master #59
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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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@ -69,32 +73,22 @@ 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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.longAccumulator("error_loading_json_found");
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LongAccumulator errorLoadingXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_xml_found");
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LongAccumulator errorParsingXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_parsing_xml_found");
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LongAccumulator downloadedRecordsAcc = spark.sparkContext().longAccumulator("downloaded_records");
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LongAccumulator errorsAcc = spark.sparkContext().longAccumulator("errors");
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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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@ -106,11 +100,10 @@ public class SparkDownloadOrcidWorks {
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if (statusCode.equals("200")) {
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String compressedData = getJsonValue(jElement, "compressedData");
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if (StringUtils.isEmpty(compressedData)) {
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errorLoadingJsonFoundAcc.add(1);
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} else {
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String authorSummary = ArgumentApplicationParser.decompressValue(compressedData);
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if (StringUtils.isEmpty(authorSummary)) {
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errorLoadingXMLFoundAcc.add(1);
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} else {
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try {
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workIdLastModifiedDate = XMLRecordParser
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@ -125,22 +118,38 @@ 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 +158,7 @@ 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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@ -167,7 +176,6 @@ public class SparkDownloadOrcidWorks {
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} else {
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downloaded.setStatusCode(-4);
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}
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errorsAcc.add(1);
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}
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long endReq = System.currentTimeMillis();
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long reqTime = endReq - startReq;
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@ -176,7 +184,6 @@ public class SparkDownloadOrcidWorks {
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}
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if (downloadCompleted) {
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downloaded.setStatusCode(200);
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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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@ -185,24 +192,69 @@ 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 = null;
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try {
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splittedWorks = XMLRecordParser
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.splitWorks(orcidId, works.getBytes(StandardCharsets.UTF_8));
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} catch (Throwable t) {
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final DownloadedRecordData errDownloaded = new DownloadedRecordData();
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errDownloaded.setOrcidId(orcidId);
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errDownloaded.setLastModifiedDate(lastModifiedDate);
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errDownloaded.setStatusCode(-10);
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errDownloaded.setErrorMessage(t.getMessage());
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splittedDownloadedWorks.add(errDownloaded.toTuple2());
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errorParsingXMLFoundAcc.add(1);
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return splittedDownloadedWorks.iterator();
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}
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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 (Throwable t) {
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downloaded.setStatusCode(-11);
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downloaded.setErrorMessage(t.getMessage());
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}
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splittedDownloadedWorks.add(downloaded.toTuple2());
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downloadedRecordsAcc.add(1);
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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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logger.info("errorParsingXMLFoundAcc: {}", errorParsingXMLFoundAcc.value());
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logger.info("downloadedRecordsAcc: {}", downloadedRecordsAcc.value());
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logger.info("errorsAcc: {}", errorsAcc.value());
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});
