Orcid Update Procedure #394
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@ -0,0 +1,244 @@
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package eu.dnetlib.dhp.collection.orcid;
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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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import javax.swing.*;
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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 eu.dnetlib.dhp.common.collection.HttpClientParams;
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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,
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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
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.error(
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"Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}", id, apiUrl,
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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,
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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) {
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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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} else {
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file.append(new Text(orcidId), new Text(response));
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file.hflush();
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}
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} else
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log.error("Thread {} response is null for {} URL:{}", id, url, orcidId);
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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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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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// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
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// hence
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// the time between two http request in a thread must be 1 second
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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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// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
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// hence
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// the time between two http request in a thread must be 1 second
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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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// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
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// hence
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// the time between two http request in a thread must be 1 second
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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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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)
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|| 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 +1,172 @@
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package eu.dnetlib.dhp.collection.orcid;
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import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
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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.Objects;
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import java.util.concurrent.ArrayBlockingQueue;
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import java.util.concurrent.BlockingQueue;
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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.FSDataInputStream;
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import org.apache.hadoop.fs.FSDataOutputStream;
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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.apache.spark.sql.SparkSession;
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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 eu.dnetlib.dhp.common.collection.HttpClientParams;
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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 Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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OrcidGetUpdatesFile.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json")))
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);
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parser.parseArgument(args);
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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 master = parser.get("master");
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log.info("got variable master: {}", master);
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final String targetPath = parser.get("targetPath");
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log.info("got variable targetPath: {}", targetPath);
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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 String graphPath = parser.get("graphPath");
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log.info("got variable graphPath: {}", graphPath);
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final SparkSession spark = SparkSession
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.builder()
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.appName(OrcidGetUpdatesFile.class.getName())
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.master(master)
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.getOrCreate();
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final String latestDate = spark
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.read()
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.load(graphPath + "/Authors")
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.selectExpr("max(lastModifiedDate)")
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.first()
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.getString(0);
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log.info("latest date is {}", latestDate);
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final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode));
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new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, latestDate);
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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,
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final String accessToken, FileSystem fileSystem) throws Exception {
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return ORCIDWorker
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.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,
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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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Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz");
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final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true);
