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From: Irina 2. <iri...@ho...> - 2011-06-13 06:52:50
|
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: ni...@th... > To: bas...@li... > 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 > > bas...@li... > > unsubscribe: send a mail with subject "unsubscribe" to > > bas...@li... > > > > ------------------------------------------------------------------------------ > 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 > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Nicklas N. <ni...@th...> - 2011-06-10 06:45:37
|
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 > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
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From: Irina 2. <iri...@ho...> - 2011-06-10 06:17:38
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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. 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. 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. 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. 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$ControlRunnable.run(ThreadPool.java:690) ...at java.lang.Thread.run(Thread.java:636) Could you tell me what I done wrong or missed in Experiment? (I don't need any Labels) Regards,Irina |
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From: Nicklas N. <ni...@th...> - 2011-05-26 05:53:11
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On 2011-05-26 07:24, Irina 264 wrote: > Dear team, > > I install Tab2MageExporter plugin into /base/plugins directory and > addition copy Tab2MageExporter.jar and ebi-plugins-utils.jar into > /base/www/WEB-INF/lib directory Never install the same jar file in two locations. It can result in random failures. > I have an error message, when I export Experiment with Tab2Mage exporter: > > *View job -- Run plugin: Tab2Mage exporter* > > *Status* > > > > Error: > > *Stack trace* > > java.lang.NullPointerException > at uk.ac.ebi.nugo.plugins.Tab2MageExporter.run(Tab2MageExporter.java:354) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) > at java.lang.Thread.run(Thread.java:636) > > Could you, please, tell me what is wrong or what I missed? I recommend that you use the "Experiment overview" first to ensure that there are no error messges and warnings. Select your experiment from the list and then go to the "Overview" tab and click on the "Validate" button. The Tab2Mage exporter assumes that your experiment includes a lot of information all the way up to BioSource items. The exception in your case seems to come from not having specified a scan for the raw bioassay. /Nicklas |
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From: Irina 2. <iri...@ho...> - 2011-05-26 05:24:33
|
Dear team, I install Tab2MageExporter plugin into /base/plugins directory and addition copy Tab2MageExporter.jar and ebi-plugins-utils.jar into /base/www/WEB-INF/lib directory I have an error message, when I export Experiment with Tab2Mage exporter: View job -- Run plugin: Tab2Mage exporter Status Error: Stack trace java.lang.NullPointerException at uk.ac.ebi.nugo.plugins.Tab2MageExporter.run(Tab2MageExporter.java:354) 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) Could you, please, tell me what is wrong or what I missed? Regards, Irina |
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From: Jari H. <ja...@th...> - 2011-05-23 08:11:53
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Can the problem be that the jobagent does not get enough memory? CATALINA OPTS will only influence the BASE core server and if there are separate jobagent processed then these may need an increased memory setting? I may be completely off here but just a thought. Jari On 2011-05-23 08.27, Nicklas Nordborg wrote: > It's difficult to say something about out of memory errors. 2GB should > be more than enough. Have you verified in the Help -> About -> > Configuration dialog that you really have 2GB? > > /Nicklas > > On 2011-05-23 04:03, Irina 264 wrote: >> Dear Team, >> >> I run Illumina plugin and had error: "Java heap space". I have increased >> CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem: >> >> "Error: GC overhead limit exceeded" >> >> View job -- Run plugin: Illumina raw data importer >> >> java.lang.OutOfMemoryError: GC overhead limit exceeded >> at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182) >> at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198) >> at >> org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898) >> at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327) >> at >> org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254) >> at >> org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123) >> at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66) >> at net.sf.basedb.core.RawDataBatcher.<init>(RawDataBatcher.java:263) >> at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104) >> at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119) >> at >> net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520) >> at >> net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691) >> at >> net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) >> 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) >> >> Did I gave too much memory? >> >> Regards, >> Irina >> >> >> >> ------------------------------------------------------------------------------ >> What Every C/C++ and Fortran developer Should Know! >> Read this article and learn how Intel has extended the reach of its >> next-generation tools to help Windows* and Linux* C/C++ and Fortran >> developers boost performance applications - including clusters. >> http://p.sf.net/sfu/intel-dev2devmay >> >> >> >> _______________________________________________ >> The BASE general discussion mailing list >> bas...@li... >> unsubscribe: send a mail with subject "unsubscribe" to >> bas...@li... > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
