Details

    • Story Points:
      3
    • Sprint:
      Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16

      Description

      Situation: In IGB, when a user selects File > Open Genome from File... a window opens that allows the user to provide a Reference Sequence for the new genome. However, only local files are allowed, not URLs.

      Task: Add ability to use URLs when opening custom genomes.

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          aloraine Ann Loraine added a comment -

          Kindly provide comments describing work thus far.

          Show
          aloraine Ann Loraine added a comment - Kindly provide comments describing work thus far.
          Hide
          karthik Karthik Raveendran added a comment -

          In the new changes, the 'Reference Sequence' text field in 'Open Genome from File UI' can be used to enter a URL as well as a local system file path to load a custom genome. The new logic checks the prefix of the link to determine if its URL or local file path.
          The changes need testing against different file paths that includes special characters or spaces.

          Show
          karthik Karthik Raveendran added a comment - In the new changes, the 'Reference Sequence' text field in 'Open Genome from File UI' can be used to enter a URL as well as a local system file path to load a custom genome. The new logic checks the prefix of the link to determine if its URL or local file path. The changes need testing against different file paths that includes special characters or spaces.
          Show
          nfreese Nowlan Freese added a comment - Karthik's branch installers: https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/ Test loading the following files both online (by adding the URL) or locally (by downloading the file and choosing it locally): https://data.cyverse.org/dav-anon/iplant/home/nowlanf/nowlanTESTDontChange/relativeFixed/E_unicornis_Jul_2043/down%20stream/E_unicornis_Jul_2043.2bit http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Karthik Raveendran

          Can this import be removed: import static com.affymetrix.genometry.symloader.ProtocolConstants.FILE_PROTOCOL_SCHEME;

          Tested the above 2bit files on Mac and they worked correctly, could load the sequence.

          I also tested the fasta file: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/S_SARS-CoV-2_Wuhan-Hu-1_Jan_2020.fa
          It was able to load the correct chromosome and sequence.

          Show
          nfreese Nowlan Freese added a comment - - edited Karthik Raveendran Can this import be removed: import static com.affymetrix.genometry.symloader.ProtocolConstants.FILE_PROTOCOL_SCHEME; Tested the above 2bit files on Mac and they worked correctly, could load the sequence. I also tested the fasta file: https://data.cyverse.org/dav-anon/iplant/home/nowlanf/S_SARS-CoV-2_Wuhan-Hu-1_Jan_2020.fa It was able to load the correct chromosome and sequence.
          Hide
          nfreese Nowlan Freese added a comment -

          Looks good, recommend pull request.

          Show
          nfreese Nowlan Freese added a comment - Looks good, recommend pull request.
          Hide
          aloraine Ann Loraine added a comment -

          Pull request is merged. Master branch installers are been built and ready for testing.

          Show
          aloraine Ann Loraine added a comment - Pull request is merged. Master branch installers are been built and ready for testing.
          Hide
          rweidenh Rachel Weidenhammer (Inactive) added a comment -

          Tested on Windows 10
          All of the files in the previous comments do load correctly via URL.
          I also tested the unicorn link locally and it works that way as well.

          Looks good. Moving to Done.

          Show
          rweidenh Rachel Weidenhammer (Inactive) added a comment - Tested on Windows 10 All of the files in the previous comments do load correctly via URL. I also tested the unicorn link locally and it works that way as well. Looks good. Moving to Done.

            People

            • Assignee:
              karthik Karthik Raveendran
              Reporter:
              nfreese Nowlan Freese
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                Updated:
                Resolved:

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