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  1. IGB
  2. IGBF-3655

Replace DAS requirements in IGB and disable DAS by default

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.1.0
        • Labels:
          None

          Description

          Situation: Now that the UCSC REST data source has been implemented in IGB, we should be able to disable DAS by default. Previously, DAS was required for the External View tab (IGBF-2776) and the View Region in UCSC Browser (IGBF-2777). This was because the code was using the internal data source object to retrieve a listing of UCSC genome names. This dependency was changed to use the UCSC JSON endpoint in IGBF-2863.

          Task:

          • Search for and replace any DAS requirements in IGB - though there may not be any left.
          • Set DAS to disabled by default in igbDefaultPrefs.json

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-2863 Use UCSC JSON endpoint to get list of genomes for External View tab

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-3129 [ 21675 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-2863 [ IGBF-2863 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 6 [ 190 ] Spring 7 [ 191 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 [ 191 ] Spring 7, Spring 8 [ 191, 192 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7, Spring 8 [ 191, 192 ] Spring 7, Spring 8, Spring 9 [ 191, 192, 193 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-05-10 at 3.36.12 PM.png [ 18376 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-05-10 at 3.27.59 PM.png [ 18377 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment Screenshot 2024-05-10 at 3.28.58 PM.png [ 18378 ]
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                jsirigin Jaya Sravani Sirigineedi added a comment - - edited

                Disabled UCSC DAS Data Provider by default and tested a few functionalities to make sure disabling DAS isn't causing any issues. Everything is working as usual. Updated code is at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3655. Below are screenshots of few tested scenarios:
                Loading of human genome with updated UCSC REST code and after disabling DAS (took around 3-4 secs to load):

                External View loaded correctly without any issue:

                Redirect to UCSC genome browser also worked fine:

                Please review and let me know if there are any issues.
                To Test:

                1. Make sure your igb preferences are reset before running the above branch installer jar or building the application from the above branch.
                2. Now, after IGB is started, click on the configure button in the available data panel and check whether UCSC DAS is disabled by default.
                3. Also, select any genome and check whether the DAS tracks are not being loaded.
                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - - edited Disabled UCSC DAS Data Provider by default and tested a few functionalities to make sure disabling DAS isn't causing any issues. Everything is working as usual. Updated code is at the branch: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3655 . Below are screenshots of few tested scenarios: Loading of human genome with updated UCSC REST code and after disabling DAS (took around 3-4 secs to load): External View loaded correctly without any issue: Redirect to UCSC genome browser also worked fine: Please review and let me know if there are any issues. To Test: Make sure your igb preferences are reset before running the above branch installer jar or building the application from the above branch. Now, after IGB is started, click on the configure button in the available data panel and check whether UCSC DAS is disabled by default. Also, select any genome and check whether the DAS tracks are not being loaded.
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7, Spring 8, Spring 9 [ 191, 192, 193 ] Spring 7, Spring 8, Spring 9, Spring 10 [ 191, 192, 193, 194 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Story Points 1 0.5
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                nfreese Nowlan Freese added a comment -

                Tested Sravani's branch on Mac.

                DAS was disabled by default. External View and the View Region in UCSC Browser menu option worked correctly. I also tested the trackhubs page (https://www.bioviz.org/public-trackhubs.html) as there was an issue (IGBF-3053) that describes needing DAS enabled by default. The UCSC REST data provider works to provide the same functionality that DAS had previously provided, and the trackhubs were able to be added and the genomes viewed. There is a separate issue (IGBF-2862) that should be addressed, but is not directly related to this ticket.

                Ready for pull request.

                Show
                nfreese Nowlan Freese added a comment - Tested Sravani's branch on Mac. DAS was disabled by default. External View and the View Region in UCSC Browser menu option worked correctly. I also tested the trackhubs page ( https://www.bioviz.org/public-trackhubs.html ) as there was an issue ( IGBF-3053 ) that describes needing DAS enabled by default. The UCSC REST data provider works to provide the same functionality that DAS had previously provided, and the trackhubs were able to be added and the genomes viewed. There is a separate issue ( IGBF-2862 ) that should be addressed, but is not directly related to this ticket. Ready for pull request.
                nfreese Nowlan Freese made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
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                jsirigin Jaya Sravani Sirigineedi added a comment -

                Raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1009. Please review and let me know if there are any issues.

                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - Raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1009 . Please review and let me know if there are any issues.
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged. Installers are build and deployed to bioviz.org "early access" section for testing.

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. Installers are build and deployed to bioviz.org "early access" section for testing.
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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                nfreese Nowlan Freese added a comment -

                Tested on main branch installer on Mac.

                DAS was disabled by default. External View and the View Region in UCSC Browser menu option worked correctly. Trackhubs page was able to open genomes available only from UCSC REST.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on main branch installer on Mac. DAS was disabled by default. External View and the View Region in UCSC Browser menu option worked correctly. Trackhubs page was able to open genomes available only from UCSC REST. Closing ticket.
                nfreese Nowlan Freese made changes -
                Assignee Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 10.1.0 [ 11000 ]

                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated:
                      Resolved: