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  1. IGB
  2. IGBF-3921

Fix second track appearing when searching for genes

        Details

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

          Description

          Situation: While testing the current main branch I found an issue where searching for a gene would cause a second track to appear and was not listed in the Data Management Table.

          Task: Fix IGB so that the second track does not appear.

          Steps to reproduce:

          1. Start IGB
          2. Select the Danio rerio species and the D_rerio_Sep_2014 genome version
          3. Sort the chromosomes by length
          4. Click Load Data for chromosomes chr7, chr5, chr3, chr6, chr2, chr1, chr9
          5. In the Advanced Search tab, search for hox
          6. Double-click on one of the results (hoxb2a)
            1. It seems like the result needs to be on a different chromosome then is currently in view in IGB
          7. A second track should appear

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              jsirigin Jaya Sravani Sirigineedi added a comment -

              The change made in this ticket IGBF-3584 (commit) is the problem, to make the type unique I have changed it to the URL variable but that URL has chromosome details as well and this in some part of code is being used as the method and method names are supposed to be only unique to the dataset, not chromosomes. Fixed this issue by changing the type variable to the contextRoot variable which is the URL without chromosomes and with track included in it, so it will be unique to each track but will be the same for all the chromosomes. Tested it for this issue and also the scenarios mentioned in IGBF-3584 by manually adding the DAS server as well, and everything is working as expected. Here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3921. Please review it and let me know if there are any issues.

              Show
              jsirigin Jaya Sravani Sirigineedi added a comment - The change made in this ticket IGBF-3584 ( commit ) is the problem, to make the type unique I have changed it to the URL variable but that URL has chromosome details as well and this in some part of code is being used as the method and method names are supposed to be only unique to the dataset, not chromosomes. Fixed this issue by changing the type variable to the contextRoot variable which is the URL without chromosomes and with track included in it, so it will be unique to each track but will be the same for all the chromosomes. Tested it for this issue and also the scenarios mentioned in IGBF-3584 by manually adding the DAS server as well, and everything is working as expected. Here is the updated code: https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3921 . Please review it and let me know if there are any issues.
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              nfreese Nowlan Freese added a comment -

              Tested using Sravani's branch on Mac.

              Unable to reproduce the issue on the new branch (good).
              I also tested useq and it is working (good).

              Ready for pull request.

              Show
              nfreese Nowlan Freese added a comment - Tested using Sravani's branch on Mac. Unable to reproduce the issue on the new branch (good). I also tested useq and it is working (good). Ready for pull request.
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              jsirigin Jaya Sravani Sirigineedi added a comment -

              Raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1041

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              jsirigin Jaya Sravani Sirigineedi added a comment - Raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1041
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              ann.loraine Ann Loraine added a comment -

              PR is merged.

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              ann.loraine Ann Loraine added a comment - PR is merged.
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              nfreese Nowlan Freese added a comment -

              Tested main branch installer on Mac.

              Unable to reproduce the original issue.

              Closing ticket.

              Show
              nfreese Nowlan Freese added a comment - Tested main branch installer on Mac. Unable to reproduce the original issue. Closing ticket.

                People

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

                  Dates

                  • Created:
                    Updated:
                    Resolved: