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    OpenSpecimen does not start

    Technical Questions
    #1

    Hello.

    I have build and deployed the current OpenSpecimen version from source according to the instructions on https://openspecimen.atlassian.net/wiki/pages/viewpage.action?pageId=1115955

    However, the application does not start, probably because the following error found in the Tomcat log:

    OpenSpecimen, a Krishagni Product
    Build Version :
    Build Date : Mon Feb 06 16:21:25 CET 2017
    Commit :
    Present Time : Mon Feb 06 17:46:01 CET 2017

    log4j:WARN No appenders could be found for logger (com.krishagni.catissueplus.core.init.AppServletContextListener).
    log4j:WARN Please initialize the log4j system properly.
    log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
    log4j:ERROR Could not read configuration file [/usr/local/tomcat7/openspecimen-logs/].
    java.io.FileNotFoundException: /usr/local/tomcat7/openspecimen-logs (Is a directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.(FileInputStream.java:138)
    at java.io.FileInputStream.(FileInputStream.java:93)
    at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:372)
    at org.apache.log4j.PropertyWatchdog.doOnChange(PropertyConfigurator.java:922)
    at org.apache.log4j.helpers.FileWatchdog.checkAndConfigure(FileWatchdog.java:89)
    at org.apache.log4j.helpers.FileWatchdog.(FileWatchdog.java:58)
    at org.apache.log4j.PropertyWatchdog.(PropertyConfigurator.java:914)
    at org.apache.log4j.PropertyConfigurator.configureAndWatch(PropertyConfigurator.java:461)
    at org.apache.log4j.PropertyConfigurator.configureAndWatch(PropertyConfigurator.java:443)
    at com.krishagni.catissueplus.core.init.AppServletContextListener.initLogging(AppServletContextListener.java:107)
    at com.krishagni.catissueplus.core.init.AppServletContextListener.contextInitialized(AppServletContextListener.java:62)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5118)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
    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:1092)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1984)
    at java.util.concurrent.Executors$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)
    log4j:ERROR Ignoring configuration file [/usr/local/tomcat7/openspecimen-logs/].
    Feb 06, 2017 5:46:03 PM org.apache.catalina.core.StandardContext startInternal
    SEVERE: One or more listeners failed to start. Full details will be found in the appropriate container log file

    Many thanks for help !!

    #2

    It seems to be a wrong configuration of the log4j logger. I have disabled the logger to proceed, but I struggle now with the error:

    OpenSpecimen, a Krishagni Product
    Build Version : master
    Build Date : Tue Feb 07 21:37:09 CET 2017
    Commit : 00eb7a2
    Present Time : Tue Feb 07 22:24:45 CET 2017

    INFO 07.02.17 22:24: liquibase: Successfully acquired change log lock
    INFO 07.02.17 22:24: liquibase: Reading from osdb.DATABASECHANGELOG
    INFO 07.02.17 22:24: liquibase: Successfully released change log lock
    INFO 07.02.17 22:24: liquibase: Successfully acquired change log lock
    INFO 07.02.17 22:24: liquibase: Reading from osdb.DATABASECHANGELOG
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    WARNING 07.02.17 22:24: liquibase: modifyDataType will lose primary key/autoincrement/not null settings for mysql. Use and re-specify all configuration if this is the case
    INFO 07.02.17 22:24: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani ran successfully in 1ms
    INFO 07.02.17 22:24: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha: ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha ran successfully in 0ms
    INFO 07.02.17 22:24: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘FKB025CFC7FFA96920’; check that column/key exists
    INFO 07.02.17 22:24: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha: Change set db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘WUSTLKEY’; check that column/key exists
    INFO 07.02.17 22:24: liquibase: classpath:db/db-os-changelog-master-fresh.xml: db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte: Change set db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte failed, but failOnError was false. Error: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can’t DROP ‘CSM_USER_ID_UNIQUE_KEY’; check that column/key exists

    I would be happy, if somebody has an idea to fix this issue. Much thanks and best regards!

    #3

    Hi @Michael_Scharfe,

    The errors shown in log are harmless and server should have started successfully.
    Please check if any further error message is appeared or server is started successfully.
    You should be able to access the app, if not then please provide log excerpts after the given errors.

    #4

    Dear Chetan_Khilosiya

    Thanks for your reply.
    I can not find more logging information. The tomcat log stops there and tomcat causes about 100% CPU load.
    I can reach the tomcat default pate localhost:8080 and it looks fine. But localhost:8080/openspecimen is not loading …

    I have installed tomcat7 from ubuntu repository - maybe I should try to install it from official source?
    Do you have any further idea?

    Thanks and best regards

    #5

    Hi @Michael_Scharfe ,

    The path of tomcat log directory will be ${tomcat_home}/logs. Please attach zipped log directory to forum.
    We will have a look at it and reply you back.

    #6

    Hi @Michael_Scharfe ,

    About 100% CPU load, the recommended memory for OpenSpecimen is 2GB.
    To configure Tomcat refer document https://openspecimen.atlassian.net/wiki/x/0Q77B

    #7

    Hello Chetan Khilosiya.

    Thanks for your reply. OS is running now! It seems there was a problem with the Tomcat installation from Ubuntu repository. I have reinstalled Tomcat from the official source and it works.

    One thing I am slightly confused about:
    According to the Build Instructions the build.properties should contain the parameter:

    app_log_conf = “folder for log files”

    However, it is only working if I reference a log4j.properties file, e.g.

    app_log_conf = “folder for log files”/log4j.properties

    Is this the expected behaviour or did I something wrong?

    Best regards

    #8

    Hi @Michael_Scharfe,

    The app_log_conf is used to specify path of logging configuration file.
    If left blank, default logging configuration shipped with app is used
    (${TOMCAT_HOME}/webapps/openspecimen/WEB-INF/classes/default-log4j.properties).

    #9

    Hello.

    Today I’ve tried to install OS on a second server. I am pretty sure I’ve followed the same procedure as for the first server (where OS is running now). However, OS seems to run (Browser title is shown), but nothing else appears - no login window and so on…

    Here is the (truncated) content of the log file:
    #################################
    2017-03-28 15:37:40,187 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.AppServletContextListener- Initialised logging configuration from following file: file:/opt/tomcat/openspecimen-logs/log4j.properties
    2017-03-28 15:37:40,195 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.AppServletContextListener-

    OpenSpecimen, a Krishagni Product
    Build Version :
    Build Date : Tue Mar 28 15:36:03 CEST 2017
    Commit :
    Present Time : Tue Mar 28 15:37:40 CEST 2017

    2017-03-28 15:37:40,195 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.AppServletContextListener- Loading plugins from /opt/tomcat/openspecimen-plugins
    2017-03-28 15:37:40,308 [localhost-startStop-1] INFO org.springframework.web.context.ContextLoader- Root WebApplicationContext: initialization started
    2017-03-28 15:37:40,383 [localhost-startStop-1] INFO org.springframework.web.context.support.XmlWebApplicationContext- Refreshing Root WebApplicationContext: startup date [Tue Mar 28 15:37:40 CEST 2017]; root of context hierarchy
    2017-03-28 15:37:40,422 [localhost-startStop-1] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/applicationContext.xml]
    2017-03-28 15:37:40,940 [localhost-startStop-1] INFO org.springframework.security.core.SpringSecurityCoreVersion- You are running with Spring Security Core 3.2.7.RELEASE
    2017-03-28 15:37:40,944 [localhost-startStop-1] INFO org.springframework.security.config.SecurityNamespaceHandler- Spring Security ‘config’ module version is 3.2.7.RELEASE
    2017-03-28 15:37:41,340 [localhost-startStop-1] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/migrationContext.xml]
    2017-03-28 15:37:41,575 [localhost-startStop-1] INFO org.springframework.beans.factory.config.PropertiesFactoryBean- Loading properties file from class path resource [application.properties]
    2017-03-28 15:37:41,664 [localhost-startStop-1] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler- Initializing ExecutorService ‘taskScheduler’
    2017-03-28 15:37:41,665 [localhost-startStop-1] INFO org.springframework.web.context.support.XmlWebApplicationContext- Bean ‘taskScheduler’ of type [class org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
    2017-03-28 15:37:41,727 [localhost-startStop-1] INFO org.springframework.beans.factory.support.DefaultListableBeanFactory- Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@3ac9c8c: defining beans [appProps,placeholderConfig,dataSource,de-liquibase,os-liquibase,sessionFactory,transactionManager,serviceInterceptor,listenerInterceptor,cfgSvc,passwordEncoder,biospecimenDaoFactory,deDaoFactory,rbacDaoFactory,multipartResolver,org.springframework.aop.config.internalAutoProxyCreator,localDbParticipantLookup,defaultParticipantLookupFlow,rbacSvc,extnPvLabelToken,visitTokenRegistrar,visitNameGenerator,sprText2PdfGenerator,visitService,cpCopier,cpFactory,cpeFactory,srFactory,cpSvc,participantFactory,specimenFactory,visitFactory,cprFactory,consentResponsesFactory,participantSvc,participantAnonymizer,cprSvc,ppidTokensRegistrar,ppidGenerator,userFact,userSvc,domainFact,domainRegSvc,auditService,userAuthService,specimenResolver,specimenSvc,spmnTypePropsSvc,specimenTokenRegistrar,specimenLabelGenerator,specimenListFactory,specimenListSvc,formDataMgr,formDao,formSvc,specimenEventsSvc,userDao,queryFolderFactory,querySvc,catalogSettingFact,catalogSvc,reportSettingsFact,instituteFact,instSvc,siteFactory,siteService,containerTokenRegistrar,containerNameGenerator,storageContainerFactory,containerMapExporter,containerSelectionStrategyFactory,storageContainerSvc,containerTypeFactory,containerTypeSvc,distributionProtocolFactory,distributionProtocolService,distributionFactory,distributionOrderService,dpRequirementFactory,scheduledJobFactory,scheduledTaskMgr,scheduledJobSvc,pvValidator,permissibleValueSvc,commonSvc,messageSource,appCtxProvider,org.springframework.security.authentication.dao.DaoAuthenticationProvider#0,org.springframework.security.authentication.DefaultAuthenticationEventPublisher#0,org.springframework.security.authenticationManager,samlFilter,authTokenFilter,velocityEngine,templateService,emailService,specimenPrintLabelTokensRegistrar,visitPrintLabelTokensRegistrar,defaultSpecimenLabelPrinter,defaultVisitLabelPrinter,taskExecutor,deInitializer,importQueryForms,importSpeForms,importJobDao,objectSchemaFactory,objectImporterFactory,importEntityForms,importDeForms,importObjectsSvc,importDefaultQueries,supportService,shipmentFactory,shipmentSvc,jdbcTemplate,upgradeLogUpdater,objectStateParamsResolver,listGenerator,taskScheduler,org.springframework.context.annotation.internalAsyncAnnotationProcessor,org.springframework.context.annotation.internalScheduledAnnotationProcessor,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,org.springframework.context.config.internalBeanConfigurerAspect,migrationProps,migrationDao,migrationSvc,migrateCntnrRestrictions,migrateSprs,migrateConsents,org.springframework.context.annotation.ConfigurationClassPostProcessor.importAwareProcessor]; root of factory hierarchy
    2017-03-28 15:37:46,697 [localhost-startStop-1] INFO org.hibernate.annotations.common.Version- Hibernate Commons Annotations 3.2.0.Final
    2017-03-28 15:37:46,703 [localhost-startStop-1] INFO org.hibernate.Version- HHH000412: Hibernate Core {4.2.18.Final}
    2017-03-28 15:37:46,705 [localhost-startStop-1] INFO org.hibernate.cfg.Environment- HHH000206: hibernate.properties not found
    2017-03-28 15:37:46,707 [localhost-startStop-1] INFO org.hibernate.cfg.Environment- HHH000021: Bytecode provider name : javassist
    2017-03-28 15:37:46,766 [localhost-startStop-1] WARN org.hibernate.internal.util.xml.DTDEntityResolver- HHH000223: Recognized obsolete hibernate namespace http://hibernate.sourceforge.net/. Use namespace http://www.hibernate.org/dtd/ instead. Refer to Hibernate 3.6 Migration Guide!
    2017-03-28 15:37:46,815 [localhost-startStop-1] WARN org.hibernate.internal.util.xml.DTDEntityResolver- HHH000223: Recognized obsolete hibernate namespace http://hibernate.sourceforge.net/. Use namespace http://www.hibernate.org/dtd/ instead. Refer to Hibernate 3.6 Migration Guide!

