0ntologies diagnostics (January 2022) - Ontologies with DIFF ERROR

[syphax-bouazzouni]

From the Admin UI

• [x] SMLC-TEST => fixed after reprocessing
• [x] LPT
• [x] CO_020
• [ ] AFEO => first it was an error in the previous submission that didn't had an ontology file (see https://github.com/agroportal/documentation/issues/226)
• [x] GEMET
• [x] CO_121
• [x] SOY => fixed after reprocessing
• [x] OEEV => fixed after reprocessing
• [x] SOSA => fixed after reprocessing
• [x] AGROVOC => Problem present but another issue is pen #178

Problem diagnostic

See Logs of the ncbo_ontology_process script

Using the script bin/ncbo_ontology_process -o AFEO -t diff (e.g with AFEO) we can see that diff process fails with no details

Performing diff failed.  Reason: null

Using the source code of bubastis

We can found the source code here : https://github.com/EBISPOT/bubastis

And after enabling the exception printing, we can see :

Error type 1: Update owlapi

• [ ] Update owlapi from 4.5.8 to 4.5.17

Error type 2: Missing imports

For the case of

• [x] #231

Error type 3: Ziped files

• [x] https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/12

Error type 4: Output folder not found

For those ressources

• CO_020

• CO_121

• [x] https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/13

Error type 5: Can't parse the previous versions

• [x] #232

[jonquet]

• For the problem of missing imports the suggestion is to create a complimentary/additional error status that will be triggered when the missing import is detected during parsing and that will explicitly inform the admin user of the problem.
  Up to us to know that we need to fix missing imports before addressing diff issues. https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/14

• For the problem of zip files => we need to patch the code to test if this is a zip file before transferring to bubastis.

• For the problem of previosu version => case by case fix the previous versions if they really don't parse

[syphax-bouazzouni]

The diff errors were resolved. It is still only AFEO, we continue its specific tracking their https://github.com/agroportal/documentation/issues/231 Same for the new feature request of https://github.com/ontoportal-lirmm/ontologies_linked_data/issues/14