#2 demo webapp bug by substructure search

[toni007]

1) from http://localhost:8080/struct_search/ I select "Search with Jchempaint applet"
2) I enter a pentane,
select substructure search,
with top n result = 20,
Strict stereo match for substructure = N
Exact match ?=N

submit

and I get the following errors:

ORA-06553: PLS-306: numéro ou types d'arguments erronés dans appel à 'SEARCH'

at oracle.jdbc.driver.SQLStateMapping.newSQLException \( SQLStateMapping.java:70 \)
at oracle.jdbc.driver.DatabaseError.newSQLException \( DatabaseError.java:110 \)
at oracle.jdbc.driver.DatabaseError.throwSqlException \( DatabaseError.java:171 \)
at oracle.jdbc.driver.T4CTTIoer.processError \( T4CTTIoer.java:455 \)
at oracle.jdbc.driver.T4CTTIoer.processError \( T4CTTIoer.java:413 \)
at oracle.jdbc.driver.T4C8Oall.receive \( T4C8Oall.java:1030 \)
at oracle.jdbc.driver.T4CPreparedStatement.doOall8 \( T4CPreparedStatement.java:194 \)
at oracle.jdbc.driver.T4CPreparedStatement.executeForDescribe \( T4CPreparedStatement.java:785 \)
at oracle.jdbc.driver.T4CPreparedStatement.executeMaybeDescribe \( T4CPreparedStatement.java:860 \)
at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout \( OracleStatement.java:1186 \)
at oracle.jdbc.driver.OraclePreparedStatement.executeInternal \( OraclePreparedStatement.java:3381 \)
at oracle.jdbc.driver.OraclePreparedStatement.executeQuery \( OraclePreparedStatement.java:3425 \)
at oracle.jdbc.driver.OraclePreparedStatementWrapper.executeQuery \( OraclePreparedStatementWrapper.java:1202 \)
at uk.ac.ebi.orchem.shared.DatabaseAccess.substructureSearch \( null:-1 \)
at uk.ac.ebi.orchem.web.SearchAction.execute \( null:-1 \)
at sun.reflect.NativeMethodAccessorImpl.invoke0 \( null:-2 \)
at sun.reflect.NativeMethodAccessorImpl.invoke \( null:-1 \)
at sun.reflect.DelegatingMethodAccessorImpl.invoke \( null:-1 \)
at java.lang.reflect.Method.invoke \( null:-1 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction \( DefaultActionInvocation.java:404 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly \( DefaultActionInvocation.java:267 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:229 \)
at com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doIntercept \( DefaultWorkflowInterceptor.java:221 \)
at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept \( MethodFilterInterceptor.java:86 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept \( ValidationInterceptor.java:150 \)
at org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept \( AnnotationValidationInterceptor.java:48 \)
at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept \( MethodFilterInterceptor.java:86 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept \( ConversionErrorInterceptor.java:123 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept \( ParametersInterceptor.java:186 \)
at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept \( MethodFilterInterceptor.java:86 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept \( StaticParametersInterceptor.java:105 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.interceptor.CheckboxInterceptor.intercept \( CheckboxInterceptor.java:83 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.interceptor.FileUploadInterceptor.intercept \( FileUploadInterceptor.java:207 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept \( ModelDrivenInterceptor.java:74 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ScopedModelDrivenInterceptor.intercept \( ScopedModelDrivenInterceptor.java:127 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.interceptor.ProfilingActivationInterceptor.intercept \( ProfilingActivationInterceptor.java:107 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept \( DebuggingInterceptor.java:206 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept \( ChainingInterceptor.java:115 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept \( I18nInterceptor.java:143 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept \( PrepareInterceptor.java:121 \)
at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept \( MethodFilterInterceptor.java:86 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept \( ServletConfigInterceptor.java:170 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept \( AliasInterceptor.java:123 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercept \( ExceptionMappingInterceptor.java:176 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:224 \)
at com.opensymphony.xwork2.DefaultActionInvocation$2.doProfiling \( DefaultActionInvocation.java:223 \)
at com.opensymphony.xwork2.util.profiling.UtilTimerStack.profile \( UtilTimerStack.java:455 \)
at com.opensymphony.xwork2.DefaultActionInvocation.invoke \( DefaultActionInvocation.java:221 \)
at org.apache.struts2.impl.StrutsActionProxy.execute \( StrutsActionProxy.java:50 \)
at org.apache.struts2.dispatcher.Dispatcher.serviceAction \( Dispatcher.java:504 \)
at org.apache.struts2.dispatcher.FilterDispatcher.doFilter \( FilterDispatcher.java:419 \)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter \( ApplicationFilterChain.java:235 \)
at org.apache.catalina.core.ApplicationFilterChain.doFilter \( ApplicationFilterChain.java:206 \)
at org.apache.catalina.core.StandardWrapperValve.invoke \( StandardWrapperValve.java:233 \)
at org.apache.catalina.core.StandardContextValve.invoke \( StandardContextValve.java:175 \)
at org.apache.catalina.core.StandardHostValve.invoke \( StandardHostValve.java:128 \)
at org.apache.catalina.valves.ErrorReportValve.invoke \( ErrorReportValve.java:102 \)
at org.apache.catalina.core.StandardEngineValve.invoke \( StandardEngineValve.java:109 \)
at org.apache.catalina.connector.CoyoteAdapter.service \( CoyoteAdapter.java:263 \)
at org.apache.coyote.http11.Http11Processor.process \( Http11Processor.java:844 \)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process \( Http11Protocol.java:584 \)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run \( JIoEndpoint.java:447 \)
at java.lang.Thread.run \( null:-1 \)

If I do the same search with sql no problem

[toni007]

[Mark Rijnbeek]

The error comes from the database. I think there is a mismatch between the web app version and the database orchem version. Does the database package orchem_subsearch, function search have the exact_yn argument?

If not, a quick workaround would be to rewrite method substructureSearch in class DatabaseAccess so that exact_yn=>? is not being used.

Best would be to sync the database version with the web app version though.

[Nobody/Anonymous]

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