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  1. IGB
  2. IGBF-3650

Fix Color by... error

        Details

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

          Description

          Situation: When using the Color by... operation on a track I am seeing the below error.

          Task: Fix Color by...

          To reproduce the issue:

          1. Start IGB
          2. Open the A_thaliana_Jun_2009 genome
          3. Right-click on the Araport track name and select Color by...
          4. Select Color By > Length
          5. Click Edit
          6. Click OK
          7. Click OK
          8. Check the Log

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3716 Create patch fix for IGB 10.0.1

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment - - edited

                Tested on using IGB main installer on Windows, Linux, and Mac. I did not see the Color By error.

                Closing ticket.

                Show
                nfreese Nowlan Freese added a comment - - edited Tested on using IGB main installer on Windows, Linux, and Mac. I did not see the Color By error. Closing ticket.
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.

                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.
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                nfreese Nowlan Freese added a comment -

                Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1000

                Show
                nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1000
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                nfreese Nowlan Freese added a comment -

                Tested using the instructions above on Mac, Windows (tested alongside Kaushik), and Linux. Color by was working and there were no errors in the log.

                Show
                nfreese Nowlan Freese added a comment - Tested using the instructions above on Mac, Windows (tested alongside Kaushik), and Linux. Color by was working and there were no errors in the log.
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                nfreese Nowlan Freese added a comment - - edited

                Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3650

                To test, follow the instructions above in this ticket's description.
                Windows:

                Show
                nfreese Nowlan Freese added a comment - - edited Branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3650 To test, follow the instructions above in this ticket's description. Windows: Using my branch's installer for IGBF-3650 : https://bitbucket.org/nfreese/nowlanfork-igb/downloads/ Using my branch running locally with run_igb.bat
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                nfreese Nowlan Freese added a comment - - edited

                Great catch!

                Karthik Raveendran - I think the --add-opens java.desktop/java.awt.color=ALL-UNNAMED \ also needs to be added to the IGB main pom.xml. Though I don't remember why we have it in both locations.

                Your branch is also 26 commits behind. We are using the "main" branch now.

                Show
                nfreese Nowlan Freese added a comment - - edited Great catch! Karthik Raveendran - I think the --add-opens java.desktop/java.awt.color=ALL-UNNAMED \ also needs to be added to the IGB main pom.xml . Though I don't remember why we have it in both locations. Your branch is also 26 commits behind. We are using the "main" branch now.
                Hide
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                karthik Karthik Raveendran added a comment -

                Fixed. See Commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/cc9cbffefc43479d9f868360d3c7d9690701c399

                Show
                karthik Karthik Raveendran added a comment - Fixed. See Commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/cc9cbffefc43479d9f868360d3c7d9690701c399
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                karthik Karthik Raveendran added a comment -

                The following error appears in the log

                Exception in thread "AWT-EventQueue-0" com.google.gson.JsonIOException: Failed making field 'java.awt.color.ColorSpace#type' accessible; either increase its visibility or write a custom TypeAdapter for its declaring type.
	at com.google.gson.internal.reflect.ReflectionHelper.makeAccessible(ReflectionHelper.java:38)
	at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:286)
	at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:130)
	at com.google.gson.Gson.getAdapter(Gson.java:556)
	at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.createBoundField(ReflectiveTypeAdapterFactory.java:160)
	at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:294)
	at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:130)
	at com.google.gson.Gson.getAdapter(Gson.java:556)
	at com.google.gson.internal.bind.ArrayTypeAdapter$1.create(ArrayTypeAdapter.java:45)
	at com.google.gson.Gson.getAdapter(Gson.java:556)
	at com.google.gson.Gson.fromJson(Gson.java:1226)
	at com.google.gson.Gson.fromJson(Gson.java:1137)
	at com.google.gson.Gson.fromJson(Gson.java:1047)
	at com.google.gson.Gson.fromJson(Gson.java:982)
                Show
                karthik Karthik Raveendran added a comment - The following error appears in the log Exception in thread "AWT-EventQueue-0" com.google.gson.JsonIOException: Failed making field 'java.awt.color.ColorSpace#type' accessible; either increase its visibility or write a custom TypeAdapter for its declaring type. at com.google.gson.internal.reflect.ReflectionHelper.makeAccessible(ReflectionHelper.java:38) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:286) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:130) at com.google.gson.Gson.getAdapter(Gson.java:556) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.createBoundField(ReflectiveTypeAdapterFactory.java:160) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.getBoundFields(ReflectiveTypeAdapterFactory.java:294) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory.create(ReflectiveTypeAdapterFactory.java:130) at com.google.gson.Gson.getAdapter(Gson.java:556) at com.google.gson.internal.bind.ArrayTypeAdapter$1.create(ArrayTypeAdapter.java:45) at com.google.gson.Gson.getAdapter(Gson.java:556) at com.google.gson.Gson.fromJson(Gson.java:1226) at com.google.gson.Gson.fromJson(Gson.java:1137) at com.google.gson.Gson.fromJson(Gson.java:1047) at com.google.gson.Gson.fromJson(Gson.java:982)
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                nfreese Nowlan Freese added a comment -

                There is also an error thrown when using the Filter... operation.

                Show
                nfreese Nowlan Freese added a comment - There is also an error thrown when using the Filter... operation.

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: