445 lines
16 KiB
Java
445 lines
16 KiB
Java
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package eu.dnetlib.dhp.collection.plugin.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.HttpURLConnection;
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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.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.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpression;
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import javax.xml.xpath.XPathExpressionException;
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import javax.xml.xpath.XPathFactory;
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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.http.HttpHeaders;
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import org.apache.http.entity.ContentType;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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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import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.common.collection.HttpClientParams;
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/**
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* log.info(...) 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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* @author Jochen Schirrwagen, Aenne Loehden, Andreas Czerniak
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* @date 2020-04-09
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*
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*/
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public class RestIterator implements Iterator<String> {
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private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
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public static final String UTF_8 = "UTF-8";
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private static final int MAX_ATTEMPTS = 5;
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private final HttpClientParams clientParams;
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private final String BASIC = "basic";
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private final String baseUrl;
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private final String resumptionType;
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private final String resumptionParam;
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private final String resultFormatValue;
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private String queryParams;
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private final 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(this.resumptionInt); // string resumption token (first record to
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// harvest
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// 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 final String queryFormat;
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private final String querySize;
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private final String authMethod;
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private final String authToken;
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private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
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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
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* json. useful for cases when the target API expects a resultFormatValue != json, but the results are returned in
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* json. 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 final String resultOutputFormat;
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/**
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* RestIterator class compatible to version 1.3.33
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*/
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public RestIterator(
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final HttpClientParams clientParams,
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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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this.clientParams = clientParams;
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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.resultSizeValue = Integer.parseInt(resultSizeValueStr);
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this.queryParams = queryParams;
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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.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
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: "";
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this.querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr
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: "";
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try {
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initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
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} catch (final 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(final String resultTotalXpath, final String resumptionXpath,
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final String entityXpath)
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throws TransformerConfigurationException, XPathExpressionException {
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final TransformerFactory factory = TransformerFactory.newInstance();
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this.transformer = factory.newTransformer();
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this.transformer.setOutputProperty(OutputKeys.INDENT, "yes");
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this.transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
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this.xpath = XPathFactory.newInstance().newXPath();
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this.xprResultTotalPath = this.xpath.compile(resultTotalXpath);
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this.xprResumptionPath = this.xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
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this.xprEntity = this.xpath.compile(entityXpath);
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}
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private void initQueue() {
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this.query = this.baseUrl + "?" + this.queryParams + this.querySize + this.queryFormat;
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log.info("REST calls starting with {}", this.query);
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}
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private void disconnect() {
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// TODO close inputstream
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}
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/*
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* (non-Javadoc)
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* @see java.util.Iterator#hasNext()
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*/
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@Override
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public boolean hasNext() {
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if (this.recordQueue.isEmpty() && this.query.isEmpty()) {
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disconnect();
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return false;
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}
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return true;
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}
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/*
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* (non-Javadoc)
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* @see java.util.Iterator#next()
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*/
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@Override
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public String next() {
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synchronized (this.recordQueue) {
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while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
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try {
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this.query = downloadPage(this.query, 0);
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} catch (final CollectorException e) {
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log.debug("CollectorPlugin.next()-Exception: {}", e);
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throw new RuntimeException(e);
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}
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}
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return this.recordQueue.poll();
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}
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}
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/*
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* download page and return nextQuery (with number of attempt)
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*/
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private String downloadPage(String query, final int attempt) throws CollectorException {
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if (attempt > MAX_ATTEMPTS) {
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throw new CollectorException("Max Number of attempts reached, query:" + query);
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}
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if (attempt > 0) {
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final int delay = (attempt * 5000);
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log.debug("Attempt {} with delay {}", attempt, delay);
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try {
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Thread.sleep(delay);
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} catch (final InterruptedException e) {
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new CollectorException(e);
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}
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}
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try {
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String resultJson;
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String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
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String nextQuery = "";
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final String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
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Node resultNode = null;
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NodeList nodeList = null;
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String qUrlArgument = "";
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int urlOldResumptionSize = 0;
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InputStream theHttpInputStream;
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// check if cursor=* is initial set otherwise add it to the queryParam URL
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if ("deep-cursor".equalsIgnoreCase(this.resumptionType)) {
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log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
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if (!query.contains("&cursor=")) {
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query += "&cursor=*";
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}
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}
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try {
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log.info("requesting URL [{}]", query);
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final URL qUrl = new URL(query);
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log.debug("authMethod: {}", this.authMethod);
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if ("bearer".equalsIgnoreCase(this.authMethod)) {
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log.trace("authMethod before inputStream: {}", resultXml);
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final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
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conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + this.authToken);
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conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
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conn.setRequestMethod("GET");
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theHttpInputStream = conn.getInputStream();
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} else if (this.BASIC.equalsIgnoreCase(this.authMethod)) {
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log.trace("authMethod before inputStream: {}", resultXml);
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final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
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conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + this.authToken);
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conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
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conn.setRequestMethod("GET");
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theHttpInputStream = conn.getInputStream();
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} else {
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theHttpInputStream = qUrl.openStream();
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}
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this.resultStream = theHttpInputStream;
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if ("json".equals(this.resultOutputFormat)) {
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resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
