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: 10.1.0
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Labels:None
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Story Points:2
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Epic Link:
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Sprint:Spring 7, Spring 8, Spring 9
Description
It is very tough for a user to search for a track in the available tracks panel as there are a lot of tracks in the hg38 genome so we have to investigate a way to make folders for each file type inside the UCSC Rest folder so it becomes a little bit easier for the user to search a specific track.
Attachments
Issue Links
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Story Points | 2 |
| Sprint | Spring 7 [ 191 ] | Spring 7, Spring 8 [ 191, 192 ] |
| Rank | Ranked higher |
| Attachment | Screenshot 2024-04-16 at 9.56.30 AM.png [ 18331 ] |
I would lean towards putting all files in folders for their file type. As for naming the folders, I would stick with what the API is returning or the naming format here: https://genome.ucsc.edu/FAQ/FAQformat.html
As discussed with Nowlan Freese, keeping the folders for all the file types and naming them according to the track type names returned by the API. Code changes are done and available at https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3689. Please review and let me know if there are any issues.
To test:
- Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3689 and start the application.
- Select a particular genome.
- See whether UCSC (Rest) datasets are visible inside file type folders (like shown in below screenshot) in the Available data panel.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Nowlan Freese [ nfreese ] |
Tested Sravani's branch on my Mac.
Available files appear in their respective folders. Able to load data from each folder. No issues in log when building or running.
Ready for pull request.
| Assignee | Nowlan Freese [ nfreese ] | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Here is the raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/999
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Summary | Investigate on how to make folders inside the UCSC Rest folder | Make folders inside the UCSC Rest folder |
Merged
| Sprint | Spring 7, Spring 8 [ 191, 192 ] | Spring 7, Spring 8, Spring 9 [ 191, 192, 193 ] |
| Rank | Ranked higher |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Tested on IGB main installer on Mac. UCSC REST data appear in folders matching their file type.
Closing ticket.
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
Investigated and found the code on how to make folders, changed the code in UCSC Rest as well to make the folders. Nowlan Freese Need your input on on how to organise the folders. Is it okay if I do folders for all the file types or do you want me to make folders for only the few file types that have a lot of tracks. Please review the below screenshot.
