✨New Feature: Remove Gene Tracks from Oncoprint

[SAHU-01]

Fix cBioPortal/cbioportal#10612 (see https://help.github.com/en/articles/closing-issues-using-keywords)

Describe changes proposed in this pull request:

• Make gene tracks removable by setting removable:true in DeltaUtils.ts
• Remove gene tracks from track menu in oncoprint UI, by updating URL gene_list

Checks

• Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
• The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
• Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

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[inodb]

@SAHU-01 Thanks again for working on this!

• There's a small bug when removing the last gene. Gives an error page. Not sure what the behavior should be. Maybe the remove track button should be disabled when there's only one gene?

[SAHU-01]

@inodb thank you for pointing out the bug, I had missed this edge case, as per your suggestion now, if there is more than 1 gene track present we can delete the tracks, else the "Remove Track" option is disabled when only 1 gene track is present.

[inodb]

@SAHU-01 Thanks so much for fixing this so quickly!

[inodb]

@SAHU-01 sorry @alisman found some more bugs:

• When using the merged track feature, see e.g. this query. All the genes become unmerged when one gene is removed. The expected behavior would be that 1) when removing the merged track, the entire merged track is removed and 2) when removing the one gene, the existing merged track stays
• Other OQL modifiers also get removed when removing a track, see e.g. this query
• Same issue for DATATYPES, see this query

The documentation for OQL can be found at https://cbioportal.org/oql if helpful

Thanks in advance for looking at it!

[SAHU-01]

@inodb and @alisman regarding the bug in merged track feature, I've fixed it in the above commit and regarding OQL modifiers and DATATYPES issue, though I've found the cause yet I need some time to explore the best possible fix for it, regardless I'll fix it by tomorrow!

[SAHU-01]

@inodb and @alisman I've fixed all the above-listed bugs, do let me know if there are any more bugs or if the code/logic needs more optimization!

[alisman]

@SAHU-01 for OQL modifiers, I still see the problem IF i remove the first track (BRAF) though it works for subsequent tracks

[SAHU-01]

@SAHU-01 for OQL modifiers, I still see the problem IF i remove the first track (BRAF) though it works for subsequent tracks

@alisman on removing (BRAF), though the modifier (MUT AMP HOMDEL) of the other 2 tracks are not visible, but they still work perfectly, the thing is, when any track is removed it's modifiers are also removed from URL but in this case, in the URL the default modifier (MUT AMP HOMDEL) are not present so after (BRAF) is removed, even though the default modifier(MUT AMP HOMDEL) works as usual they are not visible in UI after deletion.

You can see it in this console where on deleting each track the sublabel shared details about the OQL modifier present

When you try removing one of the other 2 tracks first, it's works perfectly because then each track and that track's sublabel is independently pushed to URL like below, I thought specifically pushing sublabels with remaining tracks, when only default tracks remain won't be wise, but if you suggest to push sublabels in case of defaults then I can modify accordingly.

[alisman]

@SAHU-01 thanks for your careful analysis here. I am going to need to think about the right thing to do and discuss with product team. These are probably edge cases we're worried about so maybe it's ok not worry about them. Stay tuned.