forked from D-Net/dnet-hadoop
Implemented Download update of ORCID
This commit is contained in:
parent
62104790ae
commit
1a42a5c10d
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package eu.dnetlib.dhp.collection.orcid;
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import eu.dnetlib.dhp.common.collection.HttpClientParams;
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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.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.http.HttpHeaders;
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import org.jetbrains.annotations.NotNull;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.swing.*;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.util.concurrent.BlockingQueue;
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public class ORCIDWorker extends Thread {
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final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class);
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public static String JOB_COMPLETE="JOB_COMPLETE";
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private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
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private final BlockingQueue<String> queue;
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private boolean hasComplete = false;
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private final SequenceFile.Writer employments;
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private final SequenceFile.Writer summary;
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private final SequenceFile.Writer works;
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private final String token;
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private final String id;
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public static ORCIDWorkerBuilder builder() {
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return new ORCIDWorkerBuilder();
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}
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public ORCIDWorker(String id, BlockingQueue<String> myqueue, SequenceFile.Writer employments, SequenceFile.Writer summary, SequenceFile.Writer works, String token) {
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this.id= id;
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this.queue = myqueue;
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this.employments = employments;
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this.summary = summary;
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this.works = works;
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this.token = token;
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}
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public static String retrieveURL(final String id,final String apiUrl, String token) {
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try {
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final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token);
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if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) {
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InputStream input = urlConn.getInputStream();
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return IOUtils.toString(input);
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} else {
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log.error("Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}",id, apiUrl,urlConn.getResponseCode());
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}
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} catch (Exception e) {
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log.error("Thread {} Error on retrieving URL {} {}",id,apiUrl, e);
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}
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return null;
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}
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@NotNull
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private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException {
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final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection();
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final HttpClientParams clientParams = new HttpClientParams();
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urlConn.setInstanceFollowRedirects(false);
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urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
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urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
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urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
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urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token));
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return urlConn;
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}
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private static String generateSummaryURL(final String orcidId) {
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return "https://api.orcid.org/v3.0/" + orcidId + "/record";
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}
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private static String generateWorksURL(final String orcidId) {
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return "https://api.orcid.org/v3.0/" + orcidId + "/works";
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}
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private static String generateEmploymentsURL(final String orcidId) {
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return "https://api.orcid.org/v3.0/" + orcidId + "/employments";
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}
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private static void writeResultToSequenceFile(String id, String url, String token, String orcidId, SequenceFile.Writer file) throws IOException {
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final String response = retrieveURL(id, url,token);
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if (response!= null) {
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if(orcidId==null || response ==null){
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log.error("Thread {} {} {}",id, orcidId, response);
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throw new RuntimeException("null items ");
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}
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if(file==null) {
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log.error("Thread {} file is null for {} URL:{}",id, url, orcidId);
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}
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else
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file.append(new Text(orcidId),new Text(response));
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}
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}
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@Override
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public void run() {
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final Text key = new Text();
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final Text value = new Text();
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long start;
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long total_time;
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String orcidId="";
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int requests =0;
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if(summary==null || employments==null || works == null)
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throw new RuntimeException("Null files");
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while (!hasComplete) {
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try {
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orcidId = queue.take();
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if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) {
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queue.put(orcidId);
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hasComplete = true;
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} else {
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start = System.currentTimeMillis();
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writeResultToSequenceFile(id, generateSummaryURL(orcidId), token,orcidId, summary);
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total_time = System.currentTimeMillis() - start;
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requests++;
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if (total_time < 1000) {
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Thread.sleep(1000L - total_time);
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}
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start = System.currentTimeMillis();
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writeResultToSequenceFile(id, generateWorksURL(orcidId),token,orcidId, works);
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total_time = System.currentTimeMillis() - start;
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requests++;
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if (total_time < 1000) {
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Thread.sleep(1000L - total_time);
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}
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start = System.currentTimeMillis();
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writeResultToSequenceFile(id, generateEmploymentsURL(orcidId),token,orcidId, employments);
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total_time = System.currentTimeMillis() - start;
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requests++;
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if (total_time < 1000) {
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Thread.sleep(1000L - total_time);
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}
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if (requests %30 ==0)
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{
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log.info("Thread {} Downloaded {}",id, requests);
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}
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}
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} catch (Throwable e) {
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log.error("Thread {} Unable to save ORICD: {} item error",id, orcidId,e);
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}
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}
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try {
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works.close();
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summary.close();
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employments.close();
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} catch (Throwable e) {
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throw new RuntimeException(e);
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}
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log.info("Thread {} COMPLETE ", id);
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log.info("Thread {} Downloaded {}", id, requests);
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}
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public static class ORCIDWorkerBuilder {
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private String id;
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private SequenceFile.Writer employments;
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private SequenceFile.Writer summary;
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private SequenceFile.Writer works;
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private BlockingQueue<String> queue;
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private String token;
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public ORCIDWorkerBuilder withId(final String id) {
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this.id =id;
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return this;
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}
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public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) {
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this.employments = sequenceFile;
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return this;
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}
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public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) {
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this.summary = sequenceFile;
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return this;
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}
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public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) {
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this.works = sequenceFile;
