Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
vegard nygaard wrote: Dominic wrote: Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? No. I installed and tested the AnnotationTypeCvImporter with its own jar file and assumed it was the same. I now changed to use the Tab2MageImporter.jar and the plug-in finished without errors reported to the plug-in window in BASE. Though there were a bunch of error messages in the tomcat log. This is just the start: Executing job: Importing data to raw bioassay: H_PropylParabenC1T1.gpr 13:19:29,197 ERROR jobqueue:435 - Exception while executing job: Job[id=78; name=Importing data to raw bioassay: N_PropylParabenC1T2.gpr] net.sf.basedb.core.BaseException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) at java.lang.Thread.run(Thread.java:595) Caused by: net.sf.basedb.core.ItemModifiedException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.HibernateUtil.commit(HibernateUtil.java:914) at net.sf.basedb.core.DbControl.commit(DbControl.java:393) at net.sf.basedb.plugins.RawDataFlatFileImporter.end(RawDataFlatFileImporter.ja va:521) This is not a problem that hampers the Tab2mage importer, as you have observed. The tomcat messages had been identified and handled (or fixed) and will not appear with the new release of the importer. When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message Further to the information by Nicklas. With the example zip file you are running, the importer creates new protocol types e.g. (grow ) identified in the tab2mage file. You can manually identify the protocol whose protocoltype is NOT a base-known protocoltype and change to a base known protocoltype and the experiment overview should work. And of course, you could upgrade to base 2.4.4. ¬Dominic - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
Dominic wrote: Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? No. I installed and tested the AnnotationTypeCvImporter with its own jar file and assumed it was the same. I now changed to use the Tab2MageImporter.jar and the plug-in finished without errors reported to the plug-in window in BASE. Though there were a bunch of error messages in the tomcat log. This is just the start: Executing job: Importing data to raw bioassay: H_PropylParabenC1T1.gpr 13:19:29,197 ERROR jobqueue:435 - Exception while executing job: Job[id=78; name=Importing data to raw bioassay: N_PropylParabenC1T2.gpr] net.sf.basedb.core.BaseException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) at java.lang.Thread.run(Thread.java:595) Caused by: net.sf.basedb.core.ItemModifiedException: Permission denied: The item RawBioAssay[id=102] was modified by another transaction. at net.sf.basedb.core.HibernateUtil.commit(HibernateUtil.java:914) at net.sf.basedb.core.DbControl.commit(DbControl.java:393) at net.sf.basedb.plugins.RawDataFlatFileImporter.end(RawDataFlatFileImporter.ja va:521) When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message java.lang.NullPointerException ...at net.sf.basedb.util.overview.ExperimentOverview.addProtocol(ExperimentOvervie w.java:1502) ...at net.sf.basedb.util.overview.ExperimentOverview.addSample(ExperimentOverview. java:1145) ...at net.sf.basedb.util.overview.ExperimentOverview.addExtract(ExperimentOverview .java:1039) ...at net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtract(ExperimentO verview.java:914) ...at net.sf.basedb.util.overview.ExperimentOverview.addLabeledExtracts(Experiment Overview.java:841) ...at net.sf.basedb.util.overview.ExperimentOverview.addHybridization(ExperimentOv erview.java:781) ...at net.sf.basedb.util.overview.ExperimentOverview.addScan(ExperimentOverview.ja va:748) ...at net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssay(ExperimentOver view.java:604) ...at net.sf.basedb.util.overview.ExperimentOverview.addRawBioAssays(ExperimentOve rview.java:580) ...at net.sf.basedb.util.overview.ExperimentOverview.generateOverview(ExperimentOv erview.java:316) ...at net.sf.basedb.util.overview.ExperimentOverview.init(ExperimentOverview.jav a:257) ...at net.sf.basedb.util.overview.ExperimentOverview.getOverview(ExperimentOvervie w.java:188) ...at org.apache.jsp.views.experiments.overview.index_jsp._jspService(index_jsp.ja va:87) ... and more I will now go on and test the tab2mage exporter and see if I get the same as I started with. You will hear from me if I am stuck. Vegard. - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter
However, given the performance improvement you should go for 2.4.4 Jari Nicklas Nordborg wrote: vegard nygaard wrote: When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done that for me a lot and may not be caused by the tab2mage importer. Anyways here is the error message java.lang.NullPointerException This has been fixed in the 2.4.4 release. See http://base.thep.lu.se/ticket/803 for a manual workaround if you don't want to upgrade. /Nicklas - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now http://get.splunk.com/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
