Open albagarcia opened 9 years ago
hsbauer
commented
9 years ago I see you have defined your context in the path C:\Users\garciaalba68w.cts2\lexevs-service\config as lexevs-service. Our directions require that this be the name of your war folder. If that's not the case -- then you should adjust your file system so that it reflects the correct context.
albagarcia
commented
9 years ago Do you think that the problem could be related to felix plugin and tomcat 7?
hsbauer
commented
9 years ago I think this problem is caused by a problem with how the path is defined as I've outline above. Did you mean to post this to your other issue -- because that is likely an OSGI problem.
albagarcia
commented
9 years ago No I'd like to have this post here because I've abandonied the OSGi installation. My war folder is called lexevs-service
This is how my webapp directory looks like:
C:\apache-tomcat-7.0.56-lexevs61\webapps>dir
El volumen de la unidad C es OS
El número de serie del volumen es: 36C6-B1B9
Directorio de C:\apache-tomcat-7.0.56-lexevs61\webapps
14/10/2014 18:06 <DIR> .
14/10/2014 18:06 <DIR> ..
08/10/2014 14:23 <DIR> docs
08/10/2014 14:23 <DIR> examples
08/10/2014 14:23 <DIR> host-manager
14/10/2014 18:06 <DIR> lexevs-service
14/10/2014 18:06 105.751.826 lexevs-service.war
08/10/2014 14:23 <DIR> manager
08/10/2014 14:23 <DIR> ROOT
1 archivos 105.751.826 bytes
8 dirs 248.480.317.440 bytes libresI have generated the .war through mvn clean install -DskipTests=true adding to the pom.xml this properties:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<packagingExcludes>
WEB-INF/lib/icu4j*.jar,
WEB-INF/lib/axis-saaj*.jar,
WEB-INF/lib/xercesImpl*.jar,
WEB-INF/lib/commons-codec-1.2.jar,
</packagingExcludes>
**<warName>lexevs-service</warName>**
</configuration>
<executions>
<execution>
<!-- When also running maven-jar-plugin correct maven-war-plugin's
ID from "default-war" to "default-jar" -->
<id>build-war</id>
<phase>package</phase>
<goals>
<goal>war</goal>
</goals>
</execution>
</executions>
</plugin>My best suggestion is to examine all your paths for a typo, trailing white space or something similar. Your actual path should be something like User/.cts2 and not User.cts2 for instance.
albagarcia
commented
9 years ago The problem was in C:\Users\garciaalba68w.cts2\lexevs-service\config\lexevs.properties
I'have had to change the LG_CONFIG_FILE property from LG_CONFIG_FILE=C:\LexEVS\6.1.0.RC1\resources\config\lbconfig.props to LG_CONFIG_FILE=C:/LexEVS/6.1.0.RC1/resources/config/lbconfig.props
Thank you very much Scott!!
albagarcia
commented
9 years ago By the way when I try to access http://localhost:8080/lexevs-service/system/console I get HTTP 404. And in the Tomcat console I see:
WARN : org.springframework.web.servlet.PageNotFound - No mapping found for HTTP
request with URI [/lexevs-service/system/console] in DispatcherServlet with name
'appServlet'
org.springframework.web.servlet.PageNotFound WARN - 2014-10-15 13:16:39,659 - No
mapping found for HTTP request with URI [/lexevs-service/system/console] in Dis
patcherServlet with name 'appServlet'
WARN : org.springframework.web.servlet.PageNotFound - No mapping found for HTTP
request with URI [/lexevs-service/system/console] in DispatcherServlet with name
'appServlet'
org.springframework.web.servlet.PageNotFound WARN - 2014-10-15 13:17:31,063 - No
mapping found for HTTP request with URI [/lexevs-service/system/console] in Dis
patcherServlet with name 'appServlet'How can I have the console the admin available?
hsbauer
commented
9 years ago Hi Alba: We may need Kevin to chime in here, but I think the console you are hoping to see is only available when you install the service as a plugin to the framework. This is the OSGI install you looked at earlier. Is there some particular functionality you were hoping for from this? I've reviewed the documentation and don't see where it directs you to /system/console, but if you want to link me to it -- I can see if it's accurate. If you are planning to use the OSGI install you may have to use an earlier version of Tomcat. I believe this was tested on Tomcat 5.
kevinpeterson
commented
9 years ago Yes, that is correct - you will not see anything at /system/console if you deploy LexEVS as stand-alone (meaning, not in the OSGi container). That is why all config must be done through those config files, rather than through the OSGi configuration GUI.
hsbauer
commented
9 years ago If we have resolved this issue please close it. If you have another issue feel welcome to start a new thread.
jmiddleton
commented
8 years ago Hi there,
I'm trying to install CTS2 on Tomcat, however I'm not able to see if the war is deployed correctly or not. The app keeps logging that is waiting for a Configuration Service.
I have configured the following two files:
osgi.suppress=trueLG_CONFIG_FILE=/opt/LexGrid/LexEVS/6.3.0.FINAL/resources/config/lbconfig.props
service.pid=edu.mayo.cts2.framework.plugin.service.lexevs
lexevsRemoteApiUrl=
useRemoteApi=false
uriResolutionServiceUrl=https://172.30.1.185:8080/cts2/services/uriresolver/And deployed the ware on the same tomcat server where lexevsapi63 is running. The log shows the following:
INFO: Deploying web application archive /usr/local/tomcat/webapps/lexevscts2.war
May 02, 2016 1:40:38 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags/form is already defined
May 02, 2016 1:40:38 AM org.apache.catalina.startup.TaglibUriRule body
INFO: TLD skipped. URI: http://www.springframework.org/tags is already defined
May 02, 2016 1:40:39 AM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
INFO : org.springframework.web.context.ContextLoader - Root WebApplicationContext: initialization started
INFO : org.springframework.web.context.support.XmlWebApplicationContext - Refreshing Root WebApplicationContext: startup date [Mon May 02 01:40:39 UTC 2016]; root of context hierarchy
INFO : org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from ServletContext resource [/WEB-INF/spring/root-context.xml]
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor - JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
INFO : org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@1d669acf: defining beans [edu.mayo.cts2.framework.core.config.ConfigInitializer#0,org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalPersistenceAnnotationProcessor,cts2DeploymentConfig,refreshableServerContext,jsonConverter,defaultPluginConfigManager,felixPluginManager,supplementalPropetiesLoader,delegatingMarshaller,serviceProviderFactory,codeSystemVersionNameResolver,tagResolver,metaTypeRestConfig,createHandler,deleteHandler,methodTimingAspect,multipleFiltersAspect,updateHandler,urlTemplateBindingCreator,propertiesFileExceptionCodeMapper,filterResolver,readContextResolver,sortResolver,entityDescriptionValidator,classPathScanningConformanceFactory,serviceBuilder,AssociationReadServicesEndpoint,CodeSystemCatalogQueryServicesEndpoint,CodeSystemCatalogReadServicesEndpoint,CodeSystemVersionCatalogReadServicesEndpoint,ConceptDomainCatalogReadServicesEndpoint,ConceptDomainBindingReadServicesEndpoint,EntityDescriptionReadServicesEndpoint,MapCatalogReadServicesEndpoint,MapEntryReadServicesEndpoint,MapVersionReadServicesEndpoint,StatementReadServicesEndpoint,ValueSetCatalogReadServicesEndpoint,ValueSetDefinitionReadServicesEndpoint,switchableSoapUrlMapping,edu.mayo.cts2.framework.webapp.rest.osgi.OsgiExtensionPointViewResolver#0,jsonpCallbackFilter,errorCodes,org.springframework.context.annotation.ConfigurationClassPostProcessor$ImportAwareBeanPostProcessor#0]; root of factory hierarchy
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/local/tomcat/webapps/lexevscts2/WEB-INF/lib/slf4j-log4j12-1.5.8.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/local/tomcat/webapps/lexevscts2/WEB-INF/lib/slf4j-log4j12-1.7.5.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'org/jfree'
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'org/quartz'
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'org/quartz'
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'com/opensymphony'
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'org/ofbiz'
WARN : org.twdata.pkgscanner.InternalScanner - Unable to find any resources for package 'webwork'
[INFO] Started bridged http service
INFO : org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [META-INF/spring/lexevs-context.xml]
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-250 'javax.annotation.ManagedBean' found and supported for component scanning
INFO : org.springframework.context.annotation.ClassPathBeanDefinitionScanner - JSR-330 'javax.inject.Named' annotation found and supported for component scanning
INFO : org.springframework.beans.factory.xml.XmlBeanDefinitionReader - Loading XML bean definitions from class path resource [META-INF/spring/osgi-context.xml]
INFO : org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor - JSR-330 'javax.inject.Inject' annotation found and supported for autowiring
