added workflow to generate seq(orcidId,work) and seq(orcidId,enrichedWork)

This commit is contained in:
Enrico Ottonello 2020-06-25 18:43:29 +02:00
parent fcbb4c1489
commit d6498278ed
14 changed files with 1125 additions and 231 deletions

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@ -19,7 +19,7 @@ import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.mortbay.log.Log; import org.mortbay.log.Log;
import eu.dnetlib.doiboost.orcid.json.JsonWriter; import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
import eu.dnetlib.doiboost.orcid.model.WorkData; import eu.dnetlib.doiboost.orcid.model.WorkData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;

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@ -19,7 +19,7 @@ import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.mortbay.log.Log; import org.mortbay.log.Log;
import eu.dnetlib.doiboost.orcid.json.JsonWriter; import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;

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@ -0,0 +1,16 @@
package eu.dnetlib.doiboost.orcid.json;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
public class JsonHelper {
public static String createOidWork(WorkDataNoDoi workData) {
JsonObject oidWork = new JsonObject();
oidWork.addProperty("oid", workData.getOid());
oidWork.addProperty("work", new Gson().toJson(workData));
return oidWork.toString();
}
}

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@ -0,0 +1,149 @@
package eu.dnetlib.doiboost.orcidnodoi;
import eu.dnetlib.doiboost.orcid.json.JsonHelper;
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IOUtils;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.mortbay.log.Log;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URI;
public class ActivitiesDumpReader {
private static final int MAX_XML_WORKS_PARSED = -1;
private static final int XML_WORKS_PARSED_COUNTER_LOG_INTERVAL = 100000;
public static void parseGzActivities(Configuration conf, String inputUri, Path outputPath)
throws Exception {
String uri = inputUri;
FileSystem fs = FileSystem.get(URI.create(uri), conf);
Path inputPath = new Path(uri);
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodec(inputPath);
if (codec == null) {
System.err.println("No codec found for " + uri);
System.exit(1);
}
CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
InputStream gzipInputStream = null;
try {
gzipInputStream = codec.createInputStream(fs.open(inputPath));
parseTarActivities(fs, conf, gzipInputStream, outputPath);
} finally {
Log.debug("Closing gzip stream");
IOUtils.closeStream(gzipInputStream);
}
}
private static void parseTarActivities(
FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
int counter = 0;
int noDoiFound = 0;
int errorFromOrcidFound = 0;
int xmlParserErrorFound = 0;
try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
TarArchiveEntry entry = null;
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(outputPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
while ((entry = tais.getNextTarEntry()) != null) {
String filename = entry.getName();
try {
if (entry.isDirectory() || !filename.contains("works")) {
} else {
Log.debug("XML work entry name: " + entry.getName());
counter++;
BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from
// tarInput
String line;
StringBuffer buffer = new StringBuffer();
while ((line = br.readLine()) != null) {
buffer.append(line);
}
WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi.VTDParseWorkData(buffer.toString().getBytes());
if (workDataNoDoi != null) {
if (workDataNoDoi.getErrorCode() != null) {
errorFromOrcidFound += 1;
Log
.debug(
"error from Orcid with code "
+ workDataNoDoi.getErrorCode()
+ " for entry "
+ entry.getName());
continue;
}
boolean isDoiFound = workDataNoDoi.getExtIds().stream()
.filter(e -> e.getType()!=null)
.anyMatch(e -> e.getType().equals("doi"));
if (!isDoiFound) {
String jsonData = JsonHelper.createOidWork(workDataNoDoi);
Log.debug("oid: " + workDataNoDoi.getOid() + " data: " + jsonData);
final Text key = new Text(workDataNoDoi.getOid());
final Text value = new Text(jsonData);
try {
writer.append(key, value);
} catch (IOException e) {
Log.debug("Writing to sequence file: " + e.getMessage());
Log.debug(e);
throw new RuntimeException(e);
}
noDoiFound += 1;
}
} else {
Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString());
xmlParserErrorFound += 1;
}
}
} catch (Exception e) {
Log
.warn(
"Parsing work from tar archive and xml work: " + filename + " " + e.getMessage());
Log.warn(e);
}
if ((counter % XML_WORKS_PARSED_COUNTER_LOG_INTERVAL) == 0) {
Log.info("Current xml works parsed: " + counter);
}
if ((MAX_XML_WORKS_PARSED > -1) && (counter > MAX_XML_WORKS_PARSED)) {
break;
}
}
}
} catch (IOException e) {
Log.warn("Parsing work from gzip archive: " + e.getMessage());
Log.warn(e);
throw new RuntimeException(e);
}
Log.info("Activities parse completed");
Log.info("Total XML works parsed: " + counter);
Log.info("Total no doi work found: " + noDoiFound);
Log.info("Error from Orcid found: " + errorFromOrcidFound);
Log.info("Error parsing xml work found: " + xmlParserErrorFound);
}
}

