Two more packages in JVM args for Java 16+ compatibility

[labkey-jeckels]

Rationale

Certain pipeline scenarios need access to java.util.Properties and java.awt.font.TextAttributes to be compatible with Java 16+

Changes

• Add template debug configs to match new guidance on https://www.labkey.org/Documentation/wiki-page.view?name=supported

[bbimber]

@labkey-jeckels be aware, that change might not be quite right. see:

• /home/exacloud/gscratch/prime-seq/java/current/bin/java -XX:HeapBaseMinAddress=4294967296 -Djava.io.tmpdir=/mnt/scratch/prime-seq/tmp.h4QZNQTfP4SequenceImport_20211224 --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.awt.font=ALL-UNNAMED ' '
  WARNING: package java.awt.font not in java.base
  Error: Could not find or load main class
  Caused by: java.lang.ClassNotFoundException:

I'll see if i have time today to look into this, but might not until after xmas

This seems on-point, but I only briefly scanned it

x-stream/xstream#101

[bbimber]

Updating xstreamVersion=1.2.2 might also resolve this

[labkey-jeckels]

Yes, looks like java.awt.font is in java.desktop, not java.base. Try this variant instead:

--add-opens=java.desktop/java.awt.font=ALL-UNNAMED

[labkey-jeckels]

Looking a little closer, that's a warning, not the error. Is that output the full command-line? It looks like it's missing the name of the main class, for example, and other arguments.

[bbimber]

Didnt I post one on the ONPRC issue tracker? See here:

https://prime-seq.ohsu.edu/_webdav/Labs/Bimber/708/%40files/sequenceOutputPipeline/SequenceOutput_2021-12-23_07-56-49/Single_Cell_Processing_2021-12-23_07-56-48.400959-17529355.java.log

INFO  2021-12-23 07:57:58,395 [UMOManager.3] org.mule.providers.jms.activemq.ActiveMqJmsConnector: Started: ActiveMqJmsConnector{this=14d513ca, started=true, initialised=true, name='jmsConnectorStatus', disposed=false, numberOfConcurrentTransactedReceivers=4, createMultipleTransactedReceivers=true, connected=true, supportedProtocols=[jms], serviceOverrides=null}
Starting to run task for job (NOT SUBMITTED) Single_Cell_Processing_2021-12-23_07-56-48.400959 on host: exanode-3-1
INFO  2021-12-23 07:57:58,688 [main] org.mule.extras.client.MuleClient: There is already a manager locally available to this client, no need to create a new one
INFO  2021-12-23 07:57:58,701 [main] org.mule.extras.client.MuleClient: There is already a manager locally available to this client, no need to create a new one
INFO  2021-12-23 07:57:58,701 [jmsConnectorStatus.dispatcher.1] org.mule.providers.jms.JmsMessageDispatcher: Connected: JmsMessageDispatcher{this=392acfa4, endpoint=jms://status.queue}
INFO  2021-12-23 07:57:58,702 [main] org.labkey.api.util.Job: Starting to run task 'org.labkey.sequenceanalysis.pipeline.SequenceOutputHandlerRemoteTask' for job '(NOT SUBMITTED) Single_Cell_Processing_2021-12-23_07-56-48.400959' with log file /home/groups/BimberLab/primeseq/708/@files/sequenceOutputPipeline/SequenceOutput_2021-12-23_07-56-49/Single_Cell_Processing_2021-12-23_07-56-48.400959.log
ERROR 2021-12-23 07:57:58,763 [jmsConnectorStatus.dispatcher.1] org.labkey.pipeline.mule.PipelineJobExceptionStrategy: 
********************************************************************************
Message               : Unable to initialize XStream
Type                  : org.mule.umo.transformer.TransformerException
Code                  : MULE_ERROR-64999
JavaDoc               : http://mule.mulesource.org/docs/apidocs/org/mule/umo/transformer/TransformerException.html
********************************************************************************
Exception stack is:
1. Unable to make field private static final java.util.Map java.awt.font.TextAttribute.instanceMap accessible: module java.desktop does not "opens java.awt.font" to unnamed module @88a8218 (java.lang.reflect.InaccessibleObjectException)
  java.lang.reflect.AccessibleObject:354 (null)
2. Unable to initialize XStream (org.mule.umo.transformer.TransformerException)
  org.mule.transformers.xml.AbstractXStreamTransformer:54 (http://mule.mulesource.org/docs/apidocs/org/mule/umo/transformer/TransformerException.html)
********************************************************************************
Root Exception stack trace:
java.lang.reflect.InaccessibleObjectException: Unable to make field private static final java.util.Map java.awt.font.TextAttribute.instanceMap accessible: module java.desktop does not "opens java.awt.font" to unnamed module @88a8218
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
	at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
	at com.thoughtworks.xstream.converters.reflection.FieldDictionary.buildMap(FieldDictionary.java:84)
	at com.thoughtworks.xstream.converters.reflection.FieldDictionary.serializableFieldsFor(FieldDictionary.java:38)
	at com.thoughtworks.xstream.converters.reflection.AbstractAttributedCharacterIteratorAttributeConverter.readResolve(AbstractAttributedCharacterIteratorAttributeConverter.java:73)
	at com.thoughtworks.xstream.converters.reflection.AbstractAttributedCharacterIteratorAttributeConverter.<init>(AbstractAttributedCharacterIteratorAttributeConverter.java:42)
	at com.thoughtworks.xstream.converters.extended.TextAttributeConverter.<init>(TextAttributeConverter.java:23)
	at com.thoughtworks.xstream.XStream.setupConverters(XStream.java:599)
	at com.thoughtworks.xstream.XStream.<init>(XStream.java:375)
	at com.thoughtworks.xstream.XStream.<init>(XStream.java:320)
	at org.mule.transformers.xml.XStreamFactory.<init>(XStreamFactory.java:48)
	at org.mule.transformers.xml.AbstractXStreamTransformer.getXStream(AbstractXStreamTransformer.java:46)
	at org.mule.transformers.xml.ObjectToXml.transform(ObjectToXml.java:66)
	at org.mule.transformers.AbstractEventAwareTransformer.doTransform(AbstractEventAwareTransformer.java:40)
	at org.mule.transformers.AbstractTransformer.transform(AbstractTransformer.java:250)
	at org.mule.impl.MuleEvent.getTransformedMessage(MuleEvent.java:324)
	at org.mule.providers.jms.JmsMessageDispatcher.dispatchMessage(JmsMessageDispatcher.java:142)
	at org.mule.providers.jms.JmsMessageDispatcher.doDispatch(JmsMessageDispatcher.java:65)
	at org.mule.providers.AbstractMessageDispatcher$Worker.run(AbstractMessageDispatcher.java:552)
	at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
	at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
	at java.base/java.lang.Thread.run(Thread.java:833)

********************************************************************************

ERROR 2021-12-23 07:57:58,764 [jmsConnectorStatus.dispatcher.2] org.labkey.pipeline.mule.PipelineJobExceptionStrategy: 
********************************************************************************
Message               : Unable to initialize XStream
Type                  : org.mule.umo.transformer.TransformerException
Code                  : MULE_ERROR-64999
JavaDoc               : http://mule.mulesource.org/docs/apidocs/org/mule/umo/transformer/TransformerException.html
********************************************************************************

[bbimber]

Also, when I tried:

--add-opens=java.desktop/java.awt.font=ALL-UNNAMED

It completely died with an error about not being able to find java.desktop. I can dig that up if you want me to try it.