Manager of updates to the searching database

Out of the box run on the remote

Check separate guide for remote deployment.

Local development

A configuration file for JetBrains IDEs is included which should be loaded automatically.

Build

mvn assembly:assembly -DdescriptorId=jar-with-dependencies

• output can be found in JOIntegration/target/JOIntegration-1.0-SNAPSHOT-jar-with-dependencies.jar.

Run

Project is shipped as batteries included - ready to run out of the box.

1. in the same directory as the .jar file is, create a run.properties file.
   • you can take inspiration from either in JOIntegration/src/main/resources/run.properties.example
   • or from JOIntegration/src/main/java/com/example/services/configuration/AppConfig.java which uses the file
2. make sure that the gesamt library is compiled and you know the path to the binary
   • use the path to set export LD_LIBRARY_PATH= environment variable
   • example path: /home/jakub/Documents/src/gesamt_distance/build/distance
3. run CliApp main method
   • you will need to specify which stage of the solution you want to run
   • see CliApp.java for the details and possible stages

• If you need to tunnel to the database:
  • ssh -L 13306:localhost:3306 -T <remote deployment>

Development

Managing dependencies

Gesamt library

• the library is provided in the resources/lib folder
  • the library is tested on Linux Mint 21, for non-corresponding ubuntu/debian versions you will need to compile the lib yourself
• the source code for the library can be found here: github
• compiling the library for this project requires modification of native bindigs, these modifications are on branch jo-integration of the library so you just need to compile that branch
• follow the instructions in the library's readme to compile the library, then copy the libProteinDistance.so binary to the resources folder

VMMetricSpaceTechniques, VMGenericTools, VMFSMetricSpace

• these are projects of Vladimir Mic
• they are forked to maintain control over their versions
• if you need to update them, either update the fork or point the repos to the upstream