Program: 12971
Project: 12971
Buggy source:
/** 
 * Test Scoring Algorithms
 * @throws IOException error
 */
public void testAlgorithims() throws IOException {
  log.info("String_Node_Str");
  Score Test;
  List<String> workEmail=Arrays.asList("String_Node_Str");
  List<String> blank=Arrays.asList();
  JenaConnect input;
  JenaConnect output;
  JenaConnect vivo;
  Properties inputProp=new Properties();
  inputProp.put("String_Node_Str","String_Node_Str");
  input=JenaConnect.parseConfig(this.vivoXML,inputProp);
  input.loadRdfFromStream(VFS.getManager().toFileObject(this.scoreInput).getContent().getInputStream(),null,null);
  Properties vivoProp=new Properties();
  vivoProp.put("String_Node_Str","String_Node_Str");
  vivo=JenaConnect.parseConfig(this.vivoXML,vivoProp);
  vivo.loadRdfFromStream(VFS.getManager().toFileObject(this.vivoRDF).getContent().getInputStream(),null,null);
  Properties outputProp=new Properties();
  outputProp.put("String_Node_Str","String_Node_Str");
  output=JenaConnect.parseConfig(this.vivoXML,outputProp);
  Test=new Score(input,vivo,output,false,false,blank,blank,blank,"String_Node_Str",null,null,null);
  Test.execute();
  if (Test.getScoreOutput().getJenaModel().isEmpty()) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  Test.getScoreOutput().getJenaModel().removeAll();
  Test=new Score(input,vivo,output,false,false,workEmail,blank,blank,null,null,null,null);
  Test.execute();
  if (output.getJenaModel().isEmpty()) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  Test.getScoreOutput().getJenaModel().removeAll();
  ByteArrayOutputStream baos=new ByteArrayOutputStream();
  input.getJenaModel().write(baos,"String_Node_Str");
  baos.flush();
  baos.close();
  new Score(new String[]{"String_Node_Str",this.vivoXML.getAbsolutePath(),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"}).execute();
  if (output.getJenaModel().isEmpty()) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  output.getJenaModel().removeAll();
  new Score(new String[]{"String_Node_Str",this.vivoXML.getAbsolutePath(),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"}).execute();
  if (output.getJenaModel().containsLiteral(null,null,"String_Node_Str")) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  Test.close();
  input.close();
  vivo.close();
  output.close();
  log.info("String_Node_Str");
}

Fixed version (ground truth):
/** 
 * Test Scoring Algorithms
 * @throws IOException error
 */
public void testAlgorithims() throws IOException {
  log.info("String_Node_Str");
  Score Test;
  List<String> workEmail=Arrays.asList("String_Node_Str","String_Node_Str");
  List<String> blank=Arrays.asList();
  JenaConnect input;
  JenaConnect output;
  JenaConnect vivo;
  Properties inputProp=new Properties();
  inputProp.put("String_Node_Str","String_Node_Str");
  input=JenaConnect.parseConfig(this.vivoXML,inputProp);
  input.loadRdfFromStream(VFS.getManager().toFileObject(this.scoreInput).getContent().getInputStream(),null,null);
  Properties vivoProp=new Properties();
  vivoProp.put("String_Node_Str","String_Node_Str");
  vivo=JenaConnect.parseConfig(this.vivoXML,vivoProp);
  vivo.loadRdfFromStream(VFS.getManager().toFileObject(this.vivoRDF).getContent().getInputStream(),null,null);
  Properties outputProp=new Properties();
  outputProp.put("String_Node_Str","String_Node_Str");
  output=JenaConnect.parseConfig(this.vivoXML,outputProp);
  Test=new Score(input,vivo,output,false,false,workEmail,true,"String_Node_Str");
  Test.execute();
  if (output.getJenaModel().isEmpty()) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  Test.getScoreOutput().getJenaModel().removeAll();
  ByteArrayOutputStream baos=new ByteArrayOutputStream();
  input.getJenaModel().write(baos,"String_Node_Str");
  baos.flush();
  baos.close();
  new Score(new String[]{"String_Node_Str",this.vivoXML.getAbsolutePath(),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"}).execute();
  if (output.getJenaModel().isEmpty()) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  output.getJenaModel().removeAll();
  new Score(new String[]{"String_Node_Str",this.vivoXML.getAbsolutePath(),"String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str","String_Node_Str"}).execute();
  if (output.getJenaModel().containsLiteral(null,null,"String_Node_Str")) {
    log.error("String_Node_Str");
    fail("String_Node_Str");
  }
  input.close();
  vivo.close();
  output.close();
  log.info("String_Node_Str");
}