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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: 10.0.1
        • 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

                Ascending order - Click to sort in descending order
                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Comment [ 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$1.create(ArrayTypeAdapter.java:45)
                at com.google.gson.Gson.getAdapter(Gson.java:556)
                at com.google.gson.Gson.toJson(Gson.java:834)
                at com.google.gson.Gson.toJson(Gson.java:812)
                at com.google.gson.Gson.toJson(Gson.java:759)
                at com.google.gson.Gson.toJson(Gson.java:736)
                at com.affymetrix.igb.shared.ConfigureOptionsPanel.lambda$addOptions$4(ConfigureOptionsPanel.java:299)
                at com.affymetrix.igb.shared.ConfigureOptionsPanel.getReturnValue(ConfigureOptionsPanel.java:421)
                at com.affymetrix.igb.util.ConfigureOptionsDialog.showDialog(ConfigureOptionsDialog.java:108)
                at com.affymetrix.igb.action.ColorByAction.actionPerformed(ColorByAction.java:69)
                at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972)
                at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2314)
                at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:407)
                at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
                at java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:374)
                at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1029)
                at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
                at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1073)
                at java.desktop/java.awt.Component.processMouseEvent(Component.java:6621)
                at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3398)
                at java.desktop/java.awt.Component.processEvent(Component.java:6386)
                at java.desktop/java.awt.Container.processEvent(Container.java:2266)
                at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4996)
                at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324)
                at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
                at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948)
                at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575)
                at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516)
                at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310)
                at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780)
                at java.desktop/java.awt.Component.dispatchEvent(Component.java:4828)
                at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:775)
                at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
                at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
                at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
                at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
                at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:98)
                at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:747)
                at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:745)
                at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
                at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
                at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:744)
                at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
                at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
                at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
                at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
                at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
                at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
                Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private final int java.awt.color.ColorSpace.type accessible: module java.desktop does not "opens java.awt.color" to unnamed module @214190b2
                at java.base/java.lang.reflect.AccessibleObject.throwInaccessibleObjectException(AccessibleObject.java:391)
                at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:367)
                at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:315)
                at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:183)
                at java.base/java.lang.reflect.Field.setAccessible(Field.java:177)
                at com.google.gson.internal.reflect.ReflectionHelper.makeAccessible(ReflectionHelper.java:35)
                ... 55 more
                ]
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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.
                nfreese Nowlan Freese made changes -
                Sprint Spring 5 [ 189 ] Spring 6 [ 190 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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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)
                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
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                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:
                # Start IGB
                # Open the A_thaliana_Jun_2009 genome
                # Right-click on the Araport track name and select Color by...
                # Select Color By Length
                # Click Edit
                # Click OK
                # Click OK
                # Check the Log                 		Situation: When using the Color by... operation on a track I am seeing the below error.

                Task: Fix Color by...

                To reproduce the issue:
                # Start IGB
                # Open the A_thaliana_Jun_2009 genome
                # Right-click on the Araport track name and select Color by...
                # Select Color By > Length
                # Click Edit
                # Click OK
                # Click OK
                # Check the Log
                nfreese Nowlan Freese made changes -
                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:
                # Start IGB
                # Open the A_thaliana_Jun_2009 genome
                # Right-click on the Araport track name and select Color by...
                # Select Color By > Length
                # Click Edit
                # Click OK
                # Click OK
                # Check the Log                 		Situation: When using the Color by... operation on a track I am seeing the below error.

                Task: Fix Color by...

                To reproduce the issue:
                # Start IGB
                # Open the *A_thaliana_Jun_2009* genome
                # Right-click on the *Araport* track name and select *Color by...*
                # Select *Color By* > *Length*
                # Click *Edit*
                # Click *OK*
                # Click *OK*
                # Check the Log
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                Hide
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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.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 6 [ 190 ] Spring 6, Spring 7 [ 190, 191 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ] Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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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
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Story Points 3 2
                ann.loraine Ann Loraine made changes -
                Sprint Spring 6, Spring 7 [ 190, 191 ] Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ] Spring 6, Spring 7, Spring 8, Spring 9 [ 190, 191, 192, 193 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3716 [ IGBF-3716 ]
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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.
                Hide
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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
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                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.
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Hide
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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.
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 10.0.1 [ 10901 ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: