Merge pull request 'implementation of the new collector plugin: research_fi' (#456) from research_fi_collector_plugin into beta
Reviewed-on: #456
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package eu.dnetlib.dhp.collection.plugin.researchfi;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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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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import java.util.stream.StreamSupport;
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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.NameValuePair;
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import org.apache.http.client.entity.UrlEncodedFormEntity;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpPost;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.apache.http.message.BasicNameValuePair;
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import org.json.JSONObject;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public class ResearchFiCollectorPlugin implements CollectorPlugin {
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private static final Logger log = LoggerFactory.getLogger(ResearchFiCollectorPlugin.class);
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@Override
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public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
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throws CollectorException {
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final String authUrl = api.getParams().get("auth_url");
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final String clientId = api.getParams().get("auth_client_id");
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final String clientSecret = api.getParams().get("auth_client_secret");
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final String authToken = authenticate(authUrl, clientId, clientSecret);
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final Iterator<String> iter = new ResearchFiIterator(api.getBaseUrl(), authToken);
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return StreamSupport.stream(Spliterators.spliteratorUnknownSize(iter, Spliterator.ORDERED), false);
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}
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private String authenticate(final String authUrl, final String clientId, final String clientSecret) throws CollectorException {
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try (final CloseableHttpClient client = HttpClients.createDefault()) {
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final HttpPost req = new HttpPost(authUrl);
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final List<NameValuePair> params = new ArrayList<>();
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params.add(new BasicNameValuePair("grant_type", "client_credentials"));
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params.add(new BasicNameValuePair("client_id", clientId));
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params.add(new BasicNameValuePair("client_secret", clientSecret));
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req.setEntity(new UrlEncodedFormEntity(params, "UTF-8"));
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try (final CloseableHttpResponse response = client.execute(req)) {
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final String content = IOUtils.toString(response.getEntity().getContent());
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final JSONObject obj = new JSONObject(content);
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final String token = obj.getString("access_token");
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if (StringUtils.isNotBlank(token)) { return token; }
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}
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} catch (final Throwable e) {
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log.warn("Error obtaining access token", e);
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throw new CollectorException("Error obtaining access token", e);
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}
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throw new CollectorException("Access token is missing");
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}
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}
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package eu.dnetlib.dhp.collection.plugin.researchfi;
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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 org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.math.NumberUtils;
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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.Header;
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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.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.json.JSONArray;
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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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public class ResearchFiIterator implements Iterator<String> {
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private static final Log log = LogFactory.getLog(ResearchFiIterator.class);
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private static final int PAGE_SIZE = 100;
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private final String baseUrl;
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private final String authToken;
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private int currPage;
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private int nPages;
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private final Queue<String> queue = new PriorityBlockingQueue<>();
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public ResearchFiIterator(final String baseUrl, final String authToken) {
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this.baseUrl = baseUrl;
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this.authToken = authToken;
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this.currPage = 0;
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this.nPages = 0;
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}
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private void verifyStarted() {
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if (this.currPage == 0) {
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try {
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nextCall();
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} catch (final CollectorException e) {
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throw new IllegalStateException(e);
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}
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}
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}
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@Override
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public boolean hasNext() {
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synchronized (this.queue) {
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verifyStarted();
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return !this.queue.isEmpty();
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}
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}
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@Override
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public String next() {
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synchronized (this.queue) {
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verifyStarted();
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final String res = this.queue.poll();
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while (this.queue.isEmpty() && (this.currPage < this.nPages)) {
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try {
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nextCall();
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} catch (final CollectorException e) {
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throw new IllegalStateException(e);
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}
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}
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return res;
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}
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}
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private void nextCall() throws CollectorException {
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this.currPage += 1;
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final String url;
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if (!this.baseUrl.contains("?")) {
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url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
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} else if (!this.baseUrl.contains("PageSize=")) {
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url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
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} else {
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url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
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}
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log.info("Calling url: " + url);
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try (final CloseableHttpClient client = HttpClients.createDefault()) {
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final HttpGet req = new HttpGet(url);
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req.addHeader("Authorization", "Bearer " + this.authToken);
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try (final CloseableHttpResponse response = client.execute(req)) {
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for (final Header header : response.getAllHeaders()) {
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log.debug("HEADER: " + header.getName() + " = " + header.getValue());
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if ("x-page-count".equals(header.getName())) {
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final int totalPages = NumberUtils.toInt(header.getValue());
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if (this.nPages != totalPages) {
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this.nPages = NumberUtils.toInt(header.getValue());
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log.info("Total pages: " + totalPages);
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}
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}
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}
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final String content = IOUtils.toString(response.getEntity().getContent());
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final JSONArray jsonArray = new JSONArray(content);
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jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString())));
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}
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} catch (final Throwable e) {
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log.warn("Error calling url: " + url, e);
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throw new CollectorException("Error calling url: " + url, e);
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}
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}
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}
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@ -0,0 +1,55 @@
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package eu.dnetlib.dhp.collection.plugin.researchfi;
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import java.util.HashSet;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicLong;
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import org.dom4j.DocumentException;
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import org.dom4j.DocumentHelper;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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import eu.dnetlib.dhp.collection.ApiDescriptor;
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import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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public class ResearchFiCollectorPluginTest {
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private final ResearchFiCollectorPlugin plugin = new ResearchFiCollectorPlugin();
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@Test
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@Disabled
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void testCollect() throws CollectorException {
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final ApiDescriptor api = new ApiDescriptor();
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api.setBaseUrl("https://research.fi/api/rest/v1/funding-decisions?FunderName=AKA&FundingStartYearFrom=2022");
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api.setProtocol("research_fi");
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api.getParams().put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
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api.getParams().put("auth_client_id", "");
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api.getParams().put("auth_client_secret", "");
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final AtomicLong count = new AtomicLong(0);
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final Set<String> ids = new HashSet<>();
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this.plugin.collect(api, new AggregatorReport()).forEach(s -> {
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if (count.getAndIncrement() == 0) {
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System.out.println("First: " + s);
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}
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try {
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final String id = DocumentHelper.parseText(s).valueOf("/recordWrap/funderProjectNumber");
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if (ids.contains(id)) {
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System.out.println("Id already present: " + id);
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}
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ids.add(id);
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} catch (final DocumentException e) {
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throw new RuntimeException(e);
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}
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});
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System.out.println("Total records: " + count);
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System.out.println("Total identifiers: " + ids.size());
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}
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}
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