/**
* '$RCSfile: DocumentDataPackageParser.java,v $'
*
* '$Author: leinfelder $'
* '$Date: 2009/03/27 20:21:34 $'
* '$Revision: 1.4 $'
*
* For Details: http://kepler.ecoinformatics.org
*
* Copyright (c) 2003 The Regents of the University of California.
* All rights reserved.
*
* Permission is hereby granted, without written agreement and without
* license or royalty fees, to use, copy, modify, and distribute this
* software and its documentation for any purpose, provided that the
* above copyright notice and the following two paragraphs appear in
* all copies of this software.
*
* IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
* FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
* ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN
* IF THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY
* OF SUCH DAMAGE.
*
* THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
* INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
* MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
* PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY
* OF CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
* UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
*/
package org.ecoinformatics.datamanager.parser.document;
import java.io.InputStream;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Vector;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.xpath.CachedXPathAPI;
import org.ecoinformatics.datamanager.parser.Attribute;
import org.ecoinformatics.datamanager.parser.AttributeList;
import org.ecoinformatics.datamanager.parser.DataPackage;
import org.ecoinformatics.datamanager.parser.Domain;
import org.ecoinformatics.datamanager.parser.Entity;
import org.ecoinformatics.datamanager.parser.NumericDomain;
import org.ecoinformatics.datamanager.parser.TextDomain;
import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import edu.ucsb.nceas.utilities.OrderedMap;
import edu.ucsb.nceas.utilities.XMLUtilities;
/**
* This is plugin Parser parses any XML file to
* retrieve the specified xPath elements as a Map record
*
* Note that the document
* needs to have a 'packageId' attribute as part of the root node
*
*
* @author leinfelder
*/
public class DocumentDataPackageParser implements DataPackageParserInterface
{
/*
* Class fields
*/
private static Log log = LogFactory.getLog(DocumentDataPackageParser.class);
/*
* Instance fields
*/
// previously these were constants, now member variables with defaults
protected String packageIdPath = null;
protected String packageId = null;
private DocumentDataPackage dataPackage = null;
private Map attributeXPathMap = null;
private Map record = null;
private Document doc = null;
/**
* Default constructor - no custom xpath parameter
*/
public DocumentDataPackageParser() {
this.packageIdPath = "//*/@packageId";
this.record = new HashMap();
}
public void setAttributeXPathMap(Map xpaths) {
this.attributeXPathMap = xpaths;
}
private Vector getRecordRow() {
Vector row = new Vector();
row.addAll(record.values());
return row;
}
/**
* Constructor that accepts a packageId
* Allows packageId supplied by external caller
* @param packageId specifying the desired id for the resulting data package
*/
public DocumentDataPackageParser(String packageId) {
this();
//set the param
this.packageId = packageId;
}
/* (non-Javadoc)
* @see org.ecoinformatics.datamanager.parser.generic.GenericDatasetParserInterface#parse(org.xml.sax.InputSource)
*/
public void parse(InputSource source) throws Exception
{
DocumentBuilder builder =
DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = builder.parse(source);
parseDocument();
}
/* (non-Javadoc)
* @see org.ecoinformatics.datamanager.parser.generic.GenericDatasetParserInterface#parse(java.io.InputStream)
*/
public void parse(InputStream is) throws Exception
{
DocumentBuilder builder =
DocumentBuilderFactory.newInstance().newDocumentBuilder();
doc = builder.parse(is);
parseDocument();
}
/**
* Parses the document. Uses the attributeMap to determine the
* attributes included in the returned Map record
*
* @param doc the Document object to be parsed
*/
private void parseDocument() throws Exception {
//look up the packageId if not set
if (packageId == null) {
CachedXPathAPI xpathapi = new CachedXPathAPI();
try {
// process packageid
Node packageIdNode = xpathapi.selectSingleNode(doc, packageIdPath);
if (packageIdNode != null) {
packageId = packageIdNode.getNodeValue();
}
}
catch (Exception e) {
throw new Exception(
"Error extracting packageId from root of document.");
}
}
dataPackage = new DocumentDataPackage(packageId);
}
public void generateEntity() throws Exception {
if (this.attributeXPathMap == null) {
throw new Exception(
"Must specify attribute xPaths for document->record parsing.");
}
//now get the flattened document as a map
this.record = document2Map(doc, this.attributeXPathMap);
//convert the map to an entity
Entity entity = map2Entity(this.record, dataPackage.getPackageId());
//add the entity to the datapackage
this.dataPackage.clearEntityList();
this.dataPackage.add(entity);
//set the row record data
this.dataPackage.setRecordRow(getRecordRow());
}
/* (non-Javadoc)
* @see org.ecoinformatics.datamanager.parser.generic.GenericDatasetParserInterface#getDataPackage()
*/
public DataPackage getDataPackage()
{
return dataPackage;
}
public static Entity map2Entity(Map record, String entityId) {
AttributeList attributeList = new AttributeList();
Iterator iter = record.keySet().iterator();
while (iter.hasNext()) {
String id = (String) iter.next();
String name = id;
Object value = record.get(id);
Domain domain = new TextDomain();
//TODO handle more specific numeric types?
if (value instanceof Number) {
domain = new NumericDomain("real", null, null);
}
Attribute a = new Attribute(id, name, domain);
attributeList.add(a);
}
Entity entity =
new Entity(
entityId,
entityId, // + " name",
entityId, // + " description",
attributeList);
//set some other crucial info for generating the tables and sql
entity.setPackageId(entity.getId());
entity.setEntityIdentifier(entity.getId());
return entity;
}
public static Map document2Map(Document doc, Map attributeXPaths) {
Map record = new OrderedMap();
try {
//go through the list of attribute labels (key to xpath values)
Iterator xPathIter = attributeXPaths.keySet().iterator();
while (xPathIter.hasNext()) {
String attributeLabel = (String) xPathIter.next();
String attributeXPath = (String) attributeXPaths.get(attributeLabel);
//handle NodeList, not just single Node
NodeList attributeNodeList = XMLUtilities.getNodeListWithXPath(doc.getDocumentElement(), attributeXPath);
//include placeholders for those non existent attributes but include null values
if (attributeNodeList == null) {
log.debug("no nodes found for xPath: " + attributeXPath);
record.put(attributeLabel, null);
log.debug("added null placeholder for attribute: " + attributeLabel);
continue;
}
//get the value[s] for the attribute
for (int i=0; i < attributeNodeList.getLength(); i++) {
//get the node
Node attributeNode = attributeNodeList.item(i);
//get the text value of the node
//TODO should we use DOM level 3 and assume java 1.5?
String nodeTextContent = null; //attributeNode.getTextContent();
nodeTextContent = attributeNode.getTextContent();
// if (attributeNode.getFirstChild() != null && attributeNode.getFirstChild().getNodeType() == Node.TEXT_NODE) {
// nodeTextContent = attributeNode.getFirstChild().getNodeValue();
// }
//add the attribute to the Map, taking care to handle multiples
String columnLabel = attributeLabel;
if (record.containsKey(columnLabel)) {
if (i == 1) {
//get the first original label without the number and reassign it with "_1"
Object firstValue = record.get(columnLabel);
//record.remove(columnLabel);
record.put(columnLabel + "_" + i, firstValue);
}
columnLabel = columnLabel + "_" + (i+1);
}
record.put(columnLabel, nodeTextContent);
log.debug("added flat attribute: " + columnLabel + "=" + nodeTextContent);
}
}
}
catch (Exception e) {
log.error("could not flatten attributes in document: " + e.getMessage());
e.printStackTrace();
}
return record;
}
}