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  1. IGB
  2. IGBF-2855

Investigate activating UCSC DAS source from External View tab

    Details

    • Story Points:
      2
    • 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?

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            ann.loraine Ann Loraine created issue -
            ann.loraine Ann Loraine made changes -
            Field Original Value New Value
            Epic Link IGBF-1765 [ 17855 ]
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-2793 [ IGBF-2793 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            Assignee Ann Loraine [ aloraine ]
            omarne Omkar Marne (Inactive) made changes -
            Assignee Omkar Marne [ omarne ]
            omarne Omkar Marne (Inactive) made changes -
            Status To-Do [ 10305 ] In Progress [ 3 ]
            ann.loraine Ann Loraine made changes -
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-2858 [ IGBF-2858 ]
            ann.loraine Ann Loraine made changes -
            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 ]
            ann.loraine Ann Loraine made changes -
            Rank Ranked higher
            ann.loraine Ann Loraine made changes -
            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?
            ann.loraine Ann Loraine made changes -
            Link This issue relates to IGBF-2860 [ IGBF-2860 ]
            ann.loraine Ann Loraine made changes -
            Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
            ann.loraine Ann Loraine made changes -
            Assignee Omkar Marne [ omarne ]
            ann.loraine Ann Loraine made changes -
            Story Points 0.5 2
            ann.loraine Ann Loraine made changes -
            Fix Version/s 9.1.8 Major Release [ 10605 ]
            ann.loraine Ann Loraine made changes -
            Link This issue blocks IGBF-2863 [ IGBF-2863 ]
            ann.loraine Ann Loraine made changes -
            Comment [ Pushed branch IGBF-2855 to my repository on bitbucket.org: aloraine/integrated-genome-browser.git

            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? ]
            ann.loraine Ann Loraine made changes -
            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?) ]
            ann.loraine Ann Loraine made changes -
            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} ]
            ann.loraine Ann Loraine made changes -
            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 - IGBF-2860.

            ]
            ann.loraine Ann Loraine made changes -
            Assignee Omkar Marne [ omarne ]
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
            ann.loraine Ann Loraine made changes -
            Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
            ann.loraine Ann Loraine made changes -
            Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
            ann.loraine Ann Loraine made changes -
            Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
            ann.loraine Ann Loraine made changes -
            Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
            ann.loraine Ann Loraine made changes -
            Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
            ann.loraine Ann Loraine made changes -
            Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
            ann.loraine Ann Loraine made changes -
            Resolution Done [ 10000 ]
            Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
            ann.loraine Ann Loraine made changes -
            Comment [ [~omarne] - please see above comment. ]
            ann.loraine Ann Loraine made changes -
            Link This issue blocks IGBF-2864 [ IGBF-2864 ]
            nfreese Nowlan Freese made changes -
            Link This issue relates to IGBF-2869 [ IGBF-2869 ]

              People

              • Assignee:
                omarne Omkar Marne (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                • Created:
                  Updated:
                  Resolved: