forked from D-Net/dnet-hadoop
wf to generate doi_author_list for doiboost; wf to download updated works
This commit is contained in:
parent
f2df3ead74
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@ -0,0 +1,224 @@
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package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.text.SimpleDateFormat;
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import java.util.*;
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import org.apache.commons.compress.utils.Lists;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.util.LongAccumulator;
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import org.mortbay.log.Log;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import com.ximpleware.NavException;
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import com.ximpleware.ParseException;
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import com.ximpleware.XPathEvalException;
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import com.ximpleware.XPathParseException;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import scala.Tuple2;
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public class SparkDownloadOrcidWorks {
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static Logger logger = LoggerFactory.getLogger(SparkDownloadOrcidWorks.class);
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static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
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static final String lastUpdate = "2020-09-29 00:00:00";
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public static void main(String[] args) throws IOException, Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkDownloadOrcidWorks.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String workingPath = parser.get("workingPath");
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logger.info("workingPath: ", workingPath);
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// final String outputPath = parser.get("outputPath");
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final String outputPath = "downloads/updated_works";
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logger.info("outputPath: ", outputPath);
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final String token = parser.get("token");
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// final String lambdaFileName = parser.get("lambdaFileName");
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// logger.info("lambdaFileName: ", lambdaFileName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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LongAccumulator parsedRecordsAcc = spark.sparkContext().longAccumulator("parsed_records");
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LongAccumulator modifiedRecordsAcc = spark.sparkContext().longAccumulator("to_download_records");
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LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records");
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LongAccumulator errorHTTP403Acc = spark.sparkContext().longAccumulator("error_HTTP_403");
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LongAccumulator errorHTTP409Acc = spark.sparkContext().longAccumulator("error_HTTP_409");
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LongAccumulator errorHTTP503Acc = spark.sparkContext().longAccumulator("error_HTTP_503");
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LongAccumulator errorHTTP525Acc = spark.sparkContext().longAccumulator("error_HTTP_525");
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LongAccumulator errorHTTPGenericAcc = spark.sparkContext().longAccumulator("error_HTTP_Generic");
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logger.info("Retrieving updated authors");
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JavaPairRDD<Text, Text> updatedAuthorsRDD = sc
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.sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class);
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logger.info("Updated authors retrieved: " + updatedAuthorsRDD.count());
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Function<Tuple2<Text, Text>, Iterator<String>> retrieveWorkUrlFunction = data -> {
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String orcidId = data._1().toString();
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String jsonData = data._2().toString();
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List<String> orcidIdWorkId = Lists.newArrayList();
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Map<String, String> workIdLastModifiedDate = retrieveWorkIdLastModifiedDate(jsonData);
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workIdLastModifiedDate.forEach((k, v) -> {
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if (isModified(orcidId, v)) {
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orcidIdWorkId.add(orcidId.concat("/work/").concat(k));
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}
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});
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Iterator<String> iterator = orcidIdWorkId.iterator();
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return iterator;
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};
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List<Iterator<String>> toDownloadWorksRDD = updatedAuthorsRDD
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.map(retrieveWorkUrlFunction)
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.take(1000);
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sc.parallelize(toDownloadWorksRDD).saveAsTextFile(workingPath.concat("downloads/updated_works_test/"));
