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/**
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2
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* log.debug(...) equal to log.trace(...) in the application-logs
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* <p>
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* known bug: at resumptionType 'discover' if the (resultTotal % resultSizeValue) == 0 the collecting fails -> change the resultSizeValue
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*/
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package eu.dnetlib.data.collector.plugins.rest;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.net.URL;
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import java.net.HttpURLConnection;
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import java.util.Iterator;
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import java.util.Queue;
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import java.util.concurrent.PriorityBlockingQueue;
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import javax.xml.transform.OutputKeys;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerConfigurationException;
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import javax.xml.transform.TransformerFactory;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import javax.xml.xpath.*;
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import eu.dnetlib.data.collector.plugins.oai.engine.XmlCleaner;
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import eu.dnetlib.data.collector.rmi.CollectorServiceException;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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/**
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* @author Jochen Schirrwagen, Aenne Loehden, Andreas Czerniak
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* @date 2020-03-20
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*
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*/
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public class RestIterator implements Iterator<String> {
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// TODO: clean up the comments of replaced source code
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private static final Log log = LogFactory.getLog(RestIterator.class); // NOPMD by marko on 11/24/08 5:02 PM
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private static final String wrapName = "recordWrap";
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private String baseUrl;
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private String resumptionType;
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private String resumptionParam;
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private String resultFormatValue;
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private String queryParams;
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private int resultSizeValue;
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private int resumptionInt = 0; // integer resumption token (first record to harvest)
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private int resultTotal = -1;
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private String resumptionStr = Integer.toString(resumptionInt); // string resumption token (first record to harvest or token scanned from results)
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private InputStream resultStream;
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private Transformer transformer;
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private XPath xpath;
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private String query;
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private XPathExpression xprResultTotalPath;
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private XPathExpression xprResumptionPath;
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private XPathExpression xprEntity;
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private String queryFormat;
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private String querySize;
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private String authMethod;
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private String authToken;
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private Queue<String> recordQueue = new PriorityBlockingQueue<String>();
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private int discoverResultSize = 0;
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private int pagination = 1;
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public RestIterator(
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final String baseUrl,
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final String resumptionType,
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final String resumptionParam,
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final String resumptionXpath,
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final String resultTotalXpath,
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final String resultFormatParam,
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final String resultFormatValue,
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final String resultSizeParam,
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final String resultSizeValueStr,
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final String queryParams,
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final String entityXpath
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) {
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81
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// this.baseUrl = baseUrl;
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// this.resumptionType = resumptionType;
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// this.resumptionParam = resumptionParam;
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// this.resultFormatValue = resultFormatValue;
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// this.queryParams = queryParams;
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// this.resultSizeValue = Integer.valueOf(resultSizeValueStr);
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//
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// queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue : "";
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// querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
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90
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//
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91
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// try {
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// initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
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// } catch (Exception e) {
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// throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
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// }
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// initQueue();
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this(baseUrl,resumptionType,resumptionParam,resumptionXpath,resultTotalXpath,resultFormatParam,resultFormatValue,resultSizeParam,resultSizeValueStr,queryParams,entityXpath,"", "");
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}
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public RestIterator(
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final String baseUrl,
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final String resumptionType,
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final String resumptionParam,
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final String resumptionXpath,
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final String resultTotalXpath,
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final String resultFormatParam,
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final String resultFormatValue,
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final String resultSizeParam,
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final String resultSizeValueStr,
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final String queryParams,
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final String entityXpath,
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final String authMethod,
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final String authToken
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) {
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this.baseUrl = baseUrl;
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this.resumptionType = resumptionType;
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this.resumptionParam = resumptionParam;
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this.resultFormatValue = resultFormatValue;
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this.queryParams = queryParams;
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this.resultSizeValue = Integer.valueOf(resultSizeValueStr);
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this.authMethod = authMethod;
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this.authToken = authToken;
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queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue : "";
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querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
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126
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try {
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initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
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} catch (Exception e) {
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throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
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}
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initQueue();
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}
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private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
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137
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throws TransformerConfigurationException, XPathExpressionException {
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transformer = TransformerFactory.newInstance().newTransformer();
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transformer.setOutputProperty(OutputKeys.INDENT, "yes");
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transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
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xpath = XPathFactory.newInstance().newXPath();
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xprResultTotalPath = xpath.compile(resultTotalXpath);
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xprResumptionPath = xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
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xprEntity = xpath.compile(entityXpath);
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}
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private void initQueue() {
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query = baseUrl + "?" + queryParams + querySize + queryFormat;
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}
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150
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private void disconnect() {
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// TODO close inputstream
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}
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/* (non-Javadoc)
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* @see java.util.Iterator#hasNext()
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157
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*/
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158
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@Override
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public boolean hasNext() {
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160
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if (recordQueue.isEmpty() && query.isEmpty()) {
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disconnect();
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return false;
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} else {
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return true;
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165
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}
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166
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}
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167
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168
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/* (non-Javadoc)
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169
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* @see java.util.Iterator#next()
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170
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*/
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171
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@Override
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172
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public String next() {
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173
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synchronized (recordQueue) {
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174
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while (recordQueue.isEmpty() && !query.isEmpty()) {
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175
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try {
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log.info("get Query: " + query);
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query = downloadPage(query);
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log.debug("next queryURL from downloadPage(): " + query);
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179
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} catch (CollectorServiceException e) {
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180
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log.debug("CollectorPlugin.next()-Exception: " + e);
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181
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throw new RuntimeException(e);
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182
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}
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183
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}
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184
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return recordQueue.poll();
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185
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}
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186
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}
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187
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188
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/*
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189
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* download page and return nextQuery
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190
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*/
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191
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private String downloadPage(String query) throws CollectorServiceException {
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192