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From: Nicklas N. <ni...@th...> - 2011-05-23 06:28:07
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It's difficult to say something about out of memory errors. 2GB should be more than enough. Have you verified in the Help -> About -> Configuration dialog that you really have 2GB? /Nicklas On 2011-05-23 04:03, Irina 264 wrote: > Dear Team, > > I run Illumina plugin and had error: "Java heap space". I have increased > CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem: > > "Error: GC overhead limit exceeded" > > View job -- Run plugin: Illumina raw data importer > > java.lang.OutOfMemoryError: GC overhead limit exceeded > at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182) > at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198) > at > org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898) > at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327) > at > org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254) > at > org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123) > at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66) > at net.sf.basedb.core.RawDataBatcher.<init>(RawDataBatcher.java:263) > at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104) > at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119) > at > net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691) > at > net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) > 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) > > Did I gave too much memory? > > Regards, > Irina > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > > > > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
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From: Irina 2. <iri...@ho...> - 2011-05-23 02:03:11
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Dear Team, I run Illumina plugin and had error: "Java heap space". I have increased CATALINA OPTS=-Xmx2048m, however now I have the garbage collector problem: "Error: GC overhead limit exceeded" View job -- Run plugin: Illumina raw data importer java.lang.OutOfMemoryError: GC overhead limit exceeded at org.hibernate.engine.EntityEntry.getEntityKey(EntityEntry.java:182) at org.hibernate.engine.TwoPhaseLoad.initializeEntity(TwoPhaseLoad.java:198) at org.hibernate.loader.Loader.initializeEntitiesAndCollections(Loader.java:898) at org.hibernate.loader.Loader.loadSingleRow(Loader.java:327) at org.hibernate.impl.ScrollableResultsImpl.prepareCurrentRow(ScrollableResultsImpl.java:254) at org.hibernate.impl.ScrollableResultsImpl.next(ScrollableResultsImpl.java:123) at net.sf.basedb.core.ScrollIterator.hasNext(ScrollIterator.java:66) at net.sf.basedb.core.RawDataBatcher.<init>(RawDataBatcher.java:263) at net.sf.basedb.core.RawDataBatcher.getNew(RawDataBatcher.java:104) at net.sf.basedb.core.RawBioAssay.getRawDataBatcher(RawBioAssay.java:1119) at net.sf.basedb.plugins.IlluminaRawDataImporter.beginData(IlluminaRawDataImporter.java:520) at net.sf.basedb.plugins.AbstractFlatFileImporter.doImport(AbstractFlatFileImporter.java:691) at net.sf.basedb.plugins.AbstractFlatFileImporter.run(AbstractFlatFileImporter.java:468) 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) Did I gave too much memory? Regards, Irina |
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From: Irina 2. <iri...@ho...> - 2011-05-22 01:24:36
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Thanks, I look forwatd to this. irina > Date: Fri, 20 May 2011 11:01:39 +0200 > From: ni...@th... > To: bas...@li... > Subject: Re: [base] reporters on MergeBioAssay plug-in > > Thanks for the stacktrace. It seems to be a bug in the > Base1PluginExecuter plug-in. It is trying to remap the raw data > associations after the bioassays have been merged. Obviously, this is > not possible if there is no raw data stored in the first place. The > Base1PluginExecuter need to be fixed with a check for this case. > > I have created a ticket for this fix to be included with the BASE 2.17.2 > release. Unfortunately there is no workaround. > > http://base.thep.lu.se/ticket/1610 > > /Nicklas > > > > On 2011-05-20 10:12, Irina 264 wrote: > > > > > > from "Stack trace" tab: > > > > > > > > View job -- Run plugin: Base1PluginExecuter > > <javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')> > > > > Name Run plugin: Base1PluginExecuter > > Description > > Priority 5 (1 = highest, 10 = lowest) > > Status Error: Raw data for raw data type: Affymetrix is not stored in > > the database. > > Percent complete > > unknown > > > > 100% > > > > Created 2011-05-20 18:10:30 > > Scheduled 2011-05-20 18:11:10 > > Started 2011-05-20 18:11:28 > > Ended 2011-05-20 18:11:42 > > Running time 14 seconds > > Server vera097.its.monash.edu.au > > Job agent /- none -/ > > User Irina Rusinova > > Experiment E-GEOD-6257 > > Plugin Base1PluginExecuter (version 2.16.0) > > Configuration MergeBioAssay > > > > net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix > > is not stored in the database. > > at > > net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261) > > at > > net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510) > > at > > net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346) > > at > > net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471) > > at > > net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774) > > 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) > > > > > > > > > > > > > Date: Fri, 20 May 2011 09:21:12 +0200 > > > From: ni...