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/**
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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.io.UnsupportedEncodingException;
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import java.net.URL;
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import java.net.URLEncoder;
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import java.nio.charset.StandardCharsets;
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import java.net.HttpURLConnection;
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import java.util.Iterator;
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import java.util.Map;
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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 com.google.common.collect.Maps;
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import eu.dnetlib.data.collector.plugins.utils.JsonUtils;
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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.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.HttpClients;
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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, Alessia Bardi, Miriam Baglioni
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* @date 2020-04-09
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*/
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public class RestIterator implements Iterator<String> {
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private final String AUTHBASIC = "basic";
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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 XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
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private static final String EMPTY_XML = XML_HEADER + JsonUtils.wrapName + "></" + JsonUtils.wrapName + ">";
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private JsonUtils jsonUtils;
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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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/*
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While resultFormatValue is added to the request parameter, this is used to say that the results are retrieved in json.
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useful for cases when the target API expects a resultFormatValue != json, but the results are returned in json.
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An example is the EU Open Data Portal API: resultFormatValue=standard, results are in json format.
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*/
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private String resultOutputFormat;
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/*
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Can be used to set additional request headers, like for content negotiation
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*/
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private Map<String, String> requestHeaders;
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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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final String resultOutputFormat,
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final Map<String, String> requestHeaders
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) {
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this.jsonUtils = new JsonUtils();
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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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this.resultOutputFormat = resultOutputFormat;
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this.requestHeaders = requestHeaders != null ? requestHeaders : Maps.newHashMap();
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queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue : "";
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querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
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120
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try {
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initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
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123
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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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129
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private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
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131
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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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141
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private void initQueue() {
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142
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if (queryParams.equals("") && querySize.equals("") && queryFormat.equals("")) {
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query = baseUrl;
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} else {
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query = baseUrl + "?" + queryParams + querySize + queryFormat;
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146
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}
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log.info("RestIterator.initQueue():: REST calls starting with " + query);
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}
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150
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151
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private void disconnect() {
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// TODO close inputstream
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153
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}
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155
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/* (non-Javadoc)
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156
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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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159
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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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162
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return false;
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} else {
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164
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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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176
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log.debug("RestIterator.next():: get Query: " + query);
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177
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query = downloadPage(query);
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178
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log.debug("RestIterator.next():: 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("RestIterator.next():: 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_HEADER;
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194
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String nextQuery = "";
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195
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Node resultNode = null;
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196
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NodeList nodeList = null;
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197
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String qUrlArgument = "";
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198
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int urlOldResumptionSize = 0;
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199
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InputStream theHttpInputStream;
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200
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201
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// check if cursor=* is initial set otherwise add it to the queryParam URL
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202
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if (resumptionType.equalsIgnoreCase("deep-cursor")) {
|
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203
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log.debug("RestIterator.downloadPage():: check resumptionType deep-cursor and check cursor=*?" + query);
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204
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if (!query.contains("&cursor=")) {
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205
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query += "&cursor=*";
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206
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}
|
|
207
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}
|
|
208
|
|
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209
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try {
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210
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URL qUrl = new URL(query);
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|
211
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log.debug("authMethod :" + authMethod);
|
|
212
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if (this.authMethod == "bearer") {
|
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213
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log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
|
|
214
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requestHeaders.put("Authorization", "Bearer " + authToken);
|
|
215
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//requestHeaders.put("Content-Type", "application/json");
|
|
216
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} else if (AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
|
|
217
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log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
|
|
218
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requestHeaders.put("Authorization", "Basic " + authToken);
|
|
219
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//requestHeaders.put("accept", "application/xml");
|
|
220
|
}
|
|
221
|
|
|
222
|
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
|
|
223
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conn.setRequestMethod("GET");
|
|
224
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this.setRequestHeader(conn);
|
|
225
|
resultStream = conn.getInputStream();
|
|
226
|
|
|
227
|
if ("json".equals(resultOutputFormat)) {
|
|
228
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resultJson = IOUtils.toString(resultStream, "UTF-8");
|
|
229
|
resultXml = jsonUtils.convertToXML(resultJson);
|
|
230
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resultStream = IOUtils.toInputStream(resultXml, "UTF-8");
|
|
231
|
}
|
|
232
|
|
|
233
|
if (!isEmptyXml(resultXml)) {
|
|
234
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resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
|
|
235
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nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
|
|
236
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log.debug("RestIterator.downloadPage():: nodeList.length=" + nodeList.getLength());
|
|
237
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for (int i = 0; i < nodeList.getLength(); i++) {
|
|
238
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StringWriter sw = new StringWriter();
|
|
239
|
transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
|
|
240
|
String toEnqueue = sw.toString();
|
|
241
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if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
|
|
242
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log.warn("RestIterator.downloadPage():: The following record resulted in empty item for the feeding queue: " + resultXml);
|
|
243
|
} else {
|
|
244
|
recordQueue.add(sw.toString());
|
|
245
|
}
|
|
246
|
}
|
|
247
|
} else {
|
|
248
|
log.warn("resultXml is equal with emptyXml");
|
|
249
|
}
|
|
250
|
|
|
251
|
resumptionInt += resultSizeValue;
|
|
252
|
|
|
253
|
switch (resumptionType.toLowerCase()) {
|
|
254
|
case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
|
|
255
|
resumptionStr = xprResumptionPath.evaluate(resultNode);
|
|
256
|
break;
|
|
257
|
|
|
258
|
case "count": // begin at one step for all records, iterate over items
|
|
259
|
resumptionStr = Integer.toString(resumptionInt);
|
|
260
|
break;
|
|
261
|
|
|
262
|
case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
|
|
263
|
if (resultSizeValue < 2) {
|
|
264
|
