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
- blocks
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IGBF-2863 Use UCSC JSON endpoint to get list of genomes for External View tab
- Closed
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IGBF-2864 Improve External View error message displayed when no genome is selected
- Closed
- relates to
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IGBF-2860 Disable Ensembl external view
- Closed
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IGBF-2869 Investigate adding UCSC JSON API as a new data provider
- Closed
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IGBF-2858 Write R or python notebook to compare data retrieved from UCSC DAS and JSON APIs
- To-Do
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IGBF-2793 Restore DASv1 support
- Closed
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. ] |
Before we design the interface, we need to look at the implementation of the panel that is shown when the user clicks "update". We need to know what the actual problem is here, and whether we can simply fix a bug and not have to change the UI.
The current "External View" interface shows an empty panel with three components at the bottom of the panel:
When users click "update," some code in IGB sends requests to either UCSC or Ensembl genome browser systems to retrieve image files corresponding to the currently visible region in the IGB main window.
However, as you know, this sometimes fails if (a) the genome being viewed in IGB does not exist in the requested external system or (b) DAS data source is de-activated.
DAS data source activation is controlled in Preferences > Data Sources tab.
When the UCSC option is selected within the External View tab and the user clicks "update," probably what happens is that IGB then requests data from the UCSC DAS data source. (DAS stands for: Distributed Annotation Service.)
If and when this call fails to retrieve the expected data, the External View interface then displays a message that reads:
There are actually three (possibly more) situations when this message is displayed. These include:
Situation 1: The user has launched IGB but has not yet selected a genome. If the user then opens the "External View" tab and clicks "update", the error message will be displayed.
Situation 2: User has launched IGB and selected a genome for which there is no external view available from UCSC. If the user clicks the "update" button they will see the error message.
Situation 3: User has launched IGB, selected a genome for which there is indeed an external view available at UCSC, but the DAS data source is not active. In this case, the error message will be displayed, as well.
It is possible there could be a very simple fix that not require changing anything apart from how the External View code is contacting and using the UCSC genome browser resource. It depends on what information the External View is needing to retrieve from the data source. It may be something that does not actually require the Distributed Annotation Service. Or it could be a piece of information we can get from a better, more robust source, such as the newer JSON REST service - see: http://genome.ucsc.edu/goldenPath/help/api.html