date:20070907

Re: [base] BASE 2.4 on Windows

2007-09-07 Thread jesse paquette

That was it, thanks!

Jesse

From: Nicklas Nordborg [EMAIL PROTECTED]
Reply-To: BASE ML basedb-users@lists.sourceforge.net
To: BASE ML basedb-users@lists.sourceforge.net
Subject: Re: [base] BASE 2.4 on Windows
Date: Fri, 07 Sep 2007 09:16:21 +0200

jesse paquette wrote:
  Thanks Jari,

  Was the above the only things you needed to do to get BASE to run on MS
  Windows?

  Not completely.  I submitted a bug ticket via user base.  On the 
Create
  plugin page, I get a java.lang.ClassFormatError (page
  admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 
in
  class file se/lu/thep/affymetrix/RMAExpress

It is probably a bug in Java. Upgrade to the latest 1.5 or 1.6.
For more info see: http://base.thep.lu.se/ticket/747

/Nicklas

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[base] following 2.1 getting started

2007-09-07 Thread jesse paquette

Hello all,

In section 1c the getting started manual asks me to configure a Reporter map 
importer plugin for Genepix.  I've set up the Reporter importer and Raw data 
importer plugins, but there is no entry in the plugins list for Reporter 
map importer.  Has this been done away with between versions 2.1 and 2.4.0?

I tried to create the plugin myself using the class 
net.sf.basedb.plugins.ReporterMapFlatFileImporter, but the system doesn't 
seem to let me.

Thanks,

Jesse

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Re: [base] BASE 2.4 on Windows

2007-09-07 Thread Nicklas Nordborg

jesse paquette wrote:
 Thanks Jari,
 
 Was the above the only things you needed to do to get BASE to run on MS
 Windows?
 
 Not completely.  I submitted a bug ticket via user base.  On the Create 
 plugin page, I get a java.lang.ClassFormatError (page 
 admin/plugindefinitions/index.jsp) with message Unknown constant tag 0 in 
 class file se/lu/thep/affymetrix/RMAExpress

It is probably a bug in Java. Upgrade to the latest 1.5 or 1.6.
For more info see: http://base.thep.lu.se/ticket/747

/Nicklas


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Re: [base] Error uploading CDF file

2007-09-07 Thread jesse paquette

  I'm trying to get BASE up and running, and I've hit a snag attempting to
  load a CDF file.  The HTTP Status 500 page popped up with the following
  information:
 
  org.apache.jasper.JasperException: Unable to compile class for JSP:
 

We know about this problem (http://base.thep.lu.se/ticket/736). It will
be fixed in the 2.4.1 release. The problem only happens because the file
upload has already failed for some other reason. The error message below
is coming from the page that should take care of and display the
original error. Unfortunately the original error is lost so there is no
way to know what is causing the upload to fail. It could for example be
a permission problem, lack of quota, a network timeout, etc. File
uploads that are successful are not affected by this bug.

/Nicklas

Ok, I deleted the extra line at the end of the show_exception file.  The new 
error message is:

File creation in base.config[userfiles] failed

With a stack trace of:

...at File.getNewFile(File.java:1002)
...at File.getUploadStream(File.java:878)
...at 
org.apache.jsp.filemanager.upload.upload_jsp._jspService(upload_jsp.java:175)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
...at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:393)
...at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)

...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
...at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
...at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
...at 
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72)
...at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
...at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
...at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
...at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
...at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
...at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
...at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
...at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:263)
...at 
org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:852)
...at 
org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:584)
...at 
org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1508)
...at java.lang.Thread.run(Unknown Source)

Caused by: java.io.IOException
...at java.io.WinNTFileSystem.createFileExclusively(Native Method)
...at java.io.File.createNewFile(Unknown Source)
...at File.getNewFile(File.java:998)
...at File.getUploadStream(File.java:878)
...at 
org.apache.jsp.filemanager.upload.upload_jsp._jspService(upload_jsp.java:175)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
...at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:393)
...at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
...at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
...at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
...at 
net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:72)
...at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
...at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
...at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
...at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
...at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
...at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
...at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
...at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:263)
...at 
org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:852)
...at 
org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:584)
...at

Re: [base] Error uploading CDF file

2007-09-07 Thread Nicklas Nordborg

jesse paquette wrote:
 Ok, I deleted the extra line at the end of the show_exception file.  The new 
 error message is:
 
 File creation in base.config[userfiles] failed

There can be two reasons:

1) The path specified in base.config for the userfiles property doesn't 
exists
2) The user that Tomcat runs as doesn't have permission to create new 
files in that directory

/Nicklas

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Re: [base] BASE 2.4 on Windows

[base] following 2.1 getting started

Re: [base] BASE 2.4 on Windows

Re: [base] Error uploading CDF file

Re: [base] Error uploading CDF file

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