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  1. IGB
  2. IGBF-3920

Load UCSC REST RefSeq All data by default if RefGene is not present

        Details

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

          Description

          Implement logic to load UCSC REST RefSeq All data by default if RefGene is not present

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              relates to

              Task - A task that needs to be done. IGBF-3633 Load UCSC REST data by default

              • Major - Major loss of function.
              • Closed

                Activity

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                jsirigin Jaya Sravani Sirigineedi created issue -
                jsirigin Jaya Sravani Sirigineedi made changes -
                Field Original Value New Value
                Epic Link IGBF-3129 [ 21675 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Link This issue relates to IGBF-3633 [ IGBF-3633 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment RefGene.png [ 18514 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment RefSeqAll_with_no_data.png [ 18515 ]
                jsirigin Jaya Sravani Sirigineedi made changes -
                Attachment RefSeqAll_with_data.png [ 18516 ]
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                jsirigin Jaya Sravani Sirigineedi added a comment - - edited

                Code changes are done and tested the application. Working as expected, updated code is present at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3920. Please review and let me know if there are any issues. Below are the scenarios tested:

                • IGB is not present for the genome and RefGene is present in the available tracks: RefGene gets loaded
                • IGB is not present for the genome and RefGene is not present in the available tracks: RefSeq gets loaded and the data is loaded only if it's present for the first chromosome else empty track gets loaded

                Here is the pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1040

                Show
                jsirigin Jaya Sravani Sirigineedi added a comment - - edited Code changes are done and tested the application. Working as expected, updated code is present at: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3920 . Please review and let me know if there are any issues. Below are the scenarios tested: IGB is not present for the genome and RefGene is present in the available tracks: RefGene gets loaded IGB is not present for the genome and RefGene is not present in the available tracks: RefSeq gets loaded and the data is loaded only if it's present for the first chromosome else empty track gets loaded Here is the pull request : https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1040
                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 ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                nfreese Nowlan Freese added a comment - - edited

                Tested using Sravani's branch on Mac.

                Built IGB successfully with tests.
                Loaded the human hg38 genome (has IGB Quickload) UCSC REST did not load annotations (good).
                Loaded the zebrafish sep 2014 genome (no IGB Quickload, has refGene and ncbiRefSeq UCSC REST tracks), refGene was loaded by default (good).
                Loaded the human T2T genome (no IGB Quickload right now, has ncbiRefSeq UCSC REST track), ncbiRefSeq was loaded by default (good).
                No errors in IGB log.

                Ready for pull request.

                PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1040

                Show
                nfreese Nowlan Freese added a comment - - edited Tested using Sravani's branch on Mac. Built IGB successfully with tests. Loaded the human hg38 genome (has IGB Quickload) UCSC REST did not load annotations (good). Loaded the zebrafish sep 2014 genome (no IGB Quickload, has refGene and ncbiRefSeq UCSC REST tracks), refGene was loaded by default (good). Loaded the human T2T genome (no IGB Quickload right now, has ncbiRefSeq UCSC REST track), ncbiRefSeq was loaded by default (good). No errors in IGB log. Ready for pull request. PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1040
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese 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 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment -

                PR is merged and new installers are built and deployed to bioviz.org early access section.
                Ready for testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is merged and new installers are built and deployed to bioviz.org early access section. Ready for testing.
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
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                nfreese Nowlan Freese added a comment -

                Tested on main branch installer, was able to see ncbiRefSeq or refGene load correctly from UCSC. No errors in log.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - Tested on main branch installer, was able to see ncbiRefSeq or refGene load correctly from UCSC. No errors in log. Closing ticket.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Jaya Sravani Sirigineedi [ jsirigin ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    jsirigin Jaya Sravani Sirigineedi
                    Reporter:
                    jsirigin Jaya Sravani Sirigineedi
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: