Ontologies processing code

https://github.com/ontoportal-lirmm/ontologies_linked_data/blob/master/lib/ontologies_linked_data/services/submission_process/submission_processor.rb

Ontologies upload / processing steps.

Command to process an ontology

Up-to-date guide with all options: Process an ontology

bin/ncbo_ontology_process -o ontology-acronym

(To be done in this path: /srv/ontoportal/ncbo_cron)

Command to copy a file from the server to local

scp -r -p username@agroportal.lirmm.fr:/srv/ontoportal/data/repository/ontology_acronym .

Script to archive old submissions for all ontologies

bin/ncbo_ontology_archive_old_submissions

(To be done in this path: /srv/ontoportal/ncbo_cron)

Commands that may help

bin/ncbo_cron --console Run NCBO Cron console (To be done in this path: /srv/ontoportal/ncbo_cron)

sudo opstatus To see the status of all services (running/stoped)

sudo oprestart To restart all services

sudo systemctl restart 4s-httpd To restart a particular service

Issues that you may face

Unable to launch httpd service

This issue might be related to the semaphore limit being reached. To confirm, you can use the following command: ipcs -s

To clean up all the semaphores used by apache for example you can run this command:

sudo bash -c 'for semid in $(ipcs -s | grep apache | awk "{print $2}"); do ipcrm -s $semid; done'