Add Models tab to gene product pages

[pkalita-lbl]

These changes add a Models tab to gene product pages.

• When the page is loaded it queries http://barista.berkeleybop.org/search/models for models that involve the gene product for that page. This endpoint will need to be changed later. It's being used here for the time being because unlike https://api.geneontology.xyz/gp/{id}/models it doesn't require a full identifiers.org URI. Hopefully the new GO API can take that into account, and once it is deployed we can use it instead of http://barista.berkeleybop.org/search/models.
• Once a list of models is loaded it sets up a select box to choose one and a <wc-gocam-viz> element to display the selected one. If the query returns no models a "no data" message and a link to https://geneontology.cloud/home is displayed.

[pkalita-lbl]

Update to my first point: it sounds like the new GO API already has a version of the /gp/{id}/models endpoint that accepts a CURIE. @sierra-moxon will be working on standing up a dev server. Once that's available I can updated the endpoint being used for the Models tab.

[kltm]

I'm also curious on your docker development workflow. To get it working for me, I basically did:

    git config --global user.email "foo@bar.com"
    git config --global user.name "Nemo"
    git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*"
    git fetch
    git checkout issue-677
    git pull
    npm install
    ./node_modules/.bin/gulp build
    ./node_modules/.bin/gulp install
    cp ./perl/bin/config.pl /etc/perl/

What does your setup look like?

[pkalita-lbl]

hard you think it would be to add a count (or any other indication) for models available for viewing

Not hard. I can add that.

What does your setup look like?

This is probably going to be an unsatisfying answer to you but I use VS Code's remote development features to attach VS Code to the running container.

[pkalita-lbl]

Requested changes have been made.

Plus the barista API call has been replaced by a call to the new GO API. It's controlled by config variable called GO_API_URL (can rename if that's not clear enough). I added the specific URL that works right now (https://api-sierra.geneontology.io) to conf/examples/amigo.yaml.localhost_docker_loader because that's the only example file that I really understand how it gets used 😁 The other conf/examples/amigo.yaml.* files just have an empty string as the GO_API_URL value because I wasn't sure about propagating https://api-sierra.geneontology.io in too many places.

[kltm]

@pkalita-lbl It's fine to propagate it everywhere and/or have api.geneontology.org be the default route if not defined. Better to be explicit and wrong than have shifting behavior.

[kltm]

@pkalita-lbl I wanted to note here for you that for AmiGO, right now, the master is the "production" branch. With that , since we're waiting for the new API and location to go live, we'd be leaving this as a branch that we can test for the moment. Does that sound okay to you?

[pkalita-lbl]

we'd be leaving this as a branch that we can test for the moment. Does that sound okay to you?

Yeah that's fine. I assume this branch will still be unmerged when I get a chance to work on https://github.com/geneontology/amigo/issues/678. If that's the case I'll add those changes to this branch, since that'll be based off this work. I will also make the API URL changes suggested above at that time.

[kltm]

@pkalita-lbl That sounds about right to me. The new page path is largely unrelated code-wise internally, so we can demonstrate work done with the previous part at any time.

[pkalita-lbl]

@cmungall Here's a screenshot of the in-development work on the gene product details page. A list of models is fetched from the new GO API (deployed at https://api-sierra.geneontology.io). If the list is not empty a model selection box and the GO-CAM widget are shown:

If no models are found a bit of placeholder information is shown:

[kltm]

@pkalita-lbl Latest version on https://amigo-staging.geneontology.io Example at: https://amigo-staging.geneontology.io/amigo/model/6446bfcb00000283

[kltm]

@pkalita-lbl Some notes on this example:

• [ ] The link to GH does not work (https://amigo-staging.geneontology.io/amigo/model/6446bfcb00000283); I believe it is missing a .ttl.
• [ ] The "true" name of a server seems to be escaping in the "CytoView Workbench". This should probably be hard-coded to noctua.geneontology.org; I believe there is a variable in there that you can grab that from?
• [ ] Similar to ^ for the "Edit" link
• [ ] The gene product links do not seem to work?

If you're comfortable, we can also bring Kimberly and David back into the conversation now or after another pass.

[kltm]

@pkalita-lbl This is looking great, BTW! This is going to solve a lot of problems.

[kltm]

@pkalita-lbl Looks great!