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deleted old scholix project

This commit is contained in:
Sandro La Bruzzo 2021-07-06 17:20:08 +02:00
parent 8535506c22
commit ed684874f2
88 changed files with 0 additions and 9703 deletions
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82
dhp-workflows/dhp-dedup-scholexplorer/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-dedup-scholexplorer</artifactId>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.0.1</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-graphx_2.11</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
</dependency>
</dependencies>
</project>

121
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DatePicker.java
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package eu.dnetlib.dedup;
import static java.util.Collections.reverseOrder;
import static java.util.Map.Entry.comparingByValue;
import static java.util.stream.Collectors.toMap;
import static org.apache.commons.lang.StringUtils.endsWith;
import static org.apache.commons.lang.StringUtils.substringBefore;
import java.time.Year;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Field;
public class DatePicker {
private static final String DATE_PATTERN = "\\d{4}-\\d{2}-\\d{2}";
private static final String DATE_DEFAULT_SUFFIX = "01-01";
private static final int YEAR_LB = 1300;
private static final int YEAR_UB = Year.now().getValue() + 5;
public static Field<String> pick(final Collection<String> dateofacceptance) {
final Map<String, Integer> frequencies = dateofacceptance
.parallelStream()
.filter(StringUtils::isNotBlank)
.collect(Collectors.toConcurrentMap(w -> w, w -> 1, Integer::sum));
if (frequencies.isEmpty()) {
return new Field<>();
}
final Field<String> date = new Field<>();
date.setValue(frequencies.keySet().iterator().next());
// let's sort this map by values first, filtering out invalid dates
final Map<String, Integer> sorted = frequencies
.entrySet()
.stream()
.filter(d -> StringUtils.isNotBlank(d.getKey()))
.filter(d -> d.getKey().matches(DATE_PATTERN))
.filter(d -> inRange(d.getKey()))
.sorted(reverseOrder(comparingByValue()))
.collect(
toMap(Map.Entry::getKey, Map.Entry::getValue, (e1, e2) -> e2, LinkedHashMap::new));
// shortcut
if (sorted.size() == 0) {
return date;
}
// voting method (1/3 + 1) wins
if (sorted.size() >= 3) {
final int acceptThreshold = (sorted.size() / 3) + 1;
final List<String> accepted = sorted
.entrySet()
.stream()
.filter(e -> e.getValue() >= acceptThreshold)
.map(e -> e.getKey())
.collect(Collectors.toList());
// cannot find strong majority
if (accepted.isEmpty()) {
final int max = sorted.values().iterator().next();
Optional<String> first = sorted
.entrySet()
.stream()
.filter(e -> e.getValue() == max && !endsWith(e.getKey(), DATE_DEFAULT_SUFFIX))
.map(Map.Entry::getKey)
.findFirst();
if (first.isPresent()) {
date.setValue(first.get());
return date;
}
date.setValue(sorted.keySet().iterator().next());
return date;
}
if (accepted.size() == 1) {
date.setValue(accepted.get(0));
return date;
} else {
final Optional<String> first = accepted
.stream()
.filter(d -> !endsWith(d, DATE_DEFAULT_SUFFIX))
.findFirst();
if (first.isPresent()) {
date.setValue(first.get());
return date;
}
return date;
}
// 1st non YYYY-01-01 is returned
} else {
if (sorted.size() == 2) {
for (Map.Entry<String, Integer> e : sorted.entrySet()) {
if (!endsWith(e.getKey(), DATE_DEFAULT_SUFFIX)) {
date.setValue(e.getKey());
return date;
}
}
}
// none of the dates seems good enough, return the 1st one
date.setValue(sorted.keySet().iterator().next());
return date;
}
}
private static boolean inRange(final String date) {
final int year = Integer.parseInt(substringBefore(date, "-"));
return year >= YEAR_LB && year <= YEAR_UB;
}
}

327
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java
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package eu.dnetlib.dedup;
import java.util.Collection;
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.api.java.function.PairFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class DedupRecordFactory {
public static JavaRDD<OafEntity> createDedupRecord(
final JavaSparkContext sc,
final SparkSession spark,
final String mergeRelsInputPath,
final String entitiesInputPath,
final OafEntityType entityType,
final DedupConfig dedupConf) {
long ts = System.currentTimeMillis();
// <id, json_entity>
final JavaPairRDD<String, String> inputJsonEntities = spark
.read()
.load(entitiesInputPath)
.as(Encoders.kryo(Oaf.class))
.map(
(MapFunction<Oaf, String>) p -> new org.codehaus.jackson.map.ObjectMapper().writeValueAsString(p),
Encoders.STRING())
.javaRDD()
.mapToPair(
(PairFunction<String, String, String>) it -> new Tuple2<>(
MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it));
// <source, target>: source is the dedup_id, target is the id of the mergedIn
JavaPairRDD<String, String> mergeRels = spark
.read()
.load(mergeRelsInputPath)
.as(Encoders.bean(Relation.class))
.where("relClass=='merges'")
.javaRDD()
.mapToPair(
(PairFunction<Relation, String, String>) r -> new Tuple2<String, String>(r.getTarget(), r.getSource()));
// <dedup_id, json_entity_merged>
final JavaPairRDD<String, String> joinResult = mergeRels
.join(inputJsonEntities)
.mapToPair(
(PairFunction<Tuple2<String, Tuple2<String, String>>, String, String>) Tuple2::_2);
JavaPairRDD<String, Iterable<String>> sortedJoinResult = joinResult.groupByKey();
switch (entityType) {
case publication:
return sortedJoinResult.map(p -> DedupRecordFactory.publicationMerger(p, ts));
case dataset:
return sortedJoinResult.map(d -> DedupRecordFactory.datasetMerger(d, ts));
case project:
return sortedJoinResult.map(p -> DedupRecordFactory.projectMerger(p, ts));
case software:
return sortedJoinResult.map(s -> DedupRecordFactory.softwareMerger(s, ts));
case datasource:
return sortedJoinResult.map(d -> DedupRecordFactory.datasourceMerger(d, ts));
case organization:
return sortedJoinResult.map(o -> DedupRecordFactory.organizationMerger(o, ts));
case otherresearchproduct:
return sortedJoinResult.map(o -> DedupRecordFactory.otherresearchproductMerger(o, ts));
default:
return null;
}
}
private static DLIPublication publicationMerger(Tuple2<String, Iterable<String>> e, final long ts) {
DLIPublication p = new DLIPublication(); // the result of the merge, to be returned at the end
p.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e
._2()
.forEach(
pub -> {
try {
DLIPublication publication = mapper.readValue(pub, DLIPublication.class);
p.mergeFrom(publication);
p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor()));
// add to the list if they are not null
if (publication.getDateofacceptance() != null)
dateofacceptance.add(publication.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
p.setDateofacceptance(DatePicker.pick(dateofacceptance));
if (p.getDataInfo() == null)
p.setDataInfo(new DataInfo());
p.getDataInfo().setTrust("0.9");
p.setLastupdatetimestamp(ts);
return p;
}
private static DLIDataset datasetMerger(Tuple2<String, Iterable<String>> e, final long ts) {
DLIDataset d = new DLIDataset(); // the result of the merge, to be returned at the end
d.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e
._2()
.forEach(
dat -> {
try {
Dataset dataset = mapper.readValue(dat, Dataset.class);
d.mergeFrom(dataset);
d.setAuthor(DedupUtility.mergeAuthor(d.getAuthor(), dataset.getAuthor()));
// add to the list if they are not null
if (dataset.getDateofacceptance() != null)
dateofacceptance.add(dataset.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
d.setDateofacceptance(DatePicker.pick(dateofacceptance));
if (d.getDataInfo() == null)
d.setDataInfo(new DataInfo());
d.getDataInfo().setTrust("0.9");
d.setLastupdatetimestamp(ts);
return d;
}
private static Project projectMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Project p = new Project(); // the result of the merge, to be returned at the end
p.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
if (e._2() != null)
e
._2()
.forEach(
proj -> {
try {
Project project = mapper.readValue(proj, Project.class);
p.mergeFrom(project);
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
if (p.getDataInfo() == null)
p.setDataInfo(new DataInfo());
p.getDataInfo().setTrust("0.9");
p.setLastupdatetimestamp(ts);
return p;
}
private static Software softwareMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Software s = new Software(); // the result of the merge, to be returned at the end
s.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e
._2()
.forEach(
soft -> {
try {
Software software = mapper.readValue(soft, Software.class);
s.mergeFrom(software);
s.setAuthor(DedupUtility.mergeAuthor(s.getAuthor(), software.getAuthor()));
// add to the list if they are not null
if (software.getDateofacceptance() != null)
dateofacceptance.add(software.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
s.setDateofacceptance(DatePicker.pick(dateofacceptance));
if (s.getDataInfo() == null)
s.setDataInfo(new DataInfo());
s.getDataInfo().setTrust("0.9");
s.setLastupdatetimestamp(ts);
return s;
}
private static Datasource datasourceMerger(Tuple2<String, Iterable<String>> e, final long ts) {
Datasource d = new Datasource(); // the result of the merge, to be returned at the end
d.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
if (e._2() != null)
e
._2()
.forEach(
dat -> {
try {
Datasource datasource = mapper.readValue(dat, Datasource.class);
d.mergeFrom(datasource);
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
if (d.getDataInfo() == null)
d.setDataInfo(new DataInfo());
d.getDataInfo().setTrust("0.9");
d.setLastupdatetimestamp(ts);
return d;
}
private static Organization organizationMerger(
Tuple2<String, Iterable<String>> e, final long ts) {
Organization o = new Organization(); // the result of the merge, to be returned at the end
o.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
StringBuilder trust = new StringBuilder("0.0");
if (e._2() != null)
e
._2()
.forEach(
pub -> {
try {
Organization organization = mapper.readValue(pub, Organization.class);
final String currentTrust = organization.getDataInfo().getTrust();
if (!"1.0".equals(currentTrust)) {
trust.setLength(0);
trust.append(currentTrust);
}
o.mergeFrom(organization);
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
if (o.getDataInfo() == null) {
o.setDataInfo(new DataInfo());
}
if (o.getDataInfo() == null)
o.setDataInfo(new DataInfo());
o.getDataInfo().setTrust("0.9");
o.setLastupdatetimestamp(ts);
return o;
}
private static OtherResearchProduct otherresearchproductMerger(
Tuple2<String, Iterable<String>> e, final long ts) {
OtherResearchProduct o = new OtherResearchProduct(); // the result of the merge, to be
// returned at the end
o.setId(e._1());
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
final Collection<String> dateofacceptance = Lists.newArrayList();
if (e._2() != null)
e
._2()
.forEach(
orp -> {
try {
OtherResearchProduct otherResearchProduct = mapper
.readValue(orp, OtherResearchProduct.class);
o.mergeFrom(otherResearchProduct);
o
.setAuthor(
DedupUtility.mergeAuthor(o.getAuthor(), otherResearchProduct.getAuthor()));
// add to the list if they are not null
if (otherResearchProduct.getDateofacceptance() != null)
dateofacceptance.add(otherResearchProduct.getDateofacceptance().getValue());
} catch (Exception exc) {
throw new RuntimeException(exc);
}
});
if (o.getDataInfo() == null)
o.setDataInfo(new DataInfo());
o.setDateofacceptance(DatePicker.pick(dateofacceptance));
o.getDataInfo().setTrust("0.9");
o.setLastupdatetimestamp(ts);
return o;
}
}

239
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java
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package eu.dnetlib.dedup;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkContext;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.util.LongAccumulator;
import com.google.common.collect.Sets;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.clustering.BlacklistAwareClusteringCombiner;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.model.Person;
import scala.Tuple2;
public class DedupUtility {
private static final Double THRESHOLD = 0.95;
public static Map<String, LongAccumulator> constructAccumulator(
final DedupConfig dedupConf, final SparkContext context) {
Map<String, LongAccumulator> accumulators = new HashMap<>();
String acc1 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "records per hash key = 1");
accumulators.put(acc1, context.longAccumulator(acc1));
String acc2 = String
.format(
"%s::%s",
dedupConf.getWf().getEntityType(), "missing " + dedupConf.getWf().getOrderField());
accumulators.put(acc2, context.longAccumulator(acc2));
String acc3 = String
.format(
"%s::%s",
dedupConf.getWf().getEntityType(),
String
.format(
"Skipped records for count(%s) >= %s",
dedupConf.getWf().getOrderField(), dedupConf.getWf().getGroupMaxSize()));
accumulators.put(acc3, context.longAccumulator(acc3));
String acc4 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "skip list");
accumulators.put(acc4, context.longAccumulator(acc4));
String acc5 = String.format("%s::%s", dedupConf.getWf().getEntityType(), "dedupSimilarity (x2)");
accumulators.put(acc5, context.longAccumulator(acc5));
String acc6 = String
.format(
"%s::%s", dedupConf.getWf().getEntityType(), "d < " + dedupConf.getWf().getThreshold());
accumulators.put(acc6, context.longAccumulator(acc6));
return accumulators;
}
public static JavaRDD<String> loadDataFromHDFS(String path, JavaSparkContext context) {
return context.textFile(path);
}
public static void deleteIfExists(String path) throws IOException {
Configuration conf = new Configuration();
FileSystem fileSystem = FileSystem.get(conf);
if (fileSystem.exists(new Path(path))) {
fileSystem.delete(new Path(path), true);
}
}
public static DedupConfig loadConfigFromHDFS(String path) throws IOException {
Configuration conf = new Configuration();
FileSystem fileSystem = FileSystem.get(conf);
FSDataInputStream inputStream = new FSDataInputStream(fileSystem.open(new Path(path)));
return DedupConfig.load(IOUtils.toString(inputStream, StandardCharsets.UTF_8.name()));
}
static <T> String readFromClasspath(final String filename, final Class<T> clazz) {
final StringWriter sw = new StringWriter();
try {
IOUtils.copy(clazz.getResourceAsStream(filename), sw);
return sw.toString();
} catch (final IOException e) {
throw new RuntimeException("cannot load resource from classpath: " + filename);
}
}
static Set<String> getGroupingKeys(DedupConfig conf, MapDocument doc) {
return Sets.newHashSet(BlacklistAwareClusteringCombiner.filterAndCombine(doc, conf));
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");
return null;
}
}
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
if (pa == pb) {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
} else {
base = pa > pb ? a : b;
enrich = pa > pb ? b : a;
}
enrichPidFromList(base, enrich);
return base;
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
if (base == null || enrich == null)
return;
final Map<String, Author> basePidAuthorMap = base
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap(a -> a.getPid().stream().map(p -> new Tuple2<>(p.toComparableString(), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.flatMap(
a -> a
.getPid()
.stream()
.filter(p -> !basePidAuthorMap.containsKey(p.toComparableString()))
.map(p -> new Tuple2<>(p, a)))
.collect(Collectors.toList());
pidToEnrich
.forEach(
a -> {
Optional<Tuple2<Double, Author>> simAuhtor = base
.stream()
.map(ba -> new Tuple2<>(sim(ba, a._2()), ba))
.max(Comparator.comparing(Tuple2::_1));
if (simAuhtor.isPresent() && simAuhtor.get()._1() > THRESHOLD) {
Author r = simAuhtor.get()._2();
r.getPid().add(a._1());
}
});
}
public static String createEntityPath(final String basePath, final String entityType) {
return String.format("%s/%s", basePath, entityType);
}
public static String createSimRelPath(final String basePath, final String entityType) {
return String.format("%s/%s/simRel", basePath, entityType);
}
public static String createMergeRelPath(final String basePath, final String entityType) {
return String.format("%s/%s/mergeRel", basePath, entityType);
}
private static Double sim(Author a, Author b) {
final Person pa = parse(a);
final Person pb = parse(b);
if (pa.isAccurate() & pb.isAccurate()) {
return new JaroWinkler()
.score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString()));
} else {
return new JaroWinkler()
.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
}
}
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 Person parse(Author author) {
if (StringUtils.isNotBlank(author.getSurname())) {
return new Person(author.getSurname() + ", " + author.getName(), false);
} else {
return new Person(author.getFullname(), false);
}
}
private static int countAuthorsPids(List<Author> authors) {
if (authors == null)
return 0;
return (int) authors.stream().filter(DedupUtility::hasPid).count();
}
private static int authorsSize(List<Author> authors) {
if (authors == null)
return 0;
return authors.size();
}
private static boolean hasPid(Author a) {
if (a == null || a.getPid() == null || a.getPid().size() == 0)
return false;
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
}
}

182
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/Deduper.java
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@ -1,182 +0,0 @@
package eu.dnetlib.dedup;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
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.Function2;
import org.apache.spark.api.java.function.PairFlatMapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.BlockProcessor;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Serializable;
import scala.Tuple2;
public class Deduper implements Serializable {
private static final Log log = LogFactory.getLog(Deduper.class);
/**
* @return the list of relations generated by the deduplication
* @param: the spark context
* @param: list of JSON entities to be deduped
* @param: the dedup configuration
*/
public static JavaPairRDD<String, String> dedup(
JavaSparkContext context, JavaRDD<String> entities, DedupConfig config) {
Map<String, LongAccumulator> accumulators = DedupUtility.constructAccumulator(config, context.sc());
// create vertexes of the graph: <ID, MapDocument>
JavaPairRDD<String, MapDocument> mapDocs = mapToVertexes(context, entities, config);
// create blocks for deduplication
JavaPairRDD<String, Iterable<MapDocument>> blocks = createBlocks(context, mapDocs, config);
// create relations by comparing only elements in the same group
return computeRelations(context, blocks, config);
// final RDD<Edge<String>> edgeRdd = relationRDD.map(it -> new
// Edge<>(it._1().hashCode(),
// it._2().hashCode(), "equalTo")).rdd();
//
// RDD<Tuple2<Object, MapDocument>> vertexes =
// mapDocs.mapToPair((PairFunction<Tuple2<String, MapDocument>, Object, MapDocument>) t ->
// new
// Tuple2<Object, MapDocument>((long) t._1().hashCode(), t._2())).rdd();
// accumulators.forEach((name, acc) -> log.info(name + " -> " + acc.value()));
//
// return GraphProcessor.findCCs(vertexes, edgeRdd, 20).toJavaRDD();
}
/**
* @return the list of relations generated by the deduplication
* @param: the spark context
* @param: list of blocks
* @param: the dedup configuration
*/
public static JavaPairRDD<String, String> computeRelations(
JavaSparkContext context,
JavaPairRDD<String, Iterable<MapDocument>> blocks,
DedupConfig config) {
Map<String, LongAccumulator> accumulators = DedupUtility.constructAccumulator(config, context.sc());
return blocks
.flatMapToPair(
(PairFlatMapFunction<Tuple2<String, Iterable<MapDocument>>, String, String>) it -> {
final SparkReporter reporter = new SparkReporter(accumulators);
new BlockProcessor(config).process(it._1(), it._2(), reporter);
return reporter.getRelations().iterator();
})
.mapToPair(
(PairFunction<Tuple2<String, String>, String, Tuple2<String, String>>) item -> new Tuple2<String, Tuple2<String, String>>(
item._1() + item._2(), item))
.reduceByKey((a, b) -> a)
.mapToPair(
(PairFunction<Tuple2<String, Tuple2<String, String>>, String, String>) Tuple2::_2);
}
/**
* @return the list of blocks based on clustering of dedup configuration
* @param: the spark context
* @param: list of entities: <id, entity>
* @param: the dedup configuration
*/
public static JavaPairRDD<String, Iterable<MapDocument>> createBlocks(
JavaSparkContext context, JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
return mapDocs
// the reduce is just to be sure that we haven't document with same id
.reduceByKey((a, b) -> a)
.map(Tuple2::_2)
// Clustering: from <id, doc> to List<groupkey,doc>
.flatMapToPair(
(PairFlatMapFunction<MapDocument, String, MapDocument>) a -> DedupUtility
.getGroupingKeys(config, a)
.stream()
.map(it -> new Tuple2<>(it, a))
.collect(Collectors.toList())
.iterator())
.groupByKey();
}
public static JavaPairRDD<String, List<MapDocument>> createsortedBlocks(
JavaSparkContext context, JavaPairRDD<String, MapDocument> mapDocs, DedupConfig config) {
final String of = config.getWf().getOrderField();
final int maxQueueSize = config.getWf().getGroupMaxSize();
return mapDocs
// the reduce is just to be sure that we haven't document with same id
.reduceByKey((a, b) -> a)
.map(Tuple2::_2)
// Clustering: from <id, doc> to List<groupkey,doc>
.flatMapToPair(
(PairFlatMapFunction<MapDocument, String, List<MapDocument>>) a -> DedupUtility
.getGroupingKeys(config, a)
.stream()
.map(
it -> {
List<MapDocument> tmp = new ArrayList<>();
tmp.add(a);
return new Tuple2<>(it, tmp);
})
.collect(Collectors.toList())
.iterator())
.reduceByKey(
(Function2<List<MapDocument>, List<MapDocument>, List<MapDocument>>) (v1, v2) -> {
v1.addAll(v2);
v1.sort(Comparator.comparing(a -> a.getFieldMap().get(of).stringValue()));
if (v1.size() > maxQueueSize)
return new ArrayList<>(v1.subList(0, maxQueueSize));
return v1;
});
}
/**
* @return the list of vertexes: <id, mapDocument>
* @param: the spark context
* @param: list of JSON entities
* @param: the dedup configuration
*/
public static JavaPairRDD<String, MapDocument> mapToVertexes(
JavaSparkContext context, JavaRDD<String> entities, DedupConfig config) {
return entities
.mapToPair(
(PairFunction<String, String, MapDocument>) s -> {
MapDocument mapDocument = MapDocumentUtil.asMapDocumentWithJPath(config, s);
return new Tuple2<String, MapDocument>(mapDocument.getIdentifier(), mapDocument);
});
}
public static JavaPairRDD<String, String> computeRelations2(
JavaSparkContext context, JavaPairRDD<String, List<MapDocument>> blocks, DedupConfig config) {
Map<String, LongAccumulator> accumulators = DedupUtility.constructAccumulator(config, context.sc());
return blocks
.flatMapToPair(
(PairFlatMapFunction<Tuple2<String, List<MapDocument>>, String, String>) it -> {
try {
final SparkReporter reporter = new SparkReporter(accumulators);
new BlockProcessor(config).processSortedBlock(it._1(), it._2(), reporter);
return reporter.getRelations().iterator();
} catch (Exception e) {
throw new RuntimeException(it._2().get(0).getIdentifier(), e);
}
})
.mapToPair(
(PairFunction<Tuple2<String, String>, String, Tuple2<String, String>>) item -> new Tuple2<String, Tuple2<String, String>>(
item._1() + item._2(), item))
.reduceByKey((a, b) -> a)
.mapToPair(
(PairFunction<Tuple2<String, Tuple2<String, String>>, String, String>) Tuple2::_2);
}
}

6
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/OafEntityType.java
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package eu.dnetlib.dedup;
public enum OafEntityType {
datasource, organization, project, dataset, otherresearchproduct, software, publication
}

112
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java
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package eu.dnetlib.dedup;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.PairFunction;
import org.apache.spark.graphx.Edge;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.hash.Hashing;
import eu.dnetlib.dedup.graph.ConnectedComponent;
import eu.dnetlib.dedup.graph.GraphProcessor;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class SparkCreateConnectedComponent {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateConnectedComponent.class
.getResourceAsStream(
"/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkCreateConnectedComponent.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final String inputPath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String targetPath = parser.get("targetPath");
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaPairRDD<Object, String> vertexes = spark
.read()
.load(inputPath + "/" + entity)
.as(Encoders.kryo(Oaf.class))
.map((MapFunction<Oaf, String>) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING())
.javaRDD()
.map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s))
.mapToPair(
(PairFunction<String, Object, String>) s -> new Tuple2<Object, String>(getHashcode(s), s));
final Dataset<Relation> similarityRelations = spark
.read()
.load(DedupUtility.createSimRelPath(targetPath, entity))
.as(Encoders.bean(Relation.class));
final RDD<Edge<String>> edgeRdd = similarityRelations
.javaRDD()
.map(
it -> new Edge<>(
getHashcode(it.getSource()), getHashcode(it.getTarget()), it.getRelClass()))
.rdd();
final JavaRDD<ConnectedComponent> cc = GraphProcessor
.findCCs(vertexes.rdd(), edgeRdd, dedupConf.getWf().getMaxIterations())
.toJavaRDD();
final Dataset<Relation> mergeRelation = spark
.createDataset(
cc
.filter(k -> k.getDocIds().size() > 1)
.flatMap(
(FlatMapFunction<ConnectedComponent, Relation>) c -> c
.getDocIds()
.stream()
.flatMap(
id -> {
List<Relation> tmp = new ArrayList<>();
Relation r = new Relation();
r.setSource(c.getCcId());
r.setTarget(id);
r.setRelClass(ModelConstants.MERGES);
tmp.add(r);
r = new Relation();
r.setTarget(c.getCcId());
r.setSource(id);
r.setRelClass(ModelConstants.IS_MERGED_IN);
tmp.add(r);
return tmp.stream();
})
.iterator())
.rdd(),
Encoders.bean(Relation.class));
mergeRelation
.write()
.mode("overwrite")
.save(DedupUtility.createMergeRelPath(targetPath, entity));
}
public static long getHashcode(final String id) {
return Hashing.murmur3_128().hashString(id).asLong();
}
}

59
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java
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@ -1,59 +0,0 @@
package eu.dnetlib.dedup;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.pace.config.DedupConfig;
public class SparkCreateDedupRecord {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateDedupRecord.class
.getResourceAsStream(
"/eu/dnetlib/dhp/sx/dedup/dedupRecord_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkCreateDedupRecord.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String sourcePath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String dedupPath = parser.get("dedupPath");
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
final JavaRDD<OafEntity> dedupRecord = DedupRecordFactory
.createDedupRecord(
sc,
spark,
DedupUtility.createMergeRelPath(dedupPath, entity),
DedupUtility.createEntityPath(sourcePath, entity),
OafEntityType.valueOf(entity),
dedupConf);
spark
.createDataset(dedupRecord.rdd(), Encoders.kryo(OafEntity.class))
.write()
.mode(SaveMode.Overwrite)
.save(dedupPath + "/" + entity + "/dedup_records");
//
//
// dedupRecord
// .map(
// r -> {
// ObjectMapper mapper = new ObjectMapper();
// return mapper.writeValueAsString(r);
// })
// .saveAsTextFile(dedupPath + "/" + entity + "/dedup_records");
}
}

92
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java
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@ -1,92 +0,0 @@
package eu.dnetlib.dedup;
import java.util.List;
import org.apache.commons.io.IOUtils;
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.Encoders;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.pace.config.DedupConfig;
import eu.dnetlib.pace.model.MapDocument;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
/**
* This Spark class creates similarity relations between entities, saving result
* <p>
* param request: sourcePath entityType target Path
*/
public class SparkCreateSimRels {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkCreateSimRels.class
.getResourceAsStream(
"/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkCreateSimRels.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String inputPath = parser.get("sourcePath");
final String entity = parser.get("entity");
final String targetPath = parser.get("targetPath");
// final DedupConfig dedupConf =
// DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf"));
JavaPairRDD<String, MapDocument> mapDocument = spark
.read()
.load(inputPath + "/" + entity)
.as(Encoders.kryo(Oaf.class))
.map((MapFunction<Oaf, String>) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING())
.javaRDD()
.repartition(1000)
.mapToPair(
s -> {
MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
return new Tuple2<>(d.getIdentifier(), d);
});
// create blocks for deduplication
JavaPairRDD<String, List<MapDocument>> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf);
// JavaPairRDD<String, Iterable<MapDocument>> blocks = Deduper.createBlocks(sc,
// mapDocument, dedupConf);
// create relations by comparing only elements in the same group
final JavaPairRDD<String, String> dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf);
// final JavaPairRDD<String,String> dedupRels = Deduper.computeRelations(sc, blocks,
// dedupConf);
final JavaRDD<Relation> isSimilarToRDD = dedupRels
.map(
simRel -> {
final Relation r = new Relation();
r.setSource(simRel._1());
r.setTarget(simRel._2());
r.setRelClass("isSimilarTo");
return r;
});
spark
.createDataset(isSimilarToRDD.rdd(), Encoders.bean(Relation.class))
.write()
.mode("overwrite")
.save(DedupUtility.createSimRelPath(targetPath, entity));
}
}

52
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkReporter.java
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@ -1,52 +0,0 @@
package eu.dnetlib.dedup;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.spark.util.LongAccumulator;
import eu.dnetlib.pace.util.Reporter;
import scala.Serializable;
import scala.Tuple2;
public class SparkReporter implements Serializable, Reporter {
final List<Tuple2<String, String>> relations = new ArrayList<>();
private static final Log log = LogFactory.getLog(SparkReporter.class);
Map<String, LongAccumulator> accumulators;
public SparkReporter(Map<String, LongAccumulator> accumulators) {
this.accumulators = accumulators;
}
public void incrementCounter(
String counterGroup,
String counterName,
long delta,
Map<String, LongAccumulator> accumulators) {
final String accumulatorName = String.format("%s::%s", counterGroup, counterName);
if (accumulators.containsKey(accumulatorName)) {
accumulators.get(accumulatorName).add(delta);
}
}
@Override
public void incrementCounter(String counterGroup, String counterName, long delta) {
incrementCounter(counterGroup, counterName, delta, accumulators);
}
@Override
public void emit(String type, String from, String to) {
relations.add(new Tuple2<>(from, to));
}
public List<Tuple2<String, String>> getRelations() {
return relations;
}
}

84
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/ConnectedComponent.java
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@ -1,84 +0,0 @@
package eu.dnetlib.dedup.graph;
import java.io.IOException;
import java.io.Serializable;
import java.util.Set;
import org.apache.commons.lang.StringUtils;
import org.codehaus.jackson.annotate.JsonIgnore;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dedup.DedupUtility;
import eu.dnetlib.pace.util.PaceException;
public class ConnectedComponent implements Serializable {
private Set<String> docIds;
private String ccId;
public ConnectedComponent() {
}
public ConnectedComponent(Set<String> docIds) {
this.docIds = docIds;
createID();
}
public String createID() {
if (docIds.size() > 1) {
final String s = getMin();
String prefix = s.split("\\|")[0];
ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
return ccId;
} else {
return docIds.iterator().next();
}
}
@JsonIgnore
public String getMin() {
final StringBuilder min = new StringBuilder();
docIds
.forEach(
i -> {
if (StringUtils.isBlank(min.toString())) {
min.append(i);
} else {
if (min.toString().compareTo(i) > 0) {
min.setLength(0);
min.append(i);
}
}
});
return min.toString();
}
@Override
public String toString() {
ObjectMapper mapper = new ObjectMapper();
try {
return mapper.writeValueAsString(this);
} catch (IOException e) {
throw new PaceException("Failed to create Json: ", e);
}
}
public Set<String> getDocIds() {
return docIds;
}
public void setDocIds(Set<String> docIds) {
this.docIds = docIds;
}
public String getCcId() {
return ccId;
}
public void setCcId(String ccId) {
this.ccId = ccId;
}
}

37
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/graph/GraphProcessor.scala
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@ -1,37 +0,0 @@
package eu.dnetlib.dedup.graph
import org.apache.spark.graphx._
import org.apache.spark.rdd.RDD
import scala.collection.JavaConversions;
object GraphProcessor {
def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int): RDD[ConnectedComponent] = {
val graph: Graph[String, String] = Graph(vertexes, edges).partitionBy(PartitionStrategy.RandomVertexCut) //TODO remember to remove partitionby
val cc = graph.connectedComponents(maxIterations).vertices
val joinResult = vertexes.leftOuterJoin(cc).map {
case (id, (openaireId, cc)) => {
if (cc.isEmpty) {
(id, openaireId)
}
else {
(cc.get, openaireId)
}
}
}
val connectedComponents = joinResult.groupByKey()
.map[ConnectedComponent](cc => asConnectedComponent(cc))
connectedComponents
}
def asConnectedComponent(group: (VertexId, Iterable[String])): ConnectedComponent = {
val docs = group._2.toSet[String]
val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs));
connectedComponent
}
}

78
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java
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@ -1,78 +0,0 @@
package eu.dnetlib.dedup.sx;
import org.apache.commons.io.IOUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils;
import scala.Tuple2;
public class SparkPropagateRelationsJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkPropagateRelationsJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/sx/dedup/dedup_propagate_relation_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkUpdateEntityJob.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final String relationPath = parser.get("relationPath");
final String mergeRelPath = parser.get("mergeRelPath");
final String targetRelPath = parser.get("targetRelPath");
final Dataset<Relation> merge = spark
.read()
.load(mergeRelPath)
.as(Encoders.bean(Relation.class))
.where("relClass == 'merges'");
final Dataset<Relation> rels = spark
.read()
.load(relationPath)
.as(Encoders.kryo(Relation.class))
.map(
(MapFunction<Relation, Relation>) r -> r,
Encoders.bean(Relation.class));
final Dataset<Relation> firstJoin = rels
.joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer")
.map(
(MapFunction<Tuple2<Relation, Relation>, Relation>) r -> {
final Relation mergeRelation = r._2();
final Relation relation = r._1();
if (mergeRelation != null)
relation.setSource(mergeRelation.getSource());
if (relation.getDataInfo() == null)
relation.setDataInfo(OafUtils.generateDataInfo("0.9", false));
return relation;
},
Encoders.bean(Relation.class));
final Dataset<Relation> secondJoin = firstJoin
.joinWith(merge, merge.col("target").equalTo(firstJoin.col("target")), "left_outer")
.map(
(MapFunction<Tuple2<Relation, Relation>, Relation>) r -> {
final Relation mergeRelation = r._2();
final Relation relation = r._1();
if (mergeRelation != null)
relation.setTarget(mergeRelation.getSource());
return relation;
},
Encoders.kryo(Relation.class));
secondJoin.write().mode(SaveMode.Overwrite).save(targetRelPath);
}
}

102
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityJob.java
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@ -1,102 +0,0 @@
package eu.dnetlib.dedup.sx;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.compress.GzipCodec;
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.PairFunction;
import org.apache.spark.sql.*;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;
public class SparkUpdateEntityJob {
static final String IDJSONPATH = "$.id";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkUpdateEntityJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json")));
parser.parseArgument(args);
final SparkSession spark = SparkSession
.builder()
.appName(SparkUpdateEntityJob.class.getSimpleName())
.master(parser.get("master"))
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String entityPath = parser.get("entityPath");
final String mergeRelPath = parser.get("mergeRelPath");
final String dedupRecordPath = parser.get("dedupRecordPath");
final String entity = parser.get("entity");
final String destination = parser.get("targetPath");
final Dataset<Relation> df = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class));
final JavaPairRDD<String, String> mergedIds = df
.where("relClass == 'merges'")
.select(df.col("target"))
.distinct()
.toJavaRDD()
.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
final JavaRDD<String> sourceEntity = sc.textFile(entityPath);
final JavaRDD<String> dedupEntity = sc.textFile(dedupRecordPath);
JavaPairRDD<String, String> entitiesWithId = sourceEntity
.mapToPair(
(PairFunction<String, String, String>) s -> new Tuple2<>(DHPUtils.getJPathString(IDJSONPATH, s), s));
Class<? extends Oaf> mainClass;
switch (entity) {
case "publication":
mainClass = DLIPublication.class;
break;
case "dataset":
mainClass = DLIDataset.class;
break;
case "unknown":
mainClass = DLIUnknown.class;
break;
default:
throw new IllegalArgumentException("Illegal type " + entity);
}
JavaRDD<String> map = entitiesWithId
.leftOuterJoin(mergedIds)
.map(
k -> k._2()._2().isPresent()
? updateDeletedByInference(k._2()._1(), mainClass)
: k._2()._1());
map.union(dedupEntity).saveAsTextFile(destination, GzipCodec.class);
}
private static <T extends Oaf> String updateDeletedByInference(
final String json, final Class<T> clazz) {
final ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
try {
Oaf entity = mapper.readValue(json, clazz);
if (entity.getDataInfo() == null)
entity.setDataInfo(new DataInfo());
entity.getDataInfo().setDeletedbyinference(true);
return mapper.writeValueAsString(entity);
} catch (IOException e) {
throw new RuntimeException("Unable to convert json", e);
}
}
}

75
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityWithDedupInfo.scala
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package eu.dnetlib.dedup.sx
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown, OafUtils}
import org.apache.commons.io.IOUtils
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.LoggerFactory
import org.apache.spark.sql.functions.col
object SparkUpdateEntityWithDedupInfo {
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntityWithDedupInfo.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json")))
val logger = LoggerFactory.getLogger(SparkUpdateEntityWithDedupInfo.getClass)
parser.parseArgument(args)
val workingPath: String = parser.get("workingPath")
logger.info(s"Working dir path = $workingPath")
implicit val oafEncoder: Encoder[OafEntity] = Encoders.kryo[OafEntity]
implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation])
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
val spark: SparkSession = SparkSession
.builder()
.appName(SparkUpdateEntityWithDedupInfo.getClass.getSimpleName)
.master(parser.get("master"))
.getOrCreate()
val entityPath = parser.get("entityPath")
val mergeRelPath = parser.get("mergeRelPath")
val dedupRecordPath = parser.get("dedupRecordPath")
val entity = parser.get("entity")
val destination = parser.get("targetPath")
val mergedIds = spark.read.load(mergeRelPath).as[Relation]
.where("relClass == 'merges'")
.select(col("target"))
val entities: Dataset[(String, OafEntity)] = spark
.read
.load(entityPath).as[OafEntity]
.map(o => (o.getId, o))(Encoders.tuple(Encoders.STRING, oafEncoder))
val finalDataset:Dataset[OafEntity] = entities.joinWith(mergedIds, entities("_1").equalTo(mergedIds("target")), "left")
.map(k => {
val e: OafEntity = k._1._2
val t = k._2
if (t != null && t.getString(0).nonEmpty) {
if (e.getDataInfo == null) {
e.setDataInfo(OafUtils.generateDataInfo())
}
e.getDataInfo.setDeletedbyinference(true)
}
e
})
val dedupRecords :Dataset[OafEntity] = spark.read.load(dedupRecordPath).as[OafEntity]
finalDataset.union(dedupRecords)
.repartition(1200).write
.mode(SaveMode.Overwrite).save(destination)
}
}

33
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/dedupRecord_parameters.json
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[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path of the sequential file to read",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "the type of entity to be deduped",
"paramRequired": true
},
{
"paramName": "c",
"paramLongName": "dedupConf",
"paramDescription": "dedup configuration to be used",
"compressed": true,
"paramRequired": true
},
{
"paramName": "d",
"paramLongName": "dedupPath",
"paramDescription": "dedup path to load mergeRelation",
"paramRequired": true
}
]

38
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json
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[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "ep",
"paramLongName": "entityPath",
"paramDescription": "the input entity path",
"paramRequired": true
},
{
"paramName": "mr",
"paramLongName": "mergeRelPath",
"paramDescription": "the input path of merge Rel",
"paramRequired": true
},
{
"paramName": "dr",
"paramLongName": "dedupRecordPath",
"paramDescription": "the inputPath of dedup record",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "the type of entity",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the targetPath",
"paramRequired": true
}
]

33
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/dedup_parameters.json
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[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the path of the sequential file to read",
"paramRequired": true
},
{
"paramName": "e",
"paramLongName": "entity",
"paramDescription": "the type of entity to be deduped",
"paramRequired": true
},
{
"paramName": "c",
"paramLongName": "dedupConf",
"paramDescription": "dedup configuration to be used",
"compressed": true,
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "target path to save dedup result",
"paramRequired": true
}
]

26
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/dedup_propagate_relation_parameters.json
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@ -1,26 +0,0 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "ep",
"paramLongName": "relationPath",
"paramDescription": "the input relation path",
"paramRequired": true
},
{
"paramName": "mr",
"paramLongName": "mergeRelPath",
"paramDescription": "the input path of merge Rel",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetRelPath",
"paramDescription": "the output Rel Path",
"paramRequired": true
}
]

18
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/config-default.xml
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@ -1,18 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

182
dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml
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<workflow-app name="Dedup Entities" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>entity</name>
<description>the entity that should be processed</description>
</property>
<property>
<name>dedupConf</name>
<description>the dedup Configuration</description>
</property>
<property>
<name>targetPath</name>
<description>the target path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
</parameters>
<start to="DeleteWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteWorkingPath">
<fs>
<delete path='${targetPath}/${entity}'/>
<mkdir path="${targetPath}"/>
<mkdir path="${targetPath}/${entity}"/>
</fs>
<ok to="CreateSimRels"/>
<error to="Kill"/>
</action>
<action name="CreateSimRels">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Similarity Relations</name>
<class>eu.dnetlib.dedup.SparkCreateSimRels</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupConf</arg><arg>${dedupConf}</arg>
</spark>
<ok to="CreateConnectedComponents"/>
<error to="Kill"/>
</action>
<action name="CreateConnectedComponents">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Connected Components</name>
<class>eu.dnetlib.dedup.SparkCreateConnectedComponent</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupConf</arg><arg>${dedupConf}</arg>
</spark>
<ok to="CreateDedupRecord"/>
<error to="Kill"/>
</action>
<action name="CreateDedupRecord">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create Dedup Record</name>
<class>eu.dnetlib.dedup.SparkCreateDedupRecord</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--dedupPath</arg><arg>${targetPath}</arg>
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupConf</arg><arg>${dedupConf}</arg>
</spark>
<ok to="fixRelation"/>
<error to="Kill"/>
</action>
<action name="fixRelation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Propagate Dedup Relations</name>
<class>eu.dnetlib.dedup.sx.SparkPropagateRelationsJob</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--mergeRelPath</arg><arg>${targetPath}/${entity}/mergeRel</arg>
<arg>--relationPath</arg><arg>${sourcePath}/relation</arg>
<arg>--targetRelPath</arg><arg>${targetPath}/${entity}/updated_relation</arg>
</spark>
<ok to="updateDeletedByInferenceEntity"/>
<error to="Kill"/>
</action>
<action name="updateDeletedByInferenceEntity">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Update ${entity} and add DedupRecord</name>
<class>eu.dnetlib.dedup.sx.SparkUpdateEntityWithDedupInfo</class>
<jar>dhp-dedup-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory ${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--executor-cores=${sparkExecutorCores}
${sparkExtraOPT}
</spark-opts>
<arg>-mt</arg><arg>yarn-cluster</arg>
<arg>--entityPath</arg><arg>${sourcePath}/${entity}</arg>
<arg>--mergeRelPath</arg><arg>${targetPath}/${entity}/mergeRel</arg>
<arg>--entity</arg><arg>${entity}</arg>
<arg>--dedupRecordPath</arg><arg>${targetPath}/${entity}/dedup_records</arg>
<arg>--targetPath</arg><arg>${targetPath}/${entity}/updated_record</arg>
</spark>
<ok to="replaceEntity"/>
<error to="Kill"/>
</action>
<action name="replaceEntity">
<fs>
<delete path='${sourcePath}/${entity}'/>
<delete path='${sourcePath}/relation'/>
<move source="${targetPath}/${entity}/updated_relation" target="${sourcePath}/relation" />
<move source="${targetPath}/${entity}/updated_record" target="${sourcePath}/${entity}" />
</fs>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

378
dhp-workflows/dhp-dedup-scholexplorer/src/test/resources/eu/dnetlib/dedup/sx/conf/pub_scholix.conf.json
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@ -1,378 +0,0 @@
{
"wf": {
"threshold": "0.99",
"dedupRun": "001",
"entityType": "result",
"subEntityType": "resulttype",
"subEntityValue": "publication",
"orderField": "title",
"queueMaxSize": "2000",
"groupMaxSize": "100",
"maxChildren": "100",
"slidingWindowSize": "200",
"rootBuilder": [
],
"includeChildren": "true",
"maxIterations": 20,
"idPath": "$.id"
},
"pace": {
"clustering": [
{
"name": "ngrampairs",
"fields": [
"title"
],
"params": {
"max": "1",
"ngramLen": "3"
}
},
{
"name": "suffixprefix",
"fields": [
"title"
],
"params": {
"max": "1",
"len": "3"
}
}
],
"decisionTree": {
"start": {
"fields": [
{
"field": "pid",
"comparator": "jsonListMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {
"jpath_value": "$.value",
"jpath_classid": "$.qualifier.classid"
}
}
],
"threshold": 0.5,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "layer2",
"undefined": "layer2",
"ignoreUndefined": "true"
},
"layer2": {
"fields": [
{
"field": "title",
"comparator": "titleVersionMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
},
{
"field": "authors",
"comparator": "sizeMatch",
"weight": 1.0,
"countIfUndefined": "false",
"params": {}
}
],
"threshold": 1.0,
"aggregation": "AND",
"positive": "layer3",
"negative": "NO_MATCH",
"undefined": "layer3",
"ignoreUndefined": "false"
},
"layer3": {
"fields": [
{
"field": "title",
"comparator": "levensteinTitle",
"weight": 1.0,
"countIfUndefined": "true",
"params": {}
}
],
"threshold": 0.99,
"aggregation": "AVG",
"positive": "MATCH",
"negative": "NO_MATCH",
"undefined": "NO_MATCH",
"ignoreUndefined": "true"
}
},
"model": [
{
"name": "pid",
"type": "JSON",
"path": "$.pid",
"overrideMatch": "true"
},
{
"name": "title",
"type": "String",
"path": "$.title[*].value",
"length": 250,
"size": 5
},
{
"name": "authors",
"type": "List",
"path": "$.author[*].fullname",
"size": 200
},
{
"name": "resulttype",
"type": "String",
"path": "$.resulttype.classid"
}
],
"blacklists": {
"title": [
"^Inside Front Cover$",
"^CORR Insights$",
"^Index des notions$",
"^Department of Error.$",
"^Untitled Item$",
"^Department of Error$",
"^Tome II : 1598 à 1605$",
"^(à l’exception de roi, prince, royauté, pouvoir, image… qui sont omniprésents)$",
"^Museen und Ausstellungsinstitute in Nürnberg$",
"^Text/Conference Paper$",
"^Table des illustrations$",
"^An Intimate Insight on Psychopathy and a Novel Hermeneutic Psychological Science$",
"^Index des noms$",
"^Reply by Authors.$",
"^Titelblatt - Inhalt$",
"^Index des œuvres,$",
"(?i)^Poster presentations$",
"^THE ASSOCIATION AND THE GENERAL MEDICAL COUNCIL$",
"^Problems with perinatal pathology\\.?$",
"(?i)^Cases? of Puerperal Convulsions$",
"(?i)^Operative Gyna?ecology$",
"(?i)^Mind the gap\\!?\\:?$",
"^Chronic fatigue syndrome\\.?$",
"^Cartas? ao editor Letters? to the Editor$",
"^Note from the Editor$",
"^Anesthesia Abstract$",
"^Annual report$",
"(?i)^“?THE RADICAL PREVENTION OF VENEREAL DISEASE\\.?”?$",
"(?i)^Graph and Table of Infectious Diseases?$",
"^Presentation$",
"(?i)^Reviews and Information on Publications$",
"(?i)^PUBLIC HEALTH SERVICES?$",
"(?i)^COMBINED TEXT-?BOOK OF OBSTETRICS AND GYN(Æ|ae)COLOGY$",
"(?i)^Adrese autora$",
"(?i)^Systematic Part .*\\. Catalogus Fossilium Austriae, Band 2: Echinoidea neogenica$",
"(?i)^Acknowledgement to Referees$",
"(?i)^Behçet's disease\\.?$",
"(?i)^Isolation and identification of restriction endonuclease.*$",
"(?i)^CEREBROVASCULAR DISEASES?.?$",
"(?i)^Screening for abdominal aortic aneurysms?\\.?$",
"^Event management$",
"(?i)^Breakfast and Crohn's disease.*\\.?$",
"^Cálculo de concentraciones en disoluciones acuosas. Ejercicio interactivo\\..*\\.$",
"(?i)^Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of Autism spectrum disorders?\\.?$",
"^Gushi hakubutsugaku$",
"^Starobosanski nadpisi u Bosni i Hercegovini \\(.*\\)$",
"^Intestinal spirocha?etosis$",
"^Treatment of Rodent Ulcer$",
"(?i)^\\W*Cloud Computing\\W*$",
"^Compendio mathematico : en que se contienen todas las materias mas principales de las Ciencias que tratan de la cantidad$",
"^Free Communications, Poster Presentations: Session [A-F]$",
"^“The Historical Aspects? of Quackery\\.?”$",
"^A designated centre for people with disabilities operated by St John of God Community Services (Limited|Ltd), Louth$",
"^P(er|re)-Mile Premiums for Auto Insurance\\.?$",
"(?i)^Case Report$",
"^Boletín Informativo$",
"(?i)^Glioblastoma Multiforme$",
"(?i)^Nuevos táxones animales descritos en la península Ibérica y Macaronesia desde 1994 \\(.*\\)$",
"^Zaměstnanecké výhody$",
"(?i)^The Economics of Terrorism and Counter-Terrorism: A Survey \\(Part .*\\)$",
"(?i)^Carotid body tumours?\\.?$",
"(?i)^\\[Españoles en Francia : La condición Emigrante.*\\]$",
"^Avant-propos$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Head(s)? and Capital(s)?$",
"(?i)^St\\. Patrick's Cathedral, Dublin, County Dublin - Bases?$",
"(?i)^PUBLIC HEALTH VERSUS THE STATE$",
"^Viñetas de Cortázar$",
"(?i)^Search for heavy neutrinos and W(\\[|_|\\(|_\\{|-)?R(\\]|\\)|\\})? bosons with right-handed couplings in a left-right symmetric model in pp collisions at.*TeV(\\.)?$",
"(?i)^Measurement of the pseudorapidity and centrality dependence of the transverse energy density in Pb(-?)Pb collisions at.*tev(\\.?)$",
"(?i)^Search for resonances decaying into top-quark pairs using fully hadronic decays in pp collisions with ATLAS at.*TeV$",
"(?i)^Search for neutral minimal supersymmetric standard model Higgs bosons decaying to tau pairs in pp collisions at.*tev$",
"(?i)^Relatório de Estágio (de|em) Angiologia e Cirurgia Vascular$",
"^Aus der AGMB$",
"^Znanstveno-stručni prilozi$",
"(?i)^Zhodnocení finanční situace podniku a návrhy na zlepšení$",
"(?i)^Evaluation of the Financial Situation in the Firm and Proposals to its Improvement$",
"(?i)^Hodnocení finanční situace podniku a návrhy na její zlepšení$",
"^Finanční analýza podniku$",
"^Financial analysis( of business)?$",
"(?i)^Textbook of Gyn(a)?(Æ)?(e)?cology$",
"^Jikken nihon shūshinsho$",
"(?i)^CORONER('|s)(s|') INQUESTS$",
"(?i)^(Μελέτη παραγόντων )?risk management( για ανάπτυξη και εφαρμογή ενός πληροφοριακού συστήματος| και ανάπτυξη συστήματος)?$",
"(?i)^Consultants' contract(s)?$",
"(?i)^Upute autorima$",
"(?i)^Bijdrage tot de Kennis van den Godsdienst der Dajaks van Lan(d|f)ak en Tajan$",
"^Joshi shin kokubun$",
"^Kōtō shōgaku dokuhon nōson'yō$",
"^Jinjō shōgaku shōka$",
"^Shōgaku shūjichō$",
"^Nihon joshi dokuhon$",
"^Joshi shin dokuhon$",
"^Chūtō kanbun dokuhon$",
"^Wabun dokuhon$",
"(?i)^(Analysis of economy selected village or town|Rozbor hospodaření vybrané obce či města)$",
"(?i)^cardiac rehabilitation$",
"(?i)^Analytical summary$",
"^Thesaurus resolutionum Sacrae Congregationis Concilii$",
"(?i)^Sumario analítico(\\s{1})?(Analitic summary)?$",
"^Prikazi i osvrti$",
"^Rodinný dům s provozovnou$",
"^Family house with an establishment$",
"^Shinsei chūtō shin kokugun$",
"^Pulmonary alveolar proteinosis(\\.?)$",
"^Shinshū kanbun$",
"^Viñeta(s?) de Rodríguez$",
"(?i)^RUBRIKA UREDNIKA$",
"^A Matching Model of the Academic Publication Market$",
"^Yōgaku kōyō$",
"^Internetový marketing$",
"^Internet marketing$",
"^Chūtō kokugo dokuhon$",
"^Kokugo dokuhon$",
"^Antibiotic Cover for Dental Extraction(s?)$",
"^Strategie podniku$",
"^Strategy of an Enterprise$",
"(?i)^respiratory disease(s?)(\\.?)$",
"^Award(s?) for Gallantry in Civil Defence$",
"^Podniková kultura$",
"^Corporate Culture$",
"^Severe hyponatraemia in hospital inpatient(s?)(\\.?)$",
"^Pracovní motivace$",
"^Work Motivation$",
"^Kaitei kōtō jogaku dokuhon$",
"^Konsolidovaná účetní závěrka$",
"^Consolidated Financial Statements$",
"(?i)^intracranial tumour(s?)$",
"^Climate Change Mitigation Options and Directed Technical Change: A Decentralized Equilibrium Analysis$",
"^\\[CERVECERIAS MAHOU(\\.|\\:) INTERIOR\\] \\[Material gráfico\\]$",
"^Housing Market Dynamics(\\:|\\.) On the Contribution of Income Shocks and Credit Constraint(s?)$",
"^\\[Funciones auxiliares de la música en Radio París,.*\\]$",
"^Úroveň motivačního procesu jako způsobu vedení lidí$",
"^The level of motivation process as a leadership$",
"^Pay-beds in N(\\.?)H(\\.?)S(\\.?) Hospitals$",
"(?i)^news and events$",
"(?i)^NOVOSTI I DOGAĐAJI$",
"^Sansū no gakushū$",
"^Posouzení informačního systému firmy a návrh změn$",
"^Information System Assessment and Proposal for ICT Modification$",
"^Stresové zatížení pracovníků ve vybrané profesi$",
"^Stress load in a specific job$",
"^Sunday: Poster Sessions, Pt.*$",
"^Monday: Poster Sessions, Pt.*$",
"^Wednesday: Poster Sessions, Pt.*",
"^Tuesday: Poster Sessions, Pt.*$",
"^Analýza reklamy$",
"^Analysis of advertising$",
"^Shōgaku shūshinsho$",
"^Shōgaku sansū$",
"^Shintei joshi kokubun$",
"^Taishō joshi kokubun dokuhon$",
"^Joshi kokubun$",
"^Účetní uzávěrka a účetní závěrka v ČR$",
"(?i)^The \"?Causes\"? of Cancer$",
"^Normas para la publicación de artículos$",
"^Editor('|s)(s|') [Rr]eply$",
"^Editor(’|s)(s|’) letter$",
"^Redaktoriaus žodis$",
"^DISCUSSION ON THE PRECEDING PAPER$",
"^Kōtō shōgaku shūshinsho jidōyō$",
"^Shōgaku nihon rekishi$",
"^(Theory of the flow of action currents in isolated myelinated nerve fibers).*$",
"^Préface$",
"^Occupational [Hh]ealth [Ss]ervices.$",
"^In Memoriam Professor Toshiyuki TAKESHIMA$",
"^Účetní závěrka ve vybraném podniku.*$",
"^Financial statements in selected company$",
"^Abdominal [Aa]ortic [Aa]neurysms.*$",
"^Pseudomyxoma peritonei$",
"^Kazalo autora$",
"(?i)^uvodna riječ$",
"^Motivace jako způsob vedení lidí$",
"^Motivation as a leadership$",
"^Polyfunkční dům$",
"^Multi\\-funkcional building$",
"^Podnikatelský plán$",
"(?i)^Podnikatelský záměr$",
"(?i)^Business Plan$",
"^Oceňování nemovitostí$",
"^Marketingová komunikace$",
"^Marketing communication$",
"^Sumario Analítico$",
"^Riječ uredništva$",
"^Savjetovanja i priredbe$",
"^Índice$",
"^(Starobosanski nadpisi).*$",
"^Vzdělávání pracovníků v organizaci$",
"^Staff training in organization$",
"^(Life Histories of North American Geometridae).*$",
"^Strategická analýza podniku$",
"^Strategic Analysis of an Enterprise$",
"^Sadržaj$",
"^Upute suradnicima$",
"^Rodinný dům$",
"(?i)^Fami(l)?ly house$",
"^Upute autorima$",
"^Strategic Analysis$",
"^Finanční analýza vybraného podniku$",
"^Finanční analýza$",
"^Riječ urednika$",
"(?i)^Content(s?)$",
"(?i)^Inhalt$",
"^Jinjō shōgaku shūshinsho jidōyō$",
"(?i)^Index$",
"^Chūgaku kokubun kyōkasho$",
"^Retrato de una mujer$",
"^Retrato de un hombre$",
"^Kōtō shōgaku dokuhon$",
"^Shotōka kokugo$",
"^Shōgaku dokuhon$",
"^Jinjō shōgaku kokugo dokuhon$",
"^Shinsei kokugo dokuhon$",
"^Teikoku dokuhon$",
"^Instructions to Authors$",
"^KİTAP TAHLİLİ$",
"^PRZEGLĄD PIŚMIENNICTWA$",
"(?i)^Presentación$",
"^İçindekiler$",
"(?i)^Tabl?e of contents$",
"^(CODICE DEL BEATO DE LOS REYES FERNANDO I Y SANCHA).*$",
"^(\\[MADRID\\. BIBL\\. NAC\\. N.*KING FERDINAND I.*FROM SAN ISIDORO DE LEON\\. FACUNDUS SCRIPSIT DATED.*\\]).*",
"^Editorial( Board)?$",
"(?i)^Editorial \\(English\\)$",
"^Editörden$",
"^(Corpus Oral Dialectal \\(COD\\)\\.).*$",
"^(Kiri Karl Morgensternile).*$",
"^(\\[Eksliibris Aleksandr).*\\]$",
"^(\\[Eksliibris Aleksandr).*$",
"^(Eksliibris Aleksandr).*$",
"^(Kiri A\\. de Vignolles).*$",
"^(2 kirja Karl Morgensternile).*$",
"^(Pirita kloostri idaosa arheoloogilised).*$",
"^(Kiri tundmatule).*$",
"^(Kiri Jenaer Allgemeine Literaturzeitung toimetusele).*$",
"^(Eksliibris Nikolai Birukovile).*$",
"^(Eksliibris Nikolai Issakovile).*$",
"^(WHP Cruise Summary Information of section).*$",
"^(Measurement of the top quark\\-pair production cross section with ATLAS in pp collisions at).*$",
"^(Measurement of the spin\\-dependent structure function).*",
"(?i)^.*authors['’′]? reply\\.?$",
"(?i)^.*authors['’′]? response\\.?$"
]
},
"synonyms": {}
}
}

79
dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml
View File

@ -1,79 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-graph-provision-scholexplorer</artifactId>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.0.1</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpmime</artifactId>
</dependency>
<dependency>
<groupId>org.elasticsearch</groupId>
<artifactId>elasticsearch-hadoop</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
</dependencies>
</project>

425
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
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@ -1,425 +0,0 @@
package eu.dnetlib.dhp.export
import com.fasterxml.jackson.databind.ObjectMapper
import java.time.LocalDateTime
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.common.PacePerson
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import scala.collection.JavaConverters._
case class DLIExternalReference(id: String, url: String, sitename: String, label: String, pid: String, classId: String) {}
object DLIToOAF {
val collectedFromMap: Map[String, KeyValue] = Map(
"dli_________::r3d100010527" -> generateKeyValue("10|re3data_____::c2a591f440598b63d854556beaf01591", "European Nucleotide Archive"),
"dli_________::r3d100010255" -> generateKeyValue("10|re3data_____::480d275ed6f9666ee76d6a1215eabf26", "Inter-university Consortium for Political and Social Research"),
"dli_________::r3d100011868" -> generateKeyValue("10|re3data_____::db814dc656a911b556dba42a331cebe9", "Mendeley Data"),
"dli_________::elsevier" -> generateKeyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier"),
"dli_________::openaire" -> generateKeyValue("10|infrastruct_::f66f1bd369679b5b077dcdf006089556", "OpenAIRE"),
"dli_________::thomsonreuters" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref"),
"dli_________::r3d100010216" -> generateKeyValue("10|re3data_____::0fd79429de04343dbbec705d9b5f429f", "4TU.Centre for Research Data"),
"dli_________::r3d100010134" -> generateKeyValue("10|re3data_____::9633d1e8c4309c833c2c442abeb0cfeb", "PANGAEA"),
"dli_________::ieee" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref"),
"dli_________::r3d100010197" -> generateKeyValue("10|re3data_____::9fd1d79973f7fda60cbe1d82e3819a68", "The Cambridge Structural Database"),
"dli_________::nature" -> generateKeyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature"),
"dli_________::datacite" -> generateKeyValue("10|openaire____::9e3be59865b2c1c335d32dae2fe7b254", "Datacite"),
"dli_________::r3d100010578" -> generateKeyValue("10|re3data_____::c4d751f29a7568011a4c80136b30b444", "IEDA"),
"dli_________::r3d100010464" -> generateKeyValue("10|re3data_____::23e2a81591099828f6b83a1c83150666", "Research Data Australia"),
"dli_________::r3d100010327" -> generateKeyValue("10|re3data_____::a644620b81135243dc9acc15d2362246", "Worldwide Protein Data Bank"),
"dli_________::pubmed" -> generateKeyValue("10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357", "PubMed Central"),
"dli_________::europe_pmc__" -> generateKeyValue("10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c", "Europe PubMed Central"),
"dli_________::crossref" -> generateKeyValue("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "Crossref")
)
val relationTypeMapping: Map[String, (String, String)] = Map(
"IsReferencedBy" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"References" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsRelatedTo" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsSupplementedBy" -> (ModelConstants.IS_SUPPLEMENTED_BY, ModelConstants.SUPPLEMENT),
"Documents" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"Cites" -> (ModelConstants.CITES, ModelConstants.CITATION),
"Unknown" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsSourceOf" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"IsCitedBy" -> (ModelConstants.IS_CITED_BY, ModelConstants.CITATION),
"Reviews" -> (ModelConstants.REVIEWS, ModelConstants.REVIEW),
"Describes" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
"HasAssociationWith" -> (ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP)
)
val expectecdPidType = List("uniprot", "ena", "chembl", "ncbi-n", "ncbi-p", "genbank", "pdb", "url")
val filteredURL = List(
"www.ebi.ac.uk",
"www.uniprot.org",
"f1000.com",
"en.wikipedia.org",
"flybase.org",
"www.yeastgenome.org",
"research.bioinformatics.udel.edu",
"cancer.sanger.ac.uk",
"www.iedb.org",
"www.crd.york.ac.uk",
"www.wormbase.org",
"web.expasy.org",
"www.hal.inserm.fr",
"sabiork.h-its.org",
"zfin.org",
"www.pombase.org",
"www.guidetopharmacology.org",
"reactome.org"
)
val rel_inverse: Map[String, String] = Map(
ModelConstants.IS_RELATED_TO -> ModelConstants.IS_RELATED_TO,
ModelConstants.IS_SUPPLEMENTED_BY -> ModelConstants.IS_SUPPLEMENT_TO,
ModelConstants.CITES -> ModelConstants.IS_CITED_BY,
ModelConstants.IS_CITED_BY -> ModelConstants.CITES,
ModelConstants.REVIEWS -