LinkedAnnotationAttribute.java

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/*
 * Project: Server for annotations sharing
 * Author: Ing. Jaroslav Dytrych idytrych@fit.vutbr.cz, Jan Planer xplane01@stud.fit.vutbr.cz
 * File: LinkedAnnotationAttribute.java
 * Description: Class representing attribute of type AnnotationLink
 */

package cz.vutbr.fit.knot.annotations.entity.attribute;

import cz.vutbr.fit.knot.annotations.app.AppBean;
import cz.vutbr.fit.knot.annotations.app.Constants;
import cz.vutbr.fit.knot.annotations.entity.AnnotTypeAttr;
import cz.vutbr.fit.knot.annotations.entity.Annotation;
import java.util.Iterator;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import javax.persistence.NamedQueries;
import javax.persistence.NamedQuery;
import javax.persistence.Transient;

/**
 * @file LinkedAnnotationAttribute.java
 *
 * @brief Class representing attribute of type AnnotationLink
 */

/**
 * Class representing attribute of type AnnotationLink
 *
 * @brief Class representing attribute of type AnnotationLink
 */
@Entity
@DiscriminatorValue(value = "AnnotationLink")
@NamedQueries({
  @NamedQuery(name = "Attribute.findByLinked", query = "SELECT a FROM Attribute a WHERE a.linked = :linked"),})
public class LinkedAnnotationAttribute extends BaseAttribute {

  /** Temporary id for creating links between annotations from client */
  @Transient
  private String tmpId = null;

  /**
   * Sets value of the attribute. Value should already be a native java value.
   *
   * @param value New value of the attribute
   */
  @Override
  public void setValue(Object value) {
    if (value != null) {
      this.linkedAnnotation = (Annotation) value;
      this.uri = this.linkedAnnotation.getURI();
      this.linked = linkedAnnotation.getId();
    }else{ 
      this.linkedAnnotation = null;
      this.uri = "";
      this.linked = null;
    }
  }

  /**
   * Gets value of the attribute
   *
   * @return value of the attribute
   */
  @Override
  public Object getValue() {
    return this.linkedAnnotation;
  }

  /**
   * Returns serialized informations about attribute of annotation in XML 
   * for protocol v. 2.0 without header (target and attribute specification 
   * triples)
   *
   * @param ontologyUri URI of attribute in ontology
   * @return Returns serialized informations about attribute of annotation in XML
   */
  public String toXMLStringWHV2(String ontologyUri){
    StringBuilder result = new StringBuilder();

    if(linkedAnnotation != null){
      // serialize triple with information about link
      result.append("<trix:uri>");
      result.append(linkedAnnotation.getURIV2());
      result.append("</trix:uri>");
      result.append("</trix:triple>");
      
      // <document uri><attr name><uri of type>
      result.append("<trix:triple>");
      result.append("<trix:uri>");
      result.append(this.refAnnotation.getSource()).append(this.refAnnotation.getFragmentXpointersV2());
      result.append("</trix:uri>");

      // serialize triple with name
      if (ontologyUri == null || ontologyUri.isEmpty()) {
        result.append("<trix:name>");
        result.append(this.name);
        result.append("</trix:name>");
      } else {
        result.append("<trix:uri>");
        result.append(ontologyUri);
        result.append("</trix:uri>");
      }

      // serialize triple with information about link
      result.append("<trix:uri>");
      result.append("koae:linkedAnnotation");
      result.append("</trix:uri>");
      result.append("</trix:triple>");
      
      // <document uri><attr name><type uri>
      result.append("<trix:triple>");
      result.append("<trix:uri>");
      result.append(this.refAnnotation.getSource()).append(this.refAnnotation.getFragmentXpointersV2());
      result.append("</trix:uri>");

      // serialize triple with name
      if (ontologyUri == null || ontologyUri.isEmpty()) {
        result.append("<trix:name>");
        result.append(this.name);
        result.append("</trix:name>");
      } else {
        result.append("<trix:uri>");
        result.append(ontologyUri);
        result.append("</trix:uri>");
      }

      // serialize triple with information about link
      result.append("<trix:uri>");
      result.append(linkedAnnotation.getAnnotType().getUri());
      result.append("</trix:uri>");
      result.append("</trix:triple>");
      
    }else{
      result.append("<trix:uri>");
      result.append(getAttributeType().getUri());
      result.append("</trix:uri>");
      // end of first trix
      result.append("</trix:triple>");

      // serilize triple with document uri
      result.append("<trix:triple>");
      result.append("<trix:uri>");
      result.append(this.refAnnotation.getSource()).append(this.refAnnotation.getFragmentXpointersV2());
      result.append("</trix:uri>");

      // serialize triple with name
      if(ontologyUri == null || ontologyUri.isEmpty()){
        result.append("<trix:name>");
        result.append(this.name);
        result.append("</trix:name>");
      }else{
        result.append("<trix:uri>");
        result.append(ontologyUri);
        result.append("</trix:uri>");
      }
      

      // serialize triple with information about link
      result.append("<trix:uri>");
      result.append("koae:linkedAnnotation");
      result.append("</trix:uri>");
      result.append("</trix:triple>");
    }
    
    return result.toString();
  }
  
  /**
   * Returns serialized informations about attribute of annotation in XML
   *
   * @param proto11 If true, protocol version is greater then 1.0
   * @param tmpIdForNested If true, nested annotations will have attribute tmpId
   * @param withOntology If true, URI in ontology will be serialized, if false, it will be omitted
   * @return Returns serialized informations about attribute of annotation in
   * XML
   */
  @Override
  public String toXMLString(boolean proto11, boolean tmpIdForNested, boolean withOntology) {
    String ontoString = "";

    if (withOntology) {
      if (getTypeOntologyUri() != null && !getTypeOntologyUri().isEmpty()) {
        ontoString += " typeOntologyUri=\"" + getTypeOntologyUri() + "\"";
      }

      Iterator<AnnotTypeAttr> typeAttrIt = refAnnotation.getAnnotType().getAttributes().iterator();
      while (typeAttrIt.hasNext()) {
        AnnotTypeAttr actualAttr = typeAttrIt.next();
        if (name.equals(actualAttr.getName())) {
          if (actualAttr.getUriInOntology() != null) {
            ontoString += " ontologyUri=\"" + actualAttr.getUriInOntology() + "\"";
          }
        }
      }
    }
    
    String uriString;
    
    if(uri == null || uri.isEmpty()){
      uriString = "";
    }else{
      uriString = " uri=\"" + uri + "\"";
    }

    if (this.getValue() == null && tmpId != null) {
      return "<a:attribute name=\"" + name + "\"" + ontoString + " type=\"annotationLink\" tmpId=\""
              + tmpId + "\"" + getCommentXmlPart(proto11) + ">";
    } else if(this.getValue() == null){
      if(attributeType != null){
        return "<a:attribute name=\"" + name + "\"" + ontoString + " type=\"" + attributeType.getUri() + "\"" + uriString  
                 + getCommentXmlPart(proto11) + ">";
      }else{
        if (Constants.LOG_LEVEL >= Constants.LOG_LEVEL_SERVER_INTERNAL_ERRORS) {
          String msg = "Unknown type of attribute created.";
          Logger.getLogger(LinkedAnnotationAttribute.class.getName()).log(Level.SEVERE, msg);
        }
        return "<a:attribute name=\"" + name + "\"" + ontoString + " type=\"\"" + uriString  
                 + getCommentXmlPart(proto11) + ">";
      } 
    } else {
      return "<a:attribute name=\"" + name + "\"" + ontoString + " type=\"annotationLink\"" + uriString  
               + getCommentXmlPart(proto11) + ">";
    }  
  }
  
  /**
   * Parses provided value and sets that value as a value of attribute
   *
   * @param value new value of the attribute in raw form from XML
   */
  @Override
  public void setRawValue(String value) throws IllegalArgumentException {
    if (value == null) {
      value = "";
    }
    this.uri = value;

    // try getting id of annotation by stripping off base URI
    String annotIdStr = value.replace(AppBean.getBaseAnnotUri(), "");
    Integer annotId;
    Annotation linkedAnnnot;

    // parse id of annotation
    try {
      annotId = Integer.parseInt(annotIdStr);
    } // parsing failed - it can be foreign annotation
    catch (NumberFormatException nfe) {
      annotId = null;
    }

    // if id of annotation is available
    if (annotId != null) {
      // query database for linked annotation
      Object[] params = new Object[2];
      params[0] = "id";
      params[1] = annotId;
      List aList = AppBean.getPersistenceManager().queryDB("Annotation.findById", params);

      // if annotation was found
      if (aList != null && !aList.isEmpty()) {
        linkedAnnnot = (Annotation) aList.get(0);
        this.linkedAnnotation = linkedAnnnot;
        this.setAttributeType(linkedAnnnot.getAnnotType());
        this.uri = linkedAnnnot.getURI();
      }
    }
  }  // setRawValue()

  /**
   * Gets tmpId of annotation
   *
   * @return Returns tmpId of annotation
   */
  public String getTmpId() {
    return this.tmpId;
  }

  /**
   * Sets tmpId of annotation
   *
   * @param tmpId New tmpId of annotation.
   */
  public void setTmpId(String tmpId) {
    this.tmpId = tmpId;
  }

  /**
   * Gets URI addres in ontology for this type of attribute
   *
   * @return Return URI addres in ontology for this type of attribute.
   */
  @Override
  public String getTypeOntologyUri() {
    if (this.attributeType != null) {
      return this.attributeType.getUriInOntology();
    } else {
      return "";
    }
  }
}  // class LinkedAnnotationAttribute