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DataPortal - Import Data

Note: Before proceeding the following steps (building pdx.graph DB) make sure there is no pdx.graph DB in ~/Documents/

Option 1: InteliJ

  • Menu: Run -> Edit Configuration, select Loader
  • In dialog box Run/Debug Configurations in part Enviroment/Program arguments enter -loadALL --pdxfinder.root.dir=xxx where xxx is local path to EBI data
  • Menu: Run -> Run Loader
  • Wait for 2-3 hours (!)
  • Then the graph DB is generated in folder ~/Documents/pdx.graph

Option 2: Terminal

  • Go to directory dataportal-sourcecode
  • Run mvn clean package -DskipTests
  • Run java -jar indexer/target/indexer-1.0.0.jar -loadALL --pdxfinder.root.dir=xxx where xxx is local path to EBI data
  • The graph DB is generated in folder ~/Documents/pdx.graph

Uploading data to the DataPortal server

  • Go to folder ~/Documents/pdx.graph
  • Run tar -czvf ../graph.tgz * to create archive with the data in the upper folder
  • Copy the file to DataPortal server via scp graph.tgz pdxuser@datahub.edirex.ics.muni.cz:dataportal-docker/neo4j-data/ (archive with the data muse be located just in folder neo4j-data and have just name graph.tgz)
  • Log in to Dataportal server, go to folder /home/pdxuser/dataportal-docker
  • Drop down the containers via docker-compose down
  • Delete volume with old N4J DB via docker volume rm dataportal-docker_neodata
  • Start up the containers via docker-compose up -d