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: 9.1.8 Major Release
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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 5 2021 May 17 - May 28
Description
As revealed in IGBF-2855 by Omkar Marne's investigations, the External View functionality for the UCSC Genome Browser fails when the UCSC Distributed Annotation Data source is not active.
This is because the code is using the internal data source object to retrieve a listing of UCSC genome names.
However, there is a much better way to get these information. Instead, the External View code can query the UCSC JSON API to get this same information, in JSON format.
This ticket provides a record of how we are doing this.
Attachments
Issue Links
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IGBF-2864 Improve External View error message displayed when no genome is selected
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] | |
| Sprint | Spring 5 2021 May 17 - May 28 [ 121 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Omkar Marne [ omarne ] |
Tested the External View tab functionality. Went through the commits for IGBF-2855. The genome data is getting pulled from JSON end point instead of UCSC DAS data source. The External view tab functionality is working even if the UCSC DAS data source is disabled.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
| 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 ] |
| Assignee | Ann Loraine [ aloraine ] |
Merged. Built master branch installers. Ready for testing.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | Post-merge Testing In Progress [ 10003 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Omkar Marne [ omarne ] |
Tested on Mac with master installer.
Able to load UCSC External View image when the UCSC DAS data source is disabled.
Working correctly.
Tested on Windows and Linux with master installer.
Able to load UCSC External View image when the UCSC DAS data source is disabled.
Working correctly.
Closing the issue.
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Omkar Marne [ omarne ] | Ann Loraine [ aloraine ] |
See: https://bitbucket.org/aloraine/integrated-genome-browser/branch/IGBF-2863?dest=master
This new branch uses the UCSC JSON list genomes endpoint to get a list of all supported genome names from UCSC.
It also includes test cases that fail if the endpoint stops working as expected.
This fixes "Situation Three" mentioned in
IGBF-2855in which External View tab fails when the UCSC DAS data source has been de-activated within IGB.