    …

    2017-03-28 15:37:47,515 [localhost-startStop-1] WARN org.hibernate.internal.util.xml.DTDEntityResolver- HHH000223: Recognized obsolete hibernate namespace http://hibernate.sourceforge.net/. Use namespace http://www.hibernate.org/dtd/ instead. Refer to Hibernate 3.6 Migration Guide!
    2017-03-28 15:37:47,612 [localhost-startStop-1] INFO org.hibernate.dialect.Dialect- HHH000400: Using dialect: org.hibernate.dialect.MySQLDialect
    2017-03-28 15:37:47,850 [localhost-startStop-1] INFO org.hibernate.engine.transaction.internal.TransactionFactoryInitiator- HHH000399: Using default transaction strategy (direct JDBC transactions)
    2017-03-28 15:37:47,855 [localhost-startStop-1] INFO org.hibernate.hql.internal.ast.ASTQueryTranslatorFactory- HHH000397: Using ASTQueryTranslatorFactory
    2017-03-28 15:37:49,597 [localhost-startStop-1] INFO org.springframework.orm.hibernate4.HibernateTransactionManager- Using DataSource [org.apache.tomcat.dbcp.dbcp2.BasicDataSource@67f1ec31] of Hibernate SessionFactory for HibernateTransactionManager
    2017-03-28 15:37:50,136 [localhost-startStop-1] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor- Initializing ExecutorService ‘taskExecutor’
    2017-03-28 15:37:51,427 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.biospecimen.services.impl.DefaultSpecimenLabelPrinter- Adding print rule: [label design = *, label type = Std, user = *, printer = default, tokens = Label;Specimen Type;Specimen Type;Location, cp = *, lineage = *, visit site = *, specimen class = *, specimen type = *]
    2017-03-28 15:37:51,433 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.biospecimen.services.impl.DefaultVisitLabelPrinter- Adding rule [label design = *, label type = Std, user = *, printer = default, tokens = Visit Name;Collection Protocol;Visit Date, cp = *, visit site = *]
    2017-03-28 15:37:51,634 [localhost-startStop-1] ERROR com.krishagni.catissueplus.core.de.services.impl.QueryServiceImpl- Error rendering query forms
    java.io.FileNotFoundException: class path resource [query-forms/specimen/] cannot be resolved to URL because it does not exist
    at org.springframework.core.io.ClassPathResource.getURL(ClassPathResource.java:186)
    at org.springframework.core.io.support.PathMatchingResourcePatternResolver.findPathMatchingResources(PathMatchingResourcePatternResolver.java:343)
    at org.springframework.core.io.support.PathMatchingResourcePatternResolver.getResources(PathMatchingResourcePatternResolver.java:281)
    at com.krishagni.catissueplus.core.de.services.impl.QueryServiceImpl.insertCustomQueryForms(QueryServiceImpl.java:904)
    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.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:395)
    at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:384)
    at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:173)
    at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:280)
    at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:369)
    at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:342)
    at org.apache.velocity.Template.merge(Template.java:356)
    at org.apache.velocity.Template.merge(Template.java:260)
    at org.apache.velocity.app.VelocityEngine.mergeTemplate(VelocityEngine.java:354)
    at org.apache.velocity.app.VelocityEngine.mergeTemplate(VelocityEngine.java:320)
    at org.springframework.ui.velocity.VelocityEngineUtils.mergeTemplate(VelocityEngineUtils.java:58)
    at org.springframework.ui.velocity.VelocityEngineUtils.mergeTemplateIntoString(VelocityEngineUtils.java:122)
    at com.krishagni.catissueplus.core.common.service.impl.TemplateServiceImpl.render(TemplateServiceImpl.java:35)
    at com.krishagni.catissueplus.core.init.ImportForms.preprocessForms(ImportForms.java:193)
    at com.krishagni.catissueplus.core.init.ImportForms.importForms(ImportForms.java:138)
    at com.krishagni.catissueplus.core.init.ImportForms.access$1(ImportForms.java:131)
    at com.krishagni.catissueplus.core.init.ImportForms$1.doInTransaction(ImportForms.java:103)
    at com.krishagni.catissueplus.core.init.ImportForms$1.doInTransaction(ImportForms.java:1)
    at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:131)
    at com.krishagni.catissueplus.core.init.ImportForms.importForms(ImportForms.java:98)
    at com.krishagni.catissueplus.core.init.ImportForms.afterPropertiesSet(ImportForms.java:86)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1573)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1511)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:521)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:458)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:223)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:191)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:636)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:934)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:479)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:410)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:112)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4754)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5216)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:752)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:728)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:952)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1823)
    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)
    2017-03-28 15:37:52,193 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimenBasedOnSpecimenDetails.json
    2017-03-28 15:37:52,203 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimenBasedOnSpecimenDetails.json since last import
    2017-03-28 15:37:52,203 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ShipmentDetailsBasedOnShipmentLabel.json
    2017-03-28 15:37:52,205 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ShipmentDetailsBasedOnShipmentLabel.json since last import
    2017-03-28 15:37:52,205 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ReportCountOfSpecimensByType_Container.json
    2017-03-28 15:37:52,206 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ReportCountOfSpecimensByType_Container.json since last import
    2017-03-28 15:37:52,206 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ShipmentReport.json
    2017-03-28 15:37:52,207 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ShipmentReport.json since last import
    2017-03-28 15:37:52,207 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/DistributionReport.json
    2017-03-28 15:37:52,209 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/DistributionReport.json since last import
    2017-03-28 15:37:52,209 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimensBasedOnSCG_Name.json
    2017-03-28 15:37:52,212 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimensBasedOnSCG_Name.json since last import
    2017-03-28 15:37:52,212 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ReportCountOfParticipantsByProtocol_Gender.json
    2017-03-28 15:37:52,214 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ReportCountOfParticipantsByProtocol_Gender.json since last import
    2017-03-28 15:37:52,215 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimenCatalog.json
    2017-03-28 15:37:52,216 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimenCatalog.json since last import
    2017-03-28 15:37:52,216 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/TissueSpecimensFrozenWithin15MinsOfReceivedTime.json
    2017-03-28 15:37:52,218 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/TissueSpecimensFrozenWithin15MinsOfReceivedTime.json since last import
    2017-03-28 15:37:52,218 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimensBasedOnParticipantDemographics.json
    2017-03-28 15:37:52,220 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimensBasedOnParticipantDemographics.json since last import
    2017-03-28 15:37:52,220 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/DNA_DerivedFromTumorBreastTissue.json
    2017-03-28 15:37:52,221 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/DNA_DerivedFromTumorBreastTissue.json since last import
    2017-03-28 15:37:52,221 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimensBasedOnLabel.json
    2017-03-28 15:37:52,222 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimensBasedOnLabel.json since last import
    2017-03-28 15:37:52,222 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ReportCountOfSpecimensByProtocol_Type_TissueSite.json
    2017-03-28 15:37:52,224 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ReportCountOfSpecimensByProtocol_Type_TissueSite.json since last import
    2017-03-28 15:37:52,225 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimensBasedOnPPID_MRN.json
    2017-03-28 15:37:52,226 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimensBasedOnPPID_MRN.json since last import
    2017-03-28 15:37:52,226 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/SpecimensStoredInContainer.json
    2017-03-28 15:37:52,229 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/SpecimensStoredInContainer.json since last import
    2017-03-28 15:37:52,229 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/ParticipantsWithFixedTissueBlockAndDNA.json
    2017-03-28 15:37:52,231 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/ParticipantsWithFixedTissueBlockAndDNA.json since last import
    2017-03-28 15:37:52,231 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- Importing query from file: /default-queries/TissueSpecimensHavingFrozenEvent.json
    2017-03-28 15:37:52,233 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.ImportDefaultQueries- No change found in file /default-queries/TissueSpecimensHavingFrozenEvent.json since last import
    2017-03-28 15:37:52,288 [localhost-startStop-1] INFO org.springframework.beans.factory.config.PropertiesFactoryBean- Loading properties file from class path resource [migration.properties]
    2017-03-28 15:37:52,306 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateContainerRestrictions- No storage containers to migrate. Stopping!
    2017-03-28 15:37:52,310 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Old spr directory path not spcified, either no need of migration for this version or missed it.
    2017-03-28 15:37:52,310 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Migration from static table start time: Tue Mar 28 15:37:52 CEST 2017
    2017-03-28 15:37:52,317 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- No surgical pathology reports in static table to migrate from static table
    2017-03-28 15:37:52,317 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Number of reports migrated from static table, till now: 0
    2017-03-28 15:37:52,318 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Migration from static table end time: Tue Mar 28 15:37:52 CEST 2017
    2017-03-28 15:37:52,318 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Total time for migration from static table: 0 minutes
    2017-03-28 15:37:52,318 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Migration from static table start time: Tue Mar 28 15:37:52 CEST 2017
    2017-03-28 15:37:52,318 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- No surgical pathology reports in static table to migrate from static table
