Hi BioMart Users,
I am trying to create a BioMart instance and have run into an error that I
would appreciate help diagnosing.
I set up the mart with MartBuilder 0.7 and am trying to run the configuration
and website with BioMart 0.8. Just as a side note, I am using MartBuilder 0.7
instead of 0.8 because I am needing to manage the relations between tables and
other features that I wasn't able to do with version 0.8. I am not sure what is
going wrong exactly but, I am getting an error when trying to query attributes
from a dimension table through the web interface. I have attached the error log
for this. Also when I try to use mart editor 0.7 it gives the error that the
data-sets do not exist. Also it appears as if both MartConfigurator and
MartEditor are aware of the relations all of the relationships.
I have everything setup on my local machine. I am using mySQL and connecting
with a user that has full privileges to the databases on the mySQL server.
Please let me know if there is anything I am missing or if you need any more
information. Help would be greatly appreciated.
Regards,
Adam Wright
Bioinformatics Software Developer
647-260-6479
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Toll-free: 1-866-678-6427
www.oicr.on.ca
This message and any attachments may contain confidential and/or privileged
information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in error,
please contact the sender and delete all copies. Opinions, conclusions or other
information contained in this message may not be that of the organization.
________________________________
From: Joachim Baran
Sent: 02 August 2012 16:34
To: Adam Wright
Subject: Exception.
Joachim Baran, PhD
Database/Application Programmer, Informatics and Bio-computing
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3
Tel: 647-258-4319
Toll-free: 1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca/>
This message and any attachments may contain confidential and/or privileged
information for the sole use of the intended recipient. Any review or
distribution by anyone other than the person for whom it was originally
intended is strictly prohibited. If you have received this message in error,
please contact the sender and delete all copies. Opinions, conclusions or other
information contained in this message may not be that of the organization.
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,476 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Incoming XML query: <!DOCTYPE
Query><Query client="biomartclient" processor="TSV" limit="-1"
header="1"><Dataset name="donor_mart" config="donor_config"><Attribute
name="donor__donor__main__donor_name_1016_key"/><Attribute
name="donor__donor__main__description_1029"/><Attribute
name="donor__library_seq__dm__abbr_1026"/></Dataset></Query>
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,480 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Query =
{"dataset":"donor_mart","attributes":["donor__donor__main__donor_name_1016_key","donor__donor__main__description_1029","donor__library_seq__dm__abbr_1026"],"filters":[]}
[Thread-17] INFO martconfigurator - java.util.NoSuchElementException
[Thread-17] INFO martconfigurator - at
java.util.TreeMap$PrivateEntryIterator.nextEntry(TreeMap.java:1098)
[Thread-17] INFO martconfigurator - at
java.util.TreeMap$KeyIterator.next(TreeMap.java:1154)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.searchMaterilizedSchema(QueryCompiler.java:108)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.searchSchema(QueryCompiler.java:852)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.generateQuery(QueryCompiler.java:840)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.getQuery(SubQuery.java:623)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.executeDatabaseQuery(SubQuery.java:743)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:731)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:171)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask.run(FutureTask.java:138)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask.run(FutureTask.java:138)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
[Thread-17] INFO martconfigurator - at java.lang.Thread.run(Thread.java:680)
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,482 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Total query time is 1 ms
[Thread-17] INFO martconfigurator - Aug 2, 2012 4:31:13 PM
com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException
[Thread-17] INFO martconfigurator - SEVERE: The RuntimeException could not be
mapped to a response, re-throwing to the HTTP container
[Thread-17] INFO martconfigurator - java.lang.NumberFormatException: For input
string: "error=true"
[Thread-17] INFO martconfigurator - at
java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
[Thread-17] INFO martconfigurator - at
java.lang.Integer.parseInt(Integer.java:449)
[Thread-17] INFO martconfigurator - at
java.lang.Integer.parseInt(Integer.java:499)
[Thread-17] INFO martconfigurator - at
org.biomart.api.rest.PortalResource.getQueryCount(PortalResource.java:297)
[Thread-17] INFO martconfigurator - at
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[Thread-17] INFO martconfigurator - at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
[Thread-17] INFO martconfigurator - at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
[Thread-17] INFO martconfigurator - at
java.lang.reflect.Method.invoke(Method.java:597)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:168)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:70)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:279)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:86)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:136)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:74)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1357)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1289)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1239)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1229)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:420)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:497)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:855)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:828)
[Thread-17] INFO martconfigurator - at
com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:789)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
org.biomart.web.PortalFilter.doFilter(PortalFilter.java:31)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:78)
[Thread-17] INFO martconfigurator - at
org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:131)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:134)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
org.biomart.web.LocationsFilter.doFilter(LocationsFilter.java:29)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
org.biomart.web.FlashMessageFilter.doFilter(FlashMessageFilter.java:35)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
org.biomart.web.AuthFilter.doFilter(AuthFilter.java:47)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterDefinition.doFilter(FilterDefinition.java:129)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:59)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:122)
[Thread-17] INFO martconfigurator - at
com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:110)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1157)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:388)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:765)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:418)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.Server.handle(Server.java:326)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.HttpConnection$RequestHandler.headerComplete(HttpConnection.java:924)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:549)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:212)
[Thread-17] INFO martconfigurator - at
org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
[Thread-17] INFO martconfigurator - at
org.mortbay.io.nio.SelectChannelEndPoint.run(SelectChannelEndPoint.java:409)
[Thread-17] INFO martconfigurator - at
org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,500 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Incoming XML query: <!DOCTYPE
Query><Query client="biomartclient" processor="TSVX" limit="1000"
header="1"><Dataset name="donor_mart" config="donor_config"><Attribute
name="donor__donor__main__donor_name_1016_key"/><Attribute
name="donor__donor__main__description_1029"/><Attribute
name="donor__library_seq__dm__abbr_1026"/></Dataset></Query>
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,503 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Query =
{"dataset":"donor_mart","attributes":["donor__donor__main__donor_name_1016_key","donor__donor__main__description_1029","donor__library_seq__dm__abbr_1026"],"filters":[]}
[Thread-17] INFO martconfigurator - java.util.NoSuchElementException
[Thread-17] INFO martconfigurator - at
java.util.TreeMap$PrivateEntryIterator.nextEntry(TreeMap.java:1098)
[Thread-17] INFO martconfigurator - at
java.util.TreeMap$KeyIterator.next(TreeMap.java:1154)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.searchMaterilizedSchema(QueryCompiler.java:108)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.searchSchema(QueryCompiler.java:852)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.queryCompiler.QueryCompiler.generateQuery(QueryCompiler.java:840)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.getQuery(SubQuery.java:623)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.executeDatabaseQuery(SubQuery.java:743)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:731)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:171)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73)
[Thread-17] INFO martconfigurator - at
org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask.run(FutureTask.java:138)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.FutureTask.run(FutureTask.java:138)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
[Thread-17] INFO martconfigurator - at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
[Thread-17] INFO martconfigurator - at java.lang.Thread.run(Thread.java:680)
[Thread-17] INFO martconfigurator - 2012-08-02 16:31:13,506 INFO
[2044693401@qtp-1554207397-7:Log.java:164]: Total query time is 2 m_______________________________________________
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