Hi Syed,
Thank you very much for picking up on that. I have reloaded my database
and rerun martconfigurator and everything is working as expected.
Thanks,
Iry
On 2/12/13 4:46 AM, "Syed Haider" <[email protected]> wrote:
>Iry,
>
>a piece from your error log:
>
><snip>
>com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table
>'g1biomart.G1_Biomart' doesn't exist
></snip>
>
>indicates that the offending table is a part of query but
>unfortunately doesnt exist in your database. Please check!
>
>Syed
>
>
>
>On 11 February 2013 17:59, Iry Witham <[email protected]> wrote:
>> 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(DelegatingMethodAccessorI
>>mpl.java:37)
>> at java.lang.reflect.Method.invoke(Method.java:600)
>> at
>>
>>com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDi
>>spatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchPro
>>vider.java:168)
>> at
>>
>>com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispat
>>cher.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(RightHandPa
>>thRule.java:136)
>> at
>>
>>com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceCla
>>ssRule.java:86)
>> at
>>
>>com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPa
>>thRule.java:136)
>> at
>>
>>com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootR
>>esourceClassesRule.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(W
>>ebApplicationImpl.java:1239)
>> at
>>
>>com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(W
>>ebApplicationImpl.java:1229)
>> at
>>
>>com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.ja
>>va:420)
>> at
>>
>>com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletCont
>>ainer.java:497)
>> at
>>
>>com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletCon
>>tainer.java:855)
>> at
>>
>>com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletCon
>>tainer.java:828)
>> at
>>
>>com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletCon
>>tainer.java:789)
>> at
>>
>>com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java
>>:129)
>> at
>>
>>com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvoc
>>ation.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(FilterChainInvoc
>>ation.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(FilterChainInvoc
>>ation.java:59)
>> at
>>
>>com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java
>>:134)
>> at
>>
>>com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvoc
>>ation.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(FilterChainInvoc
>>ation.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(FilterChainInvoc
>>ation.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(FilterChainInvoc
>>ation.java:59)
>> at
>>
>>com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPip
>>eline.java:122)
>> at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:110)
>> at
>>
>>org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHand
>>ler.java:1157)
>> at
>>org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
>> at
>>
>>org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:21
>>6)
>> 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$RequestHandler.headerComplete(HttpConnec
>>tion.java:924)
>> at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
>> at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
>> at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
>> at
>>
>>org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:4
>>09)
>> at
>>
>>org.mortbay.thread.QueuedThreadPool$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(DelegatingConst
>>ructorAccessorImpl.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:2
>>119)
>> 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(QueryRunnerTh
>>read.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.jav
>>a: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]>
>> Date: Monday, February 11, 2013 12:45 PM
>> To: Iry Witham <[email protected]>
>> Cc: "[email protected]" <[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]> 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]
>>> 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). 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]
>> 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). If you believe you received this email
by mistake, please notify the sender by return email as soon as possible.
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