Render Gene view using JSON

[Arnedeklerk]

Part 2 of 3. See 1 here.
Gene view to be updated to parse the returned JSON.

• 1. @marco-brandizi - ensure the code is in order (is the code from Make the output of genome API as pure JSON #655 on Master?)
• 2. @marco-brandizi make Distance and P-value numeric formats.
• 3. @marco-brandizi to ensure Distance and P-values are being returned for each evidence.
• 4. @marco-brandizi please explain to @lawal-olaotan here how to call the API with the flag.
• 5. @lawal-olaotan to update the frontend to use new JSON format Make the output of genome API as pure JSON #655. It includes "Distance" and "P-Value" KnetScore, we can use those to work on Gene Neighbourhood functionality and filtering.

[Arnedeklerk]

@marco-brandizi, @lawal-olaotan has finished the first step of this 3 part process. When you get the time, please take a look at step 1-3 on this ticket.

[marco-brandizi]

I'm aware of this, but it's not so simple. Changes remained in a branch for long time, meanwhile a lot changed (eg, config system). I need to find time to manually copy-paste the JSON output part.

[marco-brandizi]

Also, the code about infinite scrolling was way too poor yesterday, will check if it changed much, but I doubt.

[Arnedeklerk]

Cool, I know Lawal reviewed his work, made changes, then worked through it again and sent out more changes... #751

[marco-brandizi]

Those bugs are a minor aspect, a major concern is the code is still too poor, convoluted, very unreadable, even for something that we plan to replace in not so long time.

[marco-brandizi]

The API part is ready and merged to master, see #655.

==> Note the trick I've used to be able to push on master (in order to avoid the related API changes to go outdated again):

I've added some Javascript code (see geneTable2OldString() and evidenceTable2OldString() data-utils.js), which takes the new JSON and converts it back to the old TSV-in-a-string. This is a temporary hack, it makes the UI a bit slower and we shouldn't wait for too long before adapting the Javascript code to the new format. See the notes in the mentioned files regarding details about such adaptation.

[Arnedeklerk]

Great that this is working so far!

Part of this ticket is to still return P val and Distance for each evidence. @marco-brandizi when you get time please.

Then we can move to #692, which I believe @lawal-olaotan has started making mock ups for and is still using mock-data.

[marco-brandizi]

@lawal-olaotan @Arnedeklerk @KeywanHP

Now the API is returning the topological distance for each concept. As discussed, I had to change the output JSON, now it looks like this and the difference is in conceptEvidences, which reports objects, not just label strings.

As agreed, we can use "score" and "graphDistance" for filtering the gene table, for now, we're going to omit the evidence-related p-value, due to the difficulty of computation.

[Arnedeklerk]

Cool, sounds good to me @marco-brandizi, thanks :).

@lawal-olaotan to you!

[Arnedeklerk]

Working and data as expected. Thanks.

[marco-brandizi]

@Arnedeklerk Point 5) in the description isn't completed. Keep this open until that.

[Arnedeklerk]

@marco-brandizi I believe this is done, my bad for not ticking it though. Point 5 is about rendering gene view using the Json. Then it refers to other tickets which require that format. Lawal is currently working on: #692

[Arnedeklerk]

For future reference: we opted to use the Distance (available for each evidence per gene) and (instead of P val), the KnetScore (@marco-brandizi that's what the Score ended up being, by the way).

An additional API change now also changes the format to return each evidence's distance from the seed gene[s]. I think the commit above broke Ci-test but @lawal-olaotan is working on a fix. Once that's done, we can complete...

[marco-brandizi]

I don't see any gene view that uses the new JSON format from the API. Before closing a ticket, the corresponding changes must be at least pushed to github, in most cases should be tested too (on CI).

"Done on my laptop" is not like done.

[Arnedeklerk]

I must be mistaken. Best let's wait for @lawal-olaotan to comment.

[lawal-olaotan]

I should have referenced the ticket when I pushed the changes that adjusted the gene view to the new JSON format because I discussed @Arnedeklerk during our meeting; that was the last step to finish the ticket.

[marco-brandizi]

I needed to merge my fix for this and other changes around. I discovered another issue, see #777