Much clearer!
It looks like the changes for the 1366 issue were removed, so I assume that will be another branch ...?
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The commit for removing the net.sf.samtools is clearly just that.
And the formatting fixes are very simple and clearly just that.
So the code-review and the git review are good. : )
These changes are minor and only affect the pom file. We have already removed all of the import statements for the samtools library.
To make sure IGB is able to build without the net.sf.sam-exec library, I removed it from my .m2, and I cleared IGB's bundle directory, and I ran $mvn clean install.
IGB was able to build with tests, without errors, and run. The net.sf.sam-exec was not re-downloaded to .m2, so it looks like IGB is completely free of the dependency.
That's the only functional review I can think of for this, and it looks good. : )
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I'm copying these comments to issue IGBF-1371.
Branch IGBF-1371-library has to do with that issue, and now has nothing to do with this issue (IGBF-1366).
I'm not going to make any changes to this issue (except to assign back to Kiran since he's doing the ppt, and making a branch for this issue).
This error appears on startup and on each time that I refresh an app repository:
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at org.lorainelab.igb.plugin.manager.BundleInfoManager.lambda$isVersionOfBundleInstalled$48(BundleInfoManager.java:149)
at java.util.stream.MatchOps$1MatchSink.accept(MatchOps.java:90)
at java.util.Spliterators$ArraySpliterator.tryAdvance(Spliterators.java:958)
at java.util.stream.ReferencePipeline.forEachWithCancel(ReferencePipeline.java:126)
at java.util.stream.AbstractPipeline.copyIntoWithCancel(AbstractPipeline.java:498)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:485)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:230)
at java.util.stream.MatchOps$MatchOp.evaluateSequential(MatchOps.java:196)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.anyMatch(ReferencePipeline.java:449)
at org.lorainelab.igb.plugin.manager.BundleInfoManager.isVersionOfBundleInstalled(BundleInfoManager.java:149)
at org.lorainelab.igb.plugin.manager.AppManagerFxPanel.lambda$null$5(AppManagerFxPanel.java:150)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at org.lorainelab.igb.plugin.manager.AppManagerFxPanel.lambda$udpateDataEventNotification$6(AppManagerFxPanel.java:149)
at com.sun.javafx.application.PlatformImpl.lambda$null$173(PlatformImpl.java:295)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$174(PlatformImpl.java:294)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95)