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@ -0,0 +1,52 @@
package eu.dnetlib.doiboost.orcidnodoi;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.doiboost.orcid.OrcidDSManager;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.mortbay.log.Log;
import java.io.IOException;
public class GenOrcidAuthorWork extends OrcidDSManager {
private String activitiesFileNameTarGz;
private String outputWorksPath;
private String workingPath;
public static void main(String[] args) throws IOException, Exception {
GenOrcidAuthorWork genOrcidAuthorWork = new GenOrcidAuthorWork();
genOrcidAuthorWork.loadArgs(args);
genOrcidAuthorWork.generateAuthorsDOIsData();
}
public void generateAuthorsDOIsData() throws Exception {
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String tarGzUri = hdfsServerUri.concat(workingPath).concat(activitiesFileNameTarGz);
Path outputPath = new Path(hdfsServerUri.concat(workingPath).concat(outputWorksPath));
ActivitiesDumpReader.parseGzActivities(conf, tarGzUri, outputPath);
}
private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
GenOrcidAuthorWork.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
Log.info("HDFS URI: " + hdfsServerUri);
workingPath = parser.get("workingPath");
Log.info("Working Path: " + workingPath);
activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
Log.info("Activities File Name: " + activitiesFileNameTarGz);
outputWorksPath = parser.get("outputWorksPath");
Log.info("Output Author Work Data: " + outputWorksPath);
}
}

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@ -0,0 +1,119 @@
package eu.dnetlib.doiboost.orcidnodoi;
import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2;
import java.io.IOException;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class SparkGenEnrichedOrcidWorks {
public static void main(String[] args) throws IOException, Exception {
Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.class);
logger.info("[ SparkGenerateDoiAuthorList STARTED]");
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkGenEnrichedOrcidWorks.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath);
final String outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath");
logger.info("outputEnrichedWorksPath: ", outputEnrichedWorksPath);
final String outputWorksPath = parser.get("outputWorksPath");
logger.info("outputWorksPath: ", outputWorksPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<Text, Text> summariesRDD = sc
.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
Dataset<AuthorData> summariesDataset = spark
.createDataset(
summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(AuthorData.class));
JavaPairRDD<Text, Text> activitiesRDD = sc
.sequenceFile(workingPath + outputWorksPath + "works_X.seq" , Text.class, Text.class);
Dataset<WorkDataNoDoi> activitiesDataset = spark
.createDataset(
activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(WorkDataNoDoi.class));
activitiesDataset
.joinWith(
summariesDataset,
activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
.map(
(MapFunction<Tuple2<WorkDataNoDoi, AuthorData>, Tuple2<String, WorkDataNoDoi>>) value -> {
WorkDataNoDoi w = value._1;
AuthorData a = value._2;
AuthorMatcher.match(a, w.getContributors());
return new Tuple2<>(a.getOid(), w);
},
Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class)))
.filter(Objects::nonNull)
.toJavaRDD()
.saveAsTextFile(workingPath + outputEnrichedWorksPath);;
});
}
private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
AuthorData authorData = new AuthorData();
authorData.setOid(orcidId.toString());
JsonElement jElement = new JsonParser().parse(json.toString());
authorData.setName(getJsonValue(jElement, "name"));
authorData.setSurname(getJsonValue(jElement, "surname"));
authorData.setCreditName(getJsonValue(jElement, "creditname"));
return authorData;
}
private static WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) {
WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class);
return workData;
}
private static String getJsonValue(JsonElement jElement, String property) {
if (jElement.getAsJsonObject().has(property)) {
JsonElement name = null;
name = jElement.getAsJsonObject().get(property);
if (name != null && !name.isJsonNull()) {
return name.getAsString();
}
}
return null;
}
}

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@ -1,5 +1,5 @@
package eu.dnetlib.doiboost.orcid.json; package eu.dnetlib.doiboost.orcidnodoi.json;
import com.google.gson.JsonObject; import com.google.gson.JsonObject;

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@ -8,9 +8,9 @@ import eu.dnetlib.doiboost.orcid.model.AuthorData;
public class Contributor extends AuthorData implements Serializable { public class Contributor extends AuthorData implements Serializable {
private String sequence; private String sequence;
private String role; private String role;
private boolean simpleMatch = false; private transient boolean simpleMatch = false;
private Double score = 0.0; private transient Double score = 0.0;
private boolean bestMatch = false; private transient boolean bestMatch = false;
public String getSequence() { public String getSequence() {
return sequence; return sequence;

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@ -97,5 +97,4 @@ public class WorkDataNoDoi implements Serializable {
public void setContributors(List<Contributor> contributors) { public void setContributors(List<Contributor> contributors) {
this.contributors = contributors; this.contributors = contributors;
} }
} }

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@ -0,0 +1,204 @@
package eu.dnetlib.doiboost.orcidnodoi.similarity;
import java.io.IOException;
import java.text.Normalizer;
import java.util.*;
import org.apache.commons.text.similarity.JaroWinklerSimilarity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.ximpleware.NavException;
import com.ximpleware.ParseException;
import com.ximpleware.XPathEvalException;
import com.ximpleware.XPathParseException;
import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
public class AuthorMatcher {
private static final Logger logger = LoggerFactory.getLogger(AuthorMatcher.class);
private static final Double threshold = 0.8;
public static void match(AuthorData author, List<Contributor> contributors)
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
int matchCounter = 0;
List<Integer> matchCounters = Arrays.asList(matchCounter);
Contributor contributor = null;
contributors.forEach(c -> {
if (normalize(c.getCreditName()).contains(normalize(author.getName())) ||
normalize(c.getCreditName()).contains(normalize(author.getSurname())) ||
((author.getOtherName() != null)
&& normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) {
matchCounters.set(0, matchCounters.get(0) + 1);
c.setSimpleMatch(true);
}
});
logger.info("match counter: " + Integer.toString(matchCounters.get(0)));
if (matchCounters.get(0) == 1) {
updateAuthorsSimpleMatch(contributors, author);
} else if (matchCounters.get(0) > 1) {
Optional<Contributor> optCon = contributors
.stream()
.filter(c -> c.isSimpleMatch())
.map(c -> {
c.setScore(bestMatch(author.getName(), author.getSurname(), c.getCreditName()));
logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore());
return c;
})
.filter(c -> c.getScore() >= threshold)
.max(Comparator.comparing(c -> c.getScore()));
Contributor bestMatchContributor = null;
if (optCon.isPresent()) {
bestMatchContributor = optCon.get();
bestMatchContributor.setBestMatch(true);
logger.info("best match: " + bestMatchContributor.getCreditName());
updateAuthorsSimilarityMatch(contributors, author);
}
}
logger.info("UPDATED contributors: ");
contributors.forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence());
});
}
private static Double bestMatch(String authorSurname, String authorName, String contributor) {
logger.debug(authorSurname + " " + authorName + " vs " + contributor);
String[] contributorSplitted = contributor.split(" ");
if (contributorSplitted.length == 0) {
return 0.0;
}
final String contributorName = contributorSplitted[contributorSplitted.length - 1];
String contributorSurname = "";
if (contributorSplitted.length > 1) {
StringJoiner joiner = new StringJoiner(" ");
for (int i = 0; i < contributorSplitted.length - 1; i++) {
joiner.add(contributorSplitted[i]);
}
contributorSurname = joiner.toString();
}
logger
.debug(
"contributorName: " + contributorName +
" contributorSurname: " + contributorSurname);
String authorNameNrm = normalize(authorName);
String authorSurnameNrm = normalize(authorSurname);
String contributorNameNrm = normalize(contributorName);
String contributorSurnameNrm = normalize(contributorSurname);
Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm);
Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm);
if (sm1.compareTo(sm2) >= 0) {
return sm1;
}
return sm2;
}
private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) {
Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB);
logger
.debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score));
return score;
}
private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) {
return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
}
private static String normalize(final String s) {
return nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
// of large input strings
.replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
}
private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
private static String parse(String name, String surname) {
return surname + " " + name;
}
private static void updateAuthorsSimpleMatch(List<Contributor> contributors, AuthorData author) {
contributors.forEach(c -> {
if (c.isSimpleMatch()) {
logger.info("simple match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
}
});
updateRanks(contributors);
}
private static void updateAuthorsSimilarityMatch(List<Contributor> contributors, AuthorData author) {
logger.info("inside updateAuthorsSimilarityMatch ...");
contributors.forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: "
+ c.isSimpleMatch());
});
contributors
.stream()
.filter(c -> c.isBestMatch())
.forEach(c -> {
logger.info("similarity match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
});
updateRanks(contributors);
}
private static void updateRanks(List<Contributor> contributors) {
boolean seqFound = false;
if (contributors
.stream()
.filter(
c -> c.getRole() != null && c.getSequence() != null &&
c.getRole().equals("author") && (c.getSequence().equals("first") ||
c.getSequence().equals("additional")))
.count() > 0) {
seqFound = true;
logger.info("sequence data found");
}
if (!seqFound) {
List<Integer> seqIds = Arrays.asList(0);
contributors.forEach(c -> {
int currentSeq = seqIds.get(0) + 1;
seqIds.set(0, currentSeq);
c.setSequence(Integer.toString(seqIds.get(0)));
});
}
}
private static String toJson(WorkDataNoDoi work) {
GsonBuilder builder = new GsonBuilder();
Gson gson = builder.create();
return gson.toJson(work);
}
}

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@ -0,0 +1,22 @@
<configuration>
<property>
<name>oozie.action.sharelib.for.java</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
<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>
</configuration>

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@ -0,0 +1,524 @@
<workflow-app name="Gen Enriched Orcid Works" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath_activities</name>
<description>the working dir base path</description>
</property>
<property>
<name>shell_cmd_0</name>
<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz ; rm -f /tmp/ORCID_2019_activites_0.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
</property>
<property>
<name>shell_cmd_1</name>
<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz ; rm -f /tmp/ORCID_2019_activites_1.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
</property>
<property>
<name>shell_cmd_2</name>
<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz ; rm -f /tmp/ORCID_2019_activites_2.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
</property>
<property>
<name>shell_cmd_3</name>
<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz ; rm -f /tmp/ORCID_2019_activites_3.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
</property>
<property>
<name>shell_cmd_4</name>
<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz ; rm -f /tmp/ORCID_2019_activites_4.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
</property>
<property>
<name>shell_cmd_5</name>
<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz ; rm -f /tmp/ORCID_2019_activites_5.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
</property>
<property>
<name>shell_cmd_6</name>
<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz ; rm -f /tmp/ORCID_2019_activites_6.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
</property>
<property>
<name>shell_cmd_7</name>
<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz ; rm -f /tmp/ORCID_2019_activites_7.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
</property>
<property>
<name>shell_cmd_8</name>
<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz ; rm -f /tmp/ORCID_2019_activites_8.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
</property>
<property>
<name>shell_cmd_9</name>
<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz ; rm -f /tmp/ORCID_2019_activites_9.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
</property>
<property>
<name>shell_cmd_X</name>
<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz ; rm -f /tmp/ORCID_2019_activites_X.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath_activities}/no_doi_works/*'/>
<delete path='${workingPath_activities}/no_doi_enriched_works/*'/>
</fs>
<ok to="fork_gen_orcid_author_work"/>
<error to="Kill"/>
</action>
<fork name = "fork_gen_orcid_author_work">
<path start = "check_exist_on_hdfs_activities_0"/>
<path start = "check_exist_on_hdfs_activities_1"/>
<path start = "check_exist_on_hdfs_activities_2"/>
<path start = "check_exist_on_hdfs_activities_3"/>
<path start = "check_exist_on_hdfs_activities_4"/>
<path start = "check_exist_on_hdfs_activities_5"/>
<path start = "check_exist_on_hdfs_activities_6"/>
<path start = "check_exist_on_hdfs_activities_7"/>
<path start = "check_exist_on_hdfs_activities_8"/>
<path start = "check_exist_on_hdfs_activities_9"/>
<path start = "check_exist_on_hdfs_activities_X"/>
</fork>
<decision name="check_exist_on_hdfs_activities_0">
<switch>
<case to="GenOrcidAuthorWork_0">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))}
</case>
<default to="Download_0" />
</switch>
</decision>
<action name="Download_0">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_0}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_0"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_0">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_0.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_1">
<switch>
<case to="GenOrcidAuthorWork_1">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))}
</case>
<default to="Download_1" />
</switch>
</decision>
<action name="Download_1">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_1}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_1"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_1">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_1.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_2">
<switch>
<case to="GenOrcidAuthorWork_2">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))}
</case>
<default to="Download_2" />
</switch>
</decision>
<action name="Download_2">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_2}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_2"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_2">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_2.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_3">
<switch>
<case to="GenOrcidAuthorWork_3">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))}
</case>
<default to="Download_3" />
</switch>
</decision>
<action name="Download_3">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_3}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_3"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_3">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_3.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_4">
<switch>
<case to="GenOrcidAuthorWork_4">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))}
</case>
<default to="Download_4" />
</switch>
</decision>
<action name="Download_4">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_4}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_4"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_4">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_4.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_5">
<switch>
<case to="GenOrcidAuthorWork_5">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))}
</case>
<default to="Download_5" />
</switch>
</decision>
<action name="Download_5">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_5}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_5"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_5">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_5.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_6">
<switch>
<case to="GenOrcidAuthorWork_6">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))}
</case>
<default to="Download_6" />
</switch>
</decision>
<action name="Download_6">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_6}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_6"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_6">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_6.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_7">
<switch>
<case to="GenOrcidAuthorWork_7">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))}
</case>
<default to="Download_7" />
</switch>
</decision>
<action name="Download_7">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_7}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_7"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_7">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_7.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_8">
<switch>
<case to="GenOrcidAuthorWork_8">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))}
</case>
<default to="Download_8" />
</switch>
</decision>
<action name="Download_8">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_8}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_8"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_8">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_8.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_9">
<switch>
<case to="GenOrcidAuthorWork_9">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))}
</case>
<default to="Download_9" />
</switch>
</decision>
<action name="Download_9">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_9}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_9"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_9">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_9.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_X">
<switch>
<case to="GenOrcidAuthorWork_X">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))}
</case>
<default to="Download_X" />
</switch>
</decision>
<action name="Download_X">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_X}</argument>
<capture-output/>
</shell>
<ok to="GenOrcidAuthorWork_X"/>
<error to="Kill"/>
</action>
<action name="GenOrcidAuthorWork_X">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcidnodoi.GenOrcidAuthorWork</main-class>
<arg>-w</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
<arg>-ow</arg><arg>no_doi_works/works_X.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<join name = "join_node" to = "Gen_Enriched_Orcid_Works"/>
<action name="Gen_Enriched_Orcid_Works">
<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_Enriched_Orcid_Works</name>
<class>eu.dnetlib.doiboost.orcidnodoi.SparkGenEnrichedOrcidWorks</class>
<jar>dhp-doiboost-1.2.3-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 10 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
</spark-opts>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-ow</arg><arg>no_doi_works/</arg>
<arg>-oew</arg><arg>no_doi_enriched_works/</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -0,0 +1,7 @@
[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true},
{"paramName":"ow", "paramLongName":"outputWorksPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
{"paramName":"oew", "paramLongName":"outputEnrichedWorksPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true}
]

