forked from D-Net/dnet-hadoop
migrated last changes from svn (dnet45)
This commit is contained in:
parent
acbe3119a4
commit
61a2551e74
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@ -1,6 +1,7 @@
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package eu.dnetlib.dhp.collection.plugin.rest;
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import java.util.Optional;
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import java.util.Spliterator;
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import java.util.Spliterators;
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import java.util.stream.Stream;
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@ -23,6 +24,8 @@ import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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*/
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public class RestCollectorPlugin implements CollectorPlugin {
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public static final String RESULT_SIZE_VALUE_DEFAULT = "100";
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private HttpClientParams clientParams;
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public RestCollectorPlugin(HttpClientParams clientParams) {
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@ -32,6 +35,7 @@ public class RestCollectorPlugin implements CollectorPlugin {
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@Override
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public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
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final String baseUrl = api.getBaseUrl();
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final String resumptionType = api.getParams().get("resumptionType");
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final String resumptionParam = api.getParams().get("resumptionParam");
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final String resumptionXpath = api.getParams().get("resumptionXpath");
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@ -39,12 +43,14 @@ public class RestCollectorPlugin implements CollectorPlugin {
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final String resultFormatParam = api.getParams().get("resultFormatParam");
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final String resultFormatValue = api.getParams().get("resultFormatValue");
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final String resultSizeParam = api.getParams().get("resultSizeParam");
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final String resultSizeValue = (StringUtils.isBlank(api.getParams().get("resultSizeValue"))) ? "100"
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: api.getParams().get("resultSizeValue");
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final String queryParams = api.getParams().get("queryParams");
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final String entityXpath = api.getParams().get("entityXpath");
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final String authMethod = api.getParams().get("authMethod");
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final String authToken = api.getParams().get("authToken");
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final String resultSizeValue = Optional
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.ofNullable(api.getParams().get("resultSizeValue"))
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.filter(StringUtils::isNotBlank)
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.orElse(RESULT_SIZE_VALUE_DEFAULT);
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if (StringUtils.isBlank(baseUrl)) {
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throw new CollectorException("Param 'baseUrl' is null or empty");
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@ -65,6 +71,12 @@ public class RestCollectorPlugin implements CollectorPlugin {
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throw new CollectorException("Param 'entityXpath' is null or empty");
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}
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final String resultOutputFormat = Optional
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.ofNullable(api.getParams().get("resultOutputFormat"))
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.map(String::toLowerCase)
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.filter(StringUtils::isNotBlank)
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.orElse(resultFormatValue.toLowerCase());
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RestIterator it = new RestIterator(
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getClientParams(),
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baseUrl,
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@ -79,7 +91,8 @@ public class RestCollectorPlugin implements CollectorPlugin {
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queryParams,
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entityXpath,
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authMethod,
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authToken);
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authToken,
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resultOutputFormat);
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return StreamSupport
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.stream(
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@ -1,6 +1,27 @@
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package eu.dnetlib.dhp.collection.plugin.rest;
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import eu.dnetlib.dhp.collection.CollectorException;
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import eu.dnetlib.dhp.collection.HttpClientParams;
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import eu.dnetlib.dhp.collection.JsonUtils;
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import org.apache.avro.test.http.Http;
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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 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 java.io.InputStream;
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import java.io.StringWriter;
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import java.io.UnsupportedEncodingException;
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@ -12,30 +33,8 @@ 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 org.apache.commons.httpclient.HttpMethod;
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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.HttpHeaders;
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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.CollectorException;
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import eu.dnetlib.dhp.collection.HttpClientParams;
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import eu.dnetlib.dhp.collection.JsonUtils;
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/**
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* log.debug(...) equal to log.trace(...) in the application-logs
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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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@ -45,7 +44,8 @@ import eu.dnetlib.dhp.collection.JsonUtils;
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*/
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public class RestIterator implements Iterator<String> {
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private static final Log log = LogFactory.getLog(RestIterator.class);
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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 HttpClientParams clientParams;
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@ -74,65 +74,15 @@ public class RestIterator implements Iterator<String> {
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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 final Queue<String> recordQueue = new PriorityBlockingQueue<String>();
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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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* RestIterator class
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*
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* compatible to version before 1.3.33
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*
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* @param baseUrl
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* @param resumptionType
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* @param resumptionParam
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* @param resumptionXpath
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* @param resultTotalXpath
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* @param resultFormatParam
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* @param resultFormatValue
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* @param resultSizeParam
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* @param resultSizeValueStr
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* @param queryParams
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* @param entityXpath
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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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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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this(clientParams, baseUrl, resumptionType, resumptionParam, resumptionXpath, resultTotalXpath,
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resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValueStr, queryParams, entityXpath, "",
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"");
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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 resultOffsetParam) {
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this(clientParams, baseUrl, resumptionType, resumptionParam, resumptionXpath, resultTotalXpath,
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resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValueStr, queryParams, entityXpath, "",
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"");
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}
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private String resultOutputFormat;
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/** RestIterator class
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* compatible to version 1.3.33
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@ -151,17 +101,20 @@ public class RestIterator implements Iterator<String> {
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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 authToken,
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final String resultOutputFormat) {
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this.clientParams = clientParams;
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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.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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queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