INFO : org.springframework.beans.factory.support.DefaultListableBeanFactory - Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@7d487a12: defining beans [buildProperties,codeSystemVersionBulkDownloadController,searchExtensionBulkDownloader,mapVersionBulkDownloadController,mappingExtensionBulkDownloader,lexEvsChangeEventHandler,defaultCodingSchemeNameTranslator,defaultResolvedValueSetNameTranslator,defaultValueSetNameTranslator,versionNameConverter,lexevsServiceProvider,restMssoUserValidator,associatedConceptToAssociationTransform,lexEvsAssociationQueryService,codingSchemeToCodeSystemTransform,lexEvsCodeSystemVersionQueryService,lexEvsCodeSystemVersionReadService,delegatingEntityQueryService,entityNameQueryBuilder,entityTransform,entityUriResolver,lexEvsAssociationEntityQueryService,lexEvsEntityQueryService,lexEvsEntityReadService,searchExtensionEntityQueryService,codingSchemeToMapTransform,lexEvsMapQueryService,lexEvsMapReadService,lexEvsMapEntryQueryService,lexEvsMapEntryReadService,mappingToMapEntryTransform,codingSchemeToMapVersionTransform,lexEvsMapVersionQueryService,lexEvsMapVersionReadService,lexEvsResolvedValueSetQueryService,lexEvsResolvedValueSetResolutionService,resolvedCodingSchemeTransform,lexEVSValueSetQueryService,lexEVSValueSetReadService,valueSetTransform,lexEvsValueSetDefinitionQueryService,lexEvsValueSetDefinitionReadService,lexEvsValueSetDefinitionResolutionService,lexEvsValueSetDefinitionToCTS2ValueSetDefinitionTransform,codeSystemVersionUriResolver,transformUtils,delegatingUriHandler,fallbackUriHandler,lexEvsSupportedPropertiesUriHandler,restUriResolver,restUriResolverUriHandler,commonResolvedValueSetUtils,commonValueSetUtils,lexEVSResolvedValueSetServiceFactory,lexEVSValueSetDefinitionServicesFactory,mappingExtensionFactory,org.springframework.context.annotation.internalConfigurationAnnotationProcessor,org.springframework.context.annotation.internalAutowiredAnnotationProcessor,org.springframework.context.annotation.internalRequiredAnnotationProcessor,org.springframework.context.annotation.internalCommonAnnotationProcessor,org.springframework.context.annotation.internalPersistenceAnnotationProcessor,edu.mayo.cts2.framework.util.spring.UrlConstructorSpringFactory#0,org.springframework.osgi.compendium.internal.cm.ManagedServiceInstanceTrackerPostProcessor#0#lexBigServiceFactory,lexBigServiceFactory,org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean#0,org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean#1,pluginConfigManager,cts2Marshaller,org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean#2,props,org.springframework.beans.factory.config.PropertyPlaceholderConfigurer#0]; root of factory hierarchy
INFO : org.springframework.beans.factory.config.PropertiesFactoryBean - Loading properties file from class path resource [build-info.properties]
WARN : edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory - Waiting for the Configuration Service to start...
WARN : org.springframework.osgi.compendium.internal.cm.UpdateMethodAdapter - Custom method [public void edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory.updateCallback(java.util.Map)] threw exception when passing properties [{}]
java.lang.NullPointerException
at edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory.updateCallback(LexBigServiceFactory.java:93)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.osgi.util.internal.ReflectionUtils.invokeMethod(ReflectionUtils.java:108)
at org.springframework.osgi.compendium.internal.cm.UpdateMethodAdapter.invokeCustomMethods(UpdateMethodAdapter.java:114)
at org.springframework.osgi.compendium.internal.cm.UpdateMethodAdapter.invoke(UpdateMethodAdapter.java:142)
at org.springframework.osgi.compendium.internal.cm.BeanManagedUpdate.update(BeanManagedUpdate.java:43)
at org.springframework.osgi.compendium.internal.cm.CMUtils.bulkUpdate(CMUtils.java:65)
at org.springframework.osgi.compendium.internal.cm.DefaultManagedServiceBeanManager.updated(DefaultManagedServiceBeanManager.java:80)
at org.springframework.osgi.compendium.internal.cm.ConfigurationAdminManager$ConfigurationWatcher.updated(ConfigurationAdminManager.java:68)
at org.apache.felix.cm.impl.ConfigurationManager$ManagedServiceUpdate.run(ConfigurationManager.java:1160)
at org.apache.felix.cm.impl.UpdateThread.run(UpdateThread.java:104)
at java.lang.Thread.run(Thread.java:745)
WARN : edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory - Waiting for the Configuration Service to start...