View File

@ -1,15 +1,12 @@
package eu.dnetlib.doiboost.orcidnodoi.xml; package eu.dnetlib.doiboost.orcidnodoi.xml;
import com.ximpleware.NavException; import static org.junit.jupiter.api.Assertions.assertNotNull;
import com.ximpleware.ParseException;
import com.ximpleware.XPathEvalException; import java.io.IOException;
import com.ximpleware.XPathParseException; import java.text.Normalizer;
import eu.dnetlib.dhp.parser.utility.VtdException; import java.util.*;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
import jdk.nashorn.internal.ir.annotations.Ignore;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.text.similarity.JaccardSimilarity; import org.apache.commons.text.similarity.JaccardSimilarity;
import org.apache.commons.text.similarity.JaroWinklerSimilarity; import org.apache.commons.text.similarity.JaroWinklerSimilarity;
@ -17,11 +14,20 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException; import com.google.gson.Gson;
import java.text.Normalizer; import com.google.gson.GsonBuilder;
import java.util.*; import com.ximpleware.NavException;
import com.ximpleware.ParseException;
import com.ximpleware.XPathEvalException;
import com.ximpleware.XPathParseException;
import static org.junit.jupiter.api.Assertions.assertNotNull; import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
import jdk.nashorn.internal.ir.annotations.Ignore;
public class OrcidNoDoiTest { public class OrcidNoDoiTest {
@ -33,100 +39,10 @@ public class OrcidNoDoiTest {
String nameB = "K"; String nameB = "K";
String surnameB = "Abdel-Dayem"; String surnameB = "Abdel-Dayem";
String orcidIdA = "0000-0003-2760-1191"; String orcidIdA = "0000-0003-2760-1191";
Double threshold = 0.8;
@Test @Test
@Ignore @Ignore
private void similarityTest() throws Exception { private void readPublicationFieldsTest()
logger.info("running testSimilarity ....");
logger
.info(
"JaroWinklerSimilarity: "
+ Double.toString(similarityJaroWinkler(nameA, surnameA, nameB, surnameB)));
logger
.info(
"JaccardSimilarity: " + Double.toString(similarityJaccard(nameA, surnameA, nameB, surnameB)));
}
@Test
@Ignore
private void bestMatchTest() throws Exception {
logger.info("running bestMatchTest ....");
String contributor = surnameB + ", " + nameB;
logger.info("score: " + Double.toString(bestMatch(surnameA, nameA, contributor)));
}
private static Double bestMatch(String authorSurname, String authorName, String contributor) {
logger.debug(authorSurname + " " + authorName + " vs " + contributor);
String[] contributorSplitted = contributor.split(" ");
if (contributorSplitted.length == 0) {
return 0.0;
}
final String contributorName = contributorSplitted[contributorSplitted.length - 1];
String contributorSurname = "";
if (contributorSplitted.length > 1) {
StringJoiner joiner = new StringJoiner(" ");
for (int i = 0; i < contributorSplitted.length - 1; i++) {
joiner.add(contributorSplitted[i]);
}
contributorSurname = joiner.toString();
}
logger
.debug(
"contributorName: " + contributorName +
" contributorSurname: " + contributorSurname);
String authorNameNrm = normalize(authorName);
String authorSurnameNrm = normalize(authorSurname);
String contributorNameNrm = normalize(contributorName);
String contributorSurnameNrm = normalize(contributorSurname);
Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm);
Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm);
if (sm1.compareTo(sm2) >= 0) {
return sm1;
}
return sm2;
}
private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) {
Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB);
logger
.debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score));
return score;
}
private static Double similarityJaccard(String nameA, String surnameA, String nameB, String surnameB) {
return new JaccardSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
}
private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) {
return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
}
private static String parse(String name, String surname) {
return surname + " " + name;
}
private static String normalize(final String s) {
return nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
// of large input strings
.replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
}
private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
@Test
@Ignore
public void readPublicationFieldsTest()
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException { throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
logger.info("running loadPublicationFieldsTest ...."); logger.info("running loadPublicationFieldsTest ....");
String xml = IOUtils String xml = IOUtils
@ -178,78 +94,10 @@ public class OrcidNoDoiTest {
} }
private void updateRanks(List<Contributor> contributors) {
boolean seqFound = false;
if (contributors
.stream()
.filter(
c -> c.getRole() != null && c.getSequence() != null &&
c.getRole().equals("author") && (c.getSequence().equals("first") ||
c.getSequence().equals("additional")))
.count() > 0) {
seqFound = true;
logger.info("sequence data found");
}
if (!seqFound) {
List<Integer> seqIds = Arrays.asList(0);
contributors.forEach(c -> {
int currentSeq = seqIds.get(0) + 1;
seqIds.set(0, currentSeq);
c.setSequence(Integer.toString(seqIds.get(0)));
});
}
}
private void updateAuthorsSimpleMatch(List<Contributor> contributors, AuthorData author) {
contributors.forEach(c -> {
if (c.isSimpleMatch()) {
logger.info("simple match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
}
});
updateRanks(contributors);
}
private void updateAuthorsSimilarityMatch(List<Contributor> contributors, AuthorData author) {
logger.info("inside updateAuthorsSimilarityMatch ...");
contributors.forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: "
+ c.isSimpleMatch());
});
contributors
.stream()
.filter(c -> c.isBestMatch())
.forEach(c -> {
logger.info("similarity match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
});
updateRanks(contributors);
}
@Test @Test
@Ignore public void authorMatchTest() throws Exception {
public void authorSimilarityMatchTest() throws Exception {
logger.info("running authorSimilarityMatchTest ....");
authorMatchTest("activity_work_0000-0003-2760-1191-similarity.xml");
}
@Test
private void authorSimpleMatchTest() throws Exception {
logger.info("running authorSimpleMatchTest ...."); logger.info("running authorSimpleMatchTest ....");
authorMatchTest("activity_work_0000-0003-2760-1191.xml"); String orcidWork = "activity_work_0000-0003-2760-1191-similarity.xml";
}
private void authorMatchTest(String orcidWork)
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
AuthorData author = new AuthorData(); AuthorData author = new AuthorData();
author.setName(nameA); author.setName(nameA);
author.setSurname(surnameA); author.setSurname(surnameA);
@ -272,55 +120,9 @@ public class OrcidNoDoiTest {
logger.error("parsing xml", e); logger.error("parsing xml", e);
} }
assertNotNull(workData); assertNotNull(workData);
int matchCounter = 0; AuthorMatcher.match(author, workData.getContributors());
List<Integer> matchCounters = Arrays.asList(matchCounter); GsonBuilder builder = new GsonBuilder();
Contributor contributor = null; Gson gson = builder.create();
workData.getContributors().forEach(c -> { logger.info(gson.toJson(workData));
if (normalize(c.getCreditName()).contains(normalize(author.getName())) ||
normalize(c.getCreditName()).contains(normalize(author.getSurname())) ||
((author.getOtherName() != null)
&& normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) {
matchCounters.set(0, matchCounters.get(0) + 1);
c.setSimpleMatch(true);
}
});
logger.info("match counter: " + Integer.toString(matchCounters.get(0)));
if (matchCounters.get(0) == 1) {
updateAuthorsSimpleMatch(workData.getContributors(), author);
} else if (matchCounters.get(0) > 1) {
Optional<Contributor> optCon = workData
.getContributors()
.stream()
.filter(c -> c.isSimpleMatch())
.map(c -> {
c.setScore(bestMatch(nameA, surnameA, c.getCreditName()));
logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore());
return c;
})
.filter(c -> c.getScore() >= threshold)
.max(Comparator.comparing(c -> c.getScore()));
Contributor bestMatchContributor = null;
if (optCon.isPresent()) {
bestMatchContributor = optCon.get();
bestMatchContributor.setBestMatch(true);
logger.info("best match: " + bestMatchContributor.getCreditName());
updateAuthorsSimilarityMatch(workData.getContributors(), author);
}
}
logger.info("UPDATED contributors: ");
workData.getContributors().forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence());
});
} }
} }
//
// orcid_RDD = sc.textFile(ORCID_DUMP_PATH)
// no_doi_works_RDD = orcid_RDD.map(orcid_map).filter(lambda x:x is not None).map(lambda x: json.dumps(x)).saveAsTextFile(path=ORCID_OPENAIRE_PATH,compressionCodecClass="org.apache.hadoop.io.compress.GzipCodec")
//