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

Details

Type: Bug
Status: To-Do (View Workflow)
Priority: Critical
Resolution: Unresolved
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

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Nowlan Freese added a comment - 13/Mar/24 2:17 PM

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

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Nowlan Freese added a comment - 13/Mar/24 2:17 PM There is also an error thrown when using the Filter... operation.

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Karthik Raveendran added a comment - 27/Mar/24 4:30 PM

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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Karthik Raveendran added a comment - 27/Mar/24 4:30 PM 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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Karthik Raveendran added a comment - 27/Mar/24 4:32 PM

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

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Karthik Raveendran added a comment - 27/Mar/24 4:32 PM Fixed. See Commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/cc9cbffefc43479d9f868360d3c7d9690701c399

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Nowlan Freese added a comment - 28/Mar/24 3:14 PM - 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.

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Nowlan Freese added a comment - 28/Mar/24 3:14 PM - 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.

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Nowlan Freese added a comment - 10/Apr/24 3:20 PM - 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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Nowlan Freese added a comment - 10/Apr/24 3:20 PM - 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

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

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Watchers:

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Dates

Created:

13/Mar/24 2:16 PM

Updated:

Yesterday 5:01 PM