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:

Description

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).

BASEfile
section	plugin
uniqueName	molbio.mgh.harvard.edu/dpark/limitint
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\@molbio.mgh.harvard.edu.\r\n
execName	molbio.mgh.harvard.edu/dpark/basefile-general.pl
usedColumns	position\treporter\treporterId
usedFields	_allIntensities
geneAverages	0
serialFormat	0
url	
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

/usr/local/base2/www/plugins/molbio.mgh.harvard.edu/dpark

  • 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   
Bioassayset   
Experiment explorer   
Options…   
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:1.8.1.2) Gecko/20070219 Firefox/2.0.0.2
Error message 	
Stack trace 	

...at net.sf.basedb.plugins.Base1PluginExecuter.getJobParameters(Base1PluginExecuter.java:870)
...at net.sf.basedb.plugins.Base1PluginExecuter.getConfigureJobParameters(Base1PluginExecuter.java:678)
...at net.sf.basedb.plugins.Base1PluginExecuter.getRequestInformation(Base1PluginExecuter.java:233)
...at PluginConfigurationRequest.getRequestInformation(PluginConfigurationRequest.java:137)
...at org.apache.jsp.common.plugin.index_jsp.getJspPage(index_jsp.java:66)
...at org.apache.jsp.common.plugin.index_jsp._jspService(index_jsp.java:300)
...at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

...at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:332)
...at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
...at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)
...at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at net.sf.basedb.clients.web.servlet.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:71)
...at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
...at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
...at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
...at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
...at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
...at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
...at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
...at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
...at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869)
...at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664)
...at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527)
...at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80)
...at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
...at java.lang.Thread.run(Thread.java:595)

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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