CXF JAX-RS IllegalAnnotationException - Class has two properties of the same name

I am currently using Apache CXF to provide RESTful web services for the Australian PhenomeBank.

I was attempting to assign annotations of private field members of a class as follows:

    @XmlElement(name="mutationType")
    @XmlElementWrapper(name="mutationTypes")
    private Set<MutationType> mutationTypes  = EnumSet.noneOf(MutationType.class);

What I had forgot to do was assign the XmlAccessorType as follows:

@XmlRootElement(name="SearchCriteria")
@XmlAccessorType(XmlAccessType.FIELD)
public class SearchCriteria

Ant OutOfMemoryException

Currently where I work we use Ant to deploy our application to a Tomcat server. Recently, I integrated several new libraries for Apache's CXF web services and reran my ant script to do the deployment and encountered this:

deploy:
[echo] Deploying to 150.203.7.14:8080 ...

BUILD FAILED
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2786)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:94)
at sun.net.www.http.PosterOutputStream.write(PosterOutputStream.java:61)

at java.io.BufferedOutputStream.write(BufferedOutputStream.java:105)

To resolve this I ended up setting the ANT_OPTS environment variable on my Windows machine as follows:

C:\workspace\PhenomeBank>set ANT_OPTS=-Xmx500m

Searching and Displaying Terms OBO

Here is some sample code on how to search for a term and display its properties:

package au.edu.apf.phenomebank.ontology;

import java.io.File;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.util.Collection;
import java.util.LinkedList;

import org.obo.dataadapter.DefaultOBOParser;
import org.obo.dataadapter.OBOParseEngine;
import org.obo.datamodel.Dbxref;
import org.obo.datamodel.IdentifiedObject;
import org.obo.datamodel.Link;
import org.obo.datamodel.LinkDatabase;
import org.obo.datamodel.NestedValue;
import org.obo.datamodel.OBOObject;
import org.obo.datamodel.OBOSession;
import org.obo.datamodel.PropertyValue;
import org.obo.datamodel.Synonym;
import org.obo.util.TextUtil;

/**
* Testing ontology parsing
*
*
* @author Philip Wu
*/
public class OntologyTest {

  public static void main (String[] args) throws Exception {
      System.out.println("Start");
    

      DefaultOBOParser parser = new DefaultOBOParser();
      OBOParseEngine engine = new OBOParseEngine(parser);
    
      String path = "C:/Documents and Settings/a295029/Desktop/latest_MPheno_OBO.ontology";
      Collection paths = new LinkedList();
      paths.add(path);
      engine.setPaths(paths);
    
      engine.parse();
    
      OBOSession session = parser.getSession();

    
      // Using the Ontology
      IdentifiedObject obj = session.getObject("MP:0009788");
      if (obj != null) {
          if (obj instanceof OBOObject) {
              OBOObject term = (OBOObject) obj;
              dumpTerm(System.out, term);
          }          
      }
    
    
      System.out.println("Finished");
  }

  public static void dumpNestedValue(PrintStream ps, NestedValue nv) {
      if (nv!= null) {
          ps.print(" Name: "+nv.getName());
          if (nv.getPropertyValues() != null) {
              for (PropertyValue pv : nv.getPropertyValues()) {
                  ps.println("Property: "+pv.getProperty()+"="+pv.getValue());              
              }
          }
      }
  }

  public static void dumpTerm(PrintStream ps, OBOObject term) {
      String id = term.getID();
    
      ps.println("ID:"+id);
      ps.println("Name: "+term.getName());
    
      if (term.getIDExtension() != null) {
          ps.println("ID Extension: ");
          dumpNestedValue(ps, term.getIDExtension());
      }
    
      if (term.getPropertyValues() != null && term.getPropertyValues().size() > 0) {
          ps.println("Property values");
          dumpPropertyValues(ps, term.getPropertyValues());
      }
            
      ps.println("Definition: "+term.getDefinition());
      if (term.getDefinitionExtension() != null) {
          dumpNestedValue(ps, term.getDefinitionExtension());
      }
    
      for (Dbxref dbxref : TextUtil.getAllDbxrefs(term)) {
          ps.println("Def dbxref. ID: "+dbxref.getID()+ " DatabaseID: "+dbxref.getDatabaseID()+" Database: "+ dbxref.getDatabase()+" Desc: "+dbxref.getDesc());
        
      }
    
      for (Synonym syn : term.getSynonyms()) {          
          ps.println("Synonym. ID: "+syn.getID()+ " Text:"+syn.getText());      
      }
    
      for (Link link : term.getParents()) {
          ps.println("Parent. ID: "+ link.getParent().getID());
      }
  }

  public static void dumpPropertyValues(PrintStream ps, Collection<PropertyValue> propertyValues) {
      if (propertyValues != null) {
          for (PropertyValue pv : propertyValues) {
              ps.println("Property: "+pv.getProperty()+"="+pv.getValue());              
          }
      }
  }

}

Java OBO Parser

I've been task with importing a large OBO file into a database. However, I had trouble finding a parser pre-bundled as a set of JAR files. There is one Java OBO parser that exists but it lives within a much larger application found here:

http://www.geneontology.org/GO.java.obo.parser.shtml

He goes into some details about the writing some code, but isn't clear about which JAR files from the SVN source that are needed to get it working. Here I will provide the list of 3 JARs needed for a Java OBO parser:

• bbop.jar
• obo.jar
• owlapi-api.jar
  

For some sample code see below:

DefaultOBOParser parser = new DefaultOBOParser();
OBOParseEngine engine = new OBOParseEngine(parser);

String path = "C:/MPheno_OBO.ontology";
Collection paths = new LinkedList();
paths.add(path);
engine.setPaths(paths);

engine.parse();

To import the OBO file, I plan writing my own implementation of OBOParser for better memory usage.

Cheers,
Phil

Javascript Array from getElementsByTagName is LIVE!

The array returned by getElementsByTagName() function is LIVE!

What I mean by LIVE is that as you traverse the array and invoke changes to the DOM, the items in the array itself can change automatically! Here's an example:

var inputEls = divEl.getElementsByTagName('input');
for (var j=0; j < inputEls.length; j++) {
alert('inputEls length='+inputEls.length);
var inputEl = inputEls[j];
inputEl.parentNode.removeChild(inputEl);
}

What you'll actually see is that the length of the array automatically decreases with each iteration because I am removing those elements from the DOM.

To work around this issue I had to traverse the array backwards:

for(var i=inputEls.length-1;i>=0; i--) {

}

Java TreeSet missing elements

If you notice that some elements may be missing after having added them to a TreeSet then it is probably because your implementation of Comparator or Comparable is incorrect.

This is the key note to remember:

"If two elements are different but compareTo returns 0, then TreeSet will consider them equal, and the newly added element replaces the old one".

HibernateSystemException: attempted to assign id from null one-to-one property

I had a bidirectional relationship in my one-to-one mapping, however I had forgotten to set the objects in my Java code to reference each other. Once I had done that, the problem was resolved.

SpermAnalysis sa = new SpermAnalysis();
cryoSession.getControlMouse().setSpermAnalysis(sa);
// Bidirectional relationship
sa.setMouse(cryoSession.getControlMouse());