Fresh Install - Log errors

Brendan_Gilbert · January 6, 2023, 11:05am

Hi, fresh install and seeing numerous errors in the os and catalina logs

os.log example:

2023-01-06 10:45:20 [pool-6-thread-1] INFO  com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Starting bulk import jobs scheduler
2023-01-06 10:45:20 [pool-6-thread-1] ERROR com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Import jobs scheduler encountered a fatal exception. Stopping to run import jobs.
java.lang.NoClassDefFoundError: com/krishagni/catissueplus/core/common/errors/CommonErrorCode
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.doWork(TransactionalInterceptor.java:88) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.ajc$inlineAccessMethod$com_krishagni_catissueplus_core_common_TransactionalInterceptor$com_krishagni_catissueplus_core_common_TransactionalInterceptor$doWork(TransactionalInterceptor.java:1) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.startTransaction(TransactionalInterceptor.java:69) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.markInProgressJobsAsFailed(ImportServiceImpl.java:716) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.runImportJobScheduler(ImportServiceImpl.java:679) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.lambda$1(ImportServiceImpl.java:467) ~[classes/:]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_352]
	at java.lang.Thread.run(Thread.java:750) [?:1.8.0_352]
2023-01-06 10:46:20 [pool-6-thread-1] INFO  com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Starting bulk import jobs scheduler
2023-01-06 10:46:20 [pool-6-thread-1] ERROR com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Import jobs scheduler encountered a fatal exception. Stopping to run import jobs.
java.lang.NoClassDefFoundError: com/krishagni/catissueplus/core/common/errors/CommonErrorCode
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.doWork(TransactionalInterceptor.java:88) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.ajc$inlineAccessMethod$com_krishagni_catissueplus_core_common_TransactionalInterceptor$com_krishagni_catissueplus_core_common_TransactionalInterceptor$doWork(TransactionalInterceptor.java:1) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.startTransaction(TransactionalInterceptor.java:69) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.markInProgressJobsAsFailed(ImportServiceImpl.java:716) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.runImportJobScheduler(ImportServiceImpl.java:679) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.lambda$1(ImportServiceImpl.java:467) ~[classes/:]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_352]
	at java.lang.Thread.run(Thread.java:750) [?:1.8.0_352]
2023-01-06 10:47:20 [pool-6-thread-1] INFO  com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Starting bulk import jobs scheduler
2023-01-06 10:47:20 [pool-6-thread-1] ERROR com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl- Import jobs scheduler encountered a fatal exception. Stopping to run import jobs.
java.lang.NoClassDefFoundError: com/krishagni/catissueplus/core/common/errors/CommonErrorCode
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.doWork(TransactionalInterceptor.java:88) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.ajc$inlineAccessMethod$com_krishagni_catissueplus_core_common_TransactionalInterceptor$com_krishagni_catissueplus_core_common_TransactionalInterceptor$doWork(TransactionalInterceptor.java:1) ~[classes/:]
	at com.krishagni.catissueplus.core.common.TransactionalInterceptor.startTransaction(TransactionalInterceptor.java:69) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.markInProgressJobsAsFailed(ImportServiceImpl.java:716) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.runImportJobScheduler(ImportServiceImpl.java:679) ~[classes/:]
	at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.lambda$1(ImportServiceImpl.java:467) ~[classes/:]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_352]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_352]
	at java.lang.Thread.run(Thread.java:750) [?:1.8.0_352]

