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setting-up-environment.md

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Setting up local run environment

This is useful for development and debugging purposes.

All commands below are provided for IntelliJ IDEA running on Ubuntu. Prior to running them, clone the repository and open in IntelliJ IDEA.

To learn more about some variables referenced here, see instructions to run the pipeline on the cluster

1. Install and configure Java 8

By default, IDEA will use Java 11 on most modern systems. However, this project can only run on Java 8. If you don't have it, install it:

sudo apt install openjdk-8-jdk openjdk-8-jre

In IDEA, open File → Project Structure. Change the “Project SDK” to Java 8.

2. Configure Maven

  • Open File → Settings → Build, Execution, Deployment → Build Tools → Maven and change the location of the “User settings file” to settings.xml in the root of the repository. To change the setting, you will need to enable the “Override” checkbox on the right.
  • In the settings.xml file, fill in ORACLE_SSO_USERNAME and ORACLE_SSO_PASSWORD (see above).
  • In IDEA, right click on the project → Maven → Reimport. Wait for the process to complete.
  • Right click on the project → Maven → Generate sources and update folders.

3. Create and configure local Postgres database

Method 1: system installation

sudo apt install postgresql postgresql-contrib
sudo systemctl start postgresql
sudo systemctl enable postgresql
sudo -u postgres psql postgres
\password postgres

Method 2: run with Docker

docker run --name postgres -p 5432:5432 -e POSTGRES_PASSWORD=00000000 -d postgres

Type exit.

4. Configure test profiles

In metadata-load/src/test/resources/application.properties, set the following variables:

  • ena.datasource.url
  • ena.datasource.username
  • ena.datasource.password

To run the tests, open View → Tool Windows → Maven. Then open a project and click Lifecycle → test. To run tests for metadata-load, you need to be either on EBI premises or connected to its network via VPN or SSH.

5. Configure run profiles

The run profiles are useful for running import pipeline or the metadata webservice and debugging them.

metadata-load

In metadata-load/src/main/resources/application.properties, set the following variables:

  • ena.datasource.url, ena.datasource.username, ena.datasource.password — same as for testing profiles
  • metadata.datasource.url=jdbc:postgresql://localhost:5432/postgres
  • metadata.datasource.username=postgres
  • metadata.datasource.password — your local Postgres password
  • entrez.api.key

Add lines to this file:

spring.jpa.hibernate.ddl-auto=create
spring.jpa.database-platform=org.hibernate.dialect.PostgreSQLDialect
spring.jpa.generate-ddl=true

They will ensure that the local database schema and contents are erased with each import run.

metadata-ws

In metadata-ws/src/main/resources/application.properties, set the following variables:

  • spring.datasource.url, spring.datasource.username, spring.datasource.password
  • spring.jpa.hibernate.ddl-auto=create

Finally, add run configurations in IDEA for metadata-load and metadata-ws modules.

Once the environment has been set up, it makes sense to save all of the modifications as a Git stash to avoid applying them again:

git stash save 'Local run configuration'

The stash can be applied without losing it with:

git stash apply stash@{0}