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resultXml = JsonUtils.convertToXML(resultJson);
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this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
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}
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if (!(emptyXml).equalsIgnoreCase(resultXml)) {
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resultNode = (Node) this.xpath
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.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
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nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
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log.debug("nodeList.length: {}", nodeList.getLength());
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for (int i = 0; i < nodeList.getLength(); i++) {
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final StringWriter sw = new StringWriter();
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this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
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final String toEnqueue = sw.toString();
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if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue)
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|| emptyXml.equalsIgnoreCase(toEnqueue)) {
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log
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.warn(
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"The following record resulted in empty item for the feeding queue: {}", resultXml);
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} else {
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this.recordQueue.add(sw.toString());
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}
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}
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} else {
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log.warn("resultXml is equal with emptyXml");
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}
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this.resumptionInt += this.resultSizeValue;
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switch (this.resumptionType.toLowerCase()) {
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case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
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this.resumptionStr = this.xprResumptionPath.evaluate(resultNode);
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break;
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case "count": // begin at one step for all records, iterate over items
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this.resumptionStr = Integer.toString(this.resumptionInt);
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break;
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case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
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if (this.resultSizeValue < 2) {
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throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
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}
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qUrlArgument = qUrl.getQuery();
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final String[] arrayQUrlArgument = qUrlArgument.split("&");
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for (final String arrayUrlArgStr : arrayQUrlArgument) {
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if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
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final String[] resumptionKeyValue = arrayUrlArgStr.split("=");
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if (isInteger(resumptionKeyValue[1])) {
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urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
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log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
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} else {
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log.debug("discover OldResumptionSize from Url (str): {}", resumptionKeyValue[1]);
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}
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}
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}
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if (((emptyXml).equalsIgnoreCase(resultXml))
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|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
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// resumptionStr = "";
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if (nodeList != null) {
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this.discoverResultSize += nodeList.getLength();
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}
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this.resultTotal = this.discoverResultSize;
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} else {
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this.resumptionStr = Integer.toString(this.resumptionInt);
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this.resultTotal = this.resumptionInt + 1;
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if (nodeList != null) {
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this.discoverResultSize += nodeList.getLength();
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}
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}
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log.info("discoverResultSize: {}", this.discoverResultSize);
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break;
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case "pagination":
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case "page": // pagination, iterate over page numbers
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this.pagination += 1;
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if (nodeList != null) {
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this.discoverResultSize += nodeList.getLength();
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} else {
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this.resultTotal = this.discoverResultSize;
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this.pagination = this.discoverResultSize;
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}
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this.resumptionInt = this.pagination;
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this.resumptionStr = Integer.toString(this.resumptionInt);
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break;
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case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor
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// in
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// solr)
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// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode:
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// deep-cursor, Param 'resultSizeValue' is less than 2");}
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this.resumptionStr = encodeValue(this.xprResumptionPath.evaluate(resultNode));
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this.queryParams = this.queryParams.replace("&cursor=*", "");
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// terminating if length of nodeList is 0
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if ((nodeList != null) && (nodeList.getLength() < this.discoverResultSize)) {
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this.resumptionInt += ((nodeList.getLength() + 1) - this.resultSizeValue);
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} else {
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this.resumptionInt += (nodeList.getLength() - this.resultSizeValue); // subtract the
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// resultSizeValue
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// because the iteration is over
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// real length and the
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// resultSizeValue is added before
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// the switch()
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}
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this.discoverResultSize = nodeList.getLength();
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log
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.debug(
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"downloadPage().deep-cursor: resumptionStr=" + this.resumptionStr + " ; queryParams="
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+ this.queryParams + " resumptionLengthIncreased: " + this.resumptionInt);
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break;
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default: // otherwise: abort
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// resultTotal = resumptionInt;
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break;
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}
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} catch (final Exception e) {
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log.error(e.getMessage(), e);
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throw new IllegalStateException("collection failed: " + e.getMessage());
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}
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try {
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if (this.resultTotal == -1) {
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this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
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if ("page".equalsIgnoreCase(this.resumptionType) && !this.BASIC.equalsIgnoreCase(this.authMethod)) {
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this.resultTotal += 1;
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} // to correct the upper bound
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log.info("resultTotal was -1 is now: " + this.resultTotal);
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}
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} catch (final Exception e) {
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log.error(e.getMessage(), e);
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throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
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}
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log.debug("resultTotal: " + this.resultTotal);
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log.debug("resInt: " + this.resumptionInt);
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if (this.resumptionInt <= this.resultTotal) {
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nextQuery = this.baseUrl + "?" + this.queryParams + this.querySize + "&" + this.resumptionParam + "="
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+ this.resumptionStr
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+ this.queryFormat;
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} else {
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nextQuery = "";
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// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
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// resumptionInt and prevent a NullPointer Exception at mdStore
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}
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log.debug("nextQueryUrl: " + nextQuery);
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return nextQuery;
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} catch (final Throwable e) {
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log.warn(e.getMessage(), e);
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return downloadPage(query, attempt + 1);
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}
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}
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private boolean isInteger(final String s) {
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boolean isValidInteger = false;
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try {
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Integer.parseInt(s);
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// s is a valid integer
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isValidInteger = true;
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} catch (final NumberFormatException ex) {
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// s is not an integer
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}
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return isValidInteger;
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}
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// Method to encode a string value using `UTF-8` encoding scheme
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private String encodeValue(final String value) {
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try {
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return URLEncoder.encode(value, StandardCharsets.UTF_8.toString());
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} catch (final UnsupportedEncodingException ex) {
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throw new RuntimeException(ex.getCause());
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}
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}
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public String getResultFormatValue() {
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return this.resultFormatValue;
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}
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public String getResultOutputFormat() {
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return this.resultOutputFormat;
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}
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}
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