    2017-03-28 15:37:52,319 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Number of reports migrated from static table, till now: 0
    2017-03-28 15:37:52,319 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Migration from static table end time: Tue Mar 28 15:37:52 CEST 2017
    2017-03-28 15:37:52,319 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateSurgicalPathologyReports- Total time for migration from static table: 0 minutes
    2017-03-28 15:37:52,322 [localhost-startStop-1] INFO com.krishagni.catissueplus.core.init.MigrateConsents- Old consent directory path not spcified, either no need of migration for this version or missed it.
    2017-03-28 15:37:52,378 [localhost-startStop-1] INFO org.springframework.web.context.ContextLoader- Root WebApplicationContext: initialization completed in 12070 ms
    2017-03-28 15:37:52,400 [localhost-startStop-1] INFO org.springframework.web.servlet.DispatcherServlet- FrameworkServlet ‘pluginUiResources’: initialization started
    2017-03-28 15:37:52,403 [localhost-startStop-1] INFO org.springframework.web.context.support.XmlWebApplicationContext- Refreshing WebApplicationContext for namespace ‘pluginUiResources-servlet’: startup date [Tue Mar 28 15:37:52 CEST 2017]; parent: Root WebApplicationContext
    2017-03-28 15:37:52,404 [localhost-startStop-1] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/pluginUiContext.xml]
    2017-03-28 15:37:52,427 [localhost-startStop-1] INFO org.springframework.beans.factory.support.DefaultListableBeanFactory- Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@3907b43d: defining beans [org.springframework.web.servlet.resource.ResourceHttpRequestHandler#0,org.springframework.web.servlet.handler.SimpleUrlHandlerMapping#0,org.springframework.web.servlet.handler.BeanNameUrlHandlerMapping,org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter,org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter]; parent: org.springframework.beans.factory.support.DefaultListableBeanFactory@3ac9c8c
    2017-03-28 15:37:52,447 [localhost-startStop-1] INFO org.springframework.web.servlet.handler.SimpleUrlHandlerMapping- Mapped URL path [/**] onto handler ‘org.springframework.web.servlet.resource.ResourceHttpRequestHandler#0’
    2017-03-28 15:37:52,531 [localhost-startStop-1] INFO org.springframework.web.servlet.DispatcherServlet- FrameworkServlet ‘pluginUiResources’: initialization completed in 131 ms
    2017-03-28 15:37:52,533 [localhost-startStop-1] INFO org.springframework.web.servlet.DispatcherServlet- FrameworkServlet ‘restApi’: initialization started
    2017-03-28 15:37:52,535 [localhost-startStop-1] INFO org.springframework.web.context.support.XmlWebApplicationContext- Refreshing WebApplicationContext for namespace ‘restApi-servlet’: startup date [Tue Mar 28 15:37:52 CEST 2017]; parent: Root WebApplicationContext
    2017-03-28 15:37:52,537 [localhost-startStop-1] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/restApiContext.xml]
    2017-03-28 15:37:52,651 [localhost-startStop-1] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from file [/opt/tomcat/webapps/openspecimen/WEB-INF/classes/com/krishagni/openspecimen/custom/demo/apiContext.xml]
    2017-03-28 15:37:53,070 [localhost-startStop-1] INFO org.springframework.beans.factory.support.DefaultListableBeanFactory- Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@2eafb919: defining beans [mvcContentNegotiationManager,org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerMapping#0,org.springframework.format.support.FormattingConversionServiceFactoryBean#0,org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter#0,org.springframework.web.servlet.handler.MappedInterceptor#0,org.springframework.web.servlet.mvc.method.annotation.ExceptionHandlerExceptionResolver#0,org.springframework.web.servlet.mvc.annotation.ResponseStatusExceptionResolver#0,org.springframework.web.servlet.mvc.support.DefaultHandlerExceptionResolver#0,org.springframework.web.servlet.handler.BeanNameUrlHandlerMapping,org.springframework.web.servlet.mvc.HttpRequestHandlerAdapter,org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter,supportController,specimensController,specimenEventsController,authDomainController,permissibleValueController,specimenRequirementsController,configurationController,specimenTypePropsController,formFilesController,userController,institutesController,collectionProtocolsController,storageContainersController,collectionProtocolEventsController,specimenListsController,scheduledJobsController,rbacController,queryAuditLogsController,distributionProtocolController,savedQueriesController,collectionProtocolRegistrationsController,objectStateParamsResolverController,distributionOrderController,visitsController,containerTypesController,sitesController,queryController,dpRequirementController,specimenLabelPrintController,bulkObjectImportController,participantController,queryFoldersController,shipmentController,formsController,authenticationController,visitNamePrintController,unhandledExceptionsController,restErrorController,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,form,org.springframework.context.annotation.ConfigurationClassPostProcessor.importAwareProcessor]; parent: org.springframework.beans.factory.support.DefaultListableBeanFactory@3ac9c8c
    2017-03-28 15:37:53,155 [localhost-startStop-1] INFO org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerMapping- Mapped “{[/support/user-feedback],methods=[POST],params=[],headers=[],consumes=[],produces=[],custom=[]}” onto public boolean com.krishagni.catissueplus.rest.controller.SupportController.sendFeedback(com.krishagni.catissueplus.core.support.events.FeedbackDetail)

    …

    2017-03-28 15:37:53,822 [localhost-startStop-1] INFO org.springframework.web.servlet.DispatcherServlet- FrameworkServlet ‘restApi’: initialization completed in 1288 ms
    2017-03-28 15:38:53,872 [pool-3-thread-1] INFO com.krishagni.catissueplus.core.importer.services.impl.ImportRecordsTask- Woken up to bulk import records

    #################

    Has somebody an idea what is going wrong?
    Thanks and best regards

    #10

    The HTML of the appearing website stops at

    <!doctype html> <html> <head> <meta charset="utf-8"> <title>OpenSpecimen</title> <meta name="description" content=""> <meta name="viewport" content="width=device-width,height=device-height"> <!-- Place favicon.ico and apple-touch-icon.png in the root directory --> <link rel="stylesheet" href="styles/vendor.6d3ef16c.css"> <link rel="stylesheet" href="styles/app.2e7d8e79.css">  <body> <!-- ng-app="openspecimen" --> <!--[if lt IE 7]>
      <p class="browsehappy">You are using an <strong>outdated</strong> browser. Please <a href="http://browsehappy.com/">upgrade your browser</a> to improve your experience.</p>
    <![endif]--> <!-- Add your site or application content here --> <div style="height:100%" ui-view></div> <script src="scripts/vendor.64ccd84a.js"></script> <script src="scripts/scripts.a3efaed1.js"></script>

    Maybe that helps

    #11

    Did you ever figure this out? I’m getting the same with a fresh clean install of OS v4.0.