[IGBF-3650] Fix Color by... error - JIRA UNCC

Details

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

Story Points:
2
Epic Link:
Improve IGB for users
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

IGBF-3716 Create patch fix for IGB 10.0.1

Closed

Activity

Ascending order - Click to sort in descending order

Nowlan Freese created issue - 13/Mar/24 2:16 PM

Nowlan Freese made changes - 13/Mar/24 2:16 PM

Field	Original Value	New Value
Epic Link		IGBF-1765 [ 17855 ]

Nowlan Freese made changes - 13/Mar/24 2:17 PM

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
]

Nowlan Freese made changes - 15/Mar/24 11:20 AM

Sprint

Spring 5 [ 189 ]

Spring 6 [ 190 ]

Karthik Raveendran made changes - 27/Mar/24 4:24 PM

Assignee

Karthik Raveendran [ karthik ]

Karthik Raveendran made changes - 27/Mar/24 4:24 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Karthik Raveendran made changes - 27/Mar/24 4:32 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Karthik Raveendran made changes - 27/Mar/24 4:32 PM

Assignee

Karthik Raveendran [ karthik ]

Nowlan Freese made changes - 28/Mar/24 3:04 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 28/Mar/24 3:05 PM

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

Nowlan Freese made changes - 28/Mar/24 3:05 PM

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

Nowlan Freese made changes - 28/Mar/24 3:07 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 28/Mar/24 3:15 PM

Assignee

Nowlan Freese [ nfreese ]

Karthik Raveendran [ karthik ]

Nowlan Freese made changes - 28/Mar/24 3:15 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Ann Loraine made changes - 01/Apr/24 10:16 AM

Sprint

Spring 6 [ 190 ]

Spring 6, Spring 7 [ 190, 191 ]

Ann Loraine made changes - 01/Apr/24 10:16 AM

Rank

Ranked higher

Nowlan Freese made changes - 10/Apr/24 10:53 AM

Assignee

Karthik Raveendran [ karthik ]

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 10/Apr/24 10:53 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 10/Apr/24 3:21 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 10/Apr/24 3:21 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 11/Apr/24 9:44 AM

Story Points

Ann Loraine made changes - 15/Apr/24 9:44 AM

Sprint

Spring 6, Spring 7 [ 190, 191 ]

Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ]

Ann Loraine made changes - 15/Apr/24 9:44 AM

Rank

Ranked higher

Nowlan Freese made changes - 23/Apr/24 10:00 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 23/Apr/24 10:00 AM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Nowlan Freese made changes - 23/Apr/24 10:00 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 23/Apr/24 10:00 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 23/Apr/24 10:09 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 28/Apr/24 5:01 PM

Sprint

Spring 6, Spring 7, Spring 8 [ 190, 191, 192 ]

Spring 6, Spring 7, Spring 8, Spring 9 [ 190, 191, 192, 193 ]

Ann Loraine made changes - 28/Apr/24 5:01 PM

Rank

Ranked higher

Nowlan Freese made changes - 02/May/24 11:11 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 02/May/24 11:35 AM

Link

This issue relates to ~~IGBF-3716~~ [ ~~IGBF-3716~~ ]

Nowlan Freese made changes - 02/May/24 3:06 PM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 02/May/24 3:06 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 02/May/24 3:06 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 02/May/24 3:06 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Nowlan Freese made changes - 02/May/24 3:06 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 03/May/24 9:46 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 03/May/24 9:46 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Nowlan Freese made changes - 08/May/24 11:27 AM

Assignee

Karthik Raveendran [ karthik ]

Nowlan Freese made changes - 08/May/24 11:27 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Nowlan Freese made changes - 08/May/24 11:27 AM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

People

Assignee:

Karthik Raveendran

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

13/Mar/24 2:16 PM

Updated:

08/May/24 11:41 AM

Resolved:

08/May/24 11:27 AM