Re: [base] Tab2Mage exporter plugin
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
Re: [base] Tab2Mage exporter plugin
On 2011-06-13 08:51, Irina 264 wrote: 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]. Add raw bioassays to your experiment. /Nicklas -- 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
Re: [base] Tab2Mage exporter plugin
On 2011-06-13 09:17, Irina 264 wrote: Thanks, thay already there! Have you checked that the owner of the raw bioassays is the same as the owner of the experiment or that everything is shared to the same project which must also be the active project? /Nicklas -- 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
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 serverApache 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 MemoryTotal: 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 serverApache 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 MemoryTotal: 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 serverApache 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 MemoryTotal: 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
Re: [base] tab2mage exporter plugin installation problem
[EMAIL PROTECTED] wrote: now regarding your installation, it seems that the path you have indicated when configuring the plugin (i.e. usr/local/base-2.5.0/www/plugins/tab2mage/Tab2MageExporter/Tab2mageExporter.jar) differs from what it actually is. From your message, it seems that the path should be: usr/local/base-2.5.0/www/plugins/tab2mage/Tab2mageExporter.jar There seems to be a general misunderstanding that plugins should be installed in the basedir/www/plugins/ directory. This directory should only contain JSP pages and other resources (such as images, javascripts, etc.) that are needed by the plug-ins, not the actual plug-in JAR files. This has been clarified in the documentation and since the 2.5 release we are recommending that plugins are installed in the basedir/plugins/ directory (or at least in a directory that is outside the www directory). The main reason is that everything in the www directory is accessible from the internet and since BASE doesn't provide any access control to anything else that JSP files, installing plug-ins in the www directory may lead to security problems. /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] tab2mage exporter plugin installation problem
Lisa Bishop wrote: hi Sorry i think that was a typo. this is my class uk.ac.ebi.nugo.plugins.Tab2MageExporter And path usr/local/base-2.5.0/www/plugins/tab2mage/Tab2mageExporter.jar Still getting an error. for not finding the jar file i was wondering could the install of uk.ac.ebi.nugo.plugins.Tab2MageExporter be causing my problems? It seems like you are missing a / in the beginning of the path. Shouldn't it be: /usr/local... /Nicklas - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]