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 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28
Description
If the UCSC Distributed Annotation Service (DAS) data source is not active (see Preferences > Data Sources) then External View does not work. It shows a message stating that the genome is not available.
This message is very cryptic because it does not explain to the user that they need to activate the UCSC DAS data source in order to show data in the External View tab.
Investigate: Can we simply add a button or other user interface component that would let the user activate the required data source within the External View tab?
Attachments
Issue Links
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- Closed
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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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- relates to
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IGBF-2860 Disable Ensembl external view
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- Closed
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- Closed
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- To-Do
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- Closed
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Show 1 more links (1 relates to)
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | FireFoxShowingUCSCGenomesEndpoint.png [ 16150 ] |
| Sprint | Spring 4 2021 May 3 - May 14 [ 120 ] | Spring 4 2021 May 3 - May 14, Spring 5 2021 May 17 - May 28 [ 120, 121 ] |
| Rank | Ranked higher |
| Description |
If the UCSC Distributed Annotation Service (DAS) data source is not active (see Preferences > Data Sources) then External View does not work. It shows a message stating that the genome is not available.
This message is very cryptic because it does not explain to the user that they need to activate the UCSC DAS data source in order to show data in the External View tab. Investigate: Can we simply add a button or other user interface component that would let the user activate the required data source within the External View tab. |
If the UCSC Distributed Annotation Service (DAS) data source is not active (see Preferences > Data Sources) then External View does not work. It shows a message stating that the genome is not available.
This message is very cryptic because it does not explain to the user that they need to activate the UCSC DAS data source in order to show data in the External View tab. Investigate: Can we simply add a button or other user interface component that would let the user activate the required data source within the External View tab? |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Omkar Marne [ omarne ] |
| Story Points | 0.5 | 2 |
| Fix Version/s | 9.1.8 Major Release [ 10605 ] |
| Comment |
[ Pushed branch This new branch shows where and how I would recommend adding the new logic for getting UCSC genome version names from the json endpoint attn: [~omarne] - maybe take a look? ] |
| Comment | [ Attempting to add test coverage for the new method, following this tutorial: https://www.baeldung.com/integration-testing-a-rest-api (not sure if this will work outside of the spring framework; also seems like it requires oracle code, which does not appear to be available in maven central?) ] |
| Comment |
[ Please review this branch:
* https://bitbucket.org/aloraine/integrated-genome-browser/src/IGBF-2855 Note: The branch fixes "Situation 2" described above (the DAS-related problems). Still requiring a fix: "Situation 1", but I think this can be done as a different ticket. {quote} Situation 1: The user has launched IGB but has not yet selected at genome. If the user then opens the "External View" tab and clicks "update", the error message will be displayed. {quote} ] |
| Comment |
[ I looked into getting the Ensembl option to work. (Currently it does not.) It looks like the URL interface to the Ensembl genome browser site has changed, which breaks the functionality. I turned it off as part of another ticket - ] |
| Assignee | Omkar Marne [ omarne ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | 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 ] |
| 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 ] |
| Comment | [ [~omarne] - please see above comment. ] |