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IOUtils.copy(input, fsDataOutputStream);
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fsDataOutputStream.flush();
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fsDataOutputStream.close();
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FSDataInputStream updateFile = fileSystem.open(hdfsWritePath);
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TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream(
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new BufferedInputStream(
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updateFile.getWrappedStream())));
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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 < 22; 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
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.lines()
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.map(l -> l.split(","))
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.filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0)
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.map(s -> s[0])
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.forEach(s -> {
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try {
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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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|
sandro.labruzzo marked this conversation as resolved
Outdated
|
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|
||||
}
|
||||
}
|
||||
|
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for (int i = 0; i < 22; i++) {
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queue.put(ORCIDWorker.JOB_COMPLETE);
|
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}
|
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for (ORCIDWorker worker : workers) {
|
||||
worker.join();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
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|
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@ -1,11 +1,15 @@
|
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|
||||
package eu.dnetlib.dhp.collection.orcid;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
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|
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import org.apache.commons.lang3.StringUtils;
|
||||
import org.dom4j.Document;
|
||||
import org.dom4j.DocumentFactory;
|
||||
import org.dom4j.DocumentHelper;
|
||||
import org.dom4j.Node;
|
||||
import org.jetbrains.annotations.NotNull;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
|
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@ -40,8 +44,8 @@ public class OrcidParser {
|
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private static final String NS_ERROR = "error";
|
||||
private static final String NS_HISTORY = "history";
|
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private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history";
|
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private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk";
|
||||
private static final String NS_BULK = "bulk";
|
||||
private static final String NS_EMPLOYMENT = "employment";
|
||||
private static final String NS_EMPLOYMENT_URL = "http://www.orcid.org/ns/employment";
|
||||
private static final String NS_EXTERNAL = "external-identifier";
|
||||
private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier";
|
||||
|
||||
|
|
@ -61,6 +65,7 @@ public class OrcidParser {
|
|||
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
|
||||
ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL);
|
||||
ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL);
|
||||
ap.declareXPathNameSpace(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
|
||||
}
|
||||
|
||||
public Author parseSummary(final String xml) {
|
||||
|
|
@ -70,13 +75,15 @@ public class OrcidParser {
|
|||
generateParsedDocument(xml);
|
||||
List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
|
||||
.getTextValuesWithAttributes(
|
||||
ap, vn, "//record:record", Arrays.asList("path"));
|
||||
ap, vn, "//record:record", Collections.singletonList("path"));
|
||||
if (!recordNodes.isEmpty()) {
|
||||
final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
|
||||
author.setOrcid(oid);
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
final String ltm = VtdUtilityParser.getSingleValue(ap, vn, "//common:last-modified-date");
|
||||
author.setLastModifiedDate(ltm);
|
||||
List<VtdUtilityParser.Node> personNodes = VtdUtilityParser
|
||||
.getTextValuesWithAttributes(
|
||||
ap, vn, "//person:name", Arrays.asList("visibility"));
|
||||
|
|
@ -129,6 +136,64 @@ public class OrcidParser {
|
|||
}
|
||||
}
|
||||
|
||||
public List<Work> parseWorks(final String xml) {
|
||||
|
||||
try {
|
||||
String oid;
|
||||
|
||||
generateParsedDocument(xml);
|
||||
List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
|
||||
.getTextValuesWithAttributes(ap, vn, "//activities:works", Arrays.asList("path", "visibility"));
|
||||
if (!workNodes.isEmpty()) {
|
||||
oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
|
||||
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
final List<Work> works = new ArrayList<>();
|
||||
ap.selectXPath("//work:work-summary");
|
||||
|
||||
while (ap.evalXPath() != -1) {
|
||||
final Work work = new Work();
|
||||
work.setOrcid(oid);
|
||||
final AutoPilot ap1 = new AutoPilot(ap.getNav());
|
||||
ap1.selectXPath("./work:title/common:title");
|
||||
while (ap1.evalXPath() != -1) {
|
||||
int it = vn.getText();
|
||||
work.setTitle(vn.toNormalizedString(it));
|
||||
}
|
||||
ap1.selectXPath(".//common:external-id");
|
||||
while (ap1.evalXPath() != -1) {
|
||||
final Pid pid = new Pid();
|
||||
|
||||
final AutoPilot ap2 = new AutoPilot(ap1.getNav());
|
||||
|
||||
ap2.selectXPath("./common:external-id-type");
|
||||
while (ap2.evalXPath() != -1) {
|
||||
int it = vn.getText();
|
||||
pid.setSchema(vn.toNormalizedString(it));
|
||||
}
|
||||
ap2.selectXPath("./common:external-id-value");
|
||||
while (ap2.evalXPath() != -1) {
|
||||
int it = vn.getText();
|
||||
pid.setValue(vn.toNormalizedString(it));
|
||||
}
|
||||
|
||||
work.addPid(pid);
|
||||
}
|
||||
|
||||
works.add(work);
|
||||
}
|
||||
return works;
|
||||
|
||||
} catch (Throwable e) {
|
||||
log.error("Error on parsing {}", xml);
|
||||
log.error(e.getMessage());
|
||||
return null;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
public Work parseWork(final String xml) {
|
||||
|
||||
try {
|
||||
|
|
@ -176,11 +241,15 @@ public class OrcidParser {
|
|||
}
|
||||
|
||||
private String extractEmploymentDate(final String xpath) throws Exception {
|
||||
return extractEmploymentDate(xpath, ap);
|
||||
}
|
||||
|
||||
ap.selectXPath(xpath);
|
||||
private String extractEmploymentDate(final String xpath, AutoPilot pp) throws Exception {
|
||||
|
||||
pp.selectXPath(xpath);
|
||||
StringBuilder sb = new StringBuilder();
|
||||
while (ap.evalXPath() != -1) {
|
||||
final AutoPilot ap1 = new AutoPilot(ap.getNav());
|
||||
while (pp.evalXPath() != -1) {
|
||||
final AutoPilot ap1 = new AutoPilot(pp.getNav());
|
||||
ap1.selectXPath("./common:year");
|
||||
while (ap1.evalXPath() != -1) {
|
||||
int it = vn.getText();
|
||||
|
|
@ -203,6 +272,104 @@ public class OrcidParser {
|
|||
|
||||
}
|
||||
|
||||
public List<Employment> parseEmployments(final String xml) {
|
||||
try {
|
||||
String oid;
|
||||
Map<String, String> nsContext = getNameSpaceMap();
|
||||
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
|
||||
Document doc = DocumentHelper.parseText(xml);
|
||||
oid = doc.valueOf("//activities:employments/@path");
|
||||
if (oid == null || StringUtils.isEmpty(oid))
|
||||
return null;
|
||||
final String orcid = oid.split("/")[1];
|
||||
|
||||
List<Node> nodes = doc.selectNodes("//employment:employment-summary");
|
||||
return nodes.stream().map(n -> {
|
||||
final Employment e = new Employment();
|
||||
e.setOrcid(orcid);
|
||||
|
||||
final String depName = n.valueOf(".//common:department-name");
|
||||
if (StringUtils.isNotBlank(depName))
|
||||
e.setDepartmentName(depName);
|
||||
final String roleTitle = n.valueOf(".//common:role-title");
|
||||
e.setRoleTitle(roleTitle);
|
||||
final String organizationName = n.valueOf(".//common:organization/common:name");
|
||||
if (StringUtils.isEmpty(e.getDepartmentName()))
|
||||
e.setDepartmentName(organizationName);
|
||||
final Pid p = new Pid();
|
||||
final String pid = n
|
||||
.valueOf(
|
||||
"./common:organization/common:disambiguated-organization/common:disambiguated-organization-identifier");
|
||||
p.setValue(pid);
|
||||
final String pidType = n
|
||||
.valueOf("./common:organization/common:disambiguated-organization/common:disambiguation-source");
|
||||
p.setSchema(pidType);
|
||||
e.setAffiliationId(p);
|
||||
|
||||
final StringBuilder aDate = new StringBuilder();
|
||||
final String sy = n.valueOf("./common:start-date/common:year");
|
||||
if (StringUtils.isNotBlank(sy)) {
|
||||
aDate.append(sy);
|
||||
final String sm = n.valueOf("./common:start-date/common:month");
|
||||
final String sd = n.valueOf("./common:start-date/common:day");
|
||||
aDate.append("-");
|
||||
if (StringUtils.isNotBlank(sm))
|
||||
aDate.append(sm);
|
||||
else
|
||||
aDate.append("01");
|
||||
aDate.append("-");
|
||||
if (StringUtils.isNotBlank(sd))
|
||||
aDate.append(sd);
|
||||
else
|
||||
aDate.append("01");
|
||||
e.setEndDate(aDate.toString());
|
||||
}
|
||||
|
||||
final String ey = n.valueOf("./common:end-date/common:year");
|
||||
if (StringUtils.isNotBlank(ey)) {
|
||||
aDate.append(ey);
|
||||
final String em = n.valueOf("./common:end-date/common:month");
|
||||
final String ed = n.valueOf("./common:end-date/common:day");
|
||||
aDate.append("-");
|
||||
if (StringUtils.isNotBlank(em))
|
||||
aDate.append(em);
|
||||
else
|
||||
aDate.append("01");
|
||||
aDate.append("-");
|
||||
if (StringUtils.isNotBlank(ed))
|
||||
aDate.append(ed);
|
||||
else
|
||||
aDate.append("01");
|
||||
e.setEndDate(aDate.toString());
|
||||
}
|
||||
|
||||
return e;
|
||||
|
||||
}).collect(Collectors.toList());
|
||||
} catch (Throwable e) {
|
||||
log.error("Error on parsing {}", xml);
|
||||
log.error(e.getMessage());
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
@NotNull
|
||||
private static Map<String, String> getNameSpaceMap() {
|
||||
Map<String, String> nsContext = new HashMap<>();
|
||||
nsContext.put(NS_COMMON, NS_COMMON_URL);
|
||||
nsContext.put(NS_PERSON, NS_PERSON_URL);
|
||||
nsContext.put(NS_DETAILS, NS_DETAILS_URL);
|
||||
nsContext.put(NS_OTHER, NS_OTHER_URL);
|
||||
nsContext.put(NS_RECORD, NS_RECORD_URL);
|
||||
nsContext.put(NS_ERROR, NS_ERROR_URL);
|
||||
nsContext.put(NS_HISTORY, NS_HISTORY_URL);
|
||||
nsContext.put(NS_WORK, NS_WORK_URL);
|
||||
nsContext.put(NS_EXTERNAL, NS_EXTERNAL_URL);
|
||||
nsContext.put(NS_ACTIVITIES, NS_ACTIVITIES_URL);
|
||||
nsContext.put(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
|
||||
return nsContext;
|
||||
}
|
||||
|
||||
public Employment parseEmployment(final String xml) {
|
||||
try {
|
||||
final Employment employment = new Employment();
|
||||
|
|
|
|||
|
|
@ -18,6 +18,8 @@ public class Author extends ORCIDItem {
|
|||
|
||||
private String biography;
|
||||
|
||||
private String lastModifiedDate;
|
||||
|
||||
public String getBiography() {
|
||||
return biography;
|
||||
}
|
||||
|
|
@ -74,6 +76,14 @@ public class Author extends ORCIDItem {
|
|||
this.otherPids = otherPids;
|
||||
}
|
||||
|
||||
public String getLastModifiedDate() {
|
||||
return lastModifiedDate;
|
||||
}
|
||||
|
||||
public void setLastModifiedDate(String lastModifiedDate) {
|
||||
this.lastModifiedDate = lastModifiedDate;
|
||||
}
|
||||
|
||||
public void addOtherPid(final Pid pid) {
|
||||
|
||||
if (otherPids == null)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,26 @@
|
|||
[
|
||||
{
|
||||
"paramName": "m",
|
||||
"paramLongName": "master",
|
||||
"paramDescription": "the master name",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "t",
|
||||
"paramLongName": "targetPath",
|
||||
"paramDescription": "the target PATH of the DF tables",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "g",
|
||||
"paramLongName": "graphPath",
|
||||
"paramDescription": "the PATH of the current graph path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "u",
|
||||
"paramLongName": "updatePath",
|
||||
"paramDescription": "the PATH of the current graph update path",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
[ {
|
||||
"paramName": "n",
|
||||
"paramLongName": "namenode",
|
||||
"paramDescription": "the Name Node URI",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "m",
|
||||
"paramLongName": "master",
|
||||
"paramDescription": "the master name",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "t",
|
||||
"paramLongName": "targetPath",
|
||||
"paramDescription": "the target PATH where download the files",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "a",
|
||||
"paramLongName": "apiURL",
|
||||
"paramDescription": "the URL to download the tar file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "g",
|
||||
"paramLongName": "graphPath",
|
||||
"paramDescription": "the path of the input graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "at",
|
||||
"paramLongName": "accessToken",
|
||||
"paramDescription": "the accessToken to contact API",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -16,6 +16,12 @@
|
|||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the PATH of the ORCID sequence file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "fu",
|
||||
"paramLongName": "fromUpdate",
|
||||
"paramDescription": "whether we have to generate table from dump or from update",
|
||||
"paramRequired": false
|
||||
}
|
||||
|
||||
]
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,114 @@
|
|||
<workflow-app name="download_Update_ORCID" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>graphPath</name>
|
||||
<description>the path to store the original ORCID dump</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the path to store the original ORCID dump</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>apiURL</name>
|
||||
<value>http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar</value>
|
||||
<description>The URL of the update CSV list </description>
|
||||
</property>
|
||||
<property>
|
||||
<name>accessToken</name>
|
||||
<description>The access token</description>
|
||||
</property>
|
||||
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="startUpdate"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="startUpdate">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Check Latest Orcid and Download updates</name>
|
||||
<class>eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.executor.memoryOverhead=2g
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--namenode</arg><arg>${nameNode}</arg>
|
||||
<arg>--graphPath</arg><arg>${graphPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--apiURL</arg><arg>${apiURL}</arg>
|
||||
<arg>--accessToken</arg><arg>${accessToken}</arg>
|
||||
</spark>
|
||||
<ok to="generateTables"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="generateTables">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Generate ORCID Tables</name>
|
||||
<class>eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.executor.memoryOverhead=2g
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/updateTable</arg>
|
||||
<arg>--fromUpdate</arg><arg>true</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="updateTable"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="updateTable">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Update ORCID Tables</name>
|
||||
<class>eu.dnetlib.dhp.collection.orcid.SparkApplyUpdate</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.executor.memoryOverhead=2g
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphPath}</arg>
|
||||
<arg>--updatePath</arg><arg>${targetPath}/updateTable</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/newTable</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,120 @@
|
|||
package eu.dnetlib.dhp.collection.orcid
|
||||
|
||||
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||||
import org.apache.spark.sql.{DataFrame, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger)
|
||||
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||||
|
||||
/** Here all the spark applications runs this method
|
||||
* where the whole logic of the spark node is defined
|
||||
*/
|
||||
override def run(): Unit = {
|
||||
|
||||
val graphPath: String = parser.get("graphPath")
|
||||
log.info("found parameters graphPath: {}", graphPath)
|
||||
val updatePath: String = parser.get("updatePath")
|
||||
log.info("found parameters updatePath: {}", updatePath)
|
||||
val targetPath: String = parser.get("targetPath")
|
||||
log.info("found parameters targetPath: {}", targetPath)
|
||||
applyTableUpdate(spark, graphPath, updatePath, targetPath)
|
||||
checkUpdate(spark, graphPath, targetPath)
|
||||
moveTable(spark, graphPath, targetPath)
|
||||
|
||||
}
|
||||
|
||||
private def moveTable(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
|
||||
spark.read
|
||||
.load(s"$updatePath/Authors")
|
||||
.repartition(1000)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$graphPath/Authors")
|
||||
spark.read
|
||||
.load(s"$updatePath/Works")
|
||||
.repartition(1000)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$graphPath/Works")
|
||||
spark.read
|
||||
.load(s"$updatePath/Employments")
|
||||
.repartition(1000)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$graphPath/Employments")
|
||||
|
||||
}
|
||||
|
||||
private def updateDataset(
|
||||
inputDataset: DataFrame,
|
||||
idUpdate: DataFrame,
|
||||
updateDataframe: DataFrame,
|
||||
targetPath: String
|
||||
): Unit = {
|
||||
inputDataset
|
||||
.join(idUpdate, inputDataset("orcid").equalTo(idUpdate("orcid")), "leftanti")
|
||||
.select(inputDataset("*"))
|
||||
.unionByName(updateDataframe)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(targetPath)
|
||||
}
|
||||
|
||||
private def checkUpdate(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
|
||||
val totalOriginalAuthors = spark.read.load(s"$graphPath/Authors").count
|
||||
val totalOriginalWorks = spark.read.load(s"$graphPath/Works").count
|
||||
val totalOriginalEmployments = spark.read.load(s"$graphPath/Employments").count
|
||||
val totalUpdateAuthors = spark.read.load(s"$updatePath/Authors").count
|
||||
val totalUpdateWorks = spark.read.load(s"$updatePath/Works").count
|
||||
val totalUpdateEmployments = spark.read.load(s"$updatePath/Employments").count
|
||||
|
||||
log.info("totalOriginalAuthors: {}", totalOriginalAuthors)
|
||||
log.info("totalOriginalWorks: {}", totalOriginalWorks)
|
||||
log.info("totalOriginalEmployments: {}", totalOriginalEmployments)
|
||||
log.info("totalUpdateAuthors: {}", totalUpdateAuthors)
|
||||
log.info("totalUpdateWorks: {}", totalUpdateWorks)
|
||||
log.info("totalUpdateEmployments: {}", totalUpdateEmployments)
|
||||
if (
|
||||
totalUpdateAuthors < totalOriginalAuthors || totalUpdateEmployments < totalOriginalEmployments || totalUpdateWorks < totalOriginalWorks
|
||||
)
|
||||
throw new RuntimeException("The updated Graph contains less elements of the original one")
|
||||
|
||||
}
|
||||
|
||||
private def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String): Unit = {
|
||||
val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid")
|
||||
updateDataset(
|
||||
spark.read.load(s"$graphPath/Authors"),
|
||||
orcidIDUpdate,
|
||||
spark.read.load(s"$updatePath/Authors"),
|
||||
s"$targetPath/Authors"
|
||||
)
|
||||
updateDataset(
|
||||
spark.read.load(s"$graphPath/Employments"),
|
||||
orcidIDUpdate,
|
||||
spark.read.load(s"$updatePath/Employments"),
|
||||
s"$targetPath/Employments"
|
||||
)
|
||||
updateDataset(
|
||||
spark.read.load(s"$graphPath/Works"),
|
||||
orcidIDUpdate,
|
||||
spark.read.load(s"$updatePath/Works"),
|
||||
s"$targetPath/Works"
|
||||
)
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
object SparkApplyUpdate {
|
||||
|
||||
val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass)
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
new SparkApplyUpdate("/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json", args, log)
|
||||
.initialize()
|
||||
.run()
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -6,6 +6,7 @@ import org.apache.hadoop.io.Text
|
|||
import org.apache.spark.SparkContext
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger)
|
||||
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||||
|
|
@ -18,12 +19,16 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
|
|||
log.info("found parameters sourcePath: {}", sourcePath)
|
||||
val targetPath: String = parser.get("targetPath")
|
||||
log.info("found parameters targetPath: {}", targetPath)
|
||||
extractORCIDTable(spark, sourcePath, targetPath)
|
||||
extractORCIDEmploymentsTable(spark, sourcePath, targetPath)
|
||||
extractORCIDWorksTable(spark, sourcePath, targetPath)
|
||||
val fromUpdate = "true".equals(parser.get("fromUpdate"))
|
||||
val sourceSummaryPath = if (fromUpdate) s"$sourcePath/summary*" else sourcePath
|
||||
val sourceEmploymentsPath = if (fromUpdate) s"$sourcePath/employments*" else sourcePath
|
||||
val sourceWorksPath = if (fromUpdate) s"$sourcePath/works*" else sourcePath
|
||||
extractORCIDTable(spark, sourceSummaryPath, targetPath, fromUpdate)
|
||||
extractORCIDEmploymentsTable(spark, sourceEmploymentsPath, targetPath, fromUpdate)
|
||||
extractORCIDWorksTable(spark, sourceWorksPath, targetPath, fromUpdate)
|
||||
}
|
||||
|
||||
def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
|
||||
def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String, skipFilterByKey: Boolean): Unit = {
|
||||
val sc: SparkContext = spark.sparkContext
|
||||
import spark.implicits._
|
||||
val df = sc
|
||||
|
|
@ -32,8 +37,8 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
|
|||
.toDF
|
||||