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}
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@ -83,8 +83,6 @@ public class MultiAttemptsHttpConnector {
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throw new CollectorException(msg);
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}
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log.info("Request attempt {} [{}]", retryNumber, requestUrl);
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InputStream input = null;
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try {
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@ -104,9 +102,9 @@ public class MultiAttemptsHttpConnector {
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urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", getAuthToken()));
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}
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if (log.isDebugEnabled()) {
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logHeaderFields(urlConn);
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}
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// if (log.isDebugEnabled()) {
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// logHeaderFields(urlConn);
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// }
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int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
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if (is2xx(urlConn.getResponseCode())) {
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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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@ -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
|
||||
void testUpdatedRecord() throws Exception {
|
||||
final String base64CompressedRecord = IOUtils
|
||||
.toString(getClass().getResourceAsStream("0000-0003-3028-6161.compressed.base64"));
|
||||
.toString(getClass().getResourceAsStream("0000-0001-7281-6306.compressed.base64"));
|
||||
final String record = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
|
||||
logToFile(testPath, "\n\nrecord updated \n\n" + record);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -108,4 +108,12 @@ public class XMLRecordParserTest {
|
|||
work.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
|
||||
OrcidClientTest.logToFile(testPath, JsonWriter.create(work));
|
||||
}
|
||||
|
||||
@Test
|
||||
void testWorksSplit() throws Exception {
|
||||
String xml = IOUtils
|
||||
.toString(
|
||||
this.getClass().getResourceAsStream("multiple_downloaded_works.xml"));
|
||||
XMLRecordParser.splitWorks("0000-0001-7291-3210", xml.getBytes());
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
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
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,57 @@
|
|||
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
|
||||
<bulk:bulk 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">
|
||||
<work:work put-code="16639612" visibility="public">
|
||||
<common:created-date>2015-05-23T18:56:52.486Z</common:created-date>
|
||||
<common:last-modified-date>2017-02-28T08:22:12.454Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-7291-3210</common:uri>
|
||||
<common:path>0000-0001-7291-3210</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
<common:source-name>Paolo Manghi</common:source-name>
|
||||
</common:source>
|
||||
<work:title>
|
||||
<common:title>The Query Language TQL</common:title>
|
||||
</work:title>
|
||||
<work:journal-title>5th International Workshop on Web and Data Bases (WebDB02) in conjunction with ACM SIGMOD 2002</work:journal-title>
|
||||
<work:citation>
|
||||
<work:citation-type>bibtex</work:citation-type>
|
||||
<work:citation-value>@inproceedings{Conforti2002, Author= {Giovanni Conforti and Giorgio Ghelli and Antonio Albano and Dario Colazzo and Paolo Manghi and Carlo Sartiani}, Bibsource= {DBLP, http://dblp.uni-trier.de}, Booktitle= {5th International Workshop on Web and Data Bases (WebDB02) in conjunction with ACM SIGMOD 2002}, Ee= {http://www.db.ucsd.edu/webdb2002/papers/43.pdf}, Pages= {13-18}, Title= {The Query Language TQL}, Year= {2002}}
|
||||
|
||||
</work:citation-value>
|
||||
</work:citation>
|
||||
<work:type>conference-paper</work:type>
|
||||
<common:publication-date>
|
||||
<common:year>2002</common:year>
|
||||
</common:publication-date>
|
||||
<common:external-ids/>
|
||||
</work:work>
|
||||
<work:work put-code="16639628" visibility="public">
|
||||
<common:created-date>2015-05-23T18:58:18.492Z</common:created-date>
|
||||
<common:last-modified-date>2017-02-28T08:22:12.455Z</common:last-modified-date>
|
||||
<common:source>
|
||||
<common:source-orcid>
|
||||
<common:uri>https://orcid.org/0000-0001-7291-3210</common:uri>
|
||||
<common:path>0000-0001-7291-3210</common:path>
|
||||
<common:host>orcid.org</common:host>
|
||||
</common:source-orcid>
|
||||
<common:source-name>Paolo Manghi</common:source-name>
|
||||
</common:source>
|
||||
<work:title>
|
||||
<common:title>The Query Language TQL - Demo Presentation</common:title>
|
||||
</work:title>
|
||||
<work:journal-title>X Convegno nazionale su Sistemi Evoluti per Basi di Dati (SEBD)</work:journal-title>
|
||||
<work:citation>
|
||||
<work:citation-type>bibtex</work:citation-type>
|
||||
<work:citation-value>@inproceedings{Conforti2002Demo, Address= {Portoferraio, Italy}, Author= {Giovanni Conforti and Giorgio Ghelli and Antonio Albano and Dario Colazzo and Paolo Manghi and Carlo Sartiani}, Bibsource= {DBLP, http://dblp.uni-trier.de}, Booktitle= {X Convegno nazionale su Sistemi Evoluti per Basi di Dati (SEBD)}, Month= {June}, Pages= {427-431}, Title= {The Query Language TQL - Demo Presentation}, Year= {2002}}
