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.util.ArrayList; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.regex.Matcher; import java.util.regex.Pattern; import javax.xml.parsers.DocumentBuilder; import javax.xml.parsers.DocumentBuilderFactory; 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.FileImportUtil; 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.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; /** * A Harvester class for Blue Tier * * @author Tommy Wang */ @Component("BluetierHarvester") @Scope(BeanDefinition.SCOPE_PROTOTYPE) public class BlueTierHarvester implements Harvester { protected Logger logger = Logger.getLogger(BlueTierHarvester.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 BLUE_TIER_INFOSOURCE_ID = 1084; protected String contentType = "text/xml"; protected final String baseUrl = "http://www.bluetier.org/"; protected final String[] endpoints = { // "http://www.bluetier.org/images.htm", // "http://www.bluetier.org/nature/ferns.htm", "http://www.bluetier.org/nature/fungi.htm" // "http://www.bluetier.org/nature/mammals.htm", // "http://www.bluetier.org/nature/birds.htm", // "http://www.bluetier.org/nature/reptiles.htm" }; protected final String[] exceptions = { "a-archeri", "g-hypnorum", "h-chromolinonae", "h-graminicolor", "lycoperdon1", "m-affixus", "m-epipterygia", "m-hepatochrous", "m-nargan", "m-toyer laricola", "m-viscidocruenta", "o-chromacea", "p-atromarginatus", "p-squarrosipes", "r-butyracea" }; /** * 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); BlueTierHarvester h = new BlueTierHarvester(); Repository r = (Repository) context.getBean("repository"); h.setRepository(r); //set the connection params h.start(BLUE_TIER_INFOSOURCE_ID); } /** * @see org.ala.harvester.Harvester#setConnectionParams(java.util.Map) */ @Override public void setConnectionParams(Map<String, String> connectionParams) { } @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. processPages(endpoints, infosourceId); } @SuppressWarnings({ "unchecked", "rawtypes" }) private void processPages(String[] urls, int infosourceId) throws Exception { Pattern speciesPattern = Pattern.compile("(?:<a href=\")" + "([a-z0-9\\-/\\.]*\\.JPG)" + "(?:\">[\\s]*<em>)" + "([A-Za-z ]*)" + "(?:</em>[\\s]*</a>)"); Pattern speciesPattern2 = Pattern.compile("(?:<em>[\\s]*<a href=\")" + "([a-z0-9\\-/\\.]*\\.JPG)" + "(?:\">[\\s]*)" + "([A-Za-z ]*)" + "(?:[\\s]*</a>[\\s]*</em>)"); Pattern speciesPattern3 = Pattern.compile("(?:<em>[\\s]*)" + "([a-zA-Z ]*)" + "(?:</em>[\\s]*\\-[\\s]*<a href=\")" + "([a-z0-9\\-/\\.]*\\.JPG)" + "(?:\">)"); List fileList = FileImportUtil.readMetaFile(String.valueOf(BLUE_TIER_INFOSOURCE_ID)); String[] fileArray = new String[fileList.size()]; fileList.toArray(fileArray); for (String url : urls) { Map<String, String> urlNameMap = new HashMap<String, String>(); String indexStr = getIndexPageStr(url); indexStr = indexStr.replaceAll("[\\s]{1,}", " "); urlNameMap.putAll(matchStr(speciesPattern, indexStr, 1, 2)); urlNameMap.putAll(matchStr(speciesPattern2, indexStr, 1, 2)); urlNameMap.putAll(matchStr(speciesPattern3, indexStr, 2, 1)); Set<String> keySet = urlNameMap.keySet(); Iterator<String> iterator = keySet.iterator(); while (iterator.hasNext()) { String imageUrl = (String) iterator.next(); String sciName = urlNameMap.get(imageUrl); String identifier = url + "#" + sciName.replaceAll(" ", ""); boolean isexception = false; boolean isListed = false; for (String exception : exceptions) { if (imageUrl.contains(exception)) { isexception = true; } } for (String file : fileArray) { System.out.println(file); if (imageUrl.contains(file)) { isListed = true; } } System.out.println("id: " + imageUrl + ", isException: " + isexception + ", isListed: " + isListed); if (!isexception && isListed) { storeImageDoc(identifier, imageUrl, sciName, infosourceId); } } } } private Map<String, String> matchStr(Pattern p, String str, int imageUrlPosition, int sciNamePosition) { Matcher m = p.matcher(str); Map<String, String> urlNameMap = new HashMap<String, String>(); int searchIdx = 0; while (m.find(searchIdx)) { int endIdx = m.end(); // String found = content.substring(startIdx, endIdx); String imageUrl = m.group(imageUrlPosition); String sciName = m.group(sciNamePosition); imageUrl = imageUrl.replaceFirst("\\.\\./", ""); String generatedUrl = baseUrl + imageUrl; // System.out.println("URL:" + generatedUrl); // System.out.println("Name:" + sciName); // storeImageDoc(generatedUrl, sciName); urlNameMap.put(generatedUrl, sciName); searchIdx = endIdx; } return urlNameMap; } private void storeImageDoc(String identifier, String imageUrl, String sciName, int infosourceId) throws Exception { ParsedDocument pd = new ParsedDocument(); ParsedDocument imageDoc = null; if (sciName != null && !"".equals(sciName)) { List<Triple<String, String, String>> triples = pd.getTriples(); Map<String, String> dcs = pd.getDublinCore(); String subject = MappingUtils.getSubject(); pd.setGuid(identifier); pd.setContent(getContent(identifier)); pd.setContentType(contentType); dcs.put(Predicates.DC_TITLE.toString(), sciName); dcs.put(Predicates.DC_IDENTIFIER.toString(), identifier); dcs.put(Predicates.DC_LICENSE.toString(), "CC-BY"); dcs.put(Predicates.COUNTRY.toString(), "Australia"); if (sciName != null && !"".equals(sciName)) { triples.add(new Triple<String, String, String>(subject, Predicates.SCIENTIFIC_NAME.toString(), sciName)); } if (imageUrl != null && !"".equals(imageUrl)) { triples.add(new Triple<String, String, String>(subject, Predicates.IMAGE_URL.toString(), imageUrl)); imageDoc = MappingUtils.retrieveImageDocument(pd, imageUrl); imageDoc.getDublinCore().put(Predicates.DC_RIGHTS.toString(), "Photo: T. Thekathyil, bluetier.org"); imageDoc.getDublinCore().put(Predicates.DC_CREATOR.toString(), "T. Thekathyil"); } } if (pd != null && pd.getGuid() != null) { debugParsedDoc(pd); this.repository.storeDocument(infosourceId, pd); } if (imageDoc != null) { debugParsedDoc(imageDoc); this.repository.storeDocument(infosourceId, imageDoc); } } private byte[] getContent(String url) throws Exception { String contentStr = null; // Create an instance of HttpClient. HttpClient client = new HttpClient(); // Create a method instance. GetMethod method = new GetMethod(url); // 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 " + "`" + url + "`" + " returned non HTTP OK code. " + "Returned code " + statusCode + " and message " + method.getStatusLine() + "\n"; method.releaseConnection(); logger.error(errMsg); throw new Exception(errMsg); } InputStream responseStream = method.getResponseBodyAsStream(); contentStr = inputStream2String(responseStream); } catch (Exception domCreationErr) { throw new Exception(domCreationErr); } finally { // Release the connection. method.releaseConnection(); } return contentStr.getBytes(); } 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(String url) 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 = url; 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 } }