Pre-requisites:

• Installed Docker
• Installed Java 8+
• Installed Maven 3.3+

Starting the project:

• Edit class Main.java and change following paths to your location -> eg. where the hmdb file exists and where to output the sql results

  • String file = "/Users/mirekrousal/Downloads/hmdb/hmdb_metabolites.xml";
  • String results = "/Users/mirekrousal/Downloads/hmdb/results.sql";
  • Would recommend you to have these path pointed to the src/main/resources as drop and create scripts are there and in the next step you'd mount these to the docker image

• From command line run following command. Be ready to wait as it takes looong time to generate all the statements. You can check the progress using "tail -f path_to_result/results.sql"

  • mvn exec:java -Dexec.mainClass="cz.mirek.hmdb.mysql.parser.Main"

Using the generated commands in mysql:

• Starting docker container with the MySQL db

  • would recommend you to run this from the top of the project location as the drop and create scripts will be mapped from there.
  • docker run -v $(pwd)/src/main/resources:/scripts -v $(pwd)/docker-data:/var/lib/mysql -e MYSQL_ROOT_PASSWORD=start123 -d mysql:latest
  • docker ps -> to see the docker container id
  • docker exec -it INSERT_HERE_YOUR_CONTAINER_ID /bin/bash

• now you're in the container and you can run following commands to drop / create tables and insert data:

  • mysql -u root -p < dropTables.sql
  • mysql -u root -p < createDatabase.sql
  • mysql -u root -p < results.sql

• selecting data from the Docker command line:

  • mysql -u root -p
  • use metabolomics;
  • show tables;
  • select * from TABLE_YOU_WANT; ... refer to the MySQL documentation for possible queries.