.as[(String, String)]
|
||||
implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author])
|
||||
// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid])
|
||||
df.filter(r => r._1.contains("summaries"))
|
||||
val newDf = if (!skipFilterByKey) df.filter(r => r._1.contains("summaries")) else df
|
||||
newDf
|
||||
.map { r =>
|
||||
val p = new OrcidParser
|
||||
p.parseSummary(r._2)
|
||||
|
|
@ -44,7 +49,12 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
|
|||
.save(s"$targetPath/Authors")
|
||||
}
|
||||
|
||||
def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
|
||||
def extractORCIDWorksTable(
|
||||
spark: SparkSession,
|
||||
sourcePath: String,
|
||||
targetPath: String,
|
||||
skipFilterByKey: Boolean
|
||||
): Unit = {
|
||||
val sc: SparkContext = spark.sparkContext
|
||||
import spark.implicits._
|
||||
val df = sc
|
||||
|
|
@ -53,19 +63,37 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
|
|||
.toDF
|
||||
.as[(String, String)]
|
||||
implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work])
|
||||
implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
|
||||
df.filter(r => r._1.contains("works"))
|
||||
.map { r =>
|
||||
|
||||
//We are in the case of parsing ORCID UPDATE
|
||||
if (skipFilterByKey) {
|
||||
df.flatMap { r =>
|
||||
val p = new OrcidParser
|
||||
p.parseWork(r._2)
|
||||
}
|
||||
.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Works")
|
||||
p.parseWorks(r._2).asScala
|
||||
}.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Works")
|
||||
}
|
||||
//We are in the case of parsing ORCID DUMP
|
||||
else {
|
||||
df.filter(r => r._1.contains("works"))
|
||||
.map { r =>
|
||||
val p = new OrcidParser
|
||||
p.parseWork(r._2)
|
||||
}
|
||||
.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Works")
|
||||
}
|
||||
}
|
||||
|
||||
def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
|
||||
def extractORCIDEmploymentsTable(
|
||||
spark: SparkSession,
|
||||
sourcePath: String,
|
||||
targetPath: String,
|
||||
skipFilterByKey: Boolean
|
||||
): Unit = {
|
||||
val sc: SparkContext = spark.sparkContext
|
||||
import spark.implicits._
|
||||
val df = sc
|
||||
|
|
@ -74,16 +102,27 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
|
|||
.toDF
|
||||
.as[(String, String)]
|
||||
implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment])
|
||||
implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
|
||||
df.filter(r => r._1.contains("employments"))
|
||||
.map { r =>
|
||||
if (skipFilterByKey) {
|
||||
df.flatMap { r =>
|
||||
val p = new OrcidParser
|
||||
p.parseEmployment(r._2)
|
||||
}
|
||||
.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Employments")
|
||||
p.parseEmployments(r._2).asScala
|
||||
}.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Employments")
|
||||
}
|
||||
//We are in the case of parsing ORCID DUMP
|
||||
else {
|
||||
df.filter(r => r._1.contains("employments"))
|
||||
.map { r =>
|
||||
val p = new OrcidParser
|
||||
p.parseEmployment(r._2)
|
||||
}
|
||||
.filter(p => p != null)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$targetPath/Employments")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.collection.orcid;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.URI;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
|
|
@ -9,7 +10,12 @@ import java.util.Objects;
|
|||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.SequenceFile;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.io.compress.CompressionCodec;
|
||||
import org.apache.hadoop.io.compress.CompressionCodecFactory;
|
||||
import org.apache.spark.SparkContext;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
|
@ -27,6 +33,7 @@ import com.ximpleware.XPathParseException;
|
|||
|
||||
import eu.dnetlib.dhp.collection.orcid.model.Author;
|
||||
import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem;
|
||||
import eu.dnetlib.dhp.collection.orcid.model.Work;
|
||||
import eu.dnetlib.dhp.parser.utility.VtdException;
|
||||
|
||||
public class DownloadORCIDTest {
|
||||
|
|
@ -82,6 +89,34 @@ public class DownloadORCIDTest {
|
|||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParsingOrcidUpdateEmployments() throws Exception {
|
||||
final String xml = IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_employments.xml")));
|
||||
|
||||
final OrcidParser parser = new OrcidParser();
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
System.out.println(mapper.writeValueAsString(parser.parseEmployments(xml)));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParsingOrcidUpdateWorks() throws Exception {
|
||||
final String xml = IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_work.xml")));
|
||||
|
||||
final OrcidParser parser = new OrcidParser();
|
||||
final List<Work> works = parser.parseWorks(xml);
|
||||
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
System.out.println(mapper.writeValueAsString(works));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testParsingEmployments() throws Exception {
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,966 @@
|
|||
<record:record path="/0000-0001-6816-8350" xmlns:internal="http://www.orcid.org/ns/internal" xmlns:education="http://www.orcid.org/ns/education" xmlns:distinction="http://www.orcid.org/ns/distinction" xmlns:deprecated="http://www.orcid.org/ns/deprecated" xmlns:other-name="http://www.orcid.org/ns/other-name" xmlns:membership="http://www.orcid.org/ns/membership" xmlns:error="http://www.orcid.org/ns/error" xmlns:common="http://www.orcid.org/ns/common" xmlns:record="http://www.orcid.org/ns/record" xmlns:personal-details="http://www.orcid.org/ns/personal-details" xmlns:keyword="http://www.orcid.org/ns/keyword" xmlns:email="http://www.orcid.org/ns/email" xmlns:external-identifier="http://www.orcid.org/ns/external-identifier" xmlns:funding="http://www.orcid.org/ns/funding" xmlns:preferences="http://www.orcid.org/ns/preferences" xmlns:address="http://www.orcid.org/ns/address" xmlns:invited-position="http://www.orcid.org/ns/invited-position" xmlns:work="http://www.orcid.org/ns/work" xmlns:history="http://www.orcid.org/ns/history" xmlns:employment="http://www.orcid.org/ns/employment" xmlns:qualification="http://www.orcid.org/ns/qualification" xmlns:service="http://www.orcid.org/ns/service" xmlns:person="http://www.orcid.org/ns/person" xmlns:activities="http://www.orcid.org/ns/activities" xmlns:researcher-url="http://www.orcid.org/ns/researcher-url" xmlns:peer-review="http://www.orcid.org/ns/peer-review" xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:research-resource="http://www.orcid.org/ns/research-resource">
|
||||
<common:orcid-identifier>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:orcid-identifier>
|
||||
<preferences:preferences>
|
||||
<preferences:locale>en</preferences:locale>
|
||||
</preferences:preferences>
|
||||
<history:history>
|
||||
<history:creation-method>Direct</history:creation-method>
|
||||
<history:submission-date>2016-01-06T05:08:45.720Z</history:submission-date>
|
||||
<common:last-modified-date>2024-01-02T20:07:05.186Z</common:last-modified-date>
|
||||
<history:claimed>true</history:claimed>
|
||||
<history:verified-email>true</history:verified-email>
|
||||
<history:verified-primary-email>true</history:verified-primary-email>
|
||||
</history:history>
|
||||
<person:person path="/0000-0001-6816-8350/person">
|
||||