|
||||
|
||||
</work:citation-value>
|
||||
</work:citation>
|
||||
<work:type>conference-paper</work:type>
|
||||
<common:publication-date>
|
||||
<common:year>2002</common:year>
|
||||
</common:publication-date>
|
||||
<common:external-ids/>
|
||||
</work:work>
|
||||
</bulk:bulk>
|
||||
|
|
@ -7,5 +7,6 @@ log4j.appender.A1=org.apache.log4j.ConsoleAppender
|
|||
# A1 uses PatternLayout.
|
||||
log4j.logger.org = ERROR
|
||||
log4j.logger.eu.dnetlib = DEBUG
|
||||
log4j.logger.eu.dnetlib.doiboost.orcid = INFO
|
||||
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
|
||||
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
|
||||
|
|
@ -25,7 +25,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
|||
|
||||
public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
||||
|
||||
public static final String HTTP_DX_DOI_PREIFX = "https://dx.doi.org/";
|
||||
public static final String HTTP_DOI_PREIFX = "https://doi.org/";
|
||||
public static final String HTTP_HANDLE_PREIFX = "http://hdl.handle.net/";
|
||||
|
||||
public OdfToOafMapper(final VocabularyGroup vocs, final boolean invisible, final boolean shouldHashId,
|
||||
final boolean forceOrginalId) {
|
||||
|
|
@ -172,10 +173,17 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
|
|||
}
|
||||
for (final Object o : doc
|
||||
.selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='DOI']")) {
|
||||
url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
|
||||
url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim());
|
||||
}
|
||||
for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='DOI']")) {
|
||||
url.add(HTTP_DX_DOI_PREIFX + ((Node) o).getText().trim());
|
||||
url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim());
|
||||
}
|
||||
for (final Object o : doc
|
||||
.selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) {
|
||||
url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim());
|
||||
}
|
||||
for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) {
|
||||
url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim());
|
||||
}
|
||||
if (!url.isEmpty()) {
|
||||
instance.setUrl(new ArrayList<>());
|
||||
|
|
|
|||
|
|
@ -935,6 +935,18 @@ class MappersTest {
|
|||
System.out.println("***************");
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRiunet() throws IOException, DocumentException {
|
||||
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("riunet.xml")));
|
||||
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(list));
|
||||
System.out.println("***************");
|
||||
final Publication p = (Publication) list.get(0);
|
||||
assertNotNull(p.getInstance().get(0).getUrl().get(0));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testNotWellFormed() throws IOException {
|
||||
final String xml = IOUtils
|
||||
|
|
|
|||
|
|
@ -0,0 +1,71 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<record xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
|
||||
xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:oai="http://www.openarchives.org/OAI/2.0/"
|
||||
xmlns:datacite="http://datacite.org/schema/kernel-4"
|
||||
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:xs="http://www.w3.org/2001/XMLSchema"
|
||||
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:dc="http://purl.org/dc/elements/1.1/">
|
||||
<header xmlns="HTTP://www.openarchives.org/OAI/2.0/">
|
||||
<identifier xmlns="http://www.openarchives.org/OAI/2.0/">oai:riunet.upv.es:10251/178464</identifier>
|
||||
<datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2022-05-10T09:12:14Z</datestamp>
|
||||
<setSpec xmlns="http://www.openarchives.org/OAI/2.0/">com_10251_3822</setSpec>
|
||||
<setSpec xmlns="http://www.openarchives.org/OAI/2.0/">col_10251_169956</setSpec>
|
||||
<dr:dateOfTransformation>2022-09-01T07:51:12.657Z</dr:dateOfTransformation>
|
||||
<dri:objIdentifier>od______1560::8f7a139735f493882bb0f4abceb6e200</dri:objIdentifier>
|
||||
<dri:recordIdentifier>od______1560::8f7a139735f493882bb0f4abceb6e200</dri:recordIdentifier>
|
||||
<dri:dateOfCollection>2019-03-27T15:15:22.22Z</dri:dateOfCollection>
|
||||
<oaf:datasourceprefix>riunet________</oaf:datasourceprefix>
