Problems in Molgenis update

• After last update from molgenis3_3 , compilation errors:
  • Revealed an error in model :
    • Entity patient contained a field : Syndrome_id , from the old table Syndrome ,which now is User . user_id xref already exists .
      • Changed it in * <field name="PatientID" type="autoid" />
      • since there wasn't any primary key in the table(!) .
      • Also delete database , delete generated folder , Molgenis Generate again....
      • Open mysql as root :
        • mysql> create database hvp_pilot;
        • * mysql> grant all privileges on hvp_pilot.* to molgenis@localhost identified by 'molgenis'; flush privileges;
      • Clear & delete tomcat, run -->
        • Error :
          • "The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: !.:/Library/Java?/Extensions:/System/Library/Java/Extensions:/usr/lib/java"
        • Solution : ​http://www.liferay.com/web/guest/community/wiki/-/wiki/Main/Tomcat+Native+Library
        • Install tomcat native : sudo port install tomcat-native &
          • From the Terminal program, make symbolic links from the /opt/local/lib/libtcnative-1.* to /usr/lib/java:sudo ln -s /opt/local/lib/libtcnative-1.* /usr/lib/java
        • Delete & restart :
          • * SEVERE: An incompatible version 1.1.14 of the APR based Apache Tomcat Native library is installed, while Tomcat requires version 1.1.17
          • ​http://old.nabble.com/Tomcat-5.5.16---Error-configuring-application-listener-of-class-listeners.ContextListener-to3440834.html#a3487618
    • Another revealed error :
      • java.io.IOException: Cannot run program "dot": error=2, No such file or directory
        • later : install graphviz
    • Created a new project in workspace in order to debug . potential problem in lucene code ??
      • the problem is the naming of fields in DB ?