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Function<Tuple2<Text, Text>, Tuple2<String, String>> downloadRecordFunction = data -> {
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String orcidId = data._1().toString();
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String lastModifiedDate = data._2().toString();
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final DownloadedRecordData downloaded = new DownloadedRecordData();
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downloaded.setOrcidId(orcidId);
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downloaded.setLastModifiedDate(lastModifiedDate);
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try (CloseableHttpClient client = HttpClients.createDefault()) {
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HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/work");
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httpGet.addHeader("Accept", "application/vnd.orcid+xml");
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httpGet.addHeader("Authorization", String.format("Bearer %s", token));
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long startReq = System.currentTimeMillis();
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CloseableHttpResponse response = client.execute(httpGet);
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long endReq = System.currentTimeMillis();
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long reqTime = endReq - startReq;
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if (reqTime < 1000) {
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Thread.sleep(1000 - reqTime);
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}
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int statusCode = response.getStatusLine().getStatusCode();
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downloaded.setStatusCode(statusCode);
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if (statusCode != 200) {
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switch (statusCode) {
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case 403:
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errorHTTP403Acc.add(1);
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case 409:
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errorHTTP409Acc.add(1);
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case 503:
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errorHTTP503Acc.add(1);
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throw new RuntimeException("Orcid request rate limit reached (HTTP 503)");
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case 525:
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errorHTTP525Acc.add(1);
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default:
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errorHTTPGenericAcc.add(1);
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logger
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.info(
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"Downloading " + orcidId + " status code: "
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+ response.getStatusLine().getStatusCode());
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}
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return downloaded.toTuple2();
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}
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downloadedRecordsAcc.add(1);
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downloaded
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.setCompressedData(
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ArgumentApplicationParser
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.compressArgument(IOUtils.toString(response.getEntity().getContent())));
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} catch (Throwable e) {
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logger.info("Downloading " + orcidId, e.getMessage());
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downloaded.setErrorMessage(e.getMessage());
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return downloaded.toTuple2();
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}
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return downloaded.toTuple2();
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};
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// sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true");
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// logger.info("Start downloading ...");
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// updatedAuthorsRDD
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// .map(downloadRecordFunction)
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// .mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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// .saveAsNewAPIHadoopFile(
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// workingPath.concat(outputPath),
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// Text.class,
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// Text.class,
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// SequenceFileOutputFormat.class,
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// sc.hadoopConfiguration());
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// logger.info("parsedRecordsAcc: " + parsedRecordsAcc.value().toString());
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// logger.info("modifiedRecordsAcc: " + modifiedRecordsAcc.value().toString());
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// logger.info("downloadedRecordsAcc: " + downloadedRecordsAcc.value().toString());
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// logger.info("errorHTTP403Acc: " + errorHTTP403Acc.value().toString());