WARN : edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory - Waiting for the Configuration Service to start...
WARN : edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory - Waiting for the Configuration Service to start...
WARN : edu.mayo.cts2.framework.plugin.service.lexevs.LexBigServiceFactory - Waiting for the Configuration Service to start...Do I need to do something else?
Thanks, Jorge
dksharma
commented
8 years ago Hello Jorge, Based on the trace you pasted here. I noticed two things which I'd have checked:
If this does not solve the problem and me or one of us will replicate the deployment process like yours and see if we get the same error or not.
Thanks, Deepak
leetal
commented
8 years ago Hi there!
I'm having a hard time figuring out why i cannot deploy my lexevs.war-file.
I get the following error while deploying the WAR under Tomcat7:
Aug 16, 2016 1:32:31 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Aug 16, 2016 1:32:31 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Aug 16, 2016 1:32:34 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cts2DeploymentConfig' defined in URL [jar:file:/var/lib/tomcat7/webapps/lexevs/WEB-INF/lib/cts2-core-1.2.0.FINAL.jar!/edu/mayo/cts2/framework/core/config/Cts2DeploymentConfig.class]: Invocation of init method failed; nested exception is java.lang.RuntimeException: java.io.IOException: No such file or directory
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:384)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:283)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:111)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: java.io.IOException: No such file or directory
at edu.mayo.cts2.framework.core.config.ConfigUtils.createFile(ConfigUtils.java:59)
at edu.mayo.cts2.framework.core.config.Cts2DeploymentConfig.afterPropertiesSet(Cts2DeploymentConfig.java:69)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
... 25 more
Caused by: java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.createNewFile(File.java:1012)
at edu.mayo.cts2.framework.core.config.ConfigUtils.createFile(ConfigUtils.java:57)
... 28 more
Aug 16, 2016 1:32:34 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContextBy the looks of it it seems that lexevs-service cannot find a config file.. I have created the .cts2 folder under my user account like so: ~/.cts2/lexevs/config/..., with the following two files present:
cts2-deployment.properties and lexevs.properties.
lexevs.properties:
service.pid=edu.mayo.cts2.framework.plugin.service.lexevs
lexevsRemoteApiUrl=
useRemoteApi=false
LG_CONFIG_FILE=/home/leetal/LexGrid/LexEVS/6.4.0.FINAL/resources/config/lbconfig.props
uriResolutionServiceUrl=https://informatics.mayo.edu/cts2/services/uriresolver/cts2-deployment.properties:
osgi.suppress=trueIf i have understood everything correctly; I should place the ".cts2"-directory under my own user home folder, and not under the tomcat7 users home folder. Right? All files under .cts2 is chown:ed to my user, and NOT tomcat7´s user. Permissions on all files and folders are (currently) 777 to eliminate that as well.
I have built the lexevs-service from the latest source in the repository (had to skip the tests, they hung halfway through).
Running environment:
lexevs.warI'm currently at a standstill and any help would greatly be appreciated.
hsbauer
commented
8 years ago If the tomcat user is the user that Tomcat is started under then that's where the context for the configuration should be. Try moving this to the tomcat user's home and seeing if that works.
leetal
commented
8 years ago Hi @hsbauer
Thanks for the quick reply! Yes, of course that solved that problem, thank you! But as always, more problems arose..
I'm getting a lot of:
ERROR: org.springframework.web.context.ContextLoader - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'refreshableServerContext': Injection of resource dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'felixPluginManager' defined in URL [jar:file:/var/lib/tomcat7/webapps/lexevs/WEB-INF/lib/cts2-core-1.2.0.FINAL.jar!/edu/mayo/cts2/framework/core/plugin/FelixPluginManager.class]: Invocation of init method failed; nested exception is com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to start OSGi container
at org.springframework.context.annotation.CommonAnnotationBeanPostProcessor.postProcessPropertyValues(CommonAnnotationBeanPostProcessor.java:306)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1106)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:517)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:913)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:464)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:384)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:283)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:111)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5068)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5584)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:147)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1091)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1980)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'felixPluginManager' defined in URL [jar:file:/var/lib/tomcat7/webapps/lexevs/WEB-INF/lib/cts2-core-1.2.0.FINAL.jar!/edu/mayo/cts2/framework/core/plugin/FelixPluginManager.class]: Invocation of init method failed; nested exception is com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to start OSGi container
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1455)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:294)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:225)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:291)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:848)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:790)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:707)
at org.springframework.context.annotation.CommonAnnotationBeanPostProcessor.autowireResource(CommonAnnotationBeanPostProcessor.java:438)
at org.springframework.context.annotation.CommonAnnotationBeanPostProcessor.getResource(CommonAnnotationBeanPostProcessor.java:416)
at org.springframework.context.annotation.CommonAnnotationBeanPostProcessor$ResourceElement.getResourceToInject(CommonAnnotationBeanPostProcessor.java:549)
at org.springframework.beans.factory.annotation.InjectionMetadata$InjectedElement.inject(InjectionMetadata.java:150)
at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:87)
at org.springframework.context.annotation.CommonAnnotationBeanPostProcessor.postProcessPropertyValues(CommonAnnotationBeanPostProcessor.java:303)
... 26 more
Caused by: com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to start OSGi container
at edu.mayo.cts2.framework.core.plugin.FelixPluginManager.start(FelixPluginManager.java:381)
at edu.mayo.cts2.framework.core.plugin.FelixPluginManager.afterPropertiesSet(FelixPluginManager.java:134)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1514)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1452)
... 41 more
....followed by a lot of errors when trying to inject classes it cannot find:
...
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dbDriver': Post-processing of the FactoryBean's object failed; nested exception is org.aspectj.apache.bcel.classfile.ClassFormatException: File: 'java.lang.CharSequence': Invalid byte tag in constant pool: 18
...Is this something you have seen before? I thought i followed the instructions to the point, but seems like i have missed something.
hsbauer
commented
8 years ago Try deleting your plugins cache under the .cts2 directory. The URI resolver address is going to cause you problems next. You'll want to get that application up and running in this or another container, then point your resolver address to it. https://github.com/cts2/URI_Resolver
hsbauer
commented
8 years ago Also, have you verified that your lexevs installation is working properly?
leetal
commented
8 years ago Yes i've tried removing the plugins and felix caches under .cts2. No dice. I haven't verified the installation, more than by the tests (with the -v flag) and these all pass.
There is an error earlier, right after the deployment starts where it says that some string cannot be parsed as boolean. I can return with more details as soon as i return to work tomorrow, timezone here is GMT+2.
Thanks for the quick responses and for helping us resolve these problems.
leetal
commented
8 years ago Here's the first errors that appears:
*ERROR* [org.osgi.service.metatype.MetaTypeProvider, org.osgi.service.cm.ManagedService, id=6, bundle=0]: Unexpected
problem updating Configuration PID=edu.mayo.cts2.framework.webapp.rest.config, factoryPID=null, bundleLocation=Syst
em Bundle
java.lang.ClassCastException: java.lang.String cannot be cast to java.lang.Boolean
at edu.mayo.cts2.framework.webapp.rest.config.MetaTypeRestConfig.updated(MetaTypeRestConfig.java:85)
at org.apache.felix.cm.impl.ConfigurationManager$UpdateConfiguration.run(ConfigurationManager.java:1490)
at org.apache.felix.cm.impl.UpdateThread.run(UpdateThread.java:104)
at java.lang.Thread.run(Thread.java:745)
*ERROR* [org.osgi.service.metatype.MetaTypeProvider, org.osgi.service.cm.ManagedService, id=6, bundle=0]: Unexpected
problem updating Configuration PID=edu.mayo.cts2.framework.webapp.rest.config, factoryPID=null, bundleLocation=Syst
em Bundle
java.lang.ClassCastException: java.lang.String cannot be cast to java.lang.Boolean
at edu.mayo.cts2.framework.webapp.rest.config.MetaTypeRestConfig.updated(MetaTypeRestConfig.java:85)
at org.apache.felix.cm.impl.ConfigurationManager$ManagedServiceUpdate.run(ConfigurationManager.java:1160)
at org.apache.felix.cm.impl.UpdateThread.run(UpdateThread.java:104)
at java.lang.Thread.run(Thread.java:745)It seems some string cannot be parsed to boolean (perhaps the osgi.suppress=true?). Any clue what might cause this?