@th... > > > To: bas...@li... > > > Subject: Re: [base] reporters on MergeBioAssay plug-in > > > > > > On 2011-05-20 09:04, Irina 264 wrote: > > > > Hi Nicklas, > > > > > > > > Thanks for the quick reply. > > > > > > > > I run RMAExpress with Affy data, then I done filtering with equal size > > > > of arrays afterwards. > > > > > > > > Then I run MergeBioAssay (with Base1pluginExecuter) to find average > > > > between replicates (grouping assays by control and treatment with > > method > > > > ‘arithmetic mean of intensity) and have this error message: “Error: Raw > > > > data for raw data type: Affymetrix is not stored in the database.” > > > > > > > > When I use Agilent data, i have no problems. > > > > > > > > Did I explain better? > > > > > > Yes... but I still have no idea why the error about raw data is coming > > > up... As far as I know the Merge BioAssay plug-in doesn't use raw data > > > for the calculations. It would be useful to get a complete stacktrace of > > > the error in order to locate the source of the problem. > > > > > > Do you get the error while you are configuring the job? If so you should > > > be able to display more error information by clicking on the little [+] > > > icon in the configuration wizard. > > > > > > Or, if you get the error while the plug-in is running, there is a "Stack > > > trace" tab in the job dialog. > > > > > > > > > /Nicklas > > > > > > > > > > > ------------------------------------------------------------------------------ > > > What Every C/C++ and Fortran developer Should Know! > > > Read this article and learn how Intel has extended the reach of its > > > next-generation tools to help Windows* and Linux* C/C++ and Fortran > > > developers boost performance applications - including clusters. > > > http://p.sf.net/sfu/intel-dev2devmay > > > _______________________________________________ > > > The BASE general discussion mailing list > > > bas...@li... > > > unsubscribe: send a mail with subject "unsubscribe" to > > > bas...@li... > > > > > > > > ------------------------------------------------------------------------------ > > What Every C/C++ and Fortran developer Should Know! > > Read this article and learn how Intel has extended the reach of its > > next-generation tools to help Windows* and Linux* C/C++ and Fortran > > developers boost performance applications - including clusters. > > http://p.sf.net/sfu/intel-dev2devmay > > > > > > > > _______________________________________________ > > The BASE general discussion mailing list > > bas...@li... > > unsubscribe: send a mail with subject "unsubscribe" to > > bas...@li... > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Nicklas N. <ni...@th...> - 2011-05-20 09:01:48
|
Thanks for the stacktrace. It seems to be a bug in the Base1PluginExecuter plug-in. It is trying to remap the raw data associations after the bioassays have been merged. Obviously, this is not possible if there is no raw data stored in the first place. The Base1PluginExecuter need to be fixed with a check for this case. I have created a ticket for this fix to be included with the BASE 2.17.2 release. Unfortunately there is no workaround. http://base.thep.lu.se/ticket/1610 /Nicklas On 2011-05-20 10:12, Irina 264 wrote: > > > from "Stack trace" tab: > > > > View job -- Run plugin: Base1PluginExecuter > <javascript:Main.openTabControlHelp('7a1ebdaa616cc46f',%20'main',%20'null')> > > Name Run plugin: Base1PluginExecuter > Description > Priority 5 (1 = highest, 10 = lowest) > Status Error: Raw data for raw data type: Affymetrix is not stored in > the database. > Percent complete > unknown > > 100% > > Created 2011-05-20 18:10:30 > Scheduled 2011-05-20 18:11:10 > Started 2011-05-20 18:11:28 > Ended 2011-05-20 18:11:42 > Running time 14 seconds > Server vera097.its.monash.edu.au > Job agent /- none -/ > User Irina Rusinova > Experiment E-GEOD-6257 > Plugin Base1PluginExecuter (version 2.16.0) > Configuration MergeBioAssay > > net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix > is not stored in the database. > at > net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261) > at > net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510) > at > net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346) > at > net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471) > at > net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774) > 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) > > > > > > > Date: Fri, 20 May 2011 09:21:12 +0200 > > From: ni...@th... > > To: bas...@li... > > Subject: Re: [base] reporters on MergeBioAssay plug-in > > > > On 2011-05-20 09:04, Irina 264 wrote: > > > Hi Nicklas, > > > > > > Thanks for the quick reply. > > > > > > I run RMAExpress with Affy data, then I done filtering with equal size > > > of arrays afterwards. > > > > > > Then I run MergeBioAssay (with Base1pluginExecuter) to find average > > > between replicates (grouping assays by control and treatment with > method > > > ‘arithmetic mean of intensity) and have this error message: “Error: Raw > > > data for raw data type: Affymetrix is not stored in the database.” > > > > > > When I use Agilent data, i have no problems. > > > > > > Did I explain better? > > > > Yes... but I still have no idea why the error about raw data is coming > > up... As far as I know the Merge BioAssay plug-in doesn't use raw data > > for the calculations. It would be useful to get a complete stacktrace of > > the error in order to locate the source of the problem. > > > > Do you get the error while you are configuring the job? If so you should > > be able to display more error information by clicking on the little [+] > > icon in the configuration wizard. > > > > Or, if you get the error while the plug-in is running, there is a "Stack > > trace" tab in the job dialog. > > > > > > /Nicklas > > > > > > > ------------------------------------------------------------------------------ > > What Every C/C++ and Fortran developer Should Know! > > Read this article and learn how Intel has extended the reach of its > > next-generation tools to help Windows* and Linux* C/C++ and Fortran > > developers boost performance applications - including clusters. > > http://p.sf.net/sfu/intel-dev2devmay > > _______________________________________________ > > The BASE general discussion mailing list > > bas...@li... > > unsubscribe: send a mail with subject "unsubscribe" to > > bas...@li... > > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > > > > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Irina 2. <iri...@ho...> - 2011-05-20 08:16:26
|
Addition, from "Parameters" tab:
Job parameters
-- Ratio annotation type
--- Ratio annotaion value (ignored unless a Ratio annotation type is selected)
assayname
%1_%2_%3
Child description
Child name
human
Group
%3
Merge method
arithmetric mean or intensity
newname
Output directory
/home/raw data/affyExp/MergeBioAssay
- Ratio (ignored if merge method is other than 'ratio of ratio')
section
merge_bioassays settings
Bioassay set
human
Plugin configuration parameters
Parameter version
27 (27)
Name of executable
run
Plugin executables path
/opt/base2/plugins/MergeBioAssay/
Average on reporters
false
Job parameters
<jobparameters>
<parameter position="1" type="h">
<name>section</name>
<commonname>newname</commonname>
<options>10</options>
<defaultvalue>merge_bioassays settings</defaultvalue>
</parameter>
<parameter position="2" type="t">
<name>assayname</name>
<commonname>assayname</commonname>
<options>10</options>
<defaultvalue>%1</defaultvalue>
</parameter>
<parameter position="3" type="t">
<name>group</name>
<commonname>Group</commonname>
<options>10</options>
<defaultvalue>%1</defaultvalue>
</parameter>
<parameter position="4" type="t">
<name>newname</name>
<commonname>newname</commonname>
<options>10</options>
<defaultvalue />
</parameter>
<parameter position="5" type="e">
<name>mergeMethod</name>
<commonname>Merge method</commonname>
<options>30</options>
<defaultvalue>0</defaultvalue>
<enumoptions>
<value key="0">geometric mean of ratio</value>
<value key="1">arithmetric mean or ratio</value>
<value key="2">arithmetric mean or intensity</value>
<value key="3">ratio of ratio</value>
</enumoptions>
</parameter>
<parameter position="6" type="t">
<name>ratio</name>
<commonname>- Ratio (ignored if merge method is other than 'ratio of ratio')</commonname>
<options>10</options>
<defaultvalue />
</parameter>
<parameter position="7" type="n">
<name>annType</name>
<commonname>-- Ratio annotation type</commonname>
<options>30</options>
<defaultvalue>0</defaultvalue>
</parameter>
<parameter position="8" type="t">
<name>annValue</name>
<commonname>--- Ratio annotaion value (ignored unless a Ratio annotation type is selected)</commonname>
<options>10</options>
<defaultvalue />
</parameter>
</jobparameters>
Leave stdin.txt
true
Leave stdout.txt
true
Max channels
2
Min channels
1
Allow override
Resulting intensities
Data format
false
Source intensities
Columns
position\treporter
Fields
intensity1\tintensity2
Version
2.1
> Date: Fri, 20 May 2011 09:21:12 +0200
> From: ni...@th...
> To: bas...@li...
> Subject: Re: [base] reporters on MergeBioAssay plug-in
>
> On 2011-05-20 09:04, Irina 264 wrote:
> > Hi Nicklas,
> >
> > Thanks for the quick reply.
> >
> > I run RMAExpress with Affy data, then I done filtering with equal size
> > of arrays afterwards.
> >
> > Then I run MergeBioAssay (with Base1pluginExecuter) to find average
> > between replicates (grouping assays by control and treatment with method
> > ‘arithmetic mean of intensity) and have this error message: “Error: Raw
> > data for raw data type: Affymetrix is not stored in the database.”
> >
> > When I use Agilent data, i have no problems.
> >
> > Did I explain better?
>
> Yes... but I still have no idea why the error about raw data is coming
> up... As far as I know the Merge BioAssay plug-in doesn't use raw data
> for the calculations. It would be useful to get a complete stacktrace of
> the error in order to locate the source of the problem.
>
> Do you get the error while you are configuring the job? If so you should
> be able to display more error information by clicking on the little [+]
> icon in the configuration wizard.
>
> Or, if you get the error while the plug-in is running, there is a "Stack
> trace" tab in the job dialog.
>
>
> /Nicklas
>
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
|
|
From: Irina 2. <iri...@ho...> - 2011-05-20 08:12:59
|
from "Stack trace" tab: View job -- Run plugin: Base1PluginExecuter Name Run plugin: Base1PluginExecuter Description Priority 5 (1 = highest, 10 = lowest) Status Error: Raw data for raw data type: Affymetrix is not stored in the database. Percent complete unknown 100% Created 2011-05-20 18:10:30 Scheduled 2011-05-20 18:11:10 Started 2011-05-20 18:11:28 Ended 2011-05-20 18:11:42 Running time 14 seconds Server vera097.its.monash.edu.au Job agent - none - User Irina Rusinova Experiment E-GEOD-6257 Plugin Base1PluginExecuter (version 2.16.0) Configuration MergeBioAssay net.sf.basedb.core.BaseException: Raw data for raw data type: Affymetrix is not stored in the database. at net.sf.basedb.core.DynamicSpotQuery.joinRawData(DynamicSpotQuery.java:261) at net.sf.basedb.util.importer.spotdata.BaseFileImporter.createChildRawDataMapping(BaseFileImporter.java:510) at net.sf.basedb.util.importer.spotdata.BaseFileImporter.doImport(BaseFileImporter.java:346) at net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1471) at net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:774) 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) > Date: Fri, 20 May 2011 09:21:12 +0200 > From: ni...@th... > To: bas...@li... > Subject: Re: [base] reporters on MergeBioAssay plug-in > > On 2011-05-20 09:04, Irina 264 wrote: > > Hi Nicklas, > > > > Thanks for the quick reply. > > > > I run RMAExpress with Affy data, then I done filtering with equal size > > of arrays afterwards. > > > > Then I run MergeBioAssay (with Base1pluginExecuter) to find average > > between replicates (grouping assays by control and treatment with method > > ‘arithmetic mean of intensity) and have this error message: “Error: Raw > > data for raw data type: Affymetrix is not stored in the database.” > > > > When I use Agilent data, i have no problems. > > > > Did I explain better? > > Yes... but I still have no idea why the error about raw data is coming > up... As far as I know the Merge BioAssay plug-in doesn't use raw data > for the calculations. It would be useful to get a complete stacktrace of > the error in order to locate the source of the problem. > > Do you get the error while you are configuring the job? If so you should > be able to display more error information by clicking on the little [+] > icon in the configuration wizard. > > Or, if you get the error while the plug-in is running, there is a "Stack > trace" tab in the job dialog. > > > /Nicklas > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Nicklas N. <ni...@th...> - 2011-05-20 07:21:22
|
On 2011-05-20 09:04, Irina 264 wrote: > Hi Nicklas, > > Thanks for the quick reply. > > I run RMAExpress with Affy data, then I done filtering with equal size > of arrays afterwards. > > Then I run MergeBioAssay (with Base1pluginExecuter) to find average > between replicates (grouping assays by control and treatment with method > ‘arithmetic mean of intensity) and have this error message: “Error: Raw > data for raw data type: Affymetrix is not stored in the database.” > > When I use Agilent data, i have no problems. > > Did I explain better? Yes... but I still have no idea why the error about raw data is coming up... As far as I know the Merge BioAssay plug-in doesn't use raw data for the calculations. It would be useful to get a complete stacktrace of the error in order to locate the source of the problem. Do you get the error while you are configuring the job? If so you should be able to display more error information by clicking on the little [+] icon in the configuration wizard. Or, if you get the error while the plug-in is running, there is a "Stack trace" tab in the job dialog. /Nicklas |
|
From: Irina 2. <iri...@ho...> - 2011-05-20 07:04:42
|
Hi Nicklas, Thanks for the quick reply. I run RMAExpress with Affy data, then I done filtering with equal size of arrays afterwards. Then I run MergeBioAssay (with Base1pluginExecuter) to find average between replicates (grouping assays by control and treatment with method ‘arithmetic mean of intensity) and have this error message: “Error: Raw data for raw data type: Affymetrix is not stored in the database.” When I use Agilent data, i have no problems. Did I explain better? Regards, Irina > Date: Fri, 20 May 2011 07:51:52 +0200 > From: ni...@th... > To: bas...@li... > Subject: Re: [base] reporters on MergeBioAssay plug-in > > On 2011-05-20 03:46, Irina 264 wrote: > > Dear team, > > > > I am working with MergeBioAssay plug-in. I created a formula for > > reporterID using rep(‘id’) as expression, because other reporter > > parameters (Name or ExternalID) don’t work. However, when I run > > MergeBioAssay with Affy dataset I have an error message: > > > > “Error: Raw data for raw data type: Affymetrix is not stored in the > > database.” > > I don't see how this error message can be coming from the Merge BioAssay > plug-in. Can you explain better what you are doing when you get that > error message. Eg. which menus, buttons, etc. you click on to get there? > > > Could you help me, what is better way to solve it: to add Affy data > > format to the raw-data-types.xml or you have another idea? > > Affymetrix raw data should never be added to the database. There are too > many data points for this to work satisfactory. You'll have to rely on > other plug-ins for getting the data into the database. See for example > http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix > > /Nicklas > > > ------------------------------------------------------------------------------ > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Nicklas N. <ni...@th...> - 2011-05-20 05:52:03
|
On 2011-05-20 03:46, Irina 264 wrote: > Dear team, > > I am working with MergeBioAssay plug-in. I created a formula for > reporterID using rep(‘id’) as expression, because other reporter > parameters (Name or ExternalID) don’t work. However, when I run > MergeBioAssay with Affy dataset I have an error message: > > “Error: Raw data for raw data type: Affymetrix is not stored in the > database.” I don't see how this error message can be coming from the Merge BioAssay plug-in. Can you explain better what you are doing when you get that error message. Eg. which menus, buttons, etc. you click on to get there? > Could you help me, what is better way to solve it: to add Affy data > format to the raw-data-types.xml or you have another idea? Affymetrix raw data should never be added to the database. There are too many data points for this to work satisfactory. You'll have to rely on other plug-ins for getting the data into the database. See for example http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix /Nicklas |
|
From: Irina 2. <iri...@ho...> - 2011-05-20 01:46:55
|
Dear team, I am working with MergeBioAssay plug-in. I created a formula for reporterID using rep(‘id’) as expression, because other reporter parameters (Name or ExternalID) don’t work. However, when I run MergeBioAssay with Affy dataset I have an error message: “Error: Raw data for raw data type: Affymetrix is not stored in the database.” Could you help me, what is better way to solve it: to add Affy data format to the raw-data-types.xml or you have another idea? I need reporter list for the next step of analysis. Regards, Irina |
|
From: Nicklas N. <ni...@th...> - 2011-05-09 07:31:36
|
Hello all, We are happy to announce the release of BASE 2.17.1. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closed&milestone=BASE+2.17.1&group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas |
|
From: Jari H. <ja...@th...> - 2011-03-18 14:55:42
|
You may fail on another formula missing because the Base1PluginExecuter
will only report the first error since only the firts error is thrown.
The next try will reveal another missing formula but simply add that
formula and have another try. In general the BASE1 plug-ins provided on
the BASE plugins site requires 3 to 4 formulas. Of course, if you
install several BASE1 plugins the formulas are reused.
Jari
On 2011-03-18 09.13, Nicklas Nordborg wrote:
> On 2011-03-16 19:04, Thomas Person wrote:
>> Thanks that worked and am now able to see and run the Virtual Array
>> plugin. Unfortunately the plugin also fails with an error when running:
>> Error: Error during export: Item not found: Unknown reporter field:
>> reporter (you can add this field as an formula)
>
> I have tried to investigate this and I think you'll need to create a
> formula (as the error message indicates) for the VirtualArray.
> Unfortunately this is not documented in the installation instructions...
>
> In any case, here is what I think you need to do:
>
> 1. Go to View -> Formulas page and click on the "New" button.
> 2. In the popup window enter the following information:
>
> Name: reporter
> Expressions: rep('id')
> Value type: Integer
> Avg. method: None
>
> All other parameters can be left at their default values.
>
> 3. Save and then try running the VirtualArray plug-in again.
>
> I hope this works.
>
> /Nicklas
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...
|
|
From: Nicklas N. <ni...@th...> - 2011-03-18 08:13:18
|
On 2011-03-16 19:04, Thomas Person wrote:
> Thanks that worked and am now able to see and run the Virtual Array
> plugin. Unfortunately the plugin also fails with an error when running:
> Error: Error during export: Item not found: Unknown reporter field:
> reporter (you can add this field as an formula)
I have tried to investigate this and I think you'll need to create a
formula (as the error message indicates) for the VirtualArray.
Unfortunately this is not documented in the installation instructions...
In any case, here is what I think you need to do:
1. Go to View -> Formulas page and click on the "New" button.
2. In the popup window enter the following information:
Name: reporter
Expressions: rep('id')
Value type: Integer
Avg. method: None
All other parameters can be left at their default values.
3. Save and then try running the VirtualArray plug-in again.
I hope this works.