log.debug("RestIterator.downloadPage().discover:: ode: discover, Param 'resultSizeValue' must greater then 1");
|
|
265
|
throw new CollectorServiceException("Mode: discover, Param 'resultSizeValue' must greater then 1");
|
|
266
|
}
|
|
267
|
log.debug("RestIterator.downloadPage().discover:: resumptionInt="+Integer.toString(resumptionInt)+"; ");
|
|
268
|
qUrlArgument = qUrl.getQuery();
|
|
269
|
|
|
270
|
if( qUrlArgument != null ) {
|
|
271
|
String[] arrayQUrlArgument = qUrlArgument.split("&");
|
|
272
|
|
|
273
|
// check if URL arguments given
|
|
274
|
if( arrayQUrlArgument != null ) {
|
|
275
|
for (String arrayUrlArgStr : arrayQUrlArgument) {
|
|
276
|
log.debug("RestIterator.downloadPage/discover:: "+arrayUrlArgStr);
|
|
277
|
if (arrayUrlArgStr.startsWith(resumptionParam)) {
|
|
278
|
String[] resumptionKeyValue = arrayUrlArgStr.split("=");
|
|
279
|
if (isInteger(resumptionKeyValue[1])) {
|
|
280
|
urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
|
|
281
|
log.debug("RestIterator.downloadPage():discover:: OldResumptionSize from Url (int): " + urlOldResumptionSize);
|
|
282
|
} else {
|
|
283
|
log.debug("RestIterator.downloadPage().discover:: OldResumptionSize from Url (str): " + resumptionKeyValue[1]);
|
|
284
|
}
|
|
285
|
}
|
|
286
|
}
|
|
287
|
}
|
|
288
|
}
|
|
289
|
log.debug("RestIterator.downloadPage().discover:: nodeList.length=" + nodeList.getLength());
|
|
290
|
|
|
291
|
if (isEmptyXml(resultXml) || ((nodeList != null) && (nodeList.getLength() < resultSizeValue))
|
|
292
|
) {
|
|
293
|
// resumptionStr = "";
|
|
294
|
if (nodeList != null) {
|
|
295
|
discoverResultSize += nodeList.getLength();
|
|
296
|
}
|
|
297
|
resultTotal = discoverResultSize;
|
|
298
|
} else {
|
|
299
|
resumptionStr = Integer.toString(resumptionInt);
|
|
300
|
resultTotal = resumptionInt + 1;
|
|
301
|
if (nodeList != null) {
|
|
302
|
discoverResultSize += nodeList.getLength();
|
|
303
|
}
|
|
304
|
}
|
|
305
|
log.debug("RestIterator.downloadPage().discover:: discoverResultSize=" + discoverResultSize);
|
|
306
|
break;
|
|
307
|
|
|
308
|
case "pagination":
|
|
309
|
case "page": // pagination, iterate over page numbers
|
|
310
|
pagination += 1;
|
|
311
|
if (nodeList != null) {
|
|
312
|
discoverResultSize += nodeList.getLength();
|
|
313
|
} else {
|
|
314
|
resultTotal = discoverResultSize;
|
|
315
|
pagination = discoverResultSize;
|
|
316
|
}
|
|
317
|
resumptionInt = pagination;
|
|
318
|
resumptionStr = Integer.toString(resumptionInt);
|
|
319
|
break;
|
|
320
|
|
|
321
|
case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor in solr)
|
|
322
|
// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode: deep-cursor, Param 'resultSizeValue' is less than 2");}
|
|
323
|
|
|
324
|
resumptionStr = encodeValue(xprResumptionPath.evaluate(resultNode));
|
|
325
|
queryParams = queryParams.replace("&cursor=*", "");
|
|
326
|
|
|
327
|
// terminating if length of nodeList is 0
|
|
328
|
if ((nodeList != null) && (nodeList.getLength() < discoverResultSize)) {
|
|
329
|
resumptionInt += (nodeList.getLength() + 1 - resultSizeValue);
|
|
330
|
} else {
|
|
331
|
resumptionInt += (nodeList.getLength() - resultSizeValue); // subtract the resultSizeValue because the iteration is over real length and the resultSizeValue is added before the switch()
|
|
332
|
}
|
|
333
|
|
|
334
|
discoverResultSize = nodeList.getLength();
|
|
335
|
|
|
336
|
log.debug("RestIterator.downloadPage().deep-cursor:: resumptionStr=" + resumptionStr + " ; queryParams=" + queryParams + " resumptionLengthIncreased: " + resumptionInt);
|
|
337
|
|
|
338
|
break;
|
|
339
|
|
|
340
|
default: // otherwise: abort
|
|
341
|
// resultTotal = resumptionInt;
|
|
342
|
break;
|
|
343
|
}
|
|
344
|
|
|
345
|
} catch (Exception e) {
|
|
346
|
log.error(e);
|
|
347
|
throw new IllegalStateException("collection failed: " + e.getMessage());
|
|
348
|
}
|
|
349
|
|
|
350
|
try {
|
|
351
|
if (resultTotal == -1) {
|
|
352
|
resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
|
|
353
|
if (resumptionType.toLowerCase().equals("page") && !AUTHBASIC.equalsIgnoreCase(authMethod)) {
|
|
354
|
resultTotal += 1;
|
|
355
|
} // to correct the upper bound
|
|
356
|
log.info("resultTotal was -1 is now: " + resultTotal);
|
|
357
|
}
|
|
358
|
} catch (Exception e) {
|
|
359
|
log.error(e);
|
|
360
|
throw new IllegalStateException("downloadPage() resultTotal couldn't parse: " + e.getMessage());
|
|
361
|
}
|
|
362
|
log.debug("resultTotal: " + resultTotal);
|
|
363
|
log.debug("resInt: " + resumptionInt);
|
|
364
|
if (resumptionInt <= resultTotal) {
|
|
365
|
nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr + queryFormat;
|
|
366
|
} else {
|
|
367
|
nextQuery = "";
|
|
368
|
// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the resumptionInt and prevent a NullPointer Exception at mdStore
|
|
369
|
}
|
|
370
|
log.debug("downloadPage() nextQueryUrl: " + nextQuery);
|
|
371
|
return nextQuery;
|
|
372
|
|
|
373
|
|
|
374
|
}
|
|
375
|
|
|
376
|
private boolean isEmptyXml(String s){
|
|
377
|
return EMPTY_XML.equalsIgnoreCase(s);
|
|
378
|
}
|
|
379
|
|
|
380
|
|
|
381
|
private boolean isInteger(String s) {
|
|
382
|
boolean isValidInteger = false;
|
|
383
|
try {
|
|
384
|
Integer.parseInt(s);
|
|
385
|
|
|
386
|
// s is a valid integer
|
|
387
|
|
|
388
|
isValidInteger = true;
|
|
389
|
} catch (NumberFormatException ex) {
|
|
390
|
// s is not an integer
|
|
391
|
}
|
|
392
|
|
|
393
|
return isValidInteger;
|
|
394
|
}
|
|
395
|
|
|
396
|
// Method to encode a string value using `UTF-8` encoding scheme
|
|
397
|
private String encodeValue(String value) {
|
|
398
|
try {
|
|
399
|
return URLEncoder.encode(value, StandardCharsets.UTF_8.toString());
|
|
400
|
} catch (UnsupportedEncodingException ex) {
|
|
401
|
throw new RuntimeException(ex.getCause());
|
|
402
|
}
|
|
403
|
}
|
|
404
|
|
|
405
|
/**
|
|
406
|
* setRequestHeader
|
|
407
|
*
|
|
408
|
* setRequestProperty: Sets the general request property. If a property with the key already exists, overwrite its value with the new value.
|
|
409
|
* @param conn
|
|
410
|
*/
|
|
411
|
private void setRequestHeader(HttpURLConnection conn) {
|
|
412
|
if (requestHeaders != null) {
|
|
413
|
for (String key : requestHeaders.keySet()) {
|
|
414
|
conn.setRequestProperty(key, requestHeaders.get(key));
|
|
415
|
}
|
|
416
|
log.debug("Set Request Header with: " + requestHeaders);
|
|
417
|
}
|
|
418
|
|
|
419
|
}
|
|
420
|
|
|
421
|
public String getResultFormatValue() {
|
|
422
|
return resultFormatValue;
|
|
423
|
}
|
|
424
|
|
|
425
|
public String getResultOutputFormat() {
|
|
426
|
return resultOutputFormat;
|
|
427
|
}
|
|
428
|
|
|
429
|
}
|