bin/shutdown.sh 
Using CATALINA_BASE:   /home/antonakd/BBMRI
Using CATALINA_HOME:   /usr/share/tomcat6
Using CATALINA_TMPDIR: /home/antonakd/BBMRI/temp
Using JRE_HOME:        /usr
Using CLASSPATH:       /usr/share/tomcat6/bin/bootstrap.jar
antonakd@vm7:~/BBMRI$ rm conf/Catalina/localhost/bbmri_gcc.xml 
antonakd@vm7:~/BBMRI$ rm -r webapps/bbmri_gcc
antonakd@vm7:~/BBMRI$ rm webapps/bbmri_gcc.war 
antonakd@vm7:~/BBMRI$ ls -la
antonakd@vm7:~/BBMRI$ bin/startup.sh 

• * org.apache.lucene.queryParser.ParseException: Cannot parse '': Encountered "<EOF>" at line 1, column 0.
  • ​https://issues.apache.org/jira/browse/LUCENE-881
• ​http://stackoverflow.com/questions/2272908/java-io-filenotfoundexception-too-many-open-files
  • ​http://stackoverflow.com/questions/2272908/java-io-filenotfoundexception-too-many-open-files
    • Additionally the limit of open files can be altered. For example in Linux you can modify the /etc/security/limits.conf file.

lsof -p <pid of jvm>

 where pij of jvm : ps -ax: java (for antonak)

for the same pid check on /proc/6710/fd

• ​http://lucene.apache.org/java/3_0_0/api/core/org/apache/lucene/index/IndexReader.html
  • try closing the Index Reader in DBIndex Plugin . :
  • Cannot make a static reference to the non-static method close() from the type IndexReader?
    • try closing the created object : reader.close();
    • this worked ! ​http://www.molgenis.org/ticket/583

• Upload new verion in vm7 : 
• Lifelines dictionary is here in dutch .
  • translate the labels and add them in the bbmri data model . *