Data Migration (LIRMM -> INRAE)

Virtuoso

• first stop the virtuoso in both servers

• Do rsync between the two servers: sudo rsync -avzP --numeric-ids stageportal:/srv/ontoportal/data/virtuoso-opensource/ /opt/virtuoso

• Move the data to the /srv/ontoportal/data/virtuoso

  	mkdir /srv/ontoportal/data/virtuoso
  	cd /opt/virtuoso/database/
  	mv virtuoso.db virtuoso.log virtuoso.pxa virtuoso.trx virtuoso-temp.db /srv/ontoportal/data/virtuoso

• Change the config of virtuoso.ini in /opt/virtuoso/database/virtuoso.ini

  DatabaseFile = /srv/ontoportal/data/virtuoso/virtuoso.db
  ErrorLogFile = /srv/ontoportal/data/virtuoso/virtuoso.log 
  LockFile = /srv/ontoportal/data/virtuoso/virtuoso.lck
  TransactionFile = /srv/ontoportal/data/virtuoso/virtuoso.trx 
  xa_persistent_file = /srv/ontoportal/data/virtuoso/virtuoso.pxa
  ....
  DatabaseFile = /srv/ontoportal/data/virtuoso/virtuoso-temp.db 
  TransactionFile = /srv/ontoportal/data/virtuoso/virtuoso-temp.trx

• Change owner to virtuoso user

  chown -R virtuoso:virtuoso /opt/virtuoso
  chown -R virtuoso:virtuoso /srv/ontoportal/data/virtuoso

• Restart virtuoso in new server systemctl restart virtuoso.service

• Clear the cache to see it in the browser sudo opclearcaches

Tomcat

• We have to build each project into a war file and put it in the tomcat webapps directory

  • annotator.war => https://github.com/ontoportal-lirmm/annotators/tree/master/sifr-bioportal-annotator-proxy

  • annotatorplus.war => https://github.com/ontoportal-lirmm/annotators/tree/ncbo_annotator

  • fairness-assessment.war => https://github.com/agroportal/fairness

  • ncbo_proxy.war => https://github.com/ontoportal-lirmm/ncboproxy?tab=readme-ov-file#iii1-building-the-war-file-and-configuring-the-proxy

  • biomixer.war

Redis

• Stop redis on both servers

• Give the user ontoportal the permission to enter the redis_persistent folder with sudo usermod -aG redis ontoportal

• Rsync sudo rsync -avzP stageportal:/srv/ontoportal/data/redis_persistent/dump.rdb /srv/ontoportal/data/redis_persistent/

• sudo systemctl restart redis-server-persistent.service redis-server-http_cache.service redis-server-goo_cache.service

Mgrep

• Rsync the file

  rsync -avzP agroportal:/srv/ontoportal/data/mgrep/dictionary/dictionary.txt /srv/ontoportal/data/mgrep/dictionary

Mgrep-lem

• Rsync the dictionary file

  rsync -avzP agroportal:/srv/ontoportal/data/mgrep/dictionary/dictionary-lem.txt /srv/ontoportal/data/mgrep/dictionary

• add this in /etc/systemd/system/mgrep-lem.service

  [Unit]
  Description=mgrep server running on port 55557
  After=network.target
  
  [Service]
  Type=forking
  ExecStart=/opt/mgrep/mgrep --port=55557 -f /srv/ontoportal/data/mgrep/dictionary/dictionary-lem.txt -w /opt/mgrep/word_divider.txt -c /opt/mgrep/CaseFolding.txt
  StandardOutput=syslog
  StandardError=syslog
  SyslogIdentifier=mgrep-lem
  User=mgrep
  Group=ontoportal
  PermissionsStartOnly=false
  TimeoutSec=900
  TimeoutStopSec=10
  
  [Install]
  WantedBy=multi-user.target

Files

• first stop the virtuoso in both servers

• remove the repository folder if it exist in /srv/ontoportal/data

• Do rsync between the two servers: rsync -avzP --numeric-ids stageportal:/srv/ontoportal/data/repository /srv/ontoportal/data/repository

• Restart the server

• Clear the cache to see it in the browser sudo opclearcaches

Solr Indexation

• Reindexing the ontologies, agents and submissions from the admin page

• for property search and term search we can do

  • Execute this script in ncbo_cron ./bin/ncbo_ontology_index -a -l ./reindexing.log

Ontologies Report

• Regenerate it from the UI

Outline (agroportal.eu)

• https://github.com/ontoportal-lirmm/agroportal_outline

Nginx

ubuntu@localhost:/etc/nginx/sites-enabled$ ls
ontologies_api.conf  ontoportal_web_ui.conf  services.agroportal.eu.conf  wiki.agroportal.eu.conf