I upgrade BASE, but have anothe error message:
Error: [EXPORT FAILED: Experiment - Experiment[id=27; name=Agilent IFNalpha
time course] do not have a rawbiosay specified].
stack trace:
java.lang.Throwable
at uk.ac.ebi.nugo.plugins.Tab2MageExporter.run(Tab2MageExporter.java:331)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
at java.lang.Thread.run(Thread.java:636)
Regards,
Irina
> Date: Fri, 10 Jun 2011 08:45:27 +0200
> From: nick...@thep.lu.se
> To: basedb-users@lists.sourceforge.net
> Subject: Re: [base] Tab2Mage exporter plugin
>
> This was fixed in BASE 2.16.1 (http://base.thep.lu.se/ticket/1553). I
> suggest that you upgrade.
>
>
> On the other hand... the Tab2Mage plug-in may require that you specify
> labeled extracts, extracts, samples and biosources or it may not work.
>
> /Nicklas
>
> On 2011-06-10 08:17, Irina 264 wrote:
> > Dear team,
> >
> > I am working on ‘Tab2Mage exporter’ plugin. I created Agilent experiment
> > and Validate it with following message:
> >
> >
> > java.lang.NullPointerException on page
> > /base2/common/overview/index.jsp
> >
> > *Version*
> >
> >
> >
> > BASE 2.16.0 (build #5472; schema #88)
> >
> > *Web server*
> >
> >
> >
> > Apache Tomcat/6.0.29
> >
> > *Database Server*
> >
> >
> >
> > MySQL 5.0.77
> >
> > *Database Dialect*
> >
> >
> >
> > org.hibernate.dialect.MySQLInnoDBDialect
> >
> > *JDBC Driver*
> >
> >
> >
> > com.mysql.jdbc.Driver (version 5.1)
> >
> > *Java runtime*
> >
> >
> >
> > OpenJDK Runtime Environment (1.6.0_17-b17), Sun Microsystems Inc.
> > <http://java.sun.com/>
> >
> > *Operating system*
> >
> >
> >
> > Linux amd64 2.6.18-194.17.4.el5
> >
> > *Memory*
> >
> >
> >
> > Total: 924.8 MB
> > Free: 607.6 MB
> > Max: 1.8 GB
> >
> > *Browser*
> >
> >
> >
> > Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0; .NET CLR
> > 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
> > 3.5.30729; InfoPath.2; .NET4.0C)
> >
> > *Error message*
> >
> >
> >
> > *Stack trace*
> >
> >
> >
> >
> > Version BASE 2.16.0 (build #5472; schema #88)
> > Web server Apache Tomcat/6.0.29
> > Database Server MySQL 5.0.77
> > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect
> > JDBC Driver com.mysql.jdbc.Driver (version 5.1)
> > Java runtime OpenJDK Runtime Environment (1.6.0_17-b17), Sun
> > Microsystems Inc. <http://java.sun.com/>
> > Operating system Linux amd64 2.6.18-194.17.4.el5
> > Memory Total: 924.8 MB
> > Free: 607.6 MB
> > Max: 1.8 GB
> > Browser Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
> > .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
> > 3.5.30729; InfoPath.2; .NET4.0C)
> > Error message
> > Stack trace
> >
> >
> > Version BASE 2.16.0 (build #5472; schema #88)
> > Web server Apache Tomcat/6.0.29
> > Database Server MySQL 5.0.77
> > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect
> > JDBC Driver com.mysql.jdbc.Driver (version 5.1)
> > Java runtime OpenJDK Runtime Environment (1.6.0_17-b17), Sun
> > Microsystems Inc. <http://java.sun.com/>
> > Operating system Linux amd64 2.6.18-194.17.4.el5
> > Memory Total: 924.8 MB
> > Free: 607.6 MB
> > Max: 1.8 GB
> > Browser Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
> > .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
> > 3.5.30729; InfoPath.2; .NET4.0C)
> > Error message
> > Stack trace
> >
> >
> > Version BASE 2.16.0 (build #5472; schema #88)
> > Web server Apache Tomcat/6.0.29
> > Database Server MySQL 5.0.77
> > Database Dialect org.hibernate.dialect.MySQLInnoDBDialect
> > JDBC Driver com.mysql.jdbc.Driver (version 5.1)
> > Java runtime OpenJDK Runtime Environment (1.6.0_17-b17), Sun
> > Microsystems Inc. <http://java.sun.com/>
> > Operating system Linux amd64 2.6.18-194.17.4.el5
> > Memory Total: 924.8 MB
> > Free: 607.6 MB
> > Max: 1.8 GB
> > Browser Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0;
> > .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR
> > 3.5.30729; InfoPath.2; .NET4.0C)
> > Error message
> > Stack trace
> >
> >
> > java.lang.NullPointerException
> > ...at
> > net.sf.basedb.util.overview.validator.LabeledExtractValidator.postValidateFolder(LabeledExtractValidator.java:122)
> > ...at
> > net.sf.basedb.util.overview.node.NodeFactory.postValidateFolder(NodeFactory.java:224)
> > ...at
> > net.sf.basedb.util.overview.loader.BasicItemNodeLoader.postValidateFolder(BasicItemNodeLoader.java:134)
> > ...at
> > net.sf.basedb.util.overview.loader.LabeledExtractLoader.createReverseNode(LabeledExtractLoader.java:230)
> > ...at