/Nicklas
|
|
From: Thomas P. <tho...@ut...> - 2011-03-16 18:04:23
|
Thanks that worked and am now able to see and run the Virtual Array plugin. Unfortunately the plugin also fails with an error when running: Error: Error during export: Item not found: Unknown reporter field: reporter (you can add this field as an formula) Thanks again for all your help, Thomas On 03/14/2011 07:27 AM, Nicklas Nordborg wrote: > On 2011-03-11 18:13, Thomas Person wrote: >> Ok, I guess I'm missing something in the configuration of the plugin, >> for all the plugins associated with the Base1PluginExecuter. If i >> simply create the plugin under the Base1PluginExecuter but then not >> configure it, then I am given the option under the drop down to run >> it when attempting "Run an analysis plugin" but it does not function >> as it hasn't been configured. > Oh... I guess we have to look into that. Unconfigured plug-in shouldn't > really be in that list. > > > But once i do configure it, with the >> proper file and path to the run command. the option to run the plugin >> in the drop down under run an analysis plugin disappears as an option >> to run. > We have checked the installation procedure of the VirtualArray plug-in > and it turns out that the configuration file that is used is incorrect. > The problem with the 'descr' field has already been fixed but there are > two more issues: > > * The 'geneAverages' setting should be '1', not '0'. > * The 'minChannels' setting should be '1', not '2'. > > Fortunately both settings can be changed in the web gui. Start the > configuration wizard for the VirtualArray plug-in. In the first step, > make sure to NOT select a file. This will take you to a second step > where you can change the value for the two parameters mentioned above. > The 'geneAverages' setting is called 'Average on reporters' in the wizard. > > Hope this works better. > > /Nicklas > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > The BASE general discussion mailing list > bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
|
From: Nicklas N. <ni...@th...> - 2011-03-14 12:27:33
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On 2011-03-11 18:13, Thomas Person wrote: > Ok, I guess I'm missing something in the configuration of the plugin, > for all the plugins associated with the Base1PluginExecuter. If i > simply create the plugin under the Base1PluginExecuter but then not > configure it, then I am given the option under the drop down to run > it when attempting "Run an analysis plugin" but it does not function > as it hasn't been configured. Oh... I guess we have to look into that. Unconfigured plug-in shouldn't really be in that list. > But once i do configure it, with the > proper file and path to the run command. the option to run the plugin > in the drop down under run an analysis plugin disappears as an option > to run. We have checked the installation procedure of the VirtualArray plug-in and it turns out that the configuration file that is used is incorrect. The problem with the 'descr' field has already been fixed but there are two more issues: * The 'geneAverages' setting should be '1', not '0'. * The 'minChannels' setting should be '1', not '2'. Fortunately both settings can be changed in the web gui. Start the configuration wizard for the VirtualArray plug-in. In the first step, make sure to NOT select a file. This will take you to a second step where you can change the value for the two parameters mentioned above. The 'geneAverages' setting is called 'Average on reporters' in the wizard. Hope this works better. /Nicklas |
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From: Thomas P. <Tho...@UT...> - 2011-03-11 17:13:51
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Ok, I guess I'm missing something in the configuration of the plugin, for all the plugins associated with the Base1PluginExecuter. If i simply create the plugin under the Base1PluginExecuter but then not configure it, then I am given the option under the drop down to run it when attempting "Run an analysis plugin" but it does not function as it hasn't been configured. But once i do configure it, with the proper file and path to the run command. the option to run the plugin in the drop down under run an analysis plugin disappears as an option to run. Thanks again Thomas ________________________________________ From: Nicklas Nordborg [ni...@th...] Sent: Thursday, March 10, 2011 4:01 PM To: bas...@li... Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 On 2011-03-10 20:58, Jari Häkkinen wrote: > Also, Virtual array works only on 2-channel data. I was never involved in the development of this plug-in so maybe I am missing something obvious.... I had a quick lock at the code (http://baseplugins.thep.lu.se/browser/plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java) and I can't see anything in it that depends on the number of channels. As far as I can tell it is simply copying the input intensities to the output without change. The only difference is that it assigns negative position numbers. Actually I don't see any point in running the VirtualArray at all. All intensity data afterwards will be exactly the same as it was before. The only change is that position numbers are different, and as a side-effect of that the connection to raw data is lost. But... maybe I am missing something obvious... Anyone knows more about this? In any case, since there is not any dependency on the number of channels in the code, it should be safe to change 'minChannels 2' to 'minChannels 1' in the pluginVirtualArray.base file. Or (easier) directly by reconfiguring the plug-in in the web interface. There should be an option for this setting in the second step (leave the file field empty in the first step). /Nicklas ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ The BASE general discussion mailing list bas...@li... unsubscribe: send a mail with subject "unsubscribe" to bas...@li... ________________________________ UT Southwestern Medical Center The future of medicine, today. |
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From: Nicklas N. <ni...@th...> - 2011-03-10 22:01:50
