Opened 15 years ago

Closed 15 years ago

#511 closed defect (fixed)

MGH Plugins from BASE2 not working

Reported by: base Owned by: Johan Enell
Priority: major Milestone: BASE 2.2.3
Component: coreplugins Version:
Keywords: Cc:


I am trying to get the MGH plugins working under base2. I thought I would try the simple one (MGH: limit intensity). It is a single perl executable. The plugin config (as exported from BASE 1.2 is as follows).

section	plugin
versionNumber	1.1.1
name	MGH: limit intensity
descr	Enforces a minimum value for spot intensities.  Replaces all intensities below the min value specified below with that min value.  Implemented in Perl by dpark\\r\n
usedColumns	position\treporter\treporterId
usedFields	_allIntensities
geneAverages	0
serialFormat	0
minChannels	1
maxChannels	0
leaveStdin	0
leaveStdout	0
columns	position	valueType	name	commonName	options	defaultValue	enumOptions	removed
1	h	plugin			limitint		0
2	f	minval	min value	4	50		0

To install I did the following

Loggin as Admin

  • added the perl scripts under


  • imported the the base1 plugin 'plugin_MGH_ limit intensity.base' Under Plugin configurations
  • I then can see it has been added in the configuration as 'MGH: limit intensity' Analyze Base1PluginExecuter
  • when I tried to run the plugin I get a Java stack trace
Experiment explorer   
Unexpected error
java.lang.NullPointerException on page /common/plugin/index.jsp
Version 	BASE 2.2.1 (build #0; schema #29)
Web server 	Apache Tomcat/5.5.17
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_09-b03), Sun Microsystems Inc.
Operating system 	Linux amd64 2.6.19-1.2895.fc6
Memory 	Total: 277.9 MB
Free: 123.1 MB
Max: 444.5 MB
Browser 	Mozilla/5.0 (Windows; U; Windows NT 5.1; en-GB; rv: Gecko/20070219 Firefox/
Error message 	
Stack trace net.sf.basedb.plugins.Base1PluginExecuter.getJobParameters( net.sf.basedb.plugins.Base1PluginExecuter.getConfigureJobParameters( net.sf.basedb.plugins.Base1PluginExecuter.getRequestInformation( PluginConfigurationRequest.getRequestInformation( org.apache.jsp.common.plugin.index_jsp.getJspPage( 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$Http11ConnectionHandler.processConnection( org.apache.tomcat.util.threads.ThreadPool$

Change History (2)

comment:1 Changed 15 years ago by Johan Enell

Milestone: BASE 2.2.3
Status: newassigned

comment:2 Changed 15 years ago by Johan Enell

Resolution: fixed
Status: assignedclosed

(In [3195]) Fixes #511

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