> > net.sf.basedb.util.overview.loader.LabeledExtractLoader.createReverseNode(LabeledExtractLoader.java:104)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:95)
> > ...at
> > net.sf.basedb.util.overview.loader.HybridizationLoader.loadReverseChildNodes(HybridizationLoader.java:187)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)
> >
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.loadChildNodes(AutoChildNodeLoader.java:121)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:96)
> > ...at
> > net.sf.basedb.util.overview.loader.ScanLoader.loadReverseChildNodes(ScanLoader.java:171)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.loadChildNodes(AutoChildNodeLoader.java:121)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:96)
> > ...at
> > net.sf.basedb.util.overview.loader.RawBioAssayLoader.loadReverseChildNodes(RawBioAssayLoader.java:185)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfFolderNode(AbstractNodeLoader.java:142)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:108)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.loadChildNodes(AutoChildNodeLoader.java:121)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.createReverseNode(AutoChildNodeLoader.java:96)
> > ...at
> > net.sf.basedb.util.overview.loader.ExperimentLoader.loadReverseChildNodes(ExperimentLoader.java:109)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodesOfItemNode(AbstractNodeLoader.java:126)
> > ...at
> > net.sf.basedb.util.overview.loader.AbstractNodeLoader.loadChildNodes(AbstractNodeLoader.java:112)
> > ...at
> > net.sf.basedb.util.overview.loader.AutoChildNodeLoader.loadChildNodes(AutoChildNodeLoader.java:121)
> > ...at
> > net.sf.basedb.util.overview.GenericOverview.expand(GenericOverview.java:296)
> > ...at
> > org.apache.jsp.common.overview.index_jsp._jspService(index_jsp.java:115)
> > ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
> > ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
> > ...at
> > org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:377)
> > ...at
> > org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)
> > ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)
> > ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
> > ...at
> > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
> > ...at
> > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
> > ...at
> > net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:69)
> > ...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:191)
> > ...at
> > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
> > ...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:298)
> > ...at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
> > ...at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)
> > ...at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:774)
> > ...at
> > org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703)
> > ...at
> > org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:896)
> > ...at
> > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
> > ...at java.lang.Thread.run(Thread.java:636)
> >
> > Could you tell me what I done wrong or missed in Experiment? (I don't
> > need any Labels)
> >
> > Regards,
> >
> > Irina
> >
> >
> >
> > ------------------------------------------------------------------------------
> > EditLive Enterprise is the world's most technically advanced content
> > authoring tool. Experience the power of Track Changes, Inline Image
> > Editing and ensure content is compliant with Accessibility Checking.
> > http://p.sf.net/sfu/ephox-dev2dev
> >
> >
> >
> > _______________________________________________
> > The BASE general discussion mailing list
> > basedb-users@lists.sourceforge.net
> > unsubscribe: send a mail with subject "unsubscribe" to
> > basedb-users-requ...@lists.sourceforge.net
>
>
>
> ------------------------------------------------------------------------------
> EditLive Enterprise is the world's most technically advanced content
> authoring tool. Experience the power of Track Changes, Inline Image
> Editing and ensure content is compliant with Accessibility Checking.
> http://p.sf.net/sfu/ephox-dev2dev
> _______________________________________________
> The BASE general discussion mailing list
> basedb-users@lists.sourceforge.net
> unsubscribe: send a mail with subject "unsubscribe" to
> basedb-users-requ...@lists.sourceforge.net
------------------------------------------------------------------------------
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
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