Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub
https://knowledge-graph-hub.github.io/kg-obo/getting_started.html
GNU General Public License v3.0
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Transform of `foodon` fails during ROBOT convert from owl to obojson #190

Closed caufieldjh closed 2 years ago

caufieldjh commented 2 years ago

Describe the bug

Transform of foodon encounters this:

Relaxing /tmp/foodonmuj4avcz to /tmp/tmpw74_g833_foodon_relaxed.owl...
Complete.
Before relax: 146924 lines. After relax: 147853 lines.
ROBOT preprocessing: merge and convert foodon
Merging and converting /tmp/tmpw74_g833_foodon_relaxed.owl to /tmp/tmpbev5bjb1_foodon_merged.owl...
Complete.
Before merge: 147853 lines. After merge: 661386 lines.
ROBOT preprocessing: node ID normalization on foodon
Retrieving entity names in /tmp/tmpbev5bjb1_foodon_merged.owl...
Exported IDs to /tmp/tmpbev5bjb1_foodon_merged.owl.ids.csv.
Found 817 unexpected identifiers.
Will normalize 805 identifiers.
Wrote IRI maps to data/foodon/2022-08-12/update_id_maps.tsv.
ROBOT preprocessing: convert foodon
Converting /tmp/tmpw74_g833_foodon_relaxed.owl to data/foodon/2022-08-12/foodon.json...
ROBOT encountered an error: 

  RAN: /home/harry/kg-obo/robot convert --input /tmp/tmpw74_g833_foodon_relaxed.owl --format json --output data/foodon/2022-08-12/foodon.json

  STDOUT:
Cannot invoke "String.toString()" because "lv" is null
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

  STDERR:

Will try to repair...
ROBOT encountered another error: 

  RAN: /home/harry/kg-obo/robot remove --input /tmp/tmpw74_g833_foodon_relaxed.owl --select object-properties --output data/foodon/2022-08-12/foodon.json

  STDOUT:
Cannot invoke "String.toString()" because "lv" is null
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.

  STDERR:

ROBOT convert of foodon failed - skipping.

I'm getting a lot of deja vu with this issue. Will need to poke around other repos and see what may have happened before.

To Reproduce

python run.py --bucket kg-hub-public-data --save_local --get_only foodon

Expected behavior

The transform of foodon should be written to data/foodon/2022-08-12 locally, then uploaded.

Version

efc2324f040d8daad14ffaaaa6e71583d6258117

caufieldjh commented 2 years ago

Ah, here we go: https://github.com/ncbo/BioPortal-to-KGX/issues/15