multiple works download (<=100) for single request
This commit is contained in:
parent
28a32facf6
commit
657b0208a2
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@ -3,6 +3,8 @@ 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.nio.charset.StandardCharsets;
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import java.time.LocalDate;
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import java.time.format.DateTimeFormatter;
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import java.util.*;
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@ -13,6 +15,7 @@ import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.FlatMapFunction;
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import org.apache.spark.api.java.function.Function;
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@ -20,6 +23,7 @@ import org.apache.spark.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.common.collect.Lists;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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@ -42,6 +46,7 @@ public class SparkDownloadOrcidWorks {
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public static final String ORCID_XML_DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'";
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public static final DateTimeFormatter ORCID_XML_DATETIMEFORMATTER = DateTimeFormatter
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.ofPattern(ORCID_XML_DATETIME_FORMAT);
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public static final String DOWNLOAD_WORKS_REQUEST_SEPARATOR = ",";
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public static void main(String[] args) throws Exception {
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@ -56,7 +61,6 @@ public class SparkDownloadOrcidWorks {
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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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@ -69,16 +73,12 @@ public class SparkDownloadOrcidWorks {
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isSparkSessionManaged,
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spark -> {
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final String lastUpdateValue = HDFSUtil.readFromTextFile(hdfsServerUri, workingPath, "last_update.txt");
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logger.info("lastUpdateValue: ", lastUpdateValue);
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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LongAccumulator updatedAuthorsAcc = spark.sparkContext().longAccumulator("updated_authors");
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LongAccumulator parsedAuthorsAcc = spark.sparkContext().longAccumulator("parsed_authors");
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LongAccumulator parsedWorksAcc = spark.sparkContext().longAccumulator("parsed_works");
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LongAccumulator modifiedWorksAcc = spark.sparkContext().longAccumulator("modified_works");
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LongAccumulator maxModifiedWorksLimitAcc = spark
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.sparkContext()
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.longAccumulator("max_modified_works_limit");
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LongAccumulator errorCodeFoundAcc = spark.sparkContext().longAccumulator("error_code_found");
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LongAccumulator errorLoadingJsonFoundAcc = spark
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.sparkContext()
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@ -94,7 +94,8 @@ public class SparkDownloadOrcidWorks {
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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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updatedAuthorsAcc.setValue(updatedAuthorsRDD.count());
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long authorsCount = updatedAuthorsRDD.count();
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updatedAuthorsAcc.setValue(authorsCount);
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FlatMapFunction<Tuple2<Text, Text>, String> retrieveWorkUrlFunction = data -> {
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String orcidId = data._1().toString();
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@ -125,22 +126,38 @@ public class SparkDownloadOrcidWorks {
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errorCodeFoundAcc.add(1);
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}
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parsedAuthorsAcc.add(1);
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workIdLastModifiedDate.forEach((k, v) -> {
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parsedWorksAcc.add(1);
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if (isModified(orcidId, v, lastUpdateValue)) {
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modifiedWorksAcc.add(1);
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workIds.add(orcidId.concat("/work/").concat(k));
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workIds.add(k);
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}
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});
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if (workIdLastModifiedDate.size() > 50) {
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maxModifiedWorksLimitAcc.add(1);
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if (workIds.isEmpty()) {
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return new ArrayList<String>().iterator();
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}
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return workIds.iterator();
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List<String> worksDownloadUrls = new ArrayList<>();
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// Creation of url for reading multiple works (up to 100) with ORCID API
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// see this https://github.com/ORCID/ORCID-Source/blob/development/orcid-api-web/tutorial/works.md
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List<List<String>> partitionedWorks = Lists.partition(workIds, 100);
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partitionedWorks.stream().forEach(p -> {
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String worksDownloadUrl = orcidId.concat("/works/");
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final StringBuffer buffer = new StringBuffer(worksDownloadUrl);
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p.forEach(id -> {
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buffer.append(id).append(DOWNLOAD_WORKS_REQUEST_SEPARATOR);
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});
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String finalUrl = buffer.substring(0, buffer.lastIndexOf(DOWNLOAD_WORKS_REQUEST_SEPARATOR));
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worksDownloadUrls.add(finalUrl);
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});
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return worksDownloadUrls.iterator();
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};
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Function<String, Tuple2<String, String>> downloadWorkFunction = data -> {
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String relativeWorkUrl = data;
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String orcidId = relativeWorkUrl.split("/")[0];
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Function<String, Tuple2<String, String>> downloadWorksFunction = data -> {
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String relativeWorksUrl = data;
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String orcidId = relativeWorksUrl.split("/")[0];
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final DownloadedRecordData downloaded = new DownloadedRecordData();
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downloaded.setOrcidId(orcidId);
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downloaded.setLastModifiedDate(lastUpdateValue);
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@ -149,7 +166,7 @@ public class SparkDownloadOrcidWorks {
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httpConnector.setAuthMethod(MultiAttemptsHttpConnector.BEARER);
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httpConnector.setAcceptHeaderValue("application/vnd.orcid+xml");
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httpConnector.setAuthToken(token);
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String apiUrl = "https://api.orcid.org/v3.0/" + relativeWorkUrl;
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String apiUrl = "https://api.orcid.org/v3.0/" + relativeWorksUrl;
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DownloadsReport report = new DownloadsReport();
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long startReq = System.currentTimeMillis();
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boolean downloadCompleted = false;
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@ -185,18 +202,53 @@ public class SparkDownloadOrcidWorks {
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return downloaded.toTuple2();
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};
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FlatMapFunction<Tuple2<String, String>, Tuple2<String, String>> splitWorksFunction = data -> {
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List<Tuple2<String, String>> splittedDownloadedWorks = new ArrayList<>();
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String jsonData = data._2().toString();
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JsonElement jElement = new JsonParser().parse(jsonData);
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String orcidId = data._1().toString();
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String statusCode = getJsonValue(jElement, "statusCode");
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String lastModifiedDate = getJsonValue(jElement, "lastModifiedDate");
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String compressedData = getJsonValue(jElement, "compressedData");
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String errorMessage = getJsonValue(jElement, "errorMessage");
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String works = ArgumentApplicationParser.decompressValue(compressedData);
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// split a single xml containing multiple works into multiple xml (a single work for each xml)
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List<String> splittedWorks = XMLRecordParser
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.splitWorks(orcidId, works.getBytes(StandardCharsets.UTF_8));
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splittedWorks.forEach(w -> {
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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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downloaded.setStatusCode(Integer.parseInt(statusCode));
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downloaded.setErrorMessage(errorMessage);
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try {
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downloaded
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.setCompressedData(
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ArgumentApplicationParser
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.compressArgument(w));
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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splittedDownloadedWorks.add(downloaded.toTuple2());
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});
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return splittedDownloadedWorks.iterator();
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};
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updatedAuthorsRDD
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.flatMap(retrieveWorkUrlFunction)
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.repartition(100)
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.map(downloadWorkFunction)
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.mapToPair(t -> new Tuple2<>(new Text(t._1()), new Text(t._2())))
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.map(downloadWorksFunction)
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.flatMap(splitWorksFunction)
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.mapToPair(w -> new Tuple2<>(new Text(w._1()), new Text(w._2())))
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.saveAsTextFile(workingPath.concat(outputPath), GzipCodec.class);
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logger.info("updatedAuthorsAcc: {}", updatedAuthorsAcc.value());
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logger.info("parsedAuthorsAcc: {}", parsedAuthorsAcc.value());
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logger.info("parsedWorksAcc: {}", parsedWorksAcc.value());
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logger.info("modifiedWorksAcc: {}", modifiedWorksAcc.value());
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logger.info("maxModifiedWorksLimitAcc: {}", maxModifiedWorksLimitAcc.value());
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logger.info("errorCodeFoundAcc: {}", errorCodeFoundAcc.value());
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logger.info("errorLoadingJsonFoundAcc: {}", errorLoadingJsonFoundAcc.value());
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logger.info("errorLoadingXMLFoundAcc: {}", errorLoadingXMLFoundAcc.value());
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@ -1,7 +1,11 @@
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package eu.dnetlib.doiboost.orcid.xml;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import org.mortbay.log.Log;
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@ -34,6 +38,33 @@ public class XMLRecordParser {
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private static final String NS_WORK_URL = "http://www.orcid.org/ns/work";
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private static final String NS_HISTORY = "history";
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private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history";
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private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk";
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private static final String NS_BULK = "bulk";
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private static final String namespaceList = " xmlns:internal=\"http://www.orcid.org/ns/internal\"\n" +
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" xmlns:education=\"http://www.orcid.org/ns/education\"\n" +
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" xmlns:distinction=\"http://www.orcid.org/ns/distinction\"\n" +
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" xmlns:deprecated=\"http://www.orcid.org/ns/deprecated\"\n" +
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" xmlns:other-name=\"http://www.orcid.org/ns/other-name\"\n" +
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" xmlns:membership=\"http://www.orcid.org/ns/membership\"\n" +
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" xmlns:error=\"http://www.orcid.org/ns/error\" xmlns:common=\"http://www.orcid.org/ns/common\"\n" +
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" xmlns:record=\"http://www.orcid.org/ns/record\"\n" +
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" xmlns:personal-details=\"http://www.orcid.org/ns/personal-details\"\n" +
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" xmlns:keyword=\"http://www.orcid.org/ns/keyword\" xmlns:email=\"http://www.orcid.org/ns/email\"\n" +
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" xmlns:external-identifier=\"http://www.orcid.org/ns/external-identifier\"\n" +
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" xmlns:funding=\"http://www.orcid.org/ns/funding\"\n" +
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" xmlns:preferences=\"http://www.orcid.org/ns/preferences\"\n" +
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" xmlns:address=\"http://www.orcid.org/ns/address\"\n" +
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" xmlns:invited-position=\"http://www.orcid.org/ns/invited-position\"\n" +
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" xmlns:work=\"http://www.orcid.org/ns/work\" xmlns:history=\"http://www.orcid.org/ns/history\"\n" +
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" xmlns:employment=\"http://www.orcid.org/ns/employment\"\n" +
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" xmlns:qualification=\"http://www.orcid.org/ns/qualification\"\n" +
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" xmlns:service=\"http://www.orcid.org/ns/service\" xmlns:person=\"http://www.orcid.org/ns/person\"\n" +
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" xmlns:activities=\"http://www.orcid.org/ns/activities\"\n" +
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" xmlns:researcher-url=\"http://www.orcid.org/ns/researcher-url\"\n" +
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" xmlns:peer-review=\"http://www.orcid.org/ns/peer-review\"\n" +
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" xmlns:bulk=\"http://www.orcid.org/ns/bulk\"\n" +
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" xmlns:research-resource=\"http://www.orcid.org/ns/research-resource\"";
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private static final String NS_ERROR = "error";