catalina.log example

06-Jan-2023 10:53:20.890 INFO [pool-6-thread-1] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load [com.krishagni.catissueplus.core.common.TransactionalInterceptor]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
	java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load [com.krishagni.catissueplus.core.common.TransactionalInterceptor]. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
		at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1432)
		at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForClassLoading(WebappClassLoaderBase.java:1420)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1259)
		at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1220)
		at org.apache.logging.log4j.util.LoaderUtil.loadClass(LoaderUtil.java:167)
		at org.apache.logging.log4j.core.impl.ThrowableProxyHelper.loadClass(ThrowableProxyHelper.java:214)
		at org.apache.logging.log4j.core.impl.ThrowableProxyHelper.toExtendedStackTrace(ThrowableProxyHelper.java:112)
		at org.apache.logging.log4j.core.impl.ThrowableProxy.<init>(ThrowableProxy.java:112)
		at org.apache.logging.log4j.core.impl.ThrowableProxy.<init>(ThrowableProxy.java:96)
		at org.apache.logging.log4j.core.impl.Log4jLogEvent.getThrownProxy(Log4jLogEvent.java:629)
		at org.apache.logging.log4j.core.pattern.ExtendedThrowablePatternConverter.format(ExtendedThrowablePatternConverter.java:63)
		at org.apache.logging.log4j.core.pattern.PatternFormatter.format(PatternFormatter.java:44)
		at org.apache.logging.log4j.core.layout.PatternLayout$PatternFormatterPatternSerializer.toSerializable(PatternLayout.java:385)
		at org.apache.logging.log4j.core.layout.PatternLayout.toText(PatternLayout.java:241)
		at org.apache.logging.log4j.core.layout.PatternLayout.encode(PatternLayout.java:226)
		at org.apache.logging.log4j.core.layout.PatternLayout.encode(PatternLayout.java:60)
		at org.apache.logging.log4j.core.appender.AbstractOutputStreamAppender.directEncodeEvent(AbstractOutputStreamAppender.java:197)
		at org.apache.logging.log4j.core.appender.AbstractOutputStreamAppender.tryAppend(AbstractOutputStreamAppender.java:190)
		at org.apache.logging.log4j.core.appender.AbstractOutputStreamAppender.append(AbstractOutputStreamAppender.java:181)
		at org.apache.logging.log4j.core.appender.RollingFileAppender.append(RollingFileAppender.java:312)
		at org.apache.logging.log4j.core.config.AppenderControl.tryCallAppender(AppenderControl.java:161)
		at org.apache.logging.log4j.core.config.AppenderControl.callAppender0(AppenderControl.java:134)
		at org.apache.logging.log4j.core.config.AppenderControl.callAppenderPreventRecursion(AppenderControl.java:125)
		at org.apache.logging.log4j.core.config.AppenderControl.callAppender(AppenderControl.java:89)
		at org.apache.logging.log4j.core.config.LoggerConfig.callAppenders(LoggerConfig.java:542)
		at org.apache.logging.log4j.core.config.LoggerConfig.processLogEvent(LoggerConfig.java:500)
		at org.apache.logging.log4j.core.config.LoggerConfig.log(LoggerConfig.java:483)
		at org.apache.logging.log4j.core.config.LoggerConfig.log(LoggerConfig.java:417)
		at org.apache.logging.log4j.core.config.AwaitCompletionReliabilityStrategy.log(AwaitCompletionReliabilityStrategy.java:82)
		at org.apache.logging.log4j.core.Logger.log(Logger.java:161)
		at org.apache.logging.log4j.spi.AbstractLogger.tryLogMessage(AbstractLogger.java:2205)
		at org.apache.logging.log4j.spi.AbstractLogger.logMessageTrackRecursion(AbstractLogger.java:2159)
		at org.apache.logging.log4j.spi.AbstractLogger.logMessageSafely(AbstractLogger.java:2142)
		at org.apache.logging.log4j.spi.AbstractLogger.logMessage(AbstractLogger.java:2017)
		at org.apache.logging.log4j.spi.AbstractLogger.logIfEnabled(AbstractLogger.java:1983)
		at org.apache.logging.log4j.spi.AbstractLogger.error(AbstractLogger.java:750)
		at com.krishagni.catissueplus.core.common.util.LogUtil.error(LogUtil.java:81)
		at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.runImportJobScheduler(ImportServiceImpl.java:711)
		at com.krishagni.catissueplus.core.importer.services.impl.ImportServiceImpl.lambda$1(ImportServiceImpl.java:467)
		at java.util.concurrent.FutureTask.run(FutureTask.java:266)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
		at java.lang.Thread.run(Thread.java:750)

Any guidance to resolve these issues would be appreciated.

Kaustubh_Wadagavi · January 6, 2023, 11:18am

Hello Brendan,

Would you please tell us which OpenSpecimen version are you trying to deploy?
Also please send us the plugin details that you are trying to deploy with OpenSpecimen.

Regards,
Kaustubh

Brendan_Gilbert · January 6, 2023, 11:40am

Hi Kaustubh

I had an issue where pages were blank and it was recommended to deploy a plugin so I copied miabis after downloading it from os-extensions to /opt/tomcat/openspecimen/plugins/ after building it. Although this didnt work to fix the blank pages issue so followed Simon advise here Blank pages after build - #2 by Simon_Streit - which worked for me.

Kaustubh_Wadagavi · January 6, 2023, 12:38pm

Hello Brenden,

You can remove that plugin since it is not related to the problem.

Please share the openspecimen.war file with us and send the output of the below command:

jar -tvf openspecimen.war

Regards,
Kaustubh

Brendan_Gilbert · January 6, 2023, 1:01pm

Hi Kaustubh,

Although I already shared the output of the war file on another thread, Im doing so again and prefer it if we posted updates to my issue on this thread, if that’s ok with you.
war.txt (438.1 KB)

Brendan_Gilbert · January 9, 2023, 7:35am

Hi - @Kaustubh_Wadagavi - just following up on this query.

Kaustubh_Wadagavi · January 9, 2023, 8:31am

Hello @Brendan_Gilbert,

Your above output and our war file output are matched.

To debug it more we need an openspecimen.war file.

Would you please share the openspecimen.war file with us that you are trying to deploy?

Regards,
Kaustubh

Brendan_Gilbert · January 30, 2023, 8:16am

Hi @Kaustubh_Wadagavi - the openspecimen.war is 80MB in size which exceeds the maximum size that I can upload. Do you require anything specific from war?

Brendan_Gilbert · February 7, 2023, 10:50am

@Kaustubh_Wadagavi - Just quick follow-up on this