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// logger.info("errorHTTP409Acc: " + errorHTTP409Acc.value().toString());
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// logger.info("errorHTTP503Acc: " + errorHTTP503Acc.value().toString());
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// logger.info("errorHTTP525Acc: " + errorHTTP525Acc.value().toString());
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// logger.info("errorHTTPGenericAcc: " + errorHTTPGenericAcc.value().toString());
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});
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}
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private static boolean isModified(String orcidId, String modifiedDate) {
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Date modifiedDateDt = null;
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Date lastUpdateDt = null;
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try {
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if (modifiedDate.length() != 19) {
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modifiedDate = modifiedDate.substring(0, 19);
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}
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modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
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lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
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} catch (Exception e) {
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logger.info("[" + orcidId + "] Parsing date: ", e.getMessage());
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return true;
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}
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return modifiedDateDt.after(lastUpdateDt);
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}
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private static Map<String, String> retrieveWorkIdLastModifiedDate(String json)
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throws XPathEvalException, NavException, XPathParseException, ParseException {
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JsonElement jElement = new JsonParser().parse(json);
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String statusCode = getJsonValue(jElement, "statusCode");
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if (statusCode.equals("200")) {
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String compressedData = getJsonValue(jElement, "compressedData");
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String authorSummary = ArgumentApplicationParser.decompressValue(compressedData);
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return XMLRecordParser.retrieveWorkIdLastModifiedDate(authorSummary.getBytes());
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}
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return new HashMap<>();
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return new String("");
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}
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}
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@ -3,11 +3,11 @@ package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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@ -19,6 +19,7 @@ import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.slf4j.Logger;
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@ -28,10 +29,14 @@ import com.esotericsoftware.minlog.Log;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import com.ximpleware.ParseException;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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import scala.Tuple2;
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public class SparkGenerateDoiAuthorList {
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@ -56,6 +61,10 @@ public class SparkGenerateDoiAuthorList {
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logger.info("workingPath: ", workingPath);
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final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath");
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logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath);
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final String authorsPath = parser.get("authorsPath");
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logger.info("authorsPath: ", authorsPath);
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final String xmlWorksPath = parser.get("xmlWorksPath");
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logger.info("xmlWorksPath: ", xmlWorksPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> summariesRDD = sc
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.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
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.sequenceFile(workingPath.concat(authorsPath), Text.class, Text.class);
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Dataset<AuthorData> summariesDataset = spark
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.createDataset(
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summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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Encoders.bean(AuthorData.class));
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JavaPairRDD<Text, Text> activitiesRDD = sc
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.sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class);
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JavaPairRDD<Text, Text> xmlWorksRDD = sc
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.sequenceFile(workingPath.concat(xmlWorksPath), Text.class, Text.class);
