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 load --group=EurOPDX --data-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