Expose database to host machine so it can be easily inspected

[adamabeshouse]

Also add .gitignore

[inodb]

for production use often one prolly wouldn't want to expose 3306 because it opens up the port to any process on the machine. This is protected atm by running this cbioportal-database container within cbio-net network (see networks section). That is, only containers on this network are able to access 3306. To connect to the db with the mysql command you can either use exec to run a mysql command within the cbioportal-database container. Or you can start a separate mysql container on the cbio-net. Not sure if those alternatives cover your use case?

[inodb]

Discussed some more with @adamabeshouse . Use case is connecting to sequel pro locally for dev use. Can't see how to do that w/o exposing the port

@pvannierop @nr23730 any thoughts on exposing this port? I figured maybe it's not that big of a risk. Alternatively maybe we should add some dev flag (or dev compose file)

[nr23730]

I would propose to add a separate -dev compose file that may also do the following:

• Enable Debug for init script (SHOW_DEBUG_INFO: "true")
• Expose MySQL port
• Expose session service port
• Expose MongoDB port for session service

Also I may add a PR that easily allows so set a different port for cBioPortal as 8080 is very common in may already be in use. Of course it's possible for everyone to change the compose file, but that might cause unnecessary merge conflicts.

[pvannierop]

See: https://docs.docker.com/compose/extends/

This can be best done with a compose extension file like so:

db-ports.yml

services:
   cbioportal-database-container:
   ports:
      - "3306:3306"

And then run:

docker-compose -f docker-compose.yml -f db-ports.yml up -d

[pvannierop]

See: https://docs.docker.com/compose/extends/

I propose to use a compose extension strategy that will leave the docker-compose.yml unchanged.

[pvannierop]

See: https://docs.docker.com/compose/extends/

This can be best done with a compose extension file like so:

db-ports.yml

services:
   cbioportal-database-container:
   ports:
      - "3306:3306"

And then run:

docker-compose -f docker-compose.yml -f db-ports.yml up -d

[adamabeshouse]

@inodb @pvannierop @nr23730 Thanks for your comments. I have made requested changes, let me know if it looks good

[nr23730]

Lgtm!

[pvannierop]

Yes, this looks good! Minor gripe I have is with the filename. I would think that open-db-ports.yml would be better. When the idea is to open ports for other services as well in the future, I propose to leave the filename as is.