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Dataset<WorkData> activitiesDataset = spark
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.createDataset(
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activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
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xmlWorksRDD
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.map(seq -> XMLRecordParser.VTDParseWorkData(seq._2().toString().getBytes()))
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.filter(work -> work != null && work.getErrorCode() == null && work.isDoiFound())
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.rdd(),
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Encoders.bean(WorkData.class));
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Function<Tuple2<String, AuthorData>, Tuple2<String, List<AuthorData>>> toAuthorListFunction = data -> {
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@ -135,12 +148,16 @@ public class SparkGenerateDoiAuthorList {
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}
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return null;
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})
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.mapToPair(s -> {
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List<AuthorData> authorList = s._2();
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Set<String> oidsAlreadySeen = new HashSet<>();
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authorList.removeIf(a -> !oidsAlreadySeen.add(a.getOid()));
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return new Tuple2<>(s._1(), authorList);
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})
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.mapToPair(
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s -> {
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ObjectMapper mapper = new ObjectMapper();
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return new Tuple2<>(s._1(), mapper.writeValueAsString(s._2()));
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return new Tuple2<>(s._1(), JsonWriter.create(s._2()));
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})
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.repartition(10)
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.saveAsTextFile(workingPath + outputDoiAuthorListPath);
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});
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@ -1,23 +1,17 @@
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package eu.dnetlib.doiboost.orcid.xml;
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import java.util.Arrays;
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import java.util.List;
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import java.util.*;
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import org.mortbay.log.Log;
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import com.ximpleware.AutoPilot;
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import com.ximpleware.EOFException;
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import com.ximpleware.EncodingException;
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import com.ximpleware.EntityException;
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import com.ximpleware.ParseException;
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import com.ximpleware.VTDGen;
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import com.ximpleware.VTDNav;
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import com.ximpleware.*;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
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public class XMLRecordParser {
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@ -32,7 +26,8 @@ public class XMLRecordParser {
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private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record";
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private static final String NS_RECORD = "record";
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private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error";
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private static final String NS_ACTIVITIES = "activities";
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private static final String NS_ACTIVITIES_URL = "http://www.orcid.org/ns/activities";
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private static final String NS_WORK = "work";
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private static final String NS_WORK_URL = "http://www.orcid.org/ns/work";
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@ -139,6 +134,12 @@ public class XMLRecordParser {
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return retrieveOrcidId(bytes, defaultValue, NS_WORK, NS_WORK_URL, "//work:work", "put-code");
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}
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public static String retrieveWorkIdFromSummary(byte[] bytes, String defaultValue)
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throws VtdException, ParseException {
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return retrieveOrcidId(
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bytes, defaultValue, NS_ACTIVITIES, NS_ACTIVITIES_URL, "//work:work-summary", "put-code");
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}
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private static String retrieveOrcidId(byte[] bytes, String defaultValue, String ns, String nsUrl, String xpath,
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String idAttributeName)
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throws VtdException, ParseException {
