Support building from path to a mine instead of git repo

[heralden]

It seems important to be able to build a mine by its path instead of passing a git repo as an argument.

We would have to add a new argument for this, and handle it by creating a volume to mount that dir in the intermine_builder container.

[22PoojaGaur]

Hi @uosl

I think this would require two changes -

1. Adding and passing flag for the path in intermine_boot
2. Updating build.sh in docker-intermine-gradle to go into that folder if path is specified.

Does it seem fair to you? or am I missing something?

[22PoojaGaur]

For changes in docker-intermine-gradle, I still create a PR in the docker-intermine-repo right?

(And somehow update the git submodule to fetch that version in intermine_boot?)

[heralden]

Adding and passing flag for the path in intermine_boot

👍

Updating build.sh in docker-intermine-gradle to go into that folder if path is specified

Not sure about this, since we'll need to make the dir available by passing it as a volume. Currently, we mount a biotestmine volume and cd into it, right? I think we should mount a volume with the dir the path points to, and cd into that (which should only be one level deep).

For changes in docker-intermine-gradle, I still create a PR in the docker-intermine-repo right?
(And somehow update the git submodule to fetch that version in intermine_boot?)

👍
For testing you might want to replace the submodule with a symlink to your local docker-intermine-repo folder, as I'm not sure how easy it is to get a submodule to stay up-to-date with your local repo when you're trying things out.

[22PoojaGaur]

Not sure about this, since we'll need to make the dir available by passing it as a volume. Currently, we mount a biotestmine volume and cd into it, right? I think we should mount a volume with the dir the path points to, and cd into that (which should only be one level deep).

oh, right. If the folder biotestmine (or MINE_NAME) exist it should be able to use it. I'll see.

For testing you might want to replace the submodule with a symlink to your local docker-intermine-repo folder, as I'm not sure how easy it is to get a submodule to stay up-to-date with your local repo when you're trying things out.

ok.

[22PoojaGaur]

@uosl

I added a flag for datapath (datapath is a folder under which biotestmine would be present). If the flag is provided, it loads the datapath instead of creating new volumes.

For testing I just cloned the biotestmine repo in a datapath folder and pass datapath as command line argument. I think this is not sufficient, as other folders (eg dump, configs, packages) are required during intermine build.

So my question is, in building mine from path do I assume that these folders are present and the intermine_boot just needs to start the webapp ?

If not, what should I do?

[heralden]

I think the datapath folder should only replace the biotestmine volume, while the other volumes (dump, configs, packages, and intermine) should still be created and loaded as volumes.

Let me know if I misunderstood and this doesn't answer your question clearly.

[22PoojaGaur]

Yes, that's what I was asking.

Got it.