forked from D-Net/dnet-hadoop
Merge pull request 'Orcid Update Procedure' (#394) from orcid_update into beta
Reviewed-on: D-Net/dnet-hadoop#394
This commit is contained in:
commit
e468e99100
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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())));
|
||||
TarArchiveEntry entry;
|
||||
|
||||
BlockingQueue<String> queue = new ArrayBlockingQueue<String>(3000);
|
||||
final List<ORCIDWorker> workers = new ArrayList<>();
|
||||
for (int i = 0; i < 22; i++) {
|
||||
workers.add(createWorker("" + i, targetPath, queue, accessToken, fileSystem));
|
||||
}
|
||||
workers.forEach(Thread::start);
|
||||
|
||||
while ((entry = tais.getNextTarEntry()) != null) {
|
||||
|
||||
if (entry.isFile()) {
|
||||
|
||||
BufferedReader br = new BufferedReader(new InputStreamReader(tais));
|
||||
System.out.println(br.readLine());
|
||||
br
|
||||
.lines()
|
||||
.map(l -> l.split(","))
|
||||
.filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0)
|
||||
.map(s -> s[0])
|
||||
.forEach(s -> {
|
||||
try {
|
||||
queue.put(s);
|
||||
} catch (InterruptedException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < 22; i++) {
|
||||
queue.put(ORCIDWorker.JOB_COMPLETE);
|
||||
}
|
||||
for (ORCIDWorker worker : workers) {
|
||||
worker.join();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -1,11 +1,15 @@
|
|||
|
||||
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;
|
||||
|
||||
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;
|
||||
|
||||
|
|
@ -40,8 +44,8 @@ public class OrcidParser {
|
|||
private static final String NS_ERROR = "error";
|
||||
private static final String NS_HISTORY = "history";
|
||||
private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history";
|
||||
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">
|
||||
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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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||||
<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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||||
<common:path>0000-0001-6816-8350</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
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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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||||
<common:uri>https://orcid.org/client/0000-0003-1377-5676</common:uri>
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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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||||
<common:host>orcid.org</common:host>
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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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||||
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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>
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||||
<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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|
||||
<common:end-date>
|
||||
<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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||||
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|
||||
</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>
|
||||
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|
||||
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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>
|
||||
</common:disambiguated-organization>
|
||||
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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>
|
||||
<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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||||
<activities:affiliation-group>
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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>
|
||||
<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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|
||||
</employment:employment-summary>
|
||||
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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/>
|
||||
<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>
|
||||
<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>
|
||||
<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>
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||||
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Reference in New Issue