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@ -148,6 +149,7 @@ public class XMLRecordParser {
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final VTDNav vn = vg.getNav();
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final AutoPilot ap = new AutoPilot(vn);
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ap.declareXPathNameSpace(ns, nsUrl);
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ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
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List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
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.getTextValuesWithAttributes(
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ap, vn, xpath, Arrays.asList(idAttributeName));
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@ -157,4 +159,42 @@ public class XMLRecordParser {
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Log.info("id not found - default: " + defaultValue);
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return defaultValue;
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}
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public static Map<String, String> retrieveWorkIdLastModifiedDate(byte[] bytes)
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throws ParseException, XPathParseException, NavException, XPathEvalException {
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final VTDGen vg = new VTDGen();
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vg.setDoc(bytes);
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vg.parse(true);
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final VTDNav vn = vg.getNav();
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final AutoPilot ap = new AutoPilot(vn);
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ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
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ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL);
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ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL);
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ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL);
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ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL);
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ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
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ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
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ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL);
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Map<String, String> workIdLastModifiedDate = new HashMap<>();
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ap.selectXPath("//work:work-summary");
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while (ap.evalXPath() != -1) {
|
||||
String workId = "";
|
||||
String lastModifiedDate = "";
|
||||
int attr = vn.getAttrVal("put-code");
|
||||
if (attr > -1) {
|
||||
workId = vn.toNormalizedString(attr);
|
||||
workIdLastModifiedDate.put(workId, "");
|
||||
}
|
||||
if (vn.toElement(VTDNav.FIRST_CHILD, "common:last-modified-date")) {
|
||||
int val = vn.getText();
|
||||
if (val != -1) {
|
||||
lastModifiedDate = vn.toNormalizedString(val);
|
||||
workIdLastModifiedDate.put(workId, lastModifiedDate);
|
||||
}
|
||||
vn.toElement(VTDNav.PARENT);
|
||||
}
|
||||
}
|
||||
return workIdLastModifiedDate;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
|
|||
import scala.Tuple2;
|
||||
|
||||
/**
|
||||
* This spark job generates one parquet file, containing orcid publications dataset
|
||||
* This spark job generates orcid publications no doi dataset
|
||||
*/
|
||||
|
||||
public class SparkGenEnrichedOrcidWorks {
|
||||
|
|
|
|||
|
|
@ -22,6 +22,10 @@ public class JsonWriter {
|
|||
return OBJECT_MAPPER.writeValueAsString(authorData);
|
||||
}
|
||||
|
||||
public static String create(Object obj) throws JsonProcessingException {
|
||||
return OBJECT_MAPPER.writeValueAsString(obj);
|
||||
}
|
||||
|
||||
public static String create(WorkData workData) {
|
||||
JsonObject work = new JsonObject();
|
||||
work.addProperty("oid", workData.getOid());
|
||||
|
|
|
|||
|
|
@ -31,6 +31,7 @@ public class PublicationToOaf implements Serializable {
|
|||
static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class);
|
||||
|
||||
public static final String ORCID = "ORCID";
|
||||
public static final String ORCID_PID_TYPE_CLASSNAME = "Open Researcher and Contributor ID";
|
||||
public final static String orcidPREFIX = "orcid_______";
|
||||
public static final String OPENAIRE_PREFIX = "openaire____";
|
||||
public static final String SEPARATOR = "::";
|
||||
|
|
@ -79,10 +80,10 @@ public class PublicationToOaf implements Serializable {
|
|||
|
||||
{
|
||||
put("ark".toLowerCase(), new Pair<>("ark", "ark"));
|
||||
put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv"));
|
||||
put("pmc".toLowerCase(), new Pair<>("pmc", "pmc"));
|
||||
put("pmid".toLowerCase(), new Pair<>("pmid", "pmid"));
|
||||
put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid"));
|
||||
put("arxiv".toLowerCase(), new Pair<>("arXiv", "arXiv"));
|
||||
put("pmc".toLowerCase(), new Pair<>("pmc", "PubMed Central ID"));
|
||||
put("pmid".toLowerCase(), new Pair<>("pmid", "PubMed ID"));
|
||||
put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcid workid"));
|
||||
put("urn".toLowerCase(), new Pair<>("urn", "urn"));
|
||||
}
|
||||
};
|
||||
|
|
@ -152,8 +153,8 @@ public class PublicationToOaf implements Serializable {
|
|||
.keySet()
|
||||
.stream()
|
||||
.forEach(jsonExtId -> {
|
||||
final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue();
|
||||
final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey();
