Support selection from multiple lists

[LakshSingla]

Currently the user can specify only one list from which he or she can view Genes/Proteins etc. The aim of this issue is to enable a user to select from more than one list at a time (much like using "ONE OF" operator).
Here are the caveats:

• The imjs query interface supports adding only one of the list at a time.
• Selection from multiple lists can be supported using custom constraintLogic (like A or B where A and B denote the individual list constraints). But imjs query at the moment does not support changing the constraintLogic once it is set. See issue add setConstraintLogic() public method imjs#18
  For a more verbose description, refer to the discussion on PR List constraint logic  #31

[JM-Mendez]

Hi @AdrianBZG, I'm an Outreachy applicant and would love a shot at this issue.

[AdrianBZG]

Hi @JM-Mendez ,

Great! Let me know if you have any questions, I'll assign this to you 😄

[JM-Mendez]

Awesome! I'll start getting familiar with the codebase and the linked issues to better understand the requirements, and then get back to you.

Are you the mentor for this issue/project that I need to report to? Not sure how this process works.

[AdrianBZG]

That sounds like a good way to start. Yes I'm the mentor for this project, so happy to help with any issues.

[JM-Mendez]

So I came across 2 issues so far with setting up the project. I'm not familiar with coffeescript, so I just traced my way through the compiled node modules package.

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1. The only test case hangs indefinitely.

I was able to console.log the following error:

TypeError [ERR_INVALID_PROTOCOL]: Protocol "https:" not supported. Expected "http:"

in the https module of imjs. I'm not sure why it wasn't propagated up the promise chain. But changing the protocol to http succeeded.

Yet, the test still hanged. I was only able to trace it as far as the service module authorise method. I'm not entirely sure, but it looks like fetchVersion isn't resolving the promise?

EDIT: Just found this existing issue, so I will disregard this concern.
#71

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2. npm run dev does not work. The script dictates that there should be a webpack config, but I do not see one. I searched the commit history for the file but could not find it in any commit. I also do not see a gulp watch task to run on changes.

---

I doubt these 2 issues would prevent me from troubleshooting the main issue. Although without webpack or a gulp watch task, I'd have to restart the project on each change.

Would you like me to at the very least open an issue to address issue 2? I have experience setting up a dev environment using webpack and gulp, so can do it either way.

[AdrianBZG]

@JM-Mendez It would be very nice if you could set-up the dev environment, and this issue was opened to try to address that: #67.

Happy if you give it a try 😄

After that we can take a look at what happens with the other issue.

[JM-Mendez]

EDIT: Crossposted to Draft PR #82 so that I can keep track of my contributions for Outreachy.

Hi @AdrianBZG, I've managed to add multiple lists to the query using window.imTable.query.addConstraints which allows me to pass in an array of contraints.

I stepped through the debugger and for the most part it returns a result from the server, until it tries to parse the xml. Then I run into the error below. I truncated the view and constraintLogic so the code fits without scrolling

"Error: XML is not well formatted. Got 
<query model="genomic" view="Gene.symbol Gene.name..." constraintLogic="(A OR B..." >
  <constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="N" />
  <constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="N" />
</query>

Yet when I try running the query on the humanMine website, I get this xml structure:

<query model="genomic" view="Gene.name Gene.symbol..." constraintLogic="A and B">
  <constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="B" />
  <constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="A"/>
</query>

This seems well formatted to me, so I'm at a loss as to what the error means.

The stack trace throws inside the es6-promise package used by imTables. The last method called that belongs to the imTables library is Service.prototype.authorise (I'm tracing through the compiled package).

I have no idea where to go from here. Any thoughts?

Here's a screenshot of the stack trace:

[AdrianBZG]

Hi @JM-Mendez ,

In this query:

<query model="genomic" view="Gene.symbol Gene.name..." constraintLogic="(A OR B..." > <constraint path="Gene" op="IN" value="PL_BHF_UCL_cardiovascGenes" code="N" /> <constraint path="Gene" op="IN" value="PL_DiabesityGWAS_pval-4" code="N" /> </query>

You see that in the two constraints, you have the same code (N). Can you try to change that to A for the first one and B for the second one and see if the query works? If I remember correctly, it's required to add an unique code to each constraints (A,B,C,D,E...).

PS: Let's discuss that in your draft PR.