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@ -307,4 +338,65 @@ public class XMLRecordParser {
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}
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return authorHistory;
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}
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public static List<String> splitWorks(String orcidId, byte[] bytes)
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throws ParseException, XPathParseException, NavException, XPathEvalException, VtdException, ModifyException,
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IOException, TranscodeException {
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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_WORK, NS_WORK_URL);
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ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
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ap.declareXPathNameSpace(NS_BULK, NS_BULK_URL);
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List<String> works = new ArrayList<>();
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try {
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ap.selectXPath("//work:work");
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while (ap.evalXPath() != -1) {
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ByteArrayOutputStream bos = new ByteArrayOutputStream();
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long l = vn.getElementFragment();
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String xmlHeader = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>";
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bos.write(xmlHeader.getBytes(StandardCharsets.UTF_8));
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bos.write(vn.getXML().getBytes(), (int) l, (int) (l >> 32));
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works.add(bos.toString());
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bos.close();
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}
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} catch (Exception e) {
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throw new VtdException(e);
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}
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List<VTDGen> vgModifiers = Arrays.asList(new VTDGen());
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List<XMLModifier> xmModifiers = Arrays.asList(new XMLModifier());
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List<ByteArrayOutputStream> buffer = Arrays.asList(new ByteArrayOutputStream());
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List<String> updatedWorks = works.stream().map(work -> {
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vgModifiers.get(0).setDoc(work.getBytes());
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try {
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vgModifiers.get(0).parse(false);
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final VTDNav vnModifier = vgModifiers.get(0).getNav();
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xmModifiers.get(0).bind(vnModifier);
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vnModifier.toElement(VTDNav.ROOT);
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int attr = vnModifier.getAttrVal("put-code");
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if (attr > -1) {
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xmModifiers
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.get(0)
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.insertAttribute(
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" path=\"/" + orcidId + "/work/" + vnModifier.toNormalizedString(attr) + "\""
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+ " " + namespaceList);
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}
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buffer.set(0, new ByteArrayOutputStream());
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xmModifiers.get(0).output(buffer.get(0));
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buffer.get(0).close();
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return buffer.get(0).toString();
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} catch (NavException | ModifyException | IOException | TranscodeException | ParseException e) {
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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}).collect(Collectors.toList());
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return updatedWorks;
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}
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}
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@ -78,7 +78,7 @@
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</configuration>
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</global>
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<start to="ResetLambda"/>
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<start to="DownloadOrcidWorks"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -190,7 +190,7 @@
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<arg>-o</arg><arg>downloads/updated_works</arg>
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<arg>-t</arg><arg>${token}</arg>
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</spark>
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<ok to="ResetNewAuthors"/>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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@ -161,13 +161,11 @@ public class OrcidClientTest {
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@Test
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@Disabled
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void testReadBase64CompressedRecord() throws Exception {
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void testReadBase64CompressedWork() throws Exception {
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final String base64CompressedRecord = IOUtils
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.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
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.toString(getClass().getResourceAsStream("0000-0001-7281-6306.compressed.base64"));
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final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
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logToFile(testPath, "\n\ndownloaded \n\n" + recordFromSeqFile);
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final String downloadedRecord = testDownloadRecord("0000-0003-3028-6161", REQUEST_TYPE_RECORD);
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assertEquals(recordFromSeqFile, downloadedRecord);
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}
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@Test
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@ -337,7 +335,7 @@ public class OrcidClientTest {
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@Ignore
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void testUpdatedRecord() throws Exception {
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final String base64CompressedRecord = IOUtils
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.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
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.toString(getClass().getResourceAsStream("0000-0001-7281-6306.compressed.base64"));
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final String record = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
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logToFile(testPath, "\n\nrecord updated \n\n" + record);
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}
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@ -108,4 +108,12 @@ public class XMLRecordParserTest {
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work.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
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OrcidClientTest.logToFile(testPath, JsonWriter.create(work));
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}
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@Test
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void testWorksSplit() throws Exception {
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String xml = IOUtils
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.toString(
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this.getClass().getResourceAsStream("multiple_downloaded_works.xml"));
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XMLRecordParser.splitWorks("0000-0001-7291-3210", xml.getBytes());
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}
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}
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@ -0,0 +1 @@
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Loading…
Reference in New Issue