|
||||
final String classid = externalIds.get(jsonExtId.toLowerCase()).getKey();
|
||||
final String classname = externalIds.get(jsonExtId.toLowerCase()).getValue();
|
||||
final String extId = getStringValue(rootElement, jsonExtId);
|
||||
if (StringUtils.isNotBlank(extId)) {
|
||||
publication
|
||||
|
|
@ -522,21 +523,21 @@ public class PublicationToOaf implements Serializable {
|
|||
sp.setValue(orcidId);
|
||||
final Qualifier q = new Qualifier();
|
||||
q.setClassid(ORCID.toLowerCase());
|
||||
q.setClassname(ORCID.toLowerCase());
|
||||
q.setClassname(ORCID_PID_TYPE_CLASSNAME);
|
||||
q.setSchemeid(ModelConstants.DNET_PID_TYPES);
|
||||
q.setSchemename(ModelConstants.DNET_PID_TYPES);
|
||||
sp.setQualifier(q);
|
||||
final DataInfo dataInfo = new DataInfo();
|
||||
dataInfo.setDeletedbyinference(false);
|
||||
dataInfo.setInferred(false);
|
||||
dataInfo.setTrust("0.9");
|
||||
dataInfo.setTrust("0.91");
|
||||
dataInfo
|
||||
.setProvenanceaction(
|
||||
mapQualifier(
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"Harvested",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions"));
|
||||
.setProvenanceaction(
|
||||
mapQualifier(
|
||||
"sysimport:crosswalk:entityregistry",
|
||||
"Harvested",
|
||||
"dnet:provenanceActions",
|
||||
"dnet:provenanceActions"));
|
||||
sp.setDataInfo(dataInfo);
|
||||
return sp;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,3 +1,5 @@
|
|||
[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true},
|
||||
{"paramName":"a", "paramLongName":"authorsPath", "paramDescription": "the path of the authors seq file", "paramRequired": true},
|
||||
{"paramName":"xw", "paramLongName":"xmlWorksPath", "paramDescription": "the path of the works xml seq file", "paramRequired": true},
|
||||
{"paramName":"o", "paramLongName":"outputDoiAuthorListPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,18 +0,0 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>queueName</name>
|
||||
<value>default</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -1,55 +1,99 @@
|
|||
<workflow-app name="Gen_Doi_Author_List_WF" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<workflow-app name="gen_doi_author_list" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2MaxExecutors</name>
|
||||
<value>40</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working dir base path</description>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
<start to="ResetWorkingPath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath}/doi_author_list'/>
|
||||
</fs>
|
||||
<ok to="GenDoiAuthorList"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ResetWorkingPath">
|
||||
<fs>
|
||||
<delete path='${workingPath_activities}/doi_author_list'/>
|
||||
</fs>
|
||||
<ok to="Gen_Doi_Author_List"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="GenDoiAuthorList">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>GenDoiAuthorList</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.dynamicAllocation.enabled=true
|
||||
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-a</arg><arg>authors/authors.seq</arg>
|
||||
<arg>-xw</arg><arg>xml/works/*.seq</arg>
|
||||
<arg>-o</arg><arg>doi_author_list/</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="Gen_Doi_Author_List">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Gen_Doi_Author_List</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class>
|
||||
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
|
||||
<spark-opts>--num-executors 10 --conf spark.yarn.jars="hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2" --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
|
||||
</spark-opts>
|
||||
<arg>-w</arg><arg>${workingPath}/</arg>
|
||||
<arg>-o</arg><arg>doi_author_list/</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -13,13 +13,13 @@ import java.text.SimpleDateFormat;
|
|||
import java.time.Duration;
|
||||
import java.time.LocalDateTime;
|
||||
import java.time.temporal.TemporalUnit;
|
||||
import java.util.Arrays;
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
|
||||
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
|
||||
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
|
||||
import org.apache.commons.compress.utils.Lists;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
|
|
@ -30,6 +30,7 @@ import org.junit.jupiter.api.Test;
|
|||
import org.mortbay.log.Log;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||
import jdk.nashorn.internal.ir.annotations.Ignore;
|
||||
|
||||
public class OrcidClientTest {
|
||||
|
|
@ -42,6 +43,9 @@ public class OrcidClientTest {
|
|||
String toNotRetrieveDate = "2019-09-29 23:59:59.000000";
|
||||
String lastUpdate = "2019-09-30 00:00:00";
|
||||
String shortDate = "2020-05-06 16:06:11";
|
||||
final String REQUEST_TYPE_RECORD = "record";
|
||||
final String REQUEST_TYPE_WORK = "work/47652866";
|
||||
final String REQUEST_TYPE_WORKS = "works";
|
||||
|
||||
// curl -i -H "Accept: application/vnd.orcid+xml"
|
||||
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
|
||||
|
|
@ -86,25 +90,25 @@ public class OrcidClientTest {
|
|||
|
||||
@Test
|
||||
private void downloadTest(String orcid) throws Exception {
|
||||
String record = testDownloadRecord(orcid);
|
||||
String filename = "/tmp/downloaded_".concat(orcid).concat(".xml");
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_RECORD);
|
||||
String filename = "/tmp/downloaded_record_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
}
|
||||
|
||||
private String testDownloadRecord(String orcidId) throws Exception {
|
||||
private String testDownloadRecord(String orcidId, String dataType) throws Exception {
|
||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
|
||||
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/" + dataType);
|
||||
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
|
