[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gamexml TransactionXMLTemplate.java,NONE,

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Update of /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv32214/apollo/src/java/apollo/dataadapter/gamexml

Modified Files:
	TransactionXMLAdapter.java 
Added Files:
	TransactionXMLTemplate.java 
Log Message:
Use a template for transaction xml generating

--- NEW FILE: TransactionXMLTemplate.java ---
/*
 * Created on Sep 28, 2004
 *
 */
package apollo.dataadapter.gamexml;

import java.util.HashMap;
import java.util.Map;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;

import org.w3c.dom.Attr;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;

import apollo.datamodel.SeqFeatureI;
import apollo.editor.DeleteTransaction;

/**
 * This class is used to process xml template for transactions.
 * @author wgm
 */
public class TransactionXMLTemplate {
  // The definition for paramter mark
  private static final String PARAMTER_MARK = "$";
  private Document doc;
  // Default parameter values
  private Map defaultValues = new HashMap();
  // To control export format
  private String startIndent = "";
  private String indent = "    ";

  public TransactionXMLTemplate(String fileName) {
    loadTemplates(fileName);
  }

  public TransactionXMLTemplate(String fileName, String startIndent, String indent) {
    this(fileName);
    this.startIndent = startIndent;
    this.indent = indent;
  }

  public void setStartIndent(String indent) {
    this.startIndent = indent;
  }

  public void setIndent(String indent) {
    this.indent = indent;
  }

  private void loadTemplates(String fileName) {
    try {
      DocumentBuilderFactory df = DocumentBuilderFactory.newInstance();
      DocumentBuilder builder = df.newDocumentBuilder();
      doc = builder.parse(fileName);
      loadDefaultValues();
    }
    catch(Exception e) {
      System.err.println("XMLTemplate.loadTemplates(): " + e);
      e.printStackTrace();
    }
  }

  private void loadDefaultValues() {
    Element defaultElm = null;
    Element root = doc.getDocumentElement();
    NodeList children = root.getChildNodes();
    int size = children.getLength();
    for (int i = 0; i < size; i++) {
      Node node = children.item(i);
      if (node.getNodeName().equals("default")) {
        defaultElm = (Element) node;
      }
    }
    if (defaultElm != null) {
      children = defaultElm.getChildNodes();
      size = children.getLength();
      for (int i = 0; i < size; i++) {
        Node node = children.item(i);
        if (node.getNodeName().equals("parameter")) {
          Element paraElm = (Element) node;
          String name = paraElm.getAttribute("name");
          String value = paraElm.getAttribute("value");
          defaultValues.put(name, value);
        }
      }
    }    
  }

  public String createDeleteExonElement(DeleteTransaction tran) {
    Element delExonElm = getElement("delete", "exon");
    ParameterElement elm = new ParameterElement((Element)delExonElm.cloneNode(true));
    SeqFeatureI exon = tran.getSeqFeature();
    elm.setValue("$id", exon.getId());
    elm.setValue("$parentID", tran.getParentFeature().getId());
    elm.setValue("$seqlen", "" + Math.abs(exon.getEnd() - exon.getStart()));
    elm.setValue("$start", "" + exon.getStart());
    elm.setValue("$end", "" + exon.getEnd());
    elm.setValue("$phase", "" + exon.getPhase());
    elm.compile();
    return elm.toString();
  }

  public String createDeleteGeneElement(DeleteTransaction tran) {
    Element delGeneElm = getElement("delete", "gene");
    ParameterElement elm = new ParameterElement((Element)delGeneElm.cloneNode(true));
    SeqFeatureI gene = tran.getSeqFeature();
    elm.setValue("$id", gene.getId());
    elm.compile();
    return elm.toString();
  }

  public String createDeleteTranscriptElement(DeleteTransaction tran) {
    Element delTranscriptElm = getElement("delete", "transcript");
    ParameterElement elm = new ParameterElement((Element)delTranscriptElm.cloneNode(true));
    SeqFeatureI transcript = tran.getSeqFeature();
    elm.setValue("$id", transcript.getId());
    elm.setValue("$type", transcript.getType());
    elm.compile();
    return elm.toString();
  }

  private Element getElement(String operation, String type) {
    Element root = doc.getDocumentElement();
    NodeList children = root.getChildNodes();
    int size = children.getLength();
    for (int i = 0; i < size; i++) {
      Node node = children.item(i);
      if (node.getNodeName().equals(operation)) {
        Element elm = (Element) node;
        if (elm.getAttribute("type").equals(type)) {
          // Should be the first element
          NodeList list = elm.getChildNodes();
          for (int j = 0; j < list.getLength(); j++) {
            Node node1 = list.item(j);
            if (node1.getNodeType() == Node.ELEMENT_NODE)
              return (Element)node1;
          }
        }
      }
    }
    return null;
  }

  private Element getElement(String elmName) {
    // Find the root element
    Element root = doc.getDocumentElement();
    NodeList children = root.getChildNodes();
    int size = children.getLength();
    for (int i = 0; i < size; i++) {
      Node node = children.item(i);
      if (node.getNodeName().equals(elmName))
        return (Element)node;
    }
    return null;
  }

  public String getRootStartTag() {
    Element rootElm = getTxRootElement();
    StringBuffer buffer = new StringBuffer();
    buffer.append("<");
    buffer.append(rootElm.getNodeName());
    NamedNodeMap atts = rootElm.getAttributes();
    if (atts != null) {
      int size = atts.getLength();
      for (int i = 0; i < size; i++) {
        Node node = atts.item(i);
        if (node.getNodeType() == Node.ATTRIBUTE_NODE) {
          Attr att = (Attr) node;
          buffer.append(" ");
          buffer.append(att.getName());
          buffer.append("=\"");
          buffer.append(att.getName());
          buffer.append("\"");
        }
      }
    }
    buffer.append(">\n");
    return buffer.toString();
  }

  public String getRootEndTag() {
    Element txRootElm = getTxRootElement();
    return "</" + txRootElm.getNodeName() + ">\n";
  }

  private Element getTxRootElement() {
    Element rootElm = getElement("root");
    NodeList children = rootElm.getChildNodes();
    for (int i = 0; i < children.getLength(); i++) {
      Node node = children.item(i);
      if (node.getNodeType() == Node.ELEMENT_NODE) {
        return (Element)node;
      }
    }
    return null;
  }

  public String getPreambleString() {
    Element preamleElm = getElement("preamble");
    if (preamleElm != null) {
      StringBuffer buffer = new StringBuffer();
      // No need for <preamble> element
      NodeList children = preamleElm.getChildNodes();
      int size = children.getLength();
      for (int i = 0; i < size; i++) {
        Node node = children.item(i);
        if (node.getNodeType() == Node.ELEMENT_NODE)
          convertElementToString((Element)node, buffer, startIndent);
      }
      return buffer.toString();
    }
    return null;
  }

  private void convertElementToString(Element element, StringBuffer buffer, String indent1) {
    buffer.append(indent1);
    buffer.append("<");
    buffer.append(element.getNodeName());
    // Convert attributes
    NamedNodeMap attributes = element.getAttributes();
    if (attributes != null) {
      int size = attributes.getLength();
      Node node = null;
      for (int i = 0; i < size; i++) {
        node = attributes.item(i);
        if (node.getNodeType() == Node.ATTRIBUTE_NODE) {
          Attr att = (Attr) node;
          buffer.append(" ");
          buffer.append(att.getName());
          buffer.append("=\"");
          buffer.append(att.getValue());
          buffer.append("\"");
        }
      }
    }
    buffer.append(">");
    // Convert elements
    NodeList children = element.getChildNodes();
    int size = children.getLength();
    // A special case for text node
    if (size == 1 && children.item(0).getNodeType() == Node.TEXT_NODE) {
      Node textNode = children.item(0);
      buffer.append(textNode.getNodeValue());
    }
    else {
      // Close the start tag
      buffer.append("\n");
      for (int i = 0; i < size; i++) {
        Node node = children.item(i);
        if (node.getNodeType() == Node.ELEMENT_NODE) {
          convertElementToString((Element) node, buffer, indent1 + indent);
        } 
      }
      buffer.append(indent1);
    }
    buffer.append("</");
    buffer.append(element.getNodeName());
    buffer.append(">\n");
  }

  class ParameterElement {
    private Map parameters = new HashMap();
    private Element element;

    ParameterElement(Element elm) {
      this.element = elm;
    }

    public void setValue(String paraName, String value) {
      parameters.put(paraName, value);
    }

    /**
     * Convert all parameters to the specified values.
     *
     */
    public void compile() {
      compile(element);
    }

    private void compile(Element elm) {
      // Check attributes
      NamedNodeMap attMap = elm.getAttributes();
      if (attMap != null) {
        int size = attMap.getLength();
        Node node = null;
        for (int i = 0; i < size; i++) {
          node = attMap.item(i);
          if (node.getNodeType() == Node.ATTRIBUTE_NODE) {
            Attr attr = (Attr) node;
            String attrValue = attr.getValue();
            if (attrValue.startsWith(PARAMTER_MARK)) { // A mark for parameter
              String value = (String) parameters.get(attrValue);
              if (value == null) { // Check default value
                value = (String) defaultValues.get(attrValue);
              }
              if (value != null)
                attr.setValue(value);
            }
          }
        }
      }
      // Check child elements
      NodeList children = elm.getChildNodes();
      int size = children.getLength();
      // A special case for text node
      for (int i = 0; i < size; i++) {
        Node node = children.item(i);
        if (node.getNodeType() == Node.TEXT_NODE) { 
          // Should break here. There should be only one text node
          // Check if this TextNode is for paramter
          String textValue = node.getNodeValue();
          if (textValue.startsWith(PARAMTER_MARK)) {
            String value = (String) parameters.get(textValue);
            if (value == null) {
              value = (String) defaultValues.get(textValue);
            }
            if (value != null)
              node.setNodeValue(value);
          }
        }
        else if (node.getNodeType() == Node.ELEMENT_NODE) {
          compile((Element)node);
        }
      }
    }

    public String toString() {
      StringBuffer buffer = new StringBuffer();
      convertElementToString(element, buffer, startIndent);
      return buffer.toString();
    }
  }  
}

Index: TransactionXMLAdapter.java
===================================================================
RCS file: /cvsroot/gmod/apollo/src/java/apollo/dataadapter/gamexml/TransactionXMLAdapter.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** TransactionXMLAdapter.java	28 Sep 2004 18:39:43 -0000	1.2
--- TransactionXMLAdapter.java	30 Sep 2004 02:37:04 -0000	1.3
***************
*** 13,16 ****
--- 13,19 ----
  import java.util.List;

+ import apollo.datamodel.Exon;
+ import apollo.datamodel.SeqFeatureI;
+ import apollo.datamodel.Transcript;
  import apollo.editor.AddTransaction;
  import apollo.editor.DeleteTransaction;
***************
*** 59,94 ****
      System.out.println("Save transaction objects: " + transactions.size());
      StringBuffer buffer = new StringBuffer();
      buffer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
!     buffer.append("<transactions>\n");
!     String indent = "    ";
      Transaction ts = null;
      for (Iterator it = transactions.iterator(); it.hasNext();) {
        ts = (Transaction) it.next();
        if (ts instanceof DeleteTransaction) {
          DeleteTransaction delTs = (DeleteTransaction) ts;
!         buffer.append(indent);
!         // Time stamp
!         buffer.append("<delete timestamp=\"" + ts.getDate() + "\" ");
!         // parent_id
!         buffer.append("parentID=\"");
!         buffer.append(delTs.getParentFeature().getId());
!         buffer.append("\">\n");
!         buffer.append(indent + indent);
!         // Deleted feature
!         buffer.append("<");
!         buffer.append(delTs.getDeletedFeature().getType());
!         buffer.append(" id=\"");
!         buffer.append(delTs.getDeletedFeature().getId());
!         if (delTs.getSubpart() == null)
!           buffer.append("\" />\n"); // Close it. No more info is needed
!         else {
!           buffer.append(indent + indent + indent);
!           String subpart = delTs.getSubpart().toString();
!           buffer.append("<");
!           buffer.append(subpart);
!           buffer.append(" />\n");
!         }
!         buffer.append(indent);
!         buffer.append("</delete>\n");
        }
        else if (ts instanceof AddTransaction) {
--- 62,78 ----
      System.out.println("Save transaction objects: " + transactions.size());
      StringBuffer buffer = new StringBuffer();
+     TransactionXMLTemplate template = new TransactionXMLTemplate("conf" + File.separator + "transactionXMLTemplate.xml");
+     template.setStartIndent("    ");
+     template.setIndent("    ");
      buffer.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
!     buffer.append(template.getRootStartTag());
!     buffer.append(template.getPreambleString());
      Transaction ts = null;
+     String indent = "    ";
      for (Iterator it = transactions.iterator(); it.hasNext();) {
        ts = (Transaction) it.next();
        if (ts instanceof DeleteTransaction) {
          DeleteTransaction delTs = (DeleteTransaction) ts;
!         saveDeleteTransaction(delTs, buffer, template);
        }
        else if (ts instanceof AddTransaction) {
***************
*** 111,118 ****
        }
      }
!     buffer.append("</transactions>\n");
      saveToFile(buffer, fileName);
    }

    private void saveToFile(StringBuffer buffer, String fileName) throws IOException {
      FileWriter fileWriter = new FileWriter(fileName);
--- 95,115 ----
        }
      }
!     buffer.append(template.getRootEndTag());
      saveToFile(buffer, fileName);
    }

+   private void saveDeleteTransaction(DeleteTransaction transaction, StringBuffer buffer, TransactionXMLTemplate template) {
+     SeqFeatureI feature = transaction.getDeletedFeature();
+     if (feature instanceof Exon) {
+       buffer.append(template.createDeleteExonElement(transaction));
+     }
+     else if (feature instanceof Transcript) {
+       buffer.append(template.createDeleteTranscriptElement(transaction));
+     }
+     else { // Assume a Gene is deleted
+       buffer.append(template.createDeleteGeneElement(transaction));
+     }
+   }
+   
    private void saveToFile(StringBuffer buffer, String fileName) throws IOException {
      FileWriter fileWriter = new FileWriter(fileName);

[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gamexml TransactionXMLTemplate.java,NONE,

[Gmod-apollo-cmts] CVS: apollo/src/java/apollo/dataadapter/gamexml TransactionXMLTemplate.java,NONE,1.1 TransactionXMLAdapter.java,1.2,1.3