Issues when automatically pulling new ontologies

[jonquet]

Looking at the logs fixing #172 we can notice several issues with ontologies with pullLocation. I report them here :

• GEMET : no parser is found for GEMET => not sure the script "knows" it is a SKOS format and does not require OWLAPI parser. New version is available (4.2.3) but not taken by pull script. Side note : I am currently working on adding the missing version manually
• FOBI : parsing error in the OWL API parsing. Reported to FOBI GitHub : https://github.com/pcastellanoescuder/FoodBiomarkerOntology/issues/6
• CO_347 : error with latest submission reported here #175
• BIODIVTHES : it seems the script tries to reach out something not defined (pullLocation is null)

For memory, command to check the logs. cd /srv/ontoportal/ncbo_cron/logs/ tail -n 10000 scheduler-pull.log

[syphax-bouazzouni]

Todo :

• [x] https://github.com/agroportal/documentation/issues/188
• [x] https://github.com/agroportal/documentation/issues/189
• [ ] https://github.com/agroportal/documentation/issues/191

[syphax-bouazzouni]

@jonquet for the GEMET case, i tested doing a manual pull in console and it's says that there is not a new version. Did you do manual update by your self ?

[syphax-bouazzouni]

I close this issue, will continue the track of the remaining issue with NCBITAXON here: https://github.com/agroportal/documentation/issues/191