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String resultJson;
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193
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String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
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194
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String nextQuery = "";
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String emptyXml = resultXml + "<" + wrapName + "></" + wrapName + ">";
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196
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Node resultNode = null;
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197
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NodeList nodeList = null;
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198
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String qUrlArgument = "";
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199
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int urlOldResumptionSize = 0;
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200
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InputStream theHttpInputStream;
|
201
|
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202
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try {
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203
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URL qUrl = new URL(query);
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204
|
|
205
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if (this.authMethod == "bearer") {
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206
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log.trace("authMethode before inputStream: " + resultXml);
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207
|
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208
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HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
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209
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conn.setRequestProperty("Authorization","Bearer "+authToken);
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210
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conn.setRequestProperty("Content-Type","application/json");
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211
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conn.setRequestMethod("GET");
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212
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theHttpInputStream = conn.getInputStream();
|
213
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} else {
|
214
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theHttpInputStream = qUrl.openStream();
|
215
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}
|
216
|
|
217
|
resultStream = theHttpInputStream;
|
218
|
if ("json".equals(resultFormatValue.toLowerCase())) {
|
219
|
resultJson = IOUtils.toString(resultStream, "UTF-8");
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220
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resultJson = syntaxConvertJsonKeyNamens(resultJson);
|
221
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org.json.JSONObject jsonObject = new org.json.JSONObject(resultJson);
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222
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resultXml += org.json.XML.toString(jsonObject, wrapName); // wrap xml in single root element
|
223
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log.trace("before inputStream: " + resultXml);
|
224
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resultXml = XmlCleaner.cleanAllEntities(resultXml);
|
225
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log.trace("after cleaning: " + resultXml);
|
226
|
resultStream = IOUtils.toInputStream(resultXml, "UTF-8");
|
227
|
}
|
228
|
|
229
|
if (!(emptyXml.toLowerCase()).equals(resultXml.toLowerCase())) {
|
230
|
resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
|
231
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nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
|
232
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log.debug("nodeList.length: " + nodeList.getLength());
|
233
|
for (int i = 0; i < nodeList.getLength(); i++) {
|
234
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StringWriter sw = new StringWriter();
|
235
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transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
|
236
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recordQueue.add(sw.toString());
|
237
|
}
|
238
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} else { log.info("resultXml is equal with emptyXml"); }
|
239
|
|
240
|
resumptionInt += resultSizeValue;
|
241
|
|
242
|
switch (resumptionType.toLowerCase()) {
|
243
|
case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
|
244
|
resumptionStr = xprResumptionPath.evaluate(resultNode);
|
245
|
break;
|
246
|
|
247
|
case "count": // begin at one step for all records, iterate over items
|
248
|
resumptionStr = Integer.toString(resumptionInt);
|
249
|
break;
|
250
|
|
251
|
case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
|
252
|
if (resultSizeValue < 2) {throw new CollectorServiceException("Mode: discover, Param 'resultSizeValue' is less than 2");}
|
253
|
qUrlArgument = qUrl.getQuery();
|
254
|
String[] arrayQUrlArgument = qUrlArgument.split("&");
|
255
|
for (String arrayUrlArgStr : arrayQUrlArgument) {
|
256
|
if (arrayUrlArgStr.startsWith(resumptionParam)) {
|
257
|
String[] resumptionKeyValue = arrayUrlArgStr.split("=");
|
258
|
urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
|
259
|
log.debug("discover OldResumptionSize from Url: " + urlOldResumptionSize);
|
260
|
}
|
261
|
}
|
262
|
|
263
|
if (((emptyXml.toLowerCase()).equals(resultXml.toLowerCase()))
|
264
|
|| ((nodeList != null) && (nodeList.getLength() < resultSizeValue))
|
265
|
) {
|
266
|
// resumptionStr = "";
|
267
|
if (nodeList != null) { discoverResultSize += nodeList.getLength(); }
|
268
|
resultTotal = discoverResultSize;
|
269
|
} else {
|
270
|
resumptionStr = Integer.toString(resumptionInt);
|
271
|
resultTotal = resumptionInt + 1;
|
272
|
if (nodeList != null) { discoverResultSize += nodeList.getLength(); }
|
273
|
}
|
274
|
log.info("discoverResultSize: " + discoverResultSize);
|
275
|
break;
|
276
|
|
277
|
case "pagination":
|
278
|
case "page": // pagination, iterate over pages
|
279
|
pagination += 1;
|
280
|
if (nodeList != null) {
|
281
|
discoverResultSize += nodeList.getLength();
|
282
|
} else {
|
283
|
resultTotal = discoverResultSize;
|
284
|
pagination = discoverResultSize;
|
285
|
}
|
286
|
resumptionInt = pagination;
|
287
|
resumptionStr = Integer.toString(resumptionInt);
|
288
|
break;
|
289
|
|
290
|
default: // otherwise: abort
|
291
|
// resultTotal = resumptionInt;
|
292
|
break;
|
293
|
}
|
294
|
|
295
|
if (resultTotal == -1) {
|
296
|
resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
|
297
|
if (resumptionType.toLowerCase().equals("page")) { resultTotal += 1; } // to correct the upper bound
|
298
|
log.info("resultTotal was -1 is now: " + resultTotal);
|
299
|
}
|
300
|
log.info("resultTotal: " + resultTotal);
|
301
|
log.info("resInt: " + resumptionInt);
|
302
|
if (resumptionInt <= resultTotal) {
|
303
|
nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr + queryFormat;
|
304
|
} else
|
305
|
nextQuery = "";
|
306
|
|
307
|
log.debug("nextQueryUrl: " + nextQuery);
|
308
|
return nextQuery;
|
309
|
|
310
|
} catch (Exception e) {
|
311
|
log.error(e);
|
312
|
throw new IllegalStateException("collection failed: " + e.getMessage());
|
313
|
}
|
314
|
}
|
315
|
|
316
|
/**
|
317
|
* convert in JSON-KeyName 'whitespace(s)' to '_' and '/' to '_', '(' and ')' to ''
|
318
|
* check W3C XML syntax: https://www.w3.org/TR/2006/REC-xml11-20060816/#sec-starttags for valid tag names
|
319
|
* and work-around for the JSON to XML converting of org.json.XML-package.
