com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3 ; bad SQL grammar []; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3] with root cause com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3

GitHub | jjgao | 6 months ago
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    SQL error in the new implementation from sprint1

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    com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3 ; bad SQL grammar []; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3] with root cause com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3
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    com.dotmarketing.exception.DotDataException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '"float1" = 0.0 where structure_inode = '4c441ada-944a-43af-a653-9bb4f3f0cb2b'' at line 1
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    Error in SQL syntax while persisting indexed content

    GitHub | 3 years ago | lukas-vlcek
    javax.ejb.EJBException: java.lang.RuntimeException: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'clob, sys_content_type varchar(100) not null, updated timestamp )' at line 1
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    Synchronize logic that creates DB table

    GitHub | 3 years ago | lukas-vlcek
    javax.ejb.EJBException: java.lang.RuntimeException: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'data_jbossorg_project_info' already exists
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    fix /nlgroupspassword

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    com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual tha t corresponds to your MariaDB server version for the right syntax to use near 'from faction set password = 'Chubby' where group_name = 'Chubby'' at line 1

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Root Cause Analysis

  1. com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException

    You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3 ; bad SQL grammar []; nested exception is com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3] with root cause com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '."CENTER" as "sequencingCenter", "mutation"."MUTATION_STATUS" as "mutati' at line 3

    at sun.reflect.NativeConstructorAccessorImpl.newInstance0()
  2. Java RT
    Constructor.newInstance
    1. sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    2. sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    3. sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    4. java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    4 frames
  3. MySQL jdbc
    PreparedStatement.execute
    1. com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
    2. com.mysql.jdbc.Util.getInstance(Util.java:386)
    3. com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1052)
    4. com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3597)
    5. com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3529)
    6. com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1990)
    7. com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2151)
    8. com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2625)
    9. com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119)
    10. com.mysql.jdbc.PreparedStatement.execute(PreparedStatement.java:1362)
    10 frames
  4. org.apache.tomcat
    DelegatingPreparedStatement.execute
    1. org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
    2. org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:172)
    2 frames
  5. MyBatis
    DefaultSqlSession.selectList
    1. org.apache.ibatis.executor.statement.PreparedStatementHandler.query(PreparedStatementHandler.java:59)
    2. org.apache.ibatis.executor.statement.RoutingStatementHandler.query(RoutingStatementHandler.java:73)
    3. org.apache.ibatis.executor.SimpleExecutor.doQuery(SimpleExecutor.java:60)
    4. org.apache.ibatis.executor.BaseExecutor.queryFromDatabase(BaseExecutor.java:267)
    5. org.apache.ibatis.executor.BaseExecutor.query(BaseExecutor.java:137)
    6. org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:90)
    7. org.apache.ibatis.executor.CachingExecutor.query(CachingExecutor.java:77)
    8. org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:108)
    9. org.apache.ibatis.session.defaults.DefaultSqlSession.selectList(DefaultSqlSession.java:102)
    9 frames
  6. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:606)
    4 frames
  7. MyBatis-Spring
    SqlSessionTemplate$SqlSessionInterceptor.invoke
    1. org.mybatis.spring.SqlSessionTemplate$SqlSessionInterceptor.invoke(SqlSessionTemplate.java:358)
    1 frame
  8. com.sun.proxy
    $Proxy206.selectList
    1. com.sun.proxy.$Proxy206.selectList(Unknown Source)
    1 frame
  9. MyBatis-Spring
    SqlSessionTemplate.selectList
    1. org.mybatis.spring.SqlSessionTemplate.selectList(SqlSessionTemplate.java:198)
    1 frame
  10. MyBatis
    MapperProxy.invoke
    1. org.apache.ibatis.binding.MapperMethod.executeForMany(MapperMethod.java:119)
    2. org.apache.ibatis.binding.MapperMethod.execute(MapperMethod.java:63)
    3. org.apache.ibatis.binding.MapperProxy.invoke(MapperProxy.java:52)
    3 frames
  11. com.sun.proxy
    $Proxy213.getMutations
    1. com.sun.proxy.$Proxy213.getMutations(Unknown Source)
    1 frame
  12. org.cbioportal.persistence
    MutationMyBatisRepository.getMutations
    1. org.cbioportal.persistence.mybatis.MutationMyBatisRepository.getMutations(MutationMyBatisRepository.java:19)
    1 frame
  13. org.cbioportal.service
    MutationServiceImpl.getMutations
    1. org.cbioportal.service.impl.MutationServiceImpl.getMutations(MutationServiceImpl.java:20)
    1 frame
  14. org.mskcc.cbio
    ApiService$$FastClassBySpringCGLIB$$e4cf2f40.invoke
    1. org.mskcc.cbio.portal.service.ApiService.getGeneticProfileData(ApiService.java:363)
    2. org.mskcc.cbio.portal.service.ApiService$$FastClassBySpringCGLIB$$e4cf2f40.invoke(<generated>)
    2 frames
  15. Spring Core
    MethodProxy.invoke
    1. org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
    1 frame
  16. Spring AOP
    ReflectiveMethodInvocation.proceed
    1. org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:708)
    2. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    2 frames
  17. Spring Tx
    TransactionInterceptor.invoke
    1. org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:98)
    2. org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:262)
    3. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:95)
    3 frames
  18. Spring AOP
    CglibAopProxy$DynamicAdvisedInterceptor.intercept
    1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    2. org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:644)
    2 frames
  19. org.mskcc.cbio
    ApiController.getGeneticProfileData
    1. org.mskcc.cbio.portal.service.ApiService$$EnhancerBySpringCGLIB$$426659a7.getGeneticProfileData(<generated>)
    2. org.mskcc.cbio.portal.web.api.ApiController.getGeneticProfileData(ApiController.java:314)
    2 frames
  20. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    4. java.lang.reflect.Method.invoke(Method.java:606)
    4 frames
  21. Spring
    InvocableHandlerMethod.invokeForRequest
    1. org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
    2. org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
    2 frames
  22. Spring MVC
    FrameworkServlet.doPost
    1. org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
    2. org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:749)
    3. org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:689)
    4. org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:83)
    5. org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:938)
    6. org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:870)
    7. org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:961)
    8. org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:863)
    8 frames
  23. JavaServlet
    HttpServlet.service
    1. javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
    1 frame
  24. Spring MVC
    FrameworkServlet.service
    1. org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:837)
    1 frame
  25. JavaServlet
    HttpServlet.service
    1. javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
    1 frame
  26. Glassfish Core
    ApplicationFilterChain.doFilter
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    2 frames
  27. org.mskcc.cbio
    XssFilter.doFilter
    1. org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
    1 frame
  28. Glassfish Core
    ApplicationFilterChain.doFilter
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    2 frames
  29. Spring Security
    FilterChainProxy.doFilter
    1. org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
    2. org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
    2 frames
  30. Spring
    DelegatingFilterProxy.doFilter
    1. org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
    2. org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
    2 frames
  31. Glassfish Core
    CoyoteAdapter.service
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    3. org.apache.catalina.filters.CorsFilter.handleSimpleCORS(CorsFilter.java:302)
    4. org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:170)
    5. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
    6. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    7. org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
    8. org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
    9. org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
    10. org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
    11. org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
    12. org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
    13. org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
    14. org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
    14 frames
  32. org.apache.coyote
    AjpProcessor.process
    1. org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:200)
    1 frame
  33. Grizzly HTTP
    JIoEndpoint$SocketProcessor.run
    1. org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
    2. org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
    2 frames
  34. Java RT
    Thread.run
    1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    3. java.lang.Thread.run(Thread.java:745)
    3 frames