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

[syphax-bouazzouni]

From the Admin UI

• SMLC-TEST => fixed after reprocessing
• LPT
• CO_020
• AFEO => first it was an error in the previous submission that didn't had an ontology file (see Clean AFEO and OEEV empty submissions #226)
• GEMET
• CO_121
• SOY => fixed after reprocessing
• OEEV => fixed after reprocessing
• SOSA => fixed after reprocessing
• AGROVOC => Problem present but another issue is pen AGROVOC does not pull automatically and does not parse anymore #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

• AFEO Could not load imported ontology #231

Error type 3: Ziped files

• Diff use the zipped version of the resource (GEMET case) ontoportal-lirmm/ontologies_linked_data#12

Error type 4: Output folder not found

For those ressources

• CO_020

• CO_121

• erroneous generated diff output folder  ontoportal-lirmm/ontologies_linked_data#13

Error type 5: Can't parse the previous versions

• Fix the previous submission of LPT so that it can be parsed for the DIFF #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. add parsing error status for missing imports  ontoportal-lirmm/ontologies_linked_data#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 #231
Same for the new feature request of ontoportal-lirmm/ontologies_linked_data#14