Here's the step by step path: 1. Go to Administrate -> Plugins -> Configurations 2. Click on the name of my genepix configuration with Plugin definition=raw data importer 3. Click 'Save and Configure' 4. Raw data type selection is GenePix, click next 5. I have previously entered in the regular expressions to parse the files, so I click 'Test with file' button 6. Click 'Browse' and select a .gpr file that I've imported, click ok and then 'Parse File' button 7. Then I get:
Could not parse the file /home/admin/raw data/N+L3[17]_N-L3[9]_090806.gpr 1. Start of data couldn't be found. Please try again with different settings. And after reviewing the parsing, I recognize that my data header is on line 32, the first row with Type='Unknown'. So I select Use as='Data Header' from the dropdown options on that line and click ok. 8. Then I am put back to the screen where I can select the 'Test with File' button again. I do this, browse for my data file, and select "Parse File' button again. The file parses correctly, and I select ok. 9. Now, I am back at the screen where I was selecting 'Test with File', but now since it parses correctly I just hit 'Next'. I get this error, which I don't remember seeing Friday, but I am getting by doing this now: Unexpected error BaseException on page /base2/common/plugin/index.jsp Version BASE 2.2.1 (build #0; schema #29) Web server Apache Tomcat/5.5.23 Database Dialect org.hibernate.dialect.MySQLInnoDBDialect JDBC Driver com.mysql.jdbc.Driver (version 5.0) Java runtime Java(TM) 2 Runtime Environment, Standard Edition (1.5.0_11-b03), Sun Microsystems Inc. Operating system Linux i386 2.6.20-1.2933.fc6xen Memory Total: 32.4 MB Free: 12.6 MB Max: 63.6 MB Browser Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.6) Gecko/20050328 Fedora/1.7.6-1.2.5 Error message could not insert collection: [net.sf.basedb.core.data.TextParameterValueData.values#440] Stack trace ...at HibernateUtil.commit(HibernateUtil.java:869) ...at DbControl.commit(DbControl.java:383) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:484) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) ...at java.lang.Thread.run(Thread.java:595) 45 more... 10. BUT if I now hit the 'Back' button, and then try the 'Next' button again, I get the error I was getting on Friday: Unexpected error BaseException on page /base2/common/plugin/index.jsp Version BASE 2.2.1 (build #0; schema #29) Web server Apache Tomcat/5.5.23 Database Dialect org.hibernate.dialect.MySQLInnoDBDialect JDBC Driver com.mysql.jdbc.Driver (version 5.0) Java runtime Java(TM) 2 Runtime Environment, Standard Edition (1.5.0_11-b03), Sun Microsystems Inc. Operating system Linux i386 2.6.20-1.2933.fc6xen Memory Total: 32.4 MB Free: 12.5 MB Max: 63.6 MB Browser Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.6) Gecko/20050328 Fedora/1.7.6-1.2.5 Error message Stack trace ...at net.sf.basedb.plugins.RawDataFlatFileImporter.getRequestInformation(RawDataFlatFileImporter.java:322) ...at PluginConfigurationRequest.getRequestInformation(PluginConfigurationRequest.java:137) ...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:364) ...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:98) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:328) ...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:315) ...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:265) ...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71) ...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) ...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) ...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:210) ...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174) ...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) ...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) ...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) ...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:151) ...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870) ...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) ...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) ...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) ...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685) ...at java.lang.Thread.run(Thread.java:595) 18 more... Hope that helps? Thanks for taking a look. I appreciate it! Marie~ > Marie Mooney wrote: >> I'm trying to import some genepix raw data files (.gpr) with the raw >> data >> importer. In configuring the plugin, I define the fields and test the >> file >> parsing, but it doesn't recognize the data header line the way I >> expressed >> it. When I select the option to make the 'unknown' line the data header, >> the file parses correctly and everything looks the way I want, but when >> I >> hit 'Next' I get the error printout below. Could anyone give me some >> direction about what I'm doing wrong here? > > I am not able to reproduce the error, though I am not sure that I am > doing it exactly the same way as you. Can you give a step-by-step path > to follow that leads to the error? > > For example: > 1. Go to Administrate -> Plugins -> Definitions > 2. Find the 'Raw data importer' and click on it's name > 3. Click on the 'New configuration' button > 4. ... please fill in here... > > > /Nicklas > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] > -- Marie Mooney [EMAIL PROTECTED] ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
