Hi Arek, 1. I have checked to confirm that data does exist. However, the data field for the filter that I used is blank. This is a non-issue.
2. Here is the tail of the stdouterr.20130211.log: 2013-02-11 11:53:35,161 INFO [1329745730@qtp-1188579032-5:Log.java:164]: Total query time is 63 ms Feb 11, 2013 11:53:35 AM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException SEVERE: The RuntimeException could not be mapped to a response, re-throwing to the HTTP container Throwable occurred: java.lang.NumberFormatException: For input string: "error=true" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:60) at java.lang.Integer.parseInt(Integer.java:461) at java.lang.Integer.parseInt(Integer.java:511) at org.biomart.api.rest.PortalResource.getQueryCount(PortalResource.java:297) at sun.reflect.GeneratedMethodAccessor57.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37) at java.lang.reflect.Method.invoke(Method.java:600) at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168) at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70) at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136) at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:86) at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136) at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357) at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239) at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229) at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420) at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497) at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:855) at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:828) at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:789) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at org.biomart.web.PortalFilter.doFilter(PortalFilter.java:31) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78) at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:134) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at org.biomart.web.LocationsFilter.doFilter(LocationsFilter.java:29) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at org.biomart.web.FlashMessageFilter.doFilter(FlashMessageFilter.java:35) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at org.biomart.web.AuthFilter.doFilter(AuthFilter.java:47) at com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129) at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59) at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:122) at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:110) at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157) at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388) at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216) at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182) at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765) at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418) at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114) at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152) at org.mortbay.jetty.Server.handle(Server.java:326) at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542) at org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924) at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549) at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212) at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404) at org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409) at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582) com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'g1biomart.G1_Biomart' doesn't exist at sun.reflect.GeneratedConstructorAccessor15.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:39) at java.lang.reflect.Constructor.newInstance(Constructor.java:516) at com.mysql.jdbc.Util.handleNewInstance(Util.java:407) at com.mysql.jdbc.Util.getInstance(Util.java:382) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1052) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3603) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3535) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1989) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2150) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2119) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2281) at org.biomart.queryEngine.SubQuery.executeDatabaseQuery(SubQuery.java:761) at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:731) at org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:171) at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73) at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:315) at java.util.concurrent.FutureTask.run(FutureTask.java:150) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:453) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:315) at java.util.concurrent.FutureTask.run(FutureTask.java:150) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:736) 2013-02-11 11:53:35,178 INFO [1390236381@qtp-1188579032-9:Log.java:164]: Total query time is 23 ms Thanks, Iry From: Arek Kasprzyk <[email protected]<mailto:[email protected]>> Date: Monday, February 11, 2013 12:45 PM To: Iry Witham <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [BioMart Users] 'Error has occurred' Hi Iry, 1. "No results found" would indicate that there is no data in your database that would satisfy your query. I suggest you use SQL to verify this (Ideally, SQL compiled by the BioMart application from the logs). 2. "Error has occurred". Please check the log and see what exactly the error is. We need more information about the problem a On Mon, Feb 11, 2013 at 4:54 PM, Iry Witham <[email protected]<mailto:[email protected]>> wrote: Hi Biomart Team, I have setup a biomart with my own specific data and when I submit a query I get one of two results. I get the 'error has occurred' message or 'no results found' The following is the query that results in the error: <!DOCTYPE Query><Query client="biomartclient" processor="TSV" limit="-1" header="1"><Dataset name="g1biomart" config="G1_Biomart_config"><Filter name="G1_Biomart__G1_101_key_101" value="Pfkfb2"/><Attribute name="G1_Biomart__Consequence_101_101"/></Dataset></Query> Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ Users mailing list [email protected]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). 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