Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Critical
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
-
Sprint:Spring 6, Spring 7, Spring 8, Spring 9
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
Attachments
Issue Links
- relates to
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IGBF-3716 Create patch fix for IGB 10.0.1
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| 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 ] |
| Sprint | Spring 5 [ 189 ] | Spring 6 [ 190 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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)
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| 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 |
| 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 |
| Assignee | Nowlan Freese [ nfreese ] |
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.
| Assignee | Nowlan Freese [ nfreese ] | Karthik Raveendran [ karthik ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Sprint | Spring 6 [ 190 ] | Spring 6, Spring 7 [ 190, 191 ] |
| Rank | Ranked higher |
| Assignee | Karthik Raveendran [ karthik ] | Nowlan Freese [ nfreese ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Story Points | 3 | 2 |
| Sprint | Spring 6, Spring 7 [ 190, 191 ] | Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ] | Spring 6, Spring 7, Spring 8, Spring 9 [ 190, 191, 192, 193 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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.
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Tested on using IGB main installer on Windows, Linux, and Mac. I did not see the Color By error.
Closing ticket.
| Assignee | Karthik Raveendran [ karthik ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
There is also an error thrown when using the Filter... operation.