Re: [base] Problems running Tab2Mage Importer, "NOT sufficient Disk Space"
Jari Häkkinen wrote: > Just for your information: > > Dominic Oyeniran wrote: >> This is a known issue and has been documented here: >> http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. >> Please scroll to the usage section right after the installation section. > > We prefer to use links to the more generic http://baseplugins.thep.lu.se > since lev is merely the current host of the baseplugins (and base) and > it may changes in the future. That is the above link should be a more > archive safe > http://baseplugins.thep.lu.se/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt > Noted Jari. Thanks. However, I actually got the link from the base website. (At that time I could not remember the website link) This is the flow of what I did: 1. From here: http://base.thep.lu.se/, I clicked on Base plugins website at the Plug-ins section, which takes me to: http://lev.thep.lu.se/trac/baseplugins. 2. Clicking on 'download page' on the plugins site (want to be a downloader?) section takes me to: http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload etc .. Hope this is useful a information. Thanks. ¬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]
[base] multiple/compound experimental factors in BASE
Hi, While we're on the subject... how do people (and how does BASE) handle multiple experimental factors. Say a two-colour experiment was testing the following "conditions" mutantX vs. wild type in males mutantY vs. wild type in males mutantX vs. wild type in females mutantY vs. wild type in females There are are two experimental factors here, "GeneticModification" and "Sex". I guess the correct way to handle the downstream analysis (e.g. averaging and colouring in ExperimentExplorer) is to treat this as a compound annotation e.g. GeneticModification:Sex. I don't think BASE would handle this at the moment (you can only select one annotation at a time in the "Annotation summary" menu), although it might be possible to produce the desired outcome by crudely creating a "GeneticModification:Sex" AnnotationType. Would you ever have two or more experimental factors that should not be treated in this manner? I can't think of a scenario off the top of my head. cheers, Bob. -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - 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]
[base] Tab2Mage Importer has problems finding AnnotationTypeCvImporter
Hi. This is for Dominic I guess. The last error I reported yesterday was from my own shortcutting and is fixed. (I had not yet made a design). Today I got an error when the plug-in tried to use the AnnotationTypeCvImporter. BASE error message: IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage specification This was the error message from tomcat: . . auto-detecting PluginConfiguration net.sf.basedb.core.InvalidDataException: Plugin does not implement uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter: Plugin definition[id=28; name=Annotation Type and CV Loader] at net.sf.basedb.core.PluginDefinition.newInstance(PluginDefinition.java:944) at uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs(PluginConfigDete ctor.java:179) at uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.detectPluginConfig(PluginCo nfigDetector.java:114) at uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat ionTypesWriter.java:84) at uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java :89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) at java.lang.Thread.run(Thread.java:595) 15:08:07,097 ERROR AnnotationTypesWriter:87 - No suitable plugin configuration found for this plugin in NutriBase. java.lang.NullPointerException at uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat ionTypesWriter.java:142) at uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java :89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) at java.lang.Thread.run(Thread.java:595) 15:08:07,191 ERROR jobqueue:435 - Exception while executing job: Job[id=73; name=Run plugin: Tab2Mage Importer] net.sf.basedb.core.BaseException at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429) at java.lang.Thread.run(Thread.java:595) Caused by: java.lang.NullPointerException at uk.ac.ebi.nugo.plugins.tab2mageimport.io.AnnotationTypesWriter.write(Annotat ionTypesWriter.java:142) at uk.ac.ebi.nugo.plugins.Tab2MageImporter.run(Tab2MageImporter.java:330) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java :89) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421) ... 1 more I had installed the AnnotationTypeCvImporter with the annotationtypecvimporter.xml config. I found the annotation file made by the importer (anntype.txt) on BASE2's file system and successfully imported it using only AnnotationTypeCvImporter. I did all this as the same user with admin role. Somehow the importer plug-in was not able to find the AnnotationTypeCvImporter I could manually find and use. When I tried to debug in eclipse I found that the top java ref was not in my source code; uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs. It was at uk\ac\ebi\nugo\plugins\util\tab2mage\PluginConfigDetector.java in the source code I downloaded from http://lev.thep.lu.se/trac/baseplugins/browser/trunk. So I think the jar file is out of sync with the source code. This problem might have been fixed but not included in the jar file. I hope this is the case. Best Regards Vegard Nygaard Software Engineer Department of Tumor Biology (Montebello) Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo Bioinformatics user support (NMC) Phone 0047 22935590 - 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 problems finding AnnotationTypeCvImporter
vegard nygaard wrote: > Hi. > This is for Dominic I guess. > > The last error I reported yesterday was from my own shortcutting and is > fixed. (I had not yet made a design). > > Today I got an error when the plug-in tried to use the > AnnotationTypeCvImporter. > > BASE error message: > IMPORT FAILS: The tab2mage file supplied is not compliant with the tab2mage > specification > > This was the error message from tomcat: > . > . > auto-detecting PluginConfiguration > net.sf.basedb.core.InvalidDataException: Plugin does not implement > uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter: Plugin definition[id=28; > name=Annotation Type and CV Loader] > at Quick question, are using the AnnotationTypeCvImporter plugin contained in the Tab2MageImporter.jar file? > > I had installed the AnnotationTypeCvImporter with the > annotationtypecvimporter.xml config. I found the annotation file made by the > importer (anntype.txt) on BASE2's file system and successfully imported it > using only AnnotationTypeCvImporter. I did all this as the same user with > admin role. Somehow the importer plug-in was not able to find the > AnnotationTypeCvImporter I could manually find and use. When I tried to > debug in eclipse I found that the top java ref was not in my source code; > uk.ac.ebi.nugo.plugins.util.PluginConfigDetector.getConfigs. It was at > uk\ac\ebi\nugo\plugins\util\tab2mage\PluginConfigDetector.java in the source > code I downloaded from http://lev.thep.lu.se/trac/baseplugins/browser/trunk. > So I think the jar file is out of sync with the source code. This problem > might have been fixed but not included in the jar file. I hope this is the > case. > > Sorry, I have made some improvement to the code to fix bugs, enhancements e.g. pooling support and also working on an enhanced validation routine. A sub branch to hold previous version would suffice but Jari is the expert on this. May I also refer you to Jari's email on links. Please use this link for the source. http://baseplugins.thep.lu.se/browser/trunk/uk/ ¬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]
