Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 5, Spring 6, Spring 7
Description
Add group mapping for GenArk tracks in hub facade to make folders similar to how UCSC shows the GenArk genome tracks on their site. Refer the already implemented code in the ucsc module.
Attachments
Activity
As discussed, created a PR for the ticket: https://bitbucket.org/lorainelab/hub-facade/pull-requests/38. Please review and let me know if there are any issues.
Reviewed the code and it looks good.
Ready for PR: https://bitbucket.org/lorainelab/hub-facade/pull-requests/38
Updated the PR https://bitbucket.org/lorainelab/hub-facade/pull-requests/38 to make it in sync with the latest changes with the loraine lab hu-facade main.
Hub facade PR is merged and the new code is deployed to translate.bioviz.org. Ready for testing.
Testing main branch on Mac.
Tracks are in the UCSC groups, however, I'm seeing a few strange groupings. I'm looking at the Apis florea GCF_000184785.3 GenArk (UCSC hub, UCSC Genome Browser) in IGB, and in the Available Data panel each folder has some of the data in a folder labeled cpgIslands, but I don't think it is supposed to be in the folder. Seems like extra cpgIslands folders?
Investigated the issue, a small code change got removed in another pull request: https://bitbucket.org/lorainelab/hub-facade/pull-requests/40/diff#Ligb_trackhub/api/create_resources.pyF242. Here is the PR including those changes: https://bitbucket.org/lorainelab/hub-facade/pull-requests/44.
Tested the changes and everything's working as expected.
PR is merged and new code is deployed to translate.bioviz.org. Ready for testing.
Tested main branch on Mac.
The folder logic is fixed and looks great!
I noticed one other nitpicky thing I wanted to run by Jaya Sravani Sirigineedi. The logic for the available data labels differs from what we have for UCSC REST. For example:
- UCSC REST data labels are determined by: shortLabel (track) & tooltip = longLabel
- UCSC GenArk data labels are determined by: track & tooltip = longLabel
I like the labels for UCSC REST better as they match what the user sees on the UCSC Genome Browser. Would it be possible to alter the GenArk?
Added the shortlabel, here is the PR for that: https://bitbucket.org/lorainelab/hub-facade/pull-requests/45. Tested the changes, everything's working as expected.
PR is merged and new code changes are deployed to translate.bioviz.org.
Ready for testing.
Labels look good, thank you Sravani!
Closing ticket.
Implemented the changes to make the folders similar to how UCSC shows the tracks. Tested the changes and everything works as expected. Here is the updated code: https://bitbucket.org/jaya-sravani/hub-facade/branch/IGBF-4139. Please review and let me know if there's any issue.