Fix docker compose files for local env

ebi-gene-expression-group / atlas-web-bulk

Bulk Expression Atlas web application

Apache License 2.0

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Fix docker compose files for local env #166

Closed ke4 closed 9 months ago

ke4 commented 11 months ago

Changes:

Fix the service, volume names and also correct the attached volumes for Tomcat service
Add a shell script that builds and deploys the web app
Improve the build-and-deploy-webapp shell script
- Added different flags to the build-and-deploy-webapp.sh shell script to be able to build only front or back-end part of the application or both of them.
- Also added a usage/help file to the script.
- Added its usage to the README.

upendrakumbham commented 10 months ago

I have tested this PR in my local environment, all the docker-compose issues got fixed, I'm able to run all the containers successfully without issues.

upendrakumbham commented 10 months ago

When I ran the application in my local: http://localhost:8080/gxa, I got the below error:

upendrakumbham commented 10 months ago

@lingyun1010, if we both are on the same page, probably we need to fix this by running Magetab/Postgres volume scripts.

lingyun1010 commented 10 months ago

I got errors while running the solr docker volume populating command. The depends on services names are not found, which should be fixed too as the postgres one.

depends_on:
      - postgres
      - solrcloud-0
      - solrcloud-1

lingyun1010 commented 10 months ago

When I ran the application in my local: http://localhost:8080/gxa, I got the below error:

@upendrakumbham did you repopulate docker volume before starting the service in this case?

ke4 commented 10 months ago

When I ran the application in my local: http://localhost:8080/gxa, I got the below error:

@upendrakumbham We don't have E-MTAB-5423 experiment in our local environment. I suppose, your DB got corrupted or was not clean and not executed all the steps described in the README file.

lingyun1010 commented 9 months ago

@ke4 I've tested with the latest commits, but I still cannot populate the solr database in docker, having the error message below

solr-populator-1           | ls: cannot access '/root/experiments-jsonl/*.jsonl': No such file or directory
solr-populator-1 exited with code 0

I don't know if you can populate the data properly on your side or on @upendrakumbham side.

ke4 commented 9 months ago

I am going to merge this PR as we discussed it with @lingyun1010 earlier today.