[IGBF-3142] Run IGB in Java 21 - JIRA UNCC

Details

Type: Epic
Status: To-Do (View Workflow)
Priority: Major
Resolution: Unresolved
Affects Version/s: None
Fix Version/s: 10.0.0 Major Release
Labels:
None

Epic Name:
Run IGB in Java 21
Story Points:
5
Sprint:
Summer 4 2022 July 4, Spring 2 2023 Jan 16, Spring 3 2023 Feb 1

Description

IGB uses Java 1.8, a very old version of Java that is not well supported anymore.

For this task, determine if we can build and run IGB using a more up-to-date JVM.

Javafx: https://search.maven.org/artifact/org.openjfx/javafx/18.0.1/pom

For notes on how we did different parts, see: ~~IGBF-3513~~

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jdepOutput.txt
128 kB
27/Jan/23 3:37 PM

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Ann Loraine added a comment - 07/Jul/22 9:53 AM - edited

Trying JDK 18 + FX from Azul (open JDK build)

compiler crashes:

[INFO] Compiling 14 source files to /Users/aloraine/src/aloraine-integrated-genome-browser/core/heatmap-editor/target/classes
An exception has occurred in the compiler (1.8.0-internal_bootstrap). Please file a bug at the Java Developer Connection (http://java.sun.com/webapps/bugreport) after checking the Bug Parade for duplicates. Include your program and the following diagnostic in your report. Thank you.
java.lang.NullPointerException: Cannot invoke "String.length()" because "<parameter1>" is null

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Ann Loraine added a comment - 07/Jul/22 9:53 AM - edited Trying JDK 18 + FX from Azul (open JDK build) compiler crashes: [INFO] Compiling 14 source files to /Users/aloraine/src/aloraine-integrated-genome-browser/core/heatmap-editor/target/classes An exception has occurred in the compiler (1.8.0-internal_bootstrap). Please file a bug at the Java Developer Connection ( http://java.sun.com/webapps/bugreport ) after checking the Bug Parade for duplicates. Include your program and the following diagnostic in your report. Thank you. java.lang.NullPointerException: Cannot invoke "String.length()" because "<parameter1>" is null

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Nowlan Freese added a comment - 15/Feb/23 3:37 PM

osgi project that appears to be using newer osgi annotations: https://github.com/mliradelc/opencast

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Nowlan Freese added a comment - 15/Feb/23 3:37 PM osgi project that appears to be using newer osgi annotations: https://github.com/mliradelc/opencast

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Nowlan Freese added a comment - 17/Feb/23 9:55 AM

I removed the bndlib artifact as the above project and various blogs refer to bnd as being deprecated. Using osgi.cmpn and org.osgi.core in place of bnd (version 6.0.0). Able to build IGB, but still running into the same error when attempting to run IGB through the jar. Since I have been seeing this same error for a while now, my feeling is that there is something with the OSGI wiring that is incorrect currently.

09:44:48.140 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))]
org.osgi.framework.BundleException: Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring.package; (osgi.wiring.package=com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring.package; (&(osgi.wiring.package=com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))]
	at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4398)
	at org.apache.felix.framework.Felix.startBundle(Felix.java:2308)
	at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:1006)
	at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:992)
	at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83)
	at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63)
	at com.affymetrix.main.Main.main(Main.java:30)

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Nowlan Freese added a comment - 17/Feb/23 9:55 AM I removed the bndlib artifact as the above project and various blogs refer to bnd as being deprecated. Using osgi.cmpn and org.osgi.core in place of bnd (version 6.0.0). Able to build IGB, but still running into the same error when attempting to run IGB through the jar. Since I have been seeing this same error for a while now, my feeling is that there is something with the OSGI wiring that is incorrect currently. 09:44:48.140 [main] ERROR com.affymetrix.main.OSGiHandler - Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring. package ; (&(osgi.wiring. package =com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring. package ; (osgi.wiring. package =com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring. package ; (&(osgi.wiring. package =com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))] org.osgi.framework.BundleException: Unable to resolve annotation-tab [2](R 2.0): missing requirement [annotation-tab [2](R 2.0)] osgi.wiring. package ; (&(osgi.wiring. package =com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0))) [caused by: Unable to resolve genometry [30](R 30.0): missing requirement [genometry [30](R 30.0)] osgi.wiring. package ; (osgi.wiring. package =com.apple.laf)] Unresolved requirements: [[annotation-tab [2](R 2.0)] osgi.wiring. package ; (&(osgi.wiring. package =com.affymetrix.genometry.parsers)(version>=9.1.0)(!(version>=10.0.0)))] at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4398) at org.apache.felix.framework.Felix.startBundle(Felix.java:2308) at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:1006) at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:992) at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) at com.affymetrix.main.Main.main(Main.java:30)

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Nowlan Freese added a comment - 17/Feb/23 9:57 AM

Possible examples to look into: https://stackoverflow.com/questions/55829257/where-to-find-and-install-org-osgi-framework-package

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Nowlan Freese added a comment - 17/Feb/23 9:57 AM Possible examples to look into: https://stackoverflow.com/questions/55829257/where-to-find-and-install-org-osgi-framework-package

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Nowlan Freese added a comment - 22/Feb/23 1:15 PM

I have turned this ticket into an epic and have moved the related tickets to be within this epic.

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Nowlan Freese added a comment - 22/Feb/23 1:15 PM I have turned this ticket into an epic and have moved the related tickets to be within this epic.

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Nowlan Freese added a comment - 04/May/23 1:45 PM - edited

Blog on Java 11 migration: https://nipafx.dev/java-11-migration-guide/
https://nipafx.dev/maven-on-java-9/
https://nipafx.dev/java-module-system-tutorial/

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Nowlan Freese added a comment - 04/May/23 1:45 PM - edited Blog on Java 11 migration: https://nipafx.dev/java-11-migration-guide/ https://nipafx.dev/maven-on-java-9/ https://nipafx.dev/java-module-system-tutorial/

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Assignee:

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Reporter:

Ann Loraine

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Watchers:

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Dates

Created:

06/Jul/22 10:28 AM

Updated:

01/Apr/24 10:20 AM