<common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
|
||||
<other-name:other-names path="/0000-0001-6816-8350/other-names"/>
|
||||
<researcher-url:researcher-urls path="/0000-0001-6816-8350/researcher-urls">
|
||||
<common:last-modified-date>2016-02-09T09:18:18.417Z</common:last-modified-date>
|
||||
<researcher-url:researcher-url put-code="633431" visibility="public" path="/0000-0001-6816-8350/researcher-urls/633431" display-index="0">
|
||||
<common:created-date>2016-02-09T09:18:18.416Z</common:created-date>
|
||||
<common:last-modified-date>2016-02-09T09:18:18.417Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<researcher-url:url-name>Dr Michael Muchiri</researcher-url:url-name>
|
||||
<researcher-url:url>http://www.rmit.edu.au/contact/staff-contacts/academic-staff/m/muchiri-dr-michael</researcher-url:url>
|
||||
</researcher-url:researcher-url>
|
||||
</researcher-url:researcher-urls>
|
||||
<email:emails path="/0000-0001-6816-8350/email"/>
|
||||
<address:addresses path="/0000-0001-6816-8350/address">
|
||||
<common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
|
||||
<address:address put-code="897528" visibility="public" path="/0000-0001-6816-8350/address/897528" display-index="2">
|
||||
<common:created-date>2018-02-13T02:32:04.094Z</common:created-date>
|
||||
<common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<address:country>AU</address:country>
|
||||
</address:address>
|
||||
<address:address put-code="3191142" visibility="public" path="/0000-0001-6816-8350/address/3191142" display-index="1">
|
||||
<common:created-date>2023-12-02T13:32:05.260Z</common:created-date>
|
||||
<common:last-modified-date>2023-12-02T13:32:05.260Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<address:country>SA</address:country>
|
||||
</address:address>
|
||||
</address:addresses>
|
||||
<keyword:keywords path="/0000-0001-6816-8350/keywords">
|
||||
<common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
|
||||
<keyword:keyword put-code="368304" visibility="public" path="/0000-0001-6816-8350/keywords/368304" display-index="4">
|
||||
<common:created-date>2016-02-09T09:16:44.001Z</common:created-date>
|
||||
<common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<keyword:content>Organizational Behavior</keyword:content>
|
||||
</keyword:keyword>
|
||||
<keyword:keyword put-code="368303" visibility="public" path="/0000-0001-6816-8350/keywords/368303" display-index="3">
|
||||
<common:created-date>2016-02-09T09:16:27.374Z</common:created-date>
|
||||
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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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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
<common:host>orcid.org</common:host>
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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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||||
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||||
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||||
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|
||||
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||||
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|
||||
<common:host>orcid.org</common:host>
|
||||
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|
||||
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|
||||
<keyword:content>Thriving at work</keyword:content>
|
||||
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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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||||
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||||
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||||
<common:host>orcid.org</common:host>
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||||
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||||
<common:source-name>ResearcherID</common:source-name>
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||||
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|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
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||||
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||||
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||||
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||||
<common:external-id-type>ResearcherID</common:external-id-type>
|
||||
<common:external-id-value>D-1929-2018</common:external-id-value>
|
||||
<common:external-id-url>http://www.researcherid.com/rid/D-1929-2018</common:external-id-url>
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||||
<common:external-id-relationship>self</common:external-id-relationship>
|
||||
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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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|
||||
<common:last-modified-date>2016-02-09T06:55:21.838Z</common:last-modified-date>
|
||||
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|
||||
<education:education-summary put-code="1549986" display-index="0" path="/0000-0001-6816-8350/education/1549986" visibility="public">
|
||||
<common:created-date>2016-02-09T06:54:39.199Z</common:created-date>
|
||||
<common:last-modified-date>2016-02-09T06:55:21.838Z</common:last-modified-date>
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||||
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|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
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||||
<common:host>orcid.org</common:host>
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||||
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|
||||
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|
||||
<common:department-name>Management</common:department-name>
|
||||
<common:role-title>PhD</common:role-title>
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||||
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|
||||
<common:year>2021</common:year>
|
||||
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|
||||
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|
||||
<common:year>2022</common:year>
|
||||
<common:month>02</common:month>
|
||||
<common:day>12</common:day>
|
||||
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|
||||
<common:start-date>
|
||||
<common:year>2003</common:year>
|
||||
<common:month>03</common:month>
|
||||
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|
||||
<common:end-date>
|
||||
<common:year>2007</common:year>
|
||||
<common:month>03</common:month>
|
||||
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|
||||
<common:organization>
|
||||
<common:name>University of New England</common:name>
|
||||
<common:address>
|
||||
<common:city>Armidale</common:city>
|
||||
<common:region>NSW</common:region>
|
||||
<common:country>AU</common:country>
|
||||
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|
||||
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|
||||
<common:disambiguated-organization-identifier>1319</common:disambiguated-organization-identifier>
|
||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<common:last-modified-date>2018-02-13T02:33:38.225Z</common:last-modified-date>
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||||
<common:external-ids/>
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||||
