Details
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Type:
Sub-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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Sprint:Fall 7, Fall 8, Spring 1, Spring 2, Spring 3
Description
Develop code to connect to the https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 API and get the chromosomes for a selected genome
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | Develop code to connect to the https://api.genome.ucsc.edu/list/chromosomes?genome=hg38 API and get the chromosomes for a selected genome |
| Attachment | Screenshot 2024-01-16 at 11.49.03 AM.png [ 18169 ] |
Tested the code, working as expected. Able to see the chromosomes list for the selected genome. Code is available at branch https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3501
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-3501 and start the application.
- Select a particular genome, preferably one that doesn't have data in IGB quick load.
- See whether Chromosomes are visible in the Current Genome side 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 ] |
Testing on Mac:
- Cloned Sravani's
IGBF-3501branch and started IGB. - Disabled all data providers except for UCSC REST in the Data Sources tab.
- Selected the galGal6 genome (the galGal6 genome is available from UCSC but we do not have it in IGB Quickload).
- The chromosomes and their lengths are visible.
- There are no errors in the IGB logs.
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Jaya Sravani Sirigineedi [ jsirigin ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| 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 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
As discussed, closing this ticket because the data loading part is not implemented yet, will be done as part of this https://jira.bioviz.org/browse/IGBF-3528 subtask.
| Story Points | 2 |
| Comment | [ [~nfreese] While testing the application I observed one thing, the list of chromosomes differs for each track, click on the below links to see the no of chromosomes returned for each. Right now in our implementations, we are calling the chromosomes API only once at the start without any track parameter. Because of this, when we are trying to load data for the chromosomes that are not present in the current track we are receiving empty response from the UCSC API. ] |
| Fix Version/s | 10.1.0 [ 11000 ] |
Developed the code to integrate the API and get the chromosomes for the selected genome. Testing is in progress.