leetal
commented
8 years ago I have now run the tests of lexevs-service and i get one failed test with the following result:
-------------------------------------------------------------------------------
Test set: edu.mayo.cts2.framework.plugin.service.lexevs.service.resolvedvalueset.LexEVSResolvedValuesetResolutionServiceTestIT
-------------------------------------------------------------------------------
Tests run: 14, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 14.237 sec <<< FAILURE!
testGetResolutionEntitiesWithEntityRestriction(edu.mayo.cts2.framework.plugin.service.lexevs.service.resolvedvalueset.LexEVSResolvedValuesetResolutionServiceTestIT) Time elapsed: 0.023 sec <<< FAILURE!
java.lang.AssertionError:
at org.junit.Assert.fail(Assert.java:91)
at org.junit.Assert.assertTrue(Assert.java:43)
at org.junit.Assert.assertTrue(Assert.java:54)
at edu.mayo.cts2.framework.plugin.service.lexevs.service.resolvedvalueset.LexEVSResolvedValuesetResolutionServiceTestIT.testGetResolutionEntitiesWithEntityRestriction(LexEVSResolvedValuesetResolutionServiceTestIT.java:203)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:28)
at org.springframework.test.context.junit4.statements.RunBeforeTestMethodCallbacks.evaluate(RunBeforeTestMethodCallbacks.java:74)
at org.springframework.test.context.junit4.statements.RunAfterTestMethodCallbacks.evaluate(RunAfterTestMethodCallbacks.java:83)
at org.springframework.test.context.junit4.statements.SpringRepeat.evaluate(SpringRepeat.java:72)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.runChild(SpringJUnit4ClassRunner.java:231)
at org.LexGrid.LexBIG.test.LexEvsTestRunner.runChild(LexEvsTestRunner.java:36)
at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
at org.springframework.test.context.junit4.statements.RunBeforeTestClassCallbacks.evaluate(RunBeforeTestClassCallbacks.java:61)
at org.springframework.test.context.junit4.statements.RunAfterTestClassCallbacks.evaluate(RunAfterTestClassCallbacks.java:71)
at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
at org.springframework.test.context.junit4.SpringJUnit4ClassRunner.run(SpringJUnit4ClassRunner.java:174)
at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:234)
at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:133)
at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:114)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:188)
at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:166)
at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:86)
at org.apache.maven.plugin.surefire.InPluginVMSurefireStarter.runSuitesInProcess(InPluginVMSurefireStarter.java:75)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:194)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAllProviders(AbstractSurefireMojo.java:176)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:134)
at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:97)
at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)All our tests are running clean for the lexevs-service at this point. We have seen the string parsing issue before and traced it to an aspectj jar in the cts2-framework application. Not sure this would be your issue however. If it was is would require some rebuilding of source jars for the framework which shouldn't be necessary. So we can't quite account for your failures on the lexevs-service but let's get a little more information about your environment:
leetal
commented
8 years ago Thanks for your reply!
Thought I'd chime in and mention that i solved the problem... Seems some of my built files (not all, probably due to me copying and pasting) were compiled with JDK 8, instead of JDK 7. This caused lots of commotion when CTS2 Framework/osgi were trying to inject classes. Thus the "18 byte misalignment" problem i mentioned earlier.
I have now successfully built lexevs_service (based on master, or 1.5.0.FINAL tag). I can get it up and running (though it shows the default screen for CTS2 framework if i try the URL of the deployed WAR in a browser). I only have some testdata in LexEVS at the moment so i do not think i can query lexevs-service for that data. the /codesystemversions URI does not report any entries since none is loaded. I'll continue by tomorrow to load the latest HL7 code system into LexEVS and see how that goes. 👍
I also have the uriresolver installed and working locally. 👍
Thanks for your help @hsbauer
hsbauer
commented
8 years ago Glad to hear it. Let us know if you have any other questions. Our MIF loader for HL7 is relatively new and we'd be interested in any feedback you may have.
Hi, I'm following the instructions on https://github.com/cts2/lexevs-service/blob/master/README.md#installation-non-osgi but when I try to start my tomcat instance I'm facing this issue:
This is my C:\Users\garciaalba68w.cts2\lexevs-service\config\lexevs.properties file:
I'm starting my tmcat through
C:\apache-tomcat-7.0.56-lexevs61\bin>catalina.bat runI've renamed the .war created under C:\LexEVS\lexevs-service\target from lexevs-service-0.1.0-SNAPSHOT.war to lexevs-service.war and placed it under my
C:\apache-tomcat-7.0.56-lexevs61\webappsdirectory.Has anybody faced this issue?
Thanks in advance!