|
320
|
*
|
321
|
* known bugs: doesn't prevent "key name":" ["sexy name",": penari","erotic dance"],
|
322
|
*
|
323
|
* @param jsonInput
|
324
|
* @return convertedJsonKeynameOutput
|
325
|
*/
|
326
|
private String syntaxConvertJsonKeyNamens(String jsonInput) {
|
327
|
|
328
|
log.trace("before convertJsonKeyNames: " + jsonInput);
|
329
|
// pre-clean json - rid spaces of element names (misinterpreted as elements with attributes in xml)
|
330
|
// replace ' 's in JSON Namens with '_'
|
331
|
while (jsonInput.matches(".*\"([^\"]*)\\s+([^\"]*)\":.*")) {
|
332
|
jsonInput = jsonInput.replaceAll("\"([^\"]*)\\s+([^\"]*)\":", "\"$1_$2\":");
|
333
|
}
|
334
|
|
335
|
// replace forward-slash (sign '/' ) in JSON Names with '_'
|
336
|
while (jsonInput.matches(".*\"([^\"]*)/([^\"]*)\":.*")) {
|
337
|
jsonInput = jsonInput.replaceAll("\"([^\"]*)/([^\"]*)\":", "\"$1_$2\":");
|
338
|
}
|
339
|
|
340
|
// replace '(' in JSON Names with ''
|
341
|
while (jsonInput.matches(".*\"([^\"]*)[(]([^\"]*)\":.*")) {
|
342
|
jsonInput = jsonInput.replaceAll("\"([^\"]*)[(]([^\"]*)\":", "\"$1$2\":");
|
343
|
}
|
344
|
|
345
|
// replace ')' in JSON Names with ''
|
346
|
while (jsonInput.matches(".*\"([^\"]*)[)]([^\"]*)\":.*")) {
|
347
|
jsonInput = jsonInput.replaceAll("\"([^\"]*)[)]([^\"]*)\":", "\"$1$2\":");
|
348
|
}
|
349
|
|
350
|
// add prefix of startNumbers in JSON Keynames with 'n_'
|
351
|
while (jsonInput.matches(".*\"([^\"][0-9])([^\"]*)\":.*")) {
|
352
|
jsonInput = jsonInput.replaceAll("\"([^\"][0-9])([^\"]*)\":", "\"n_$1$2\":");
|
353
|
}
|
354
|
// add prefix of only numbers in JSON Keynames with 'm_'
|
355
|
while (jsonInput.matches(".*\"([0-9]+)\":.*")) {
|
356
|
jsonInput = jsonInput.replaceAll("\"([0-9]+)\":", "\"m_$1\":");
|
357
|
}
|
358
|
|
359
|
// replace ':' between number like '2018-08-28T11:05:00Z' in JSON keynames with ''
|
360
|
while (jsonInput.matches(".*\"([^\"]*[0-9]):([0-9][^\"]*)\":.*")) {
|
361
|
jsonInput = jsonInput.replaceAll("\"([^\"]*[0-9]):([0-9][^\"]*)\":", "\"$1$2\":");
|
362
|
}
|
363
|
|
364
|
// replace ',' in JSON Keynames with '.' to prevent , in xml tagnames.
|
365
|
// while (jsonInput.matches(".*\"([^\"]*),([^\"]*)\":.*")) {
|
366
|
// jsonInput = jsonInput.replaceAll("\"([^\"]*),([^\"]*)\":", "\"$1.$2\":");
|
367
|
// }
|
368
|
|
369
|
// replace '=' in JSON Keynames with '-'
|
370
|
while (jsonInput.matches(".*\"([^\"]*)=([^\"]*)\":.*")) {
|
371
|
jsonInput = jsonInput.replaceAll("\"([^\"]*)=([^\"]*)\":", "\"$1-$2\":");
|
372
|
}
|
373
|
|
374
|
log.trace("after syntaxConvertJsonKeyNames: " + jsonInput);
|
375
|
return jsonInput;
|
376
|
}
|
377
|
|
378
|
/**
|
379
|
*
|
380
|
* https://www.w3.org/TR/REC-xml/#charencoding shows character enoding in entities
|
381
|
* *
|
382
|
* @param bufferStr - XML string
|
383
|
* @return
|
384
|
*/
|
385
|
private static String cleanUnwantedJsonCharsInXmlTagnames(String bufferStr) {
|
386
|
|
387
|
while (bufferStr.matches(".*<([^<>].*),(.)>.*")) {
|
388
|
bufferStr = bufferStr.replaceAll("<([^<>.*),(.*)>", "<$1$2>");
|
389
|
}
|
390
|
|
391
|
// replace [#x10-#x1f] with ''
|
392
|
// while (bufferStr.matches(".*[0-9a-f].*")) {
|
393
|
// bufferStr = bufferStr.replaceAll("([0-9a-fA-F])", "");
|
394
|
// }
|
395
|
|
396
|
return bufferStr;
|
397
|
}
|
398
|
|
399
|
}
|