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:
> []
> Stack trace
> HibernateUtil.commit(
> DbControl.commit(
> org.apache.jsp.common.plugin.index_jsp._jspService(
> org.apache.jasper.runtime.HttpJspBase.service(
> javax.servlet.http.HttpServlet.service(
> org.apache.jasper.servlet.JspServletWrapper.service(
> org.apache.jasper.servlet.JspServlet.serviceJspFile(
> org.apache.jasper.servlet.JspServlet.service(
> javax.servlet.http.HttpServlet.service(
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
> org.apache.catalina.core.ApplicationFilterChain.doFilter(
> net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
> org.apache.catalina.core.ApplicationFilterChain.doFilter(
> org.apache.catalina.core.StandardWrapperValve.invoke(
> org.apache.catalina.core.StandardContextValve.invoke(
> org.apache.catalina.core.StandardHostValve.invoke(
> org.apache.catalina.valves.ErrorReportValve.invoke(
> org.apache.catalina.core.StandardEngineValve.invoke(
> org.apache.catalina.connector.CoyoteAdapter.service(
> org.apache.coyote.http11.Http11Processor.process(
> org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(
> org.apache.tomcat.util.threads.ThreadPool$
>    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.


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