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  1. IGB
  2. IGBF-2848

Fix 2bit file name when loading custom genome

    Details

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

      Description

      Situation: When loading a custom genome the 2bit file is supposed to show up as a file under Available Data with the file name. A change in the 9.1.8 master is hiding the 2bit file name.

      Task: Implement a fix so that the 2bit file name shows correctly under Available Data when loading a custom genome.

        Attachments

          Activity

          Hide
          nfreese Nowlan Freese added a comment -

          Issue was that fileName variable was not being set in NewGenomeAction.java

          Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3c32f05bba8da598fb6d256a2f0bbb0ce9f1d3df?at=IGBF-2848

          To test:
          Download my branch installer for IGBF-2848
          Install and open IGB
          Select File > Open Genome from File...
          In the Reference Sequence box paste this url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit
          Click OK
          Select the Data Access tab and look at the Available Data box.
          Under Local Files the name A_thaliana_Jun_2009.2bit should appear.

          Show
          nfreese Nowlan Freese added a comment - Issue was that fileName variable was not being set in NewGenomeAction.java Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3c32f05bba8da598fb6d256a2f0bbb0ce9f1d3df?at=IGBF-2848 To test: Download my branch installer for IGBF-2848 Install and open IGB Select File > Open Genome from File... In the Reference Sequence box paste this url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit Click OK Select the Data Access tab and look at the Available Data box. Under Local Files the name A_thaliana_Jun_2009.2bit should appear.
          Hide
          aloraine Ann Loraine added a comment -

          Should the sequence data file be listed under "available data"? Note that the "available data" section lets users add and remove data sets from tracks by clicking the boxes. There is logic there that might not interact well with reference sequence data.

          Show
          aloraine Ann Loraine added a comment - Should the sequence data file be listed under "available data"? Note that the "available data" section lets users add and remove data sets from tracks by clicking the boxes. There is logic there that might not interact well with reference sequence data.
          Hide
          nfreese Nowlan Freese added a comment -

          The sequence data file has shown up under available data since at least 2015. Sequence files are handled differently with custom genomes and it may require significant changes in logic for the sequence file to not be displayed under available data. We could create a new ticket for removing the sequence file from available data and include it as part of 9.1.10.

          Show
          nfreese Nowlan Freese added a comment - The sequence data file has shown up under available data since at least 2015. Sequence files are handled differently with custom genomes and it may require significant changes in logic for the sequence file to not be displayed under available data. We could create a new ticket for removing the sequence file from available data and include it as part of 9.1.10.
          Hide
          aloraine Ann Loraine added a comment -

          OK thank you for the explanation! In that case, the new change is fine.

          Show
          aloraine Ann Loraine added a comment - OK thank you for the explanation! In that case, the new change is fine.
          Hide
          inaylor Irvin Naylor added a comment -

          1st-level review: Can confirm, the correct file .2bit file name for A_thaliana_Jun_2009 is showing up when I use Dr. Freese's branch installers. The code change itself looks good too! Recommending pull request.

          Show
          inaylor Irvin Naylor added a comment - 1st-level review: Can confirm, the correct file .2bit file name for A_thaliana_Jun_2009 is showing up when I use Dr. Freese's branch installers. The code change itself looks good too! Recommending pull request.
          Show
          nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/877/igbf-2848-get-name-of-refseq-file
          Hide
          aloraine Ann Loraine added a comment - - edited

          Merged. Master branch installers are built. Ready for testing.

          Show
          aloraine Ann Loraine added a comment - - edited Merged. Master branch installers are built. Ready for testing.
          Hide
          inaylor Irvin Naylor added a comment -

          Can confirm, things look good! The name is showing up in the data access file on the master installer. If there are no objections, I'm moving to closed.

          Show
          inaylor Irvin Naylor added a comment - Can confirm, things look good! The name is showing up in the data access file on the master installer. If there are no objections, I'm moving to closed.

            People

            • Assignee:
              nfreese Nowlan Freese
              Reporter:
              nfreese Nowlan Freese
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              Watchers:
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              Dates

              • Created:
                Updated:
                Resolved: