Java tutorial
/** * '$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 edu.lternet.pasta.dml.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 edu.lternet.pasta.dml.parser.Attribute; import edu.lternet.pasta.dml.parser.AttributeList; import edu.lternet.pasta.dml.parser.DataPackage; import edu.lternet.pasta.dml.parser.Domain; import edu.lternet.pasta.dml.parser.Entity; import edu.lternet.pasta.dml.parser.NumericDomain; import edu.lternet.pasta.dml.parser.TextDomain; import edu.lternet.pasta.dml.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 edu.lternet.pasta.dml.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 edu.lternet.pasta.dml.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 edu.lternet.pasta.dml.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; } }