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: "";
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@ -188,6 +141,7 @@ public class RestIterator implements Iterator<String> {
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private void initQueue() {
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query = baseUrl + "?" + queryParams + querySize + queryFormat;
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log.info("REST calls starting with " + query);
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}
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private void disconnect() {
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@ -217,9 +171,7 @@ public class RestIterator implements Iterator<String> {
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synchronized (recordQueue) {
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while (recordQueue.isEmpty() && !query.isEmpty()) {
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try {
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log.debug("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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} catch (CollectorException e) {
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log.debug("CollectorPlugin.next()-Exception: " + e);
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throw new RuntimeException(e);
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@ -235,9 +187,12 @@ public class RestIterator implements Iterator<String> {
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private String downloadPage(String query) throws CollectorException {
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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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String emptyXml = resultXml + "<" + JsonUtils.wrapName + "></" + JsonUtils.wrapName + ">";
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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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@ -249,20 +204,22 @@ public class RestIterator implements Iterator<String> {
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}
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try {
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log.info("requestig URL [{}]", query);
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URL qUrl = new URL(query);
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log.debug("authMethod :" + authMethod);
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if (this.authMethod == "bearer") {
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if ("bearer".equalsIgnoreCase(this.authMethod)) {
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log.trace("authMethod before inputStream: " + resultXml);
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HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
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conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
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conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/json");
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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 (BASIC.equalsIgnoreCase(this.authMethod)) {
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log.trace("authMethod before inputStream: " + resultXml);
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HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
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conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
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conn.setRequestProperty(HttpHeaders.ACCEPT, "application/xml");
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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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@ -270,10 +227,10 @@ public class RestIterator implements Iterator<String> {
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}
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resultStream = theHttpInputStream;
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if ("json".equalsIgnoreCase(resultFormatValue)) {
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resultJson = IOUtils.toString(resultStream, "UTF-8");
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if ("json".equals(resultOutputFormat)) {
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resultJson = IOUtils.toString(resultStream, UTF_8);
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resultXml = jsonUtils.convertToXML(resultJson);
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resultStream = IOUtils.toInputStream(resultXml, "UTF-8");
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resultStream = IOUtils.toInputStream(resultXml, UTF_8);
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}
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if (!(emptyXml).equalsIgnoreCase(resultXml)) {
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@ -283,15 +240,19 @@ public class RestIterator implements Iterator<String> {
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for (int i = 0; i < nodeList.getLength(); i++) {
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StringWriter sw = new StringWriter();
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transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
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String toEnqueue = sw.toString();
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if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
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log.warn("The following record resulted in empty item for the feeding queue: " + resultXml);
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} else {
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recordQueue.add(sw.toString());
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}
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}
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} else {
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log.info("resultXml is equal with emptyXml");
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log.warn("resultXml is equal with emptyXml");
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}
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resumptionInt += resultSizeValue;
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String qUrlArgument = "";
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switch (resumptionType.toLowerCase()) {
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case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
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resumptionStr = xprResumptionPath.evaluate(resultNode);
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@ -307,7 +268,6 @@ public class RestIterator implements Iterator<String> {
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}
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qUrlArgument = qUrl.getQuery();
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String[] arrayQUrlArgument = qUrlArgument.split("&");
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int urlOldResumptionSize = 0;
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for (String arrayUrlArgStr : arrayQUrlArgument) {
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if (arrayUrlArgStr.startsWith(resumptionParam)) {
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String[] resumptionKeyValue = arrayUrlArgStr.split("=");
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@ -334,7 +294,7 @@ public class RestIterator implements Iterator<String> {
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discoverResultSize += nodeList.getLength();
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}
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}
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log.debug("discoverResultSize: " + discoverResultSize);
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log.info("discoverResultSize: {}", discoverResultSize);
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break;
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case "pagination":
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@ -384,25 +344,24 @@ public class RestIterator implements Iterator<String> {
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}
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} catch (Exception e) {
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log.error(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 (resultTotal == -1) {
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resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
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if (resumptionType.toLowerCase().equals("page") && !BASIC.equalsIgnoreCase(authMethod)) {
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if (resumptionType.equalsIgnoreCase("page") && !BASIC.equalsIgnoreCase(authMethod)) {
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resultTotal += 1;
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} // to correct the upper bound
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log.info("resultTotal was -1 is now: " + resultTotal);
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}
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} catch (Exception e) {
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log.error(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: " + resultTotal);
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log.debug("resInt: " + resumptionInt);
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String nextQuery;
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if (resumptionInt <= resultTotal) {
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nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr
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+ queryFormat;
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@ -413,6 +372,7 @@ public class RestIterator implements Iterator<String> {
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}
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log.debug("nextQueryUrl: " + nextQuery);
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return nextQuery;
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}
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private boolean isInteger(String s) {
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@ -439,4 +399,12 @@ public class RestIterator implements Iterator<String> {
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}
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}
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public String getResultFormatValue() {
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return resultFormatValue;
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}
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public String getResultOutputFormat() {
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return resultOutputFormat;
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}
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}
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