|
||||
</header>
|
||||
<metadata>
|
||||
<datacite:resource>
|
||||
<datacite:identifier identifierType="Handle">10251/178464</datacite:identifier>
|
||||
<datacite:alternateIdentifiers/>
|
||||
<datacite:relatedIdentifiers/>
|
||||
<datacite:resourceType xs:anyURI="http://purl.org/coar/resource_type/c_8544">lecture</datacite:resourceType>
|
||||
<datacite:rightsList>
|
||||
<datacite:rights rightsURI=" http://creativecommons.org/licenses/by-nc/4.0/">http://creativecommons.org/licenses/by-nc/4.0/</datacite:rights>
|
||||
<datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
|
||||
</datacite:rightsList>
|
||||
<datacite:titles>
|
||||
<datacite:title>Discurso de inauguración del curso academico 1990-1991 de la Universitat Politècnica de València</datacite:title>
|
||||
</datacite:titles>
|
||||
<datacite:descriptions>
|
||||
<datacite:description descriptionType="Abstract">[ES] Discurso de Justo Nieto en el acto de inauguración del curso académico 1990-1991</datacite:description>
|
||||
<datacite:description descriptionType="Abstract">[EN] Inaugural speech by Justo Nieto at the opening ceremony of the 1990-1991 academic year</datacite:description>
|
||||
</datacite:descriptions>
|
||||
<datacite:language>spa</datacite:language>
|
||||
<datacite:formats>
|
||||
<datacite:format>application/pdf</datacite:format>
|
||||
<datacite:format>5055377</datacite:format>
|
||||
</datacite:formats>
|
||||
<datacite:creators>
|
||||
<datacite:creator>
|
||||
<datacite:creatorName>Nieto Nieto, Justo</datacite:creatorName>
|
||||
</datacite:creator>
|
||||
</datacite:creators>
|
||||
<datacite:contributors/>
|
||||
<datacite:dates>
|
||||
<datacite:date dateType="Issued">1991</datacite:date>
|
||||
</datacite:dates>
|
||||
<datacite:subjects>
|
||||
<datacite:subject>Justo Nieto Nieto (Discursos)</datacite:subject>
|
||||
<datacite:subject>Universitat Politècnica de València (UPV)</datacite:subject>
|
||||
<datacite:subject>Presentación inaugural</datacite:subject>
|
||||
<datacite:subject>Curso académico 1990-91</datacite:subject>
|
||||
<datacite:subject>Discurso inaugural</datacite:subject>
|
||||
<datacite:subject>Inaugural speech</datacite:subject>
|
||||
<datacite:subject>Inaugural presentation</datacite:subject>
|
||||
</datacite:subjects>
|
||||
</datacite:resource>
|
||||
<oaf:identifier identifierType="Handle">10251/178464</oaf:identifier>
|
||||
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
|
||||
<oaf:dateAccepted>1991-01-01</oaf:dateAccepted>
|
||||
<oaf:accessrights>OPEN</oaf:accessrights>
|
||||
<oaf:language>spa</oaf:language>
|
||||
<oaf:hostedBy name="RiuNet" id="opendoar____::1560"/>
|
||||
<oaf:collectedFrom name="RiuNet" id="opendoar____::1560"/>
|
||||
</metadata>
|
||||
</record>
|
||||
|
|
@ -81,6 +81,21 @@ public class IndexRecordTransformerTest {
|
|||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testRiunet() throws IOException, TransformerException {
|
||||
|
||||
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
|
||||
XmlConverterJob.schemaLocation);
|
||||
|
||||
final Publication p = load("riunet.json", Publication.class);
|
||||
|
||||
final JoinedEntity je = new JoinedEntity<>(p);
|
||||
final String record = xmlRecordFactory.build(je);
|
||||
assertNotNull(record);
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureDataTransferPilot() throws IOException, TransformerException {
|
||||
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/data-transfer-pilot.xml"));
|
||||
|
|
@ -114,6 +129,8 @@ public class IndexRecordTransformerTest {
|
|||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Test
|
||||
void testDoiUrlNormalization() throws MalformedURLException {
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,470 @@
|
|||
{
|
||||
"collectedfrom": [
|
||||
{
|
||||
"key": "10|opendoar____::3a20f62a0af1aa152670bab3c602feed",
|
||||
"value": "RiuNet",
|
||||
"dataInfo": null
|
||||
}
|
||||
],
|
||||
"dataInfo": {
|
||||
"invisible": false,
|
||||
"inferred": false,
|
||||
"deletedbyinference": false,
|
||||
"trust": "0.9",
|
||||
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Loading…
Reference in New Issue