Enable atlas-web-core integration tests in Single Cell Expression Atlas Gradle container

[alfonsomunozpomer]

We’ll need magetab and experiment designs for bulk, possibly Solr, too. This could make the execute-all-tests.sh script obsolete.

Summary of changes to the prepare-dev-environment directory:

• All scripts have been changed to use docker compose instead of Docker. I described the new requirements in README.md and removed the “Troubleshooting” section since that only happened with earlier versions of Docker and the deprecated docker-compose.
• I added a -r flag to all scripts in order to remove volumes. Being able to explicitly mark which volumes shouldn’t be deleted with external:true when executing docker compose down -v is quite handy.
• I added an interactive countdown before removing volumes. I asked Copilot for help with that one and I tweaked it afterwards. Good job Copilot!
• The Solr private key is used by the populator container as a secret, rather than a volume.

For the Compose files that we use to launch and test the application:

• Got rid of the error you had some times regarding the signing key in Solr. The service only needs the key when verifying packages (i.e. when running the prepare-dev-environment script). If it’s not set it defaults to /dev/null and it’s fine.
• I added a new docker-compose-build.yml to be used in conjunction with the Tomcat service. It will build the front-end packages, the WAR, and then launch Tomcat. Use the build-and-deploy-webapp.sh script to do that. You get a .war file as a side benefit.

This is all as a result of the need to parameterise all the YAML files with PROJECT_NAME to dynamically change between gxa and scxa. It was a massive tangent. The positive side of this is that we may be able to use exactly the same files for bulk and SC, but this needs some consideration.

There are some additional changes to test classes and a few other main classes in atlas-web-core, too. See https://github.com/ebi-gene-expression-group/atlas-web-core/pull/128.

Remember that this PR makes it possible to run integration tests for atlas-web-core locally with Docker. Jenkins doesn’t do that, because we don’t have a bulk CI environemnt yet. One exmple output of execute-all-tests.sh after adding integration tests in atlas-web-core is here: https://gist.github.com/alfonsomunozpomer/61ec9437124d93e672307813ad596b61

[alfonsomunozpomer]

@ke4 Please have another look. You were right and variables that are in --env-file aren’t necessary to be declared another time in the Docker Compose YAML files.

[alfonsomunozpomer]

@ke4 I addressed or otherwise clarified the issues you raised. Feel free to resolve the conversations or comment further.

[alfonsomunozpomer]

@ke4 There’s bin an extra bit of drama related to how --env-file isn’t exactly the same as env_file or using .env by default. Docker Compose is kind of weird... Have one more look at the last commit, please.