Run time error creating LocationType table

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Shilpa
2006-04-04
2013-04-25
  • Shilpa
    Shilpa
    2006-04-04

    Hello,

    I am trying to run XmlPipeDB project within NetBeans 5.0.  It compiles but gives the following  run time error:

    "SEVERE: Unsuccessful: create table LocationType (idInternal varchar(32) not null, sequence varchar(255), begin varchar(32), position varchar(32), end varchar(32), CommentTypeImpl_id varchar(32), LocationInternal_index int4, primary key (idInternal))"

    Why is it not able to creat the LocationType table? 

    I am using PostgreSql.  Any help would be greatly appreciated.

    Thanks,
    Shilpa

     
    • Joe Boyle
      Joe Boyle
      2006-04-09

      Shilpa,
         Are you using a uniprot xsd file?  If so, under the uniprotdb project there is a tool that post processes the schema.sql and the hibernate mappings.  The problem is that in the uniprot xsd file there are strings larger than varchar(255). 

          I must also say that the XMLPipeDB will soon be replaced.  We decided to split the project up into multiple parts.  xsd2db will be used to create the necessary source, hibernate mappings, and sql files.  XMLPipeDBUtils can then be used in order to import the source generated by xsd2db into a database of your choice, not limited to Postgreql.  It will also have features that can query objects via hql calls in the near feature.  And then there is uniprotdb which can be used specifically for the uniprot xsd.  It includes all the source, hibernate mappings, and sql files for uniprot already post processed.  The post processor is also available within that project.  Lastly, if you are using GenMapp, gmbuilder will allow the user to create access databases files that can be used by GenMapp.  This feature, along with XMLPipeDBUtils is still being developed.  But xsd2db and uniprotdb should be enough to get you started if that is what you are looking for.  If you have any more questions, please let me know.  Thanks. 

      Joe

       
    • Shilpa
      Shilpa
      2006-04-10

      Joe,

      Thanks for help.  Using a different xsd got rid of that error. How do you run the ImportUniprotXML and TestDriver class?  I tried adding the following to the build.xml:

      <target name="test1" depends="compile">
            <java fork="true"
            classname="edu.lmu.xmlpipedb.ImportUniprotXML"
            classpath="{classes};.">
            </java>
        </target>

      but I am getting "failed to prepare tests" error.  I am using Netbeans and I am new Ant.  Thank you in advance for your help.

      Shilpa

       
    • Joe Boyle
      Joe Boyle
      2006-04-11

      Shilpa,
         I am not exactly sure what you are trying to do.  Where is this TestDriver class located?  I do not recall seeing that in the project at all.  In addition, are you still using the old xmlpipedb project or one of the newer sub projects?  If you are still using the old xmlpipedb project, the following code needs to be added to the ImportUniprotXML class in the loadXML method:

          Transaction transaction = null;
          try {
              transaction = saveSession.beginTransaction();
              saveSession.saveOrUpdate(object);
              transaction.commit();
          } catch(Exception ex) {
              if (transaction != null)
                  transaction.rollback();
              throw ex;
          } finally {
              saveSession.close();
          }

      This would replace this section of code:
          saveSession.saveOrUpdate(object);
          saveSession.flush();
             
          // Close the session
          saveSession.close();

      Hope this helps and let me know if you have any more questions.  Thanks. 

      Joe

       
    • Shilpa
      Shilpa
      2006-04-14

      Hello,

      After reviewing replys to some of my previous post, I think it may be better for me to download xsd2db and XMLPipeDBUtils project.  However, I am not able to conntect to cvs server.  I am getting the following error:

      cvs.exe [login aborted]: connect to cvs.sourceforge.net(66.35.250.207):2401 fail
      ed: Connection timed out.

      I am able to ping 66.35.250.207.  Any ideas why can't connect?

      Thank you in advance.
      Shilpa

       
    • Joe Boyle
      Joe Boyle
      2006-04-14

      Well I know CVS has had problems on and off all month.  So all I can say is try again later.  xsd2db should work out fine but I met with the XMLPipeDBUtils people last night and they are still working out some bugs.  So you may run into some issues, and if you do, post what they are so we can fix them.  We feel it is close to being where we want it to be though.  Good luck. 

      Joe