Marie Mooney wrote: > 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:
I do the same thing and it works just fine. I am using BASE 2.2.2 though, but I don't think anything has changed that affects this. It seems like the database is complaining about some of the values so maybe there is something strange in your parameters that isn't taken care of correctly. First, I don't think the 'Test with file' function has anything to do with the problem, but you can use it for debugging. If you don't change any other parameter values it is most probably something in the 'Data header' value that the database doesn't like. Can you check the value to see if there is something strange with it? Try cutting away pieces (say 10-20 characters at a time) from the value until the configuration can be saved correctly. Then, it should be easy to identify the part that is problematic. > > 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... Please submit the entire stack trace. I think (hope) there is some important information later on. > > 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: The back button is broken. If it doesn't work the first time you have to close the window and start over from the beginning. Normally this wouldn't be a problem since most errors are caught and you will be taken back to the previous page automatically. It seems however that this error happens when everything already has been validated. It is the last step of sending the data to the database that for some reason fails. The NullPointerException the second time happens because everything has already been cleared the first time you hit the 'Next' button. /Nicklas ------------------------------------------------------------------------- Take Surveys. Earn Cash. 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