||||
httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d");
|
||||
logToFile("start connection: " + new Date(System.currentTimeMillis()).toString());
|
||||
long start = System.currentTimeMillis();
|
||||
CloseableHttpResponse response = client.execute(httpGet);
|
||||
logToFile("end connection: " + new Date(System.currentTimeMillis()).toString());
|
||||
long end = System.currentTimeMillis();
|
||||
if (response.getStatusLine().getStatusCode() != 200) {
|
||||
System.out
|
||||
.println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
|
||||
logToFile("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
|
||||
}
|
||||
logToFile(orcidId + " " + dataType + " " + (end - start) / 1000 + " seconds");
|
||||
return IOUtils.toString(response.getEntity().getContent());
|
||||
} catch (Throwable e) {
|
||||
e.printStackTrace();
|
||||
|
|
@ -129,7 +133,7 @@ public class OrcidClientTest {
|
|||
}
|
||||
String[] values = line.split(",");
|
||||
List<String> recordInfo = Arrays.asList(values);
|
||||
testDownloadRecord(recordInfo.get(0));
|
||||
testDownloadRecord(recordInfo.get(0), REQUEST_TYPE_RECORD);
|
||||
long endReq = System.currentTimeMillis();
|
||||
nReqTmp++;
|
||||
if (nReqTmp == REQ_LIMIT) {
|
||||
|
|
@ -190,7 +194,7 @@ public class OrcidClientTest {
|
|||
.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
|
||||
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
|
||||
logToFile("\n\ndownloaded \n\n" + recordFromSeqFile);
|
||||
final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161");
|
||||
final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD);
|
||||
assertTrue(recordFromSeqFile.equals(downloadedRecord));
|
||||
}
|
||||
|
||||
|
|
@ -255,7 +259,7 @@ public class OrcidClientTest {
|
|||
logToFile("modified: " + modified);
|
||||
}
|
||||
|
||||
private void logToFile(String log)
|
||||
public static void logToFile(String log)
|
||||
throws IOException {
|
||||
log = log.concat("\n");
|
||||
Path path = Paths.get("/tmp/orcid_log.txt");
|
||||
|
|
@ -298,4 +302,72 @@ public class OrcidClientTest {
|
|||
}
|
||||
return new String("");
|
||||
}
|
||||
|
||||
@Test
|
||||
private void downloadWorkTest() throws Exception {
|
||||
String orcid = "0000-0003-0015-1952";
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORK);
|
||||
String filename = "/tmp/downloaded_work_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
}
|
||||
|
||||
@Test
|
||||
private void downloadRecordTest() throws Exception {
|
||||
String orcid = "0000-0001-5004-5918";
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_RECORD);
|
||||
String filename = "/tmp/downloaded_record_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
}
|
||||
|
||||
@Test
|
||||
private void downloadWorksTest() throws Exception {
|
||||
String orcid = "0000-0001-5004-5918";
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORKS);
|
||||
String filename = "/tmp/downloaded_works_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
}
|
||||
|
||||
@Test
|
||||
private void downloadSingleWorkTest() throws Exception {
|
||||
String orcid = "0000-0001-5004-5918";
|
||||
String record = testDownloadRecord(orcid, REQUEST_TYPE_WORK);
|
||||
String filename = "/tmp/downloaded_work_47652866_".concat(orcid).concat(".xml");
|
||||
File f = new File(filename);
|
||||
OutputStream outStream = new FileOutputStream(f);
|
||||
IOUtils.write(record.getBytes(), outStream);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void cleanAuthorListTest() throws Exception {
|
||||
AuthorData a1 = new AuthorData();
|
||||
a1.setOid("1");
|
||||
a1.setName("n1");
|
||||
a1.setSurname("s1");
|
||||
a1.setCreditName("c1");
|
||||
AuthorData a2 = new AuthorData();
|
||||
a2.setOid("1");
|
||||
a2.setName("n1");
|
||||
a2.setSurname("s1");
|
||||
a2.setCreditName("c1");
|
||||
AuthorData a3 = new AuthorData();
|
||||
a3.setOid("3");
|
||||
a3.setName("n3");
|
||||
a3.setSurname("s3");
|
||||
a3.setCreditName("c3");
|
||||
List<AuthorData> list = Lists.newArrayList();
|
||||
list.add(a1);
|
||||
list.add(a2);
|
||||
list.add(a3);
|
||||
|
||||
Set<String> namesAlreadySeen = new HashSet<>();
|
||||
assertTrue(list.size() == 3);
|
||||
list.removeIf(a -> !namesAlreadySeen.add(a.getOid()));
|
||||
assertTrue(list.size() == 2);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,10 +4,13 @@ package eu.dnetlib.doiboost.orcid.xml;
|
|||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
import java.util.Map;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||
import eu.dnetlib.doiboost.orcid.OrcidClientTest;
|
||||
import eu.dnetlib.doiboost.orcid.model.WorkData;
|
||||
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
|
||||
|
||||
|
|
@ -59,7 +62,7 @@ public class XMLRecordParserTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testOrcidOtherNamesXMLParser() throws Exception {
|
||||
private void testOrcidOtherNamesXMLParser() throws Exception {
|
||||
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
|
|
@ -74,4 +77,17 @@ public class XMLRecordParserTest {
|
|||
String jsonData = JsonWriter.create(authorData);
|
||||
assertNotNull(jsonData);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWorkIdLastModifiedDateXMLParser() throws Exception {
|
||||
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
this.getClass().getResourceAsStream("record_8888-8888-8888-8880.xml"));
|
||||
// Map<String, String> workIdLastModifiedDate = XMLRecordParser.retrieveWorkIdLastModifiedDate(xml.getBytes());
|
||||
// String LastModifiedDate = workIdLastModifiedDate.get(0);
|
||||
// OrcidClientTest.logToFile(LastModifiedDate + " -- " + workIdLastModifiedDate.get(LastModifiedDate));
|
||||
String result = XMLRecordParser.retrieveWorkIdFromSummary(xml.getBytes(), "empty");
|
||||
OrcidClientTest.logToFile(result);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue