Details

    • Story Points:
      4
    • Sprint:
      Winter 6 Mar 8 - Mar 19, Spring 1 2021 Mar 22 - Apr 2, Spring 2 2021 Apr 5 - Apr 16, Spring 3 2021 Apr 19 - Apr 30

      Description

      Situation: IGB does not appear to be handling spaces in folder names for local quickloads (tested on Mac and Windows).

      Task: Handle spaces in folder names for local quickloads.

      Note: We also need to handle spaces in file names themselves, but we have not tested whether spaces in file names for local quickloads does or does not work currently.

        Issue Links

          Activity

          Hide
          nfreese Nowlan Freese added a comment -

          When testing IGBF-510 Dr. Freese and I found that my Windows 10 machine was not loading local quickloads normally.
          Today I created new copies of the E. unicornis files tested in IGBF-510,
          expanded the annots.xml file based on the wiki,
          and added a spicies.txt file.

          It was not loading any genomic data in IGB 9.1.6 but was showing data from the contents.txt and genome.txt files.
          Changing the direction of the / characters,
          checking that tabs were used to separate text content,
          moving the files within the local quickload,
          or adding/removing content from the quickload files did not fix the problem.

          I moved the local quickload folder from my two-word user name file path down to the C drive and it began working normally.
          I then moved it up one level to "Program Files", a folder containing a space in the name, and the local quickload stopped working.
          I moved it to another folder with a path not containing any spaces and the local quickload began working again.

          Without spaces anywhere in the file path, local quickloads work on Windows 10.
          Tested on both IGB 9.1.6 and 9.1.8.

          Show
          nfreese Nowlan Freese added a comment - When testing IGBF-510 Dr. Freese and I found that my Windows 10 machine was not loading local quickloads normally. Today I created new copies of the E. unicornis files tested in IGBF-510 , expanded the annots.xml file based on the wiki, and added a spicies.txt file. It was not loading any genomic data in IGB 9.1.6 but was showing data from the contents.txt and genome.txt files. Changing the direction of the / characters, checking that tabs were used to separate text content, moving the files within the local quickload, or adding/removing content from the quickload files did not fix the problem. I moved the local quickload folder from my two-word user name file path down to the C drive and it began working normally. I then moved it up one level to "Program Files", a folder containing a space in the name, and the local quickload stopped working. I moved it to another folder with a path not containing any spaces and the local quickload began working again. Without spaces anywhere in the file path, local quickloads work on Windows 10. Tested on both IGB 9.1.6 and 9.1.8.
          Hide
          nfreese Nowlan Freese added a comment -

          IGBF-2805 contains a zip file with two quickloads that contain folders with spaces that can be used for testing.

          Show
          nfreese Nowlan Freese added a comment - IGBF-2805 contains a zip file with two quickloads that contain folders with spaces that can be used for testing.
          Hide
          nfreese Nowlan Freese added a comment -

          After extensive testing there are a number of issues with special characters (including spaces) in loading quickloads.

          The current implementation of QuickloadDataProvider.java assumes that local quickload paths, whether absolute or relative, do NOT include special characters or spaces. If the path to a local file includes special characters or spaces then that file will fail to load when the user selects the quickload.

          The solution I envision for this issue is to encode special characters in the path to local files (relative or absolute). After initial testing on mac, this appears to work well. However, additional testing will be needed on Windows and Linux.

          An additional problem is that the Quickload Saver app (IGBF-510) is currently encoding the local file paths when creating the quickload. This would lead to double-encoding assuming the implementation of my solution and would not work. I need to investigate if the unencoded file path can be saved (IGBF-2827).

          Next steps:
          If IGBF-2827 can be completed successfully, then I will implement the changes to encode local file paths in QuickloadDataProvider.java.

          Show
          nfreese Nowlan Freese added a comment - After extensive testing there are a number of issues with special characters (including spaces) in loading quickloads. The current implementation of QuickloadDataProvider.java assumes that local quickload paths, whether absolute or relative, do NOT include special characters or spaces. If the path to a local file includes special characters or spaces then that file will fail to load when the user selects the quickload. The solution I envision for this issue is to encode special characters in the path to local files (relative or absolute). After initial testing on mac, this appears to work well. However, additional testing will be needed on Windows and Linux. An additional problem is that the Quickload Saver app ( IGBF-510 ) is currently encoding the local file paths when creating the quickload. This would lead to double-encoding assuming the implementation of my solution and would not work. I need to investigate if the unencoded file path can be saved ( IGBF-2827 ). Next steps: If IGBF-2827 can be completed successfully, then I will implement the changes to encode local file paths in QuickloadDataProvider.java.
          Hide
          nfreese Nowlan Freese added a comment -

          Branch is ready for testing: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2820

          Can use the zip folder from IGBF-2805 to test

          Show
          nfreese Nowlan Freese added a comment - Branch is ready for testing: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-2820 Can use the zip folder from IGBF-2805 to test
          Hide
          nfreese Nowlan Freese added a comment -

          Rachel and I tested this issue on Mac and Windows.

          Show
          nfreese Nowlan Freese added a comment - Rachel and I tested this issue on Mac and Windows.
          Hide
          aloraine Ann Loraine added a comment -

          Looks like the branch is pretty far behind the current master branch commit.
          Can you rebase on the latest commit?

          Show
          aloraine Ann Loraine added a comment - Looks like the branch is pretty far behind the current master branch commit. Can you rebase on the latest commit?
          Show
          nfreese Nowlan Freese added a comment - Updated pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/875/igbf-2820
          Hide
          aloraine Ann Loraine added a comment -

          Merged and master branch installers are built and ready for testing.

          Show
          aloraine Ann Loraine added a comment - Merged and master branch installers are built and ready for testing.
          Hide
          nfreese Nowlan Freese added a comment - - edited

          Tested by Rachel and myself on Windows and Mac. Tested relative and absolute QuickLoad paths on local machines, as well as relative paths for a QuickLoad hosted online. Focused testing on spaces in QuickLoad paths.

          Working correctly.

          Closing issue.

          Show
          nfreese Nowlan Freese added a comment - - edited Tested by Rachel and myself on Windows and Mac. Tested relative and absolute QuickLoad paths on local machines, as well as relative paths for a QuickLoad hosted online. Focused testing on spaces in QuickLoad paths. Working correctly. Closing issue.

            People

            • Assignee:
              nfreese Nowlan Freese
              Reporter:
              nfreese Nowlan Freese
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                Updated:
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