• FEATURES
  • PRICING
  • MARKETPLACE
  • CASE STUDIES
  • BLOG
  • Error run gradle deploy

    #1

    #2

    Hi Sir,

    We’ve viewed your error. You need to install all npm/bower/grunt dependencies, so please re-install these dependencies.

    That will resolve your problem. If not, please revert.

    Thanks.

    #3

    thank u,I lost grunt.

    #4

    Hi Jack,

    It is not clear as to what error you are getting. Can you send us the log or screenshot of the error?

    Thanks,
    Vivek

    #5

    The project didnot run on my computer.Because I cannot find the way to open my website. http://localhost:8080/openspecimen this comes 404 for me.
    This error I had resolved,just run command npm install grunt,and then,gradle deploy build success.
    Now I have new question,as I say,how to open the index.html to see the project on brower.

    #6

    Hi Jack,

    After starting the Tomcat, if you created the app/data directory, then monitor the “os.log” file. It will appear in the app/data/logs directory.

    If the “os.log” file is not generated in this directory, you need to monitor the “catalina.out” file present in the tomcat/logs directory. And Check the errors.

    If the os.log file is generated, then wait until the following line:

    [main] INFO org.springframework.web.servlet.DispatcherServlet- FrameworkServlet ‘restApi’: initialization completed in 1754 ms

    After this line, you can check the output in your browser at http://localhost:8080/openspecimen

    Thanks,
    Kaustubh

    #7

    Here is the detail of os.log.
    2020-12-24 13:34:37,887 [main] INFO com.krishagni.catissueplus.core.init.AppServletContextListener- Initialised logging configuration from following file: file:/D:/apache-tomcat-9.0.39/webapps/open/WEB-INF/classes/default-log4j.properties
    2020-12-24 13:34:37,891 [main] INFO com.krishagni.catissueplus.core.init.AppServletContextListener-


    OpenSpecimen, a Krishagni Product
    Build Version :
    Build Date : Mon Dec 21 14:39:34 CST 2020
    Commit :
    Present Time : Thu Dec 24 13:34:37 CST 2020


    2020-12-24 13:34:37,891 [main] INFO com.krishagni.catissueplus.core.init.AppServletContextListener- Loading plugins from D:/plugins
    2020-12-24 13:34:37,905 [main] INFO org.springframework.web.context.ContextLoader- Root WebApplicationContext: initialization started
    2020-12-24 13:34:38,048 [main] INFO org.springframework.web.context.support.XmlWebApplicationContext- Refreshing Root WebApplicationContext: startup date [Thu Dec 24 13:34:38 CST 2020]; root of context hierarchy
    2020-12-24 13:34:38,083 [main] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/applicationContext.xml]
    2020-12-24 13:34:38,311 [main] INFO org.springframework.security.core.SpringSecurityCoreVersion- You are running with Spring Security Core 4.2.8.RELEASE
    2020-12-24 13:34:38,314 [main] INFO org.springframework.security.config.SecurityNamespaceHandler- Spring Security ‘config’ module version is 4.2.8.RELEASE
    2020-12-24 13:34:38,807 [main] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/migrationContext.xml]
    2020-12-24 13:34:38,816 [main] INFO org.springframework.beans.factory.xml.XmlBeanDefinitionReader- Loading XML bean definitions from ServletContext resource [/WEB-INF/postInitContext.xml]
    2020-12-24 13:34:39,205 [main] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler- Initializing ExecutorService ‘taskScheduler’
    2020-12-24 13:34:39,205 [main] INFO org.springframework.context.support.PostProcessorRegistrationDelegate$BeanPostProcessorChecker- Bean ‘taskScheduler’ of type [org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler] is not eligible for getting processed by all BeanPostProcessors (for example: not eligible for auto-proxying)
    2020-12-24 13:34:39,933 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT() FROM open.DATABASECHANGELOGLOCK
    2020-12-24 13:34:40,147 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT(
    ) FROM open.DATABASECHANGELOGLOCK
    2020-12-24 13:34:40,148 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT LOCKED FROM open.DATABASECHANGELOGLOCK WHERE ID=1
    2020-12-24 13:34:40,162 [main] INFO liquibase.lockservice.StandardLockService- Successfully acquired change log lock
    2020-12-24 13:34:40,811 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT MD5SUM FROM open.DATABASECHANGELOG WHERE MD5SUM IS NOT NULL LIMIT 1
    2020-12-24 13:34:40,816 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT() FROM open.DATABASECHANGELOG
    2020-12-24 13:34:40,821 [main] INFO liquibase.changelog.StandardChangeLogHistoryService- Reading from open.DATABASECHANGELOG
    2020-12-24 13:34:40,821 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT * FROM open.DATABASECHANGELOG ORDER BY DATEEXECUTED ASC, ORDEREXECUTED ASC
    2020-12-24 13:34:40,896 [main] INFO liquibase.lockservice.StandardLockService- Successfully released change log lock
    2020-12-24 13:34:40,904 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT(
    ) FROM open.DATABASECHANGELOGLOCK
    2020-12-24 13:34:40,904 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT() FROM open.DATABASECHANGELOGLOCK
    2020-12-24 13:34:40,904 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT LOCKED FROM open.DATABASECHANGELOGLOCK WHERE ID=1
    2020-12-24 13:34:40,907 [main] INFO liquibase.lockservice.StandardLockService- Successfully acquired change log lock
    2020-12-24 13:34:41,962 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT MD5SUM FROM open.DATABASECHANGELOG WHERE MD5SUM IS NOT NULL LIMIT 1
    2020-12-24 13:34:41,962 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT COUNT(
    ) FROM open.DATABASECHANGELOG
    2020-12-24 13:34:41,964 [main] INFO liquibase.changelog.StandardChangeLogHistoryService- Reading from open.DATABASECHANGELOG
    2020-12-24 13:34:41,964 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT * FROM open.DATABASECHANGELOG ORDER BY DATEEXECUTED ASC, ORDEREXECUTED ASC
    2020-12-24 13:34:42,534 [main] INFO liquibase.executor.jvm.JdbcExecutor- select @@global.default_storage_engine
    2020-12-24 13:34:42,534 [main] INFO liquibase.changelog.ChangeSet- ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the storage engine::slakhani ran successfully in 1ms
    2020-12-24 13:34:42,535 [main] INFO liquibase.executor.jvm.JdbcExecutor- SELECT MAX(ORDEREXECUTED) FROM open.DATABASECHANGELOG
    2020-12-24 13:34:42,538 [main] INFO liquibase.executor.jvm.JdbcExecutor- UPDATE open.DATABASECHANGELOG SET DATEEXECUTED = NOW(), DEPLOYMENT_ID = ‘8788081987’, EXECTYPE = ‘RERAN’, MD5SUM = ‘8:d41d8cd98f00b204e9800998ecf8427e’, ORDEREXECUTED = 1951 WHERE ID = ‘Pre condition to check the storage engine’ AND AUTHOR = ‘slakhani’ AND FILENAME = ‘db/db-os-pre-conditions.xml’
    2020-12-24 13:34:42,543 [main] INFO liquibase.executor.jvm.JdbcExecutor- select @@global.lower_case_table_names
    2020-12-24 13:34:42,544 [main] INFO liquibase.changelog.ChangeSet- ChangeSet db/db-os-pre-conditions.xml::Pre condition to check the case sensitivity::nmarwaha ran successfully in 1ms
    2020-12-24 13:34:42,544 [main] INFO liquibase.executor.jvm.JdbcExecutor- UPDATE open.DATABASECHANGELOG SET DATEEXECUTED = NOW(), DEPLOYMENT_ID = ‘8788081987’, EXECTYPE = ‘RERAN’, MD5SUM = ‘8:d41d8cd98f00b204e9800998ecf8427e’, ORDEREXECUTED = 1952 WHERE ID = ‘Pre condition to check the case sensitivity’ AND AUTHOR = ‘nmarwaha’ AND FILENAME = ‘db/db-os-pre-conditions.xml’
    2020-12-24 13:34:42,566 [main] INFO liquibase.executor.jvm.JdbcExecutor- ALTER TABLE open.CATISSUE_USER DROP FOREIGN KEY FKB025CFC7FFA96920
    2020-12-24 13:34:42,592 [main] INFO liquibase.changelog.ChangeSet- Change set db/2.0/schema.xml::Drop foreign key from CRG column in CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: Can’t DROP ‘FKB025CFC7FFA96920’; check that column/key exists [Failed SQL: ALTER TABLE open.CATISSUE_USER DROP FOREIGN KEY FKB025CFC7FFA96920]
    2020-12-24 13:34:42,594 [main] INFO liquibase.executor.jvm.JdbcExecutor- ALTER TABLE open.CATISSUE_USER DROP COLUMN WUSTLKEY
    2020-12-24 13:34:42,594 [main] INFO liquibase.changelog.ChangeSet- Change set db/2.0/schema.xml::Drop WUSTLKEY column from CATISSUE_USER::nmarwaha failed, but failOnError was false. Error: Can’t DROP ‘WUSTLKEY’; check that column/key exists [Failed SQL: ALTER TABLE open.CATISSUE_USER DROP COLUMN WUSTLKEY]
    2020-12-24 13:34:42,600 [main] INFO liquibase.executor.jvm.JdbcExecutor- ALTER TABLE open.CATISSUE_USER DROP KEY CSM_USER_ID_UNIQUE_KEY
    2020-12-24 13:34:42,601 [main] INFO liquibase.changelog.ChangeSet- Change set db/2.0/schema.xml::Drop UK on csm_user_id from catissue user table::vlonushte failed, but failOnError was false. Error: Can’t DROP ‘CSM_USER_ID_UNIQUE_KEY’; check that column/key exists [Failed SQL: ALTER TABLE open.CATISSUE_USER DROP KEY CSM_USER_ID_UNIQUE_KEY]
    2020-12-24 13:34:42,645 [main] INFO liquibase.lockservice.StandardLockService- Successfully released change log lock
    2020-12-24 13:34:42,780 [main] INFO org.hibernate.Version- HHH000412: Hibernate Core {5.3.6.Final}
    2020-12-24 13:34:42,781 [main] INFO org.hibernate.cfg.Environment- HHH000206: hibernate.properties not found
    2020-12-24 13:34:43,585 [main] INFO org.hibernate.annotations.common.Version- HCANN000001: Hibernate Commons Annotations {5.0.4.Final}
    2020-12-24 13:34:43,692 [main] INFO org.hibernate.dialect.Dialect- HHH000400: Using dialect: org.hibernate.dialect.MySQLDialect
    2020-12-24 13:34:43,716 [main] INFO org.hibernate.engine.jdbc.env.internal.LobCreatorBuilderImpl- HHH000423: Disabling contextual LOB creation as JDBC driver reported JDBC version [3] less than 4
    2020-12-24 13:34:43,724 [main] INFO org.hibernate.envers.boot.internal.EnversServiceImpl- Envers integration enabled? : true
    2020-12-24 13:34:45,493 [main] INFO org.hibernate.hql.internal.QueryTranslatorFactoryInitiator- HHH000397: Using ASTQueryTranslatorFactory
    2020-12-24 13:34:45,763 [main] INFO org.springframework.orm.hibernate5.HibernateTransactionManager- Using DataSource [org.apache.tomcat.dbcp.dbcp2.BasicDataSource@2ed7d757] of Hibernate SessionFactory for HibernateTransactionManager
    2020-12-24 13:34:46,105 [main] INFO com.krishagni.catissueplus.core.common.service.impl.ConfigurationServiceImpl- App is using the locale: zh_CN
    2020-12-24 13:34:46,356 [main] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor- Initializing ExecutorService ‘taskExecutor’
    2020-12-24 13:34:46,512 [main] INFO com.krishagni.catissueplus.core.common.service.impl.EmailServiceImpl- IMAP service is not configured. Will not poll for inbound emails.
    2020-12-24 13:34:46,718 [main] WARN org.springframework.web.context.support.XmlWebApplicationContext- Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘visitService’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘specimenSvc’ while setting bean property ‘specimenSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘specimenFactory’ while setting bean property ‘specimenFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘storageContainerSvc’ while setting bean property ‘containerSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘storageContainerSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘exportSvc’ while setting bean property ‘exportSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    2020-12-24 13:34:46,718 [main] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskExecutor- Shutting down ExecutorService ‘taskExecutor’
    2020-12-24 13:34:46,719 [main] INFO org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler- Shutting down ExecutorService ‘taskScheduler’
    2020-12-24 13:34:46,720 [main] ERROR org.springframework.web.context.ContextLoader- Context initialization failed
    org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘visitService’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘specimenSvc’ while setting bean property ‘specimenSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘specimenFactory’ while setting bean property ‘specimenFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘storageContainerSvc’ while setting bean property ‘containerSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘storageContainerSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘exportSvc’ while setting bean property ‘exportSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1534)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
    at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
    at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
    at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4716)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5177)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:717)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:690)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:706)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:978)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1848)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
    at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:112)
    at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:773)
    at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:427)
    at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1576)
    at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:309)
    at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
    at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
    at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
    at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:936)
    at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:843)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
    at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
    at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
    at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.StandardService.startInternal(StandardService.java:421)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
    at org.apache.catalina.startup.Catalina.start(Catalina.java:772)
    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.catalina.startup.Bootstrap.start(Bootstrap.java:342)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:473)
    Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘specimenFactory’ while setting bean property ‘specimenFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘storageContainerSvc’ while setting bean property ‘containerSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘storageContainerSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘exportSvc’ while setting bean property ‘exportSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1534)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    … 56 more
    Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘specimenFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘storageContainerSvc’ while setting bean property ‘containerSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘storageContainerSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘exportSvc’ while setting bean property ‘exportSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1534)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    … 66 more
    Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘storageContainerSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘exportSvc’ while setting bean property ‘exportSvc’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1534)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    … 76 more
    Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘exportSvc’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Cannot resolve reference to bean ‘objectSchemaFactory’ while setting bean property ‘schemaFactory’; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:359)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:108)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1534)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    … 86 more
    Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name ‘objectSchemaFactory’ defined in ServletContext resource [/WEB-INF/applicationContext.xml]: Error setting property values; nested exception is org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1571)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1281)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:551)
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:481)
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:312)
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:308)
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:351)
    … 96 more
    Caused by: org.springframework.beans.PropertyBatchUpdateException; nested PropertyAccessExceptions (1) are:
    PropertyAccessException 1: org.springframework.beans.MethodInvocationException: Property ‘schemaResources’ threw exception; nested exception is com.thoughtworks.xstream.io.StreamException:
    at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:121)
    at org.springframework.beans.AbstractPropertyAccessor.setPropertyValues(AbstractPropertyAccessor.java:75)
    org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1567)