<education:education-summary put-code="1549990" display-index="0" path="/0000-0001-6816-8350/education/1549990" visibility="public">
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||||
<common:created-date>2016-02-09T06:57:04.181Z</common:created-date>
|
||||
<common:last-modified-date>2018-02-13T02:33:38.225Z</common:last-modified-date>
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||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
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||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<common:department-name>Psychology</common:department-name>
|
||||
<common:role-title>Master of Science (Industrial and Organizational) Psychology</common:role-title>
|
||||
<common:start-date>
|
||||
<common:year>1998</common:year>
|
||||
<common:month>01</common:month>
|
||||
</common:start-date>
|
||||
<common:end-date>
|
||||
<common:year>2000</common:year>
|
||||
<common:month>01</common:month>
|
||||
</common:end-date>
|
||||
<common:organization>
|
||||
<common:name>Universitas Gadjah Mada</common:name>
|
||||
<common:address>
|
||||
<common:city>Yogyakarta</common:city>
|
||||
<common:region>Daerah Istimewa Yogyakart</common:region>
|
||||
<common:country>ID</common:country>
|
||||
</common:address>
|
||||
<common:disambiguated-organization>
|
||||
<common:disambiguated-organization-identifier>59166</common:disambiguated-organization-identifier>
|
||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
|
||||
</common:disambiguated-organization>
|
||||
</common:organization>
|
||||
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|
||||
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|
||||
<activities:affiliation-group>
|
||||
<common:last-modified-date>2018-02-13T02:33:35.821Z</common:last-modified-date>
|
||||
<common:external-ids/>
|
||||
<education:education-summary put-code="1549998" display-index="0" path="/0000-0001-6816-8350/education/1549998" visibility="public">
|
||||
<common:created-date>2016-02-09T06:58:59.869Z</common:created-date>
|
||||
<common:last-modified-date>2018-02-13T02:33:35.821Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
|
||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<common:department-name>Education</common:department-name>
|
||||
<common:role-title>Bachelor of Education (Honors)</common:role-title>
|
||||
<common:start-date>
|
||||
<common:year>1988</common:year>
|
||||
<common:month>03</common:month>
|
||||
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|
||||
<common:end-date>
|
||||
<common:year>1991</common:year>
|
||||
<common:month>03</common:month>
|
||||
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|
||||
<common:organization>
|
||||
<common:name>Kenyatta University</common:name>
|
||||
<common:address>
|
||||
<common:city>Nairobi</common:city>
|
||||
<common:region>Nairobi</common:region>
|
||||
<common:country>KE</common:country>
|
||||
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|
||||
<common:disambiguated-organization>
|
||||
<common:disambiguated-organization-identifier>107864</common:disambiguated-organization-identifier>
|
||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
<common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
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||||
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|
||||
<common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
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||||
<common:external-ids/>
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||||
<employment:employment-summary put-code="21884863" display-index="1" path="/0000-0001-6816-8350/employment/21884863" visibility="public">
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||||
<common:created-date>2023-12-02T13:28:26.051Z</common:created-date>
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||||
<common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
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||||
<common:source>
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||||
<common:source-orcid>
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||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
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||||
<common:host>orcid.org</common:host>
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||||
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||||
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||||
<common:department-name>Management</common:department-name>
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||||
<common:role-title>Associate Professor in Management</common:role-title>
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||||
<common:start-date>
|
||||
<common:year>2023</common:year>
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||||
<common:month>08</common:month>
|
||||
<common:day>20</common:day>
|
||||
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|
||||
<common:organization>
|
||||
<common:name>Alfaisal University</common:name>
|
||||
<common:address>
|
||||
<common:city>Riyadh</common:city>
|
||||
<common:country>SA</common:country>
|
||||
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||||
<common:disambiguated-organization>
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||||
<common:disambiguated-organization-identifier>https://ror.org/00cdrtq48</common:disambiguated-organization-identifier>
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||||
<common:disambiguation-source>ROR</common:disambiguation-source>
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||||
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||||
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||||
<common:url>https://faculty.alfaisal.edu/user/mmuchiri</common:url>
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||||
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||||
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||||
<activities:affiliation-group>
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||||
<common:last-modified-date>2016-02-09T07:00:06.052Z</common:last-modified-date>
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||||
<common:external-ids/>
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||||
<employment:employment-summary put-code="1550002" display-index="0" path="/0000-0001-6816-8350/employment/1550002" visibility="public">
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||||
<common:created-date>2016-02-09T07:00:06.052Z</common:created-date>
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||||
<common:last-modified-date>2016-02-09T07:00:06.052Z</common:last-modified-date>
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||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
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||||
<common:host>orcid.org</common:host>
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||||
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||||
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||||
<common:department-name>Management</common:department-name>
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||||
<common:role-title>Senior Lecturer</common:role-title>
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||||
<common:start-date>
|
||||
<common:year>2014</common:year>
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||||
<common:month>02</common:month>
|
||||
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|
||||
<common:organization>
|
||||
<common:name>RMIT University</common:name>
|
||||
<common:address>
|
||||
<common:city>Melbourne</common:city>
|
||||
<common:region>VIC</common:region>
|
||||
<common:country>AU</common:country>
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||||
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||||
<common:disambiguated-organization>
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||||
<common:disambiguated-organization-identifier>5376</common:disambiguated-organization-identifier>
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||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
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||||
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||||
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||||
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||||
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||||
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||||
<common:last-modified-date>2016-02-09T07:01:08.398Z</common:last-modified-date>
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||||
<common:external-ids/>
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||||
<employment:employment-summary put-code="1550007" display-index="0" path="/0000-0001-6816-8350/employment/1550007" visibility="public">
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||||
<common:created-date>2016-02-09T07:01:08.398Z</common:created-date>
|
||||
<common:last-modified-date>2016-02-09T07:01:08.398Z</common:last-modified-date>
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||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
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||||
</common:source-orcid>
|
||||
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|
||||
<common:department-name>Management</common:department-name>
|
||||
<common:role-title>Senior Lecturer in Human Resource Management</common:role-title>
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||||
<common:start-date>
|
||||
<common:year>2010</common:year>
|
||||
<common:month>01</common:month>
|
||||
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|
||||
<common:end-date>
|
||||
<common:year>2014</common:year>
|
||||
<common:month>02</common:month>
|
||||
</common:end-date>
|
||||
<common:organization>
|
||||
<common:name>Central Queensland University</common:name>
|
||||
<common:address>
|
||||
<common:city>Rockhampton</common:city>
|
||||
<common:region>QLD</common:region>
|
||||
<common:country>AU</common:country>
|
||||
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|
||||
<common:disambiguated-organization>
|
||||
<common:disambiguated-organization-identifier>273488</common:disambiguated-organization-identifier>
|
||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
|
||||
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|
||||
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|
||||
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|
||||
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||||
<activities:affiliation-group>
|
||||
<common:last-modified-date>2016-02-09T07:01:47.814Z</common:last-modified-date>
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||||
<common:external-ids/>
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||||
<employment:employment-summary put-code="1550010" display-index="0" path="/0000-0001-6816-8350/employment/1550010" visibility="public">
|
||||
<common:created-date>2016-02-09T07:01:47.814Z</common:created-date>
|
||||
<common:last-modified-date>2016-02-09T07:01:47.814Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<common:department-name>Management</common:department-name>
|
||||
<common:role-title>Lecturer in Management</common:role-title>
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||||
<common:start-date>
|
||||
<common:year>2007</common:year>
|
||||
<common:month>01</common:month>
|
||||
</common:start-date>
|
||||
<common:end-date>
|
||||
<common:year>2010</common:year>
|
||||
<common:month>01</common:month>
|
||||
</common:end-date>
|
||||
<common:organization>
|
||||
<common:name>Central Queensland University</common:name>
|
||||
<common:address>
|
||||
<common:city>Rockhampton</common:city>
|
||||
<common:region>QLD</common:region>
|
||||
<common:country>AU</common:country>
|
||||
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|
||||
<common:disambiguated-organization>
|
||||
<common:disambiguated-organization-identifier>273488</common:disambiguated-organization-identifier>
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||||
<common:disambiguation-source>RINGGOLD</common:disambiguation-source>
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||||
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||||
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||||
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||||
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||||
<activities:affiliation-group>
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||||
<common:last-modified-date>2018-02-13T02:33:13.213Z</common:last-modified-date>
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||||
<common:external-ids/>
|
||||
<employment:employment-summary put-code="1550017" display-index="0" path="/0000-0001-6816-8350/employment/1550017" visibility="public">
|
||||
<common:created-date>2016-02-09T07:03:42.180Z</common:created-date>
|
||||
<common:last-modified-date>2018-02-13T02:33:13.213Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
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||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
</common:source>
|
||||
<common:department-name>Human Resource Development Division</common:department-name>
|
||||
<common:role-title>Chief Human Resource Development Officer</common:role-title>
|
||||
<common:start-date>
|
||||
<common:year>2005</common:year>
|
||||
<common:month>01</common:month>
|
||||
</common:start-date>
|
||||
<common:end-date>
|
||||
<common:year>2007</common:year>
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Load Diff
Loading…
Reference in New Issue
I read this line as a request to shut down one worker.
I would expect instead to have 22 of those put to shut down all workers. Also I would expect this activity to be done at the end of the outermost while loop, that is before joining the workers.
When a ORCIDworker encounters a JOB_COMPLETE message before it closes itself, it re-inserts the same object back into the queue. Do you think this behavior is incorrect, or could it lead to deadlocks or other types of bugs?
A deadlock is possible if this thread (or in general producer of messages) - after putting the JOB_COMPLETE message - continues to put other messages. What could happen is that the last worker gets the last re-routed JOB_COMPLETE message and, meanwhile before reinserting the message, it gets pre-empted and the queue gets completely filled by the producers: at this point the last reinsert tentative will last forever because the queue is full and not consumed by anyone.
If I'm not reading the code wrongly, in this case the JOB_COMPLETE should be put outside the while loop also to cover cases where the tar is empty or the last entry of the tar is not a file.
Thanks for your revision Jedi Master, I've updated the code.
I Think I can merge the request