Details
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Type:
Epic
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: 10.0.0 Major Release
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Labels:None
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Epic Name:Run IGB in Java 21
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Story Points:5
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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
Attachments
Activity
I have turned this ticket into an epic and have moved the related tickets to be within this epic.
Possible examples to look into: https://stackoverflow.com/questions/55829257/where-to-find-and-install-org-osgi-framework-package
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)
osgi project that appears to be using newer osgi annotations: https://github.com/mliradelc/opencast
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
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/