    #8

    Hi Jack,

    Your contxt.xml file configuration is failed.

    Please check your context.xml file which is present in the tomcat/conf directory.

    Give the absolute path to the log4j file. (Or you can leave that blank. Because that file is optional)

    Thanks,
    Kaustubh

    #9

    context.xml

    <?xml version="1.0" encoding="UTF-8"?>
    <!-- Default set of monitored resources. If one of these changes, the    -->
    <!-- web application will be reloaded.                                   -->
    <WatchedResource>WEB-INF/web.xml</WatchedResource>
    <WatchedResource>WEB-INF/tomcat-web.xml</WatchedResource>
    <WatchedResource>${catalina.base}/conf/web.xml</WatchedResource>
    
    
    <!-- Uncomment this to disable session persistence across Tomcat restarts -->
    <!--
      
      driverClassName="com.mysql.jdbc.Driver"
      maxActive="100" 
      maxWait="10000"
    
    
      driverClassName="com.mysql.cj.jdbc.Driver"
      maxTotal="100" 
      maxWaitMillis="10000"
    <Manager pathname="" />
    -->
    
    <Resource 
      name="jdbc/open"
      auth="Container" 
      type="javax.sql.DataSource"
      maxTotal="100" 
      maxIdle="30" 
      maxWaitMillis="10000"
      username="root" 
      password="111111" 
      driverClassName="com.mysql.jdbc.Driver"
      url="jdbc:mysql://localhost:3306/open?serverTimezone=GMT%2B8"/>
    
    <Environment
      name="config/open"
      value="D:/apache-tomcat-9.0.39/conf/openspecimen.properties"
      type="java.lang.String"/>
    
    #10

    openspecimen.properties
    #######################################################################

    Windows users, please note the directories should be separated using

    forward slashes as in below example:

    D:/openspecimen/tomcat

    D:/opnespecimen/data

    D:/openspecimen/plugins

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

    This field is useful for deploying multiple OpenSpecimen

    instances on the one Tomcat server. E.g. “os-test” and

    “os-prod”.

    app.name=open

    Name of datasource configured in the Tomcat’s context.xml.

    Usually, it is “jdbc/openspecimen”.

    datasource.jndi=jdbc/open

    Value can be mysql or oracle

    database.type=mysql

    Value can be fresh or upgrade.

    This should be “upgrade” if the database was initially upgraded from caTissue.

    Note: This should be fresh for all other cases.

    datasource.type=fresh

    Absolute path where Tomcat is installed

    tomcat.dir=D:/apache-tomcat-9.0.39

    Absolute path to OpenSpecimen data directory.

    Best practice: Create a folder in parallel to ‘tomcat.dir’ with

    the name “openspecimen/data”

    app.data_dir=D:/data

    Absolute path to OpenSpecimen data directory.

    Best practice: Create a folder in parallel to ‘tomcat.dir’ with

    the name “openspecimen/plugins”

    plugin.dir=D:/plugins

    Optional. Absolute path of the customised logging configuration file.

    The configuration file should follow log4j configuration rules.

    app.log_conf=

    #11

    Hi Jack,

    Please recheck your context.xml and configure the context.xml file again.

    Thanks,
    Kaustubh

    #12

    I didn’t find the error of context.xml .
    Can u please ?
    I follow the step but it doesn’t run correctly.