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On 2011-03-10 20:58, Jari Häkkinen wrote: > Also, Virtual array works only on 2-channel data. I was never involved in the development of this plug-in so maybe I am missing something obvious.... I had a quick lock at the code (http://baseplugins.thep.lu.se/browser/plugins/base1/se.lu.onk.VirtualArray/trunk/src/virtualarray/VirtualArray.java) and I can't see anything in it that depends on the number of channels. As far as I can tell it is simply copying the input intensities to the output without change. The only difference is that it assigns negative position numbers. Actually I don't see any point in running the VirtualArray at all. All intensity data afterwards will be exactly the same as it was before. The only change is that position numbers are different, and as a side-effect of that the connection to raw data is lost. But... maybe I am missing something obvious... Anyone knows more about this? In any case, since there is not any dependency on the number of channels in the code, it should be safe to change 'minChannels 2' to 'minChannels 1' in the pluginVirtualArray.base file. Or (easier) directly by reconfiguring the plug-in in the web interface. There should be an option for this setting in the second step (leave the file field empty in the first step). /Nicklas |
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From: Thomas P. <Tho...@UT...> - 2011-03-10 21:19:12
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The only prerequisite I saw was BaseFile, and thats already included with Virtual Array, correct? Yeah, I think its all shared out appropriately, course I'm also still only using the root user for the server. Still testing everything before I deploy it for all my users and create them accounts. Since we don't have two channel data, we have Illumina "bead Chip", I guess this issue is a moot point for me. But leaves me with the question, is there another way to average the signal of arrays at the server? My users will often have 4 experimental arrays and 4 control arrays for each of their 5 or more different time points. And want to be able to easily view graphs and compare the control to the experimental. True we can do some basic processing between base and MeV or whatever they want to use, but its not that easy. Thanks again for all the help, Thomas ________________________________________ From: Jari Häkkinen [ja...@th...] Sent: Thursday, March 10, 2011 1:58 PM To: bas...@li... Subject: Re: [base] Base 1.2 plugin - Virtual Array -1.1 Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: > Thanks! > > That change allows installation but once I atmpt to use the plugin, > by clicking on the "Run an Analysis Plugin" icon when looking at an > experiment under Bioassay set, the option select the the plugin in > the drop down menu does not appear. > > Thanks again, > > Thomas ________________________________________ From: Nicklas > Nordborg [ni...@th...] Sent: Wednesday, March 09, 2011 1:11 > AM To: BASE ML Subject: Re: [base] Base 1.2 plugin - Virtual Array > -1.1 > > On 2011-03-08 22:28, Thomas Person wrote: >> Howdy All, >> >> I'm attempting to install the Virtual Array 1.1 plugin on my Base >> 2.15 server. I get two sets of errors. ( I was able to install the >> Center-2.1 Plugin with no error). > > Thanks for the report. I can verify that the VirtualArray plug-in > can't be installed as is. There seems to be a bug in BASE that is > related to the 'descr' field in the 'pluginVirtualArray.base' file. > This file has a space instead of a tab character between the 'descr' > and the rest of the line. Please change the space to a tab and then > re-try the installation. > > /Nicklas > > ------------------------------------------------------------------------------ > > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit for your > organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ The BASE general > discussion mailing list bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... > > ________________________________ > > UT Southwestern Medical Center The future of medicine, today. > > ------------------------------------------------------------------------------ > > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit for your > organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ The BASE general > discussion mailing list bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ The BASE general discussion mailing list bas...@li... unsubscribe: send a mail with subject "unsubscribe" to bas...@li... |
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From: Jari H. <ja...@th...> - 2011-03-10 20:28:42
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Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: > Thanks! > > That change allows installation but once I atmpt to use the plugin, > by clicking on the "Run an Analysis Plugin" icon when looking at an > experiment under Bioassay set, the option select the the plugin in > the drop down menu does not appear. > > Thanks again, > > Thomas ________________________________________ From: Nicklas > Nordborg [ni...@th...] Sent: Wednesday, March 09, 2011 1:11 > AM To: BASE ML Subject: Re: [base] Base 1.2 plugin - Virtual Array > -1.1 > > On 2011-03-08 22:28, Thomas Person wrote: >> Howdy All, >> >> I'm attempting to install the Virtual Array 1.1 plugin on my Base >> 2.15 server. I get two sets of errors. ( I was able to install the >> Center-2.1 Plugin with no error). > > Thanks for the report. I can verify that the VirtualArray plug-in > can't be installed as is. There seems to be a bug in BASE that is > related to the 'descr' field in the 'pluginVirtualArray.base' file. > This file has a space instead of a tab character between the 'descr' > and the rest of the line. Please change the space to a tab and then > re-try the installation. > > /Nicklas > > ------------------------------------------------------------------------------ > > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit for your > organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ The BASE general > discussion mailing list bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... > > ________________________________ > > UT Southwestern Medical Center The future of medicine, today. > > ------------------------------------------------------------------------------ > > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit for your > organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ The BASE general > discussion mailing list bas...@li... > unsubscribe: send a mail with subject "unsubscribe" to > bas...@li... |
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