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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-4086 [ 23382 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 5 [ 214 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
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.
| Sprint | Spring 5 [ 214 ] | Spring 5, Spring 6 [ 214, 215 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Reviewed the code and it looks good.
Ready for PR: https://bitbucket.org/lorainelab/hub-facade/pull-requests/38
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
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.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Hub facade PR is merged and the new code is deployed to translate.bioviz.org. Ready for testing.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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?
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Sprint | Spring 5, Spring 6 [ 214, 215 ] | Spring 5, Spring 6, Spring 7 [ 214, 215, 216 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
PR is merged and new code is deployed to translate.bioviz.org. Ready for testing.
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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?
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
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.
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
PR is merged and new code changes are deployed to translate.bioviz.org.
Ready for testing.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Labels look good, thank you Sravani!
Closing ticket.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
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.