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  1. IGB
  2. IGBF-4381

Fix the formatting of the Color by Import error

        Details

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

          Description

          Situation: When a user attempts to import a file that is improperly formatted (e.g., space-separated text file), an error appears in the Color by table. This error being displayed is incorrectly formatted. It reads, "Error: Please make sure if the file format is right.java.lang.NullPointerException: Cannot invoke "String.length()" because "regex" is null". The message itself also extends past the boundary of the window size, forcing a user to expand the Color by window to read it.

          Task: Update the error message and ensure that it does not change the formatting of the Color by window when it's thrown.

          To reproduce: In the Color by window, click Import..., then open the file attached to this ticket. See the error at the bottom of the window.

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              karthik Karthik Raveendran added a comment -

              Issues fixed in 7a5cbc5

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              karthik Karthik Raveendran added a comment - Issues fixed in 7a5cbc5
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              pkulzer Paige Kulzer (Inactive) added a comment -

              The error message has been updated and now reads "Error: Data is not formatted correctly. See IGB User's Guide". It is not being clipped/cut off by the edge of the Color By window anymore. Changes look good!

              My only question for Karthik Raveendran is whether this error should disappear when a user clicks the Clear All button. Implementing this behavior would match that of the missing SAMtag warning.

              If that is not the desired behavior, then I would recommend a PR.

              Show
              pkulzer Paige Kulzer (Inactive) added a comment - The error message has been updated and now reads " Error: Data is not formatted correctly. See IGB User's Guide ". It is not being clipped/cut off by the edge of the Color By window anymore. Changes look good! My only question for Karthik Raveendran is whether this error should disappear when a user clicks the Clear All button. Implementing this behavior would match that of the missing SAMtag warning. If that is not the desired behavior, then I would recommend a PR.
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              karthik Karthik Raveendran added a comment -

              Unlike the other error messages in this module, this message requires the user to familiarize themselves with the data format of the file and re-edit their file to the correct format for all of which they might need the User's Guide. They can just google IGB User's Guide and find it. For the entire process I would like the error message to be there for the user's reference.

              Show
              karthik Karthik Raveendran added a comment - Unlike the other error messages in this module, this message requires the user to familiarize themselves with the data format of the file and re-edit their file to the correct format for all of which they might need the User's Guide. They can just google IGB User's Guide and find it. For the entire process I would like the error message to be there for the user's reference.
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              karthik Karthik Raveendran added a comment -

              PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1096

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              karthik Karthik Raveendran added a comment - PR submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1096
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              ann.loraine Ann Loraine added a comment -

              PR is merged, installers are built and deployed to BioViz.org Early Access section.
              Ready for testing.

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              ann.loraine Ann Loraine added a comment - PR is merged, installers are built and deployed to BioViz.org Early Access section. Ready for testing.
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              pkulzer Paige Kulzer (Inactive) added a comment -

              Downloaded the Early Access release and tested on my Mac. The error is formatted correctly and is human-readable. No errors in the Log. No odd behavior in the Color by table.

              Closing ticket!

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              pkulzer Paige Kulzer (Inactive) added a comment - Downloaded the Early Access release and tested on my Mac. The error is formatted correctly and is human-readable. No errors in the Log. No odd behavior in the Color by table. Closing ticket!

                People

                • Assignee:
                  karthik Karthik Raveendran
                  Reporter:
                  pkulzer Paige Kulzer (Inactive)
                • Votes:
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                  Dates

                  • Created:
                    Updated:
                    Resolved: