Java tutorial
/*************************************************************************** * Copyright (C) 2009 Atlas of Living Australia * All Rights Reserved. * * The contents of this file are subject to the Mozilla Public * License Version 1.1 (the "License"); you may not use this file * except in compliance with the License. You may obtain a copy of * the License at http://www.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or * implied. See the License for the specific language governing * rights and limitations under the License. ***************************************************************************/ package org.ala.harvester; import java.io.BufferedReader; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import java.io.StringReader; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.regex.Matcher; import java.util.regex.Pattern; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; import javax.xml.parsers.ParserConfigurationException; import javax.xml.xpath.XPath; import javax.xml.xpath.XPathConstants; import javax.xml.xpath.XPathExpressionException; import javax.xml.xpath.XPathFactory; import org.ala.documentmapper.DocumentMapper; import org.ala.documentmapper.MappingUtils; import org.ala.repository.ParsedDocument; import org.ala.repository.Predicates; import org.ala.repository.Repository; import org.ala.repository.Triple; import org.ala.util.Response; import org.ala.util.WebUtils; import org.apache.commons.httpclient.HttpClient; import org.apache.commons.httpclient.HttpStatus; import org.apache.commons.httpclient.methods.GetMethod; import org.apache.commons.httpclient.params.HttpMethodParams; import org.apache.commons.lang.StringUtils; import org.apache.log4j.Logger; import org.springframework.beans.factory.config.BeanDefinition; import org.springframework.context.ApplicationContext; import org.springframework.context.annotation.Scope; import org.springframework.context.support.ClassPathXmlApplicationContext; import org.springframework.stereotype.Component; import org.w3c.dom.Document; import org.w3c.dom.NodeList; import org.xml.sax.InputSource; /** * A Harvester class for Western Australian Insect Study Society * * @author Tommy Wang */ @Component("WaissHarvester") @Scope(BeanDefinition.SCOPE_PROTOTYPE) public class WaissHarvester implements Harvester { protected Logger logger = Logger.getLogger(MaHarvester.class); protected String endpoint; // private String eolGroupId; // private String MorphbankRestBaseUrl; // private String MorphbankApiKey; // private int recordsPerPage; protected Repository repository; protected int timeGap = 0; // private static final int RESULT_LIMIT = 6544; private static final int WAISS_INFOSOURCE_ID = 1110; protected String contentType = "image/jpeg"; protected final String baseUrl = "http://www.museum.wa.gov.au/waiss/pages/image.htm"; /** * Main method for testing this particular Harvester * * @param args */ public static void main(String[] args) throws Exception { String[] locations = { "classpath*:spring.xml" }; ApplicationContext context = new ClassPathXmlApplicationContext(locations); WaissHarvester h = new WaissHarvester(); Repository r = (Repository) context.getBean("repository"); h.setRepository(r); //set the connection params Map<String, String> connectParams = new HashMap<String, String>(); connectParams.put("endpoint", "http://www.museum.wa.gov.au/waiss/pages/image.htm"); h.setConnectionParams(connectParams); h.start(WAISS_INFOSOURCE_ID); } /** * @see org.ala.harvester.Harvester#setConnectionParams(java.util.Map) */ @Override public void setConnectionParams(Map<String, String> connectionParams) { this.endpoint = connectionParams.get("endpoint"); } @Override public void start(int infosourceId, int timeGap) throws Exception { this.timeGap = timeGap; start(infosourceId); } /** * @see org.ala.harvester.Harvester#start() */ @SuppressWarnings("unchecked") @Override public void start(int infosourceId) throws Exception { // TODO Auto-generated method stub Thread.sleep(timeGap); // Obtains the image listing on the page number specified. // Instance variable `currentResDom` will have new // DOM representation of the result. String indexStr = getIndexPageStr(); // String xpathToImageUrls = "//div[@align='center']/a[@target='_blank']/@href"; // // Document document = getDocument(indexStr.getBytes()); // XPathFactory factory = XPathFactory.newInstance(); // XPath xpath = factory.newXPath(); // // NodeList nodes = (NodeList) xpath.evaluate(xpathToImageUrls, document, XPathConstants.NODESET); // // for (int i = 0; i < nodes.getLength(); i++) { // String imageUrl = (nodes.item(i)).getNodeValue(); // imageUrl = StringUtils.trimToNull(imageUrl); // // if (imageUrl != null && !"".equals(imageUrl)) { // imageUrl = "http://www.museum.wa.gov.au/waiss/pages/" + imageUrl; // System.out.println(imageUrl); // } // } Pattern speciesPattern = Pattern.compile("(?:<a href=\")" + "(images/[a-zA-Z0-9\\.]*)" + "(?:\" target=\"_blank\"><img src=\")" + "(?:\\.\\./a_data/[a-zA-Z0-9_]{1,}\\.jpg)" + "(?:\" width=\"[0-9]{1,}\" height=\"[0-9]{1,}\" border=\"[0-9]{1,}\"></a></div></td>[\\s]{0,}<td[ width=\"422]*>[\\s]*[<div align=\"center\">]*<span class=\"style4\"><strong>)" + "([a-zA-Z \\-']*)" + "(?:</strong>[ ]*\\([ ]*<em>)" + "([a-zA-Z ]*)"); Pattern creatorPattern = Pattern.compile("(?:Photo: )" + "([a-zA-Z ]{1,})"); Matcher m = speciesPattern.matcher(indexStr); String[] creatorArray = new String[9]; Matcher m2 = creatorPattern.matcher(indexStr); int searchIdx2 = 0; int creatorCounter = 0; while (m2.find(searchIdx2)) { int endIdx2 = m2.end(); String creator = m2.group(1); if (creator != null && !"".equals(creator)) { creatorArray[creatorCounter] = creator; creatorCounter++; } searchIdx2 = endIdx2; } int speciesCounter = 0; int searchIdx = 0; // get all the family links while (m.find(searchIdx)) { int endIdx = m.end(); // String found = content.substring(startIdx, endIdx); String url = "http://www.museum.wa.gov.au/waiss/pages/" + m.group(1); String commonName = m.group(2); String sciName = m.group(3); // String generatedUrl = this.endpoint + url; // System.out.println("URL:" + url); System.out.println("Common Name: " + commonName); System.out.println("Sci Name:" + sciName); // processSingleImage(url.trim(), commonName.trim(), sciName.trim(), infosourceId, creatorArray[speciesCounter]); speciesCounter++; // // identifiers.add(generatedUrl); searchIdx = endIdx; } System.out.println(speciesCounter); } private Document getDocument(byte[] content) throws ParserConfigurationException { DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance(); dbFactory.setNamespaceAware(false); InputSource is = new InputSource(new StringReader(new String(content))); DocumentBuilder parser = dbFactory.newDocumentBuilder(); Document document = null; try { document = parser.parse(is); } catch (Exception e) { e.printStackTrace(); } return document; } @SuppressWarnings("unchecked") public void processSingleImage(String url, String commonName, String scientificName, int infosourceId, String creator) throws Exception { ParsedDocument imageDoc = new ParsedDocument(); if (scientificName != null && !"".equals(scientificName)) { List<Triple<String, String, String>> triples = imageDoc.getTriples(); Map<String, String> dcs = imageDoc.getDublinCore(); String subject = MappingUtils.getSubject(); Response response = WebUtils.getUrlContentAsBytes(url); imageDoc.setGuid(url); imageDoc.setContent(response.getResponseAsBytes()); imageDoc.setContentType(response.getContentType()); dcs.put(Predicates.DC_TITLE.toString(), scientificName); dcs.put(Predicates.DC_IDENTIFIER.toString(), "http://www.museum.wa.gov.au/waiss/pages/image.htm"); dcs.put(Predicates.DC_CREATOR.toString(), creator); dcs.put(Predicates.DC_LICENSE.toString(), "CC BY-NC"); dcs.put(Predicates.DC_RIGHTS.toString(), "Copyright by " + creator); dcs.put(Predicates.COUNTRY.toString(), "Australia"); dcs.put(Predicates.DC_IS_PART_OF.toString(), "http://www.museum.wa.gov.au/waiss/pages/image.htm"); if (scientificName != null && !"".equals(scientificName)) { triples.add(new Triple(subject, Predicates.SCIENTIFIC_NAME.toString(), scientificName)); } if (commonName != null && !"".equals(commonName)) { triples.add(new Triple(subject, Predicates.COMMON_NAME.toString(), commonName)); } } if (imageDoc != null) { debugParsedDoc(imageDoc); this.repository.storeDocument(infosourceId, imageDoc); } } private String inputStream2String(InputStream is) throws IOException { BufferedReader in = new BufferedReader(new InputStreamReader(is)); StringBuffer buffer = new StringBuffer(); String line = ""; while ((line = in.readLine()) != null) { buffer.append(line); } return buffer.toString(); } private String getIndexPageStr() throws Exception { // Constructs the GET URL to search. // `woe_id` is Yahoo! Where On Earth ID. // Issue // http://api.Morphbank.com/services/rest/?method=Morphbank.places.find&api_key=08f5318120189e9d12669465c0113351&query=australia // to find Australia. // `woe_id` here is country level code, as opposed to continent code. String urlToSearch = this.endpoint; System.out.println("Search URL: " + urlToSearch); /* * // Default parameters if not supplied. if (this.MorphbankApiKeySupplied * == false) { urlToSearch += "&" + "api_key=" + this.MorphbankApiKey; } if * (this.currentPageNumSupplied == false) { urlToSearch += "&" + "page=" * + this.currentPageNum; } if (this.recordsPerPageSupplied == false) { * urlToSearch += "&" + "per_page=" + this.recordsPerPage; } */ // System.out.println(urlToSearch); logger.debug("URL to search is: " + "`" + urlToSearch + "`" + "\n"); // Create an instance of HttpClient. HttpClient client = new HttpClient(); // Create a method instance. GetMethod method = new GetMethod(urlToSearch); // Provide custom retry handler is necessary method.getParams().setParameter(HttpMethodParams.HTTP_CONTENT_CHARSET, "UTF-8"); method.getParams().setParameter(HttpMethodParams.HTTP_ELEMENT_CHARSET, "UTF-8"); method.getParams().setParameter(HttpMethodParams.HTTP_URI_CHARSET, "UTF-8"); try { int statusCode = client.executeMethod(method); if (statusCode != HttpStatus.SC_OK) { String errMsg = "HTTP GET to " + "`" + urlToSearch + "`" + " returned non HTTP OK code. Returned code " + statusCode + " and message " + method.getStatusLine() + "\n"; method.releaseConnection(); throw new Exception(errMsg); } // InputStream responseStream = method.getResponseBodyAsStream(); // // // Instantiates a DOM builder to create a DOM of the response. // DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); // DocumentBuilder builder = factory.newDocumentBuilder(); // return a parsed Document return method.getResponseBodyAsString(); } catch (Exception httpErr) { String errMsg = "HTTP GET to `" + urlToSearch + "` returned HTTP error."; throw new Exception(errMsg, httpErr); } finally { // Release the connection. method.releaseConnection(); } } // End of `getIndexPage` method. public void debugParsedDoc(ParsedDocument parsedDoc) { System.out.println("==============================================================================="); System.out.println("GUID: " + parsedDoc.getGuid()); System.out.println("Content-Type: " + parsedDoc.getContentType()); Map<String, String> dublinCore = parsedDoc.getDublinCore(); for (String key : dublinCore.keySet()) { System.out.println("DC: " + key + "\t" + dublinCore.get(key)); } List<Triple<String, String, String>> triples = parsedDoc.getTriples(); for (Triple<String, String, String> triple : triples) { System.out.println( "RDF: " + triple.getSubject() + "\t" + triple.getPredicate() + "\t" + triple.getObject()); } System.out.println("==============================================================================="); } /** * @see * org.ala.harvester.Harvester#setRepository(org.ala.repository.Repository) */ public void setRepository(Repository repository) { this.repository = repository; } @Override public void setDocumentMapper(DocumentMapper documentMapper) { // TODO Auto-generated method stub } }