021-12-13 --output imports/go_import.owl.tmp.owl && mv imports/go_import.owl.tmp.owl imports/go_import.owl; fi
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

Memory issues :( will up the memory in yaml file and try again

shawntanzk commented 2 years ago

of note: I run into Error 18 when trying to make mirror/chebi.owl with robot_java_args: '-Xmx24G' still facing the same issue

shawntanzk commented 2 years ago

sh run.sh make no-mirror-refresh-imports ran through without errors - however -edit file still has all the dangling terms -> will merge this into the other PR and try to fix it there