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return this;
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}
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public ORCIDWorkerBuilder withAccessToken(final String accessToken) {
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this.token = accessToken;
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return this;
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}
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public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue<String> queue) {
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this.queue = queue;
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return this;
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}
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public ORCIDWorker build() {
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if (this.summary== null || this.works==null || this.employments == null || StringUtils.isEmpty(token) || queue == null)
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throw new RuntimeException("Unable to build missing required params");
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return new ORCIDWorker(id, queue,employments,summary,works,token);
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}
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}
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}
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@ -0,0 +1,133 @@
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package eu.dnetlib.dhp.collection.orcid;
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import java.io.*;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.concurrent.ArrayBlockingQueue;
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import java.util.concurrent.BlockingQueue;
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import eu.dnetlib.dhp.common.collection.HttpClientParams;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
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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.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
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public class OrcidGetUpdatesFile {
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private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class);
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public static void main(String[] args) throws IOException {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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"/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json");
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final String namenode = parser.get("namenode");
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log.info("got variable namenode: {}", namenode);
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final String targetPath = parser.get("targetPath");
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log.info("got variable targetPath: {}", targetPath);
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//http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar
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final String apiURL = parser.get("apiURL");
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log.info("got variable apiURL: {}", apiURL);
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final String accessToken = parser.get("accessToken");
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log.info("got variable accessToken: {}", accessToken);
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final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode));
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}
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private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException {
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return SequenceFile
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.createWriter(
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fileSystem.getConf(),
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SequenceFile.Writer.file(aPath),
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SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class));
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}
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private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue<String> queue, final String accessToken, FileSystem fileSystem) throws Exception {
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return ORCIDWorker.builder()
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.withId(id)
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.withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem))
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.withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem))
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.withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem))
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.withAccessToken(accessToken)
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.withBlockingQueue(queue)
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.build();
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}
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public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath, final String startDate ) throws Exception {
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final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection();
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final HttpClientParams clientParams = new HttpClientParams();
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urlConn.setInstanceFollowRedirects(false);
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urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
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urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
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if (urlConn.getResponseCode()>199 && urlConn.getResponseCode()<300) {
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InputStream input = urlConn.getInputStream();
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TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream(
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new BufferedInputStream(
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input)));
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TarArchiveEntry entry;
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BlockingQueue<String> queue = new ArrayBlockingQueue<String>(3000);
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final List<ORCIDWorker> workers = new ArrayList<>();
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for (int i = 0; i <20; i++) {
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workers.add(createWorker(""+i,targetPath,queue,accessToken, fileSystem));
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}
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workers.forEach(Thread::start);
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while ((entry = tais.getNextTarEntry()) != null) {
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if (entry.isFile()) {
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BufferedReader br = new BufferedReader(new InputStreamReader(tais));
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System.out.println(br.readLine());
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br.lines().map(l -> l.split(",")).filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0).map(s->s[0]).limit(200).forEach(s -> {
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try {
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log.info("Adding item ");
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queue.put(s);
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} catch (InterruptedException e) {
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throw new RuntimeException(e);
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}
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});
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queue.put(ORCIDWorker.JOB_COMPLETE);
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}
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}
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for (ORCIDWorker worker : workers) {
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worker.join();
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}
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}
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}
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}
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[
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{
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"paramName": "n",
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"paramLongName": "namenode",
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"paramDescription": "the Name Node URI",
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"paramRequired": true
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},
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{
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"paramName": "t",
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"paramLongName": "targetPath",
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"paramDescription": "the target PATH where download the files",
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"paramRequired": true
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},
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{
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"paramName": "a",
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"paramLongName": "apiURL",
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"paramDescription": "the URL to download the tar file",
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"paramRequired": true
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},
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{
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"paramName": "at",
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"paramLongName": "accessToken",
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"paramDescription": "the accessToken to contact API",
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"paramRequired": true
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}
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]
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@ -2,6 +2,7 @@
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package eu.dnetlib.dhp.collection.orcid;
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import java.io.IOException;
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import java.net.URI;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Objects;
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@ -9,7 +10,12 @@ import java.util.Objects;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.spark.SparkContext;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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@ -116,4 +122,19 @@ public class DownloadORCIDTest {
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});
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}
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// @Test
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// public void testReadTar() throws Exception {
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//// new OrcidGetUpdatesFile().readTar();
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//
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// Configuration conf = new Configuration();
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// FileSystem fs = FileSystem.get(URI.create("file:///"), conf);
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// final String token ="78fdb232-7105-4086-8570-e153f4198e3d";
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//
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// new OrcidGetUpdatesFile().readTar(fs,token, "http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar", "file:///Users/sandro/orcid","2023-09-30");
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//
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//
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//
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//
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// }
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}
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@ -82,7 +82,7 @@ public class IndexRecordTransformerTest {
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void testPeerReviewed() throws IOException, TransformerException {
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final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
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XmlConverterJob.schemaLocation);
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XmlConverterJob.schemaLocation);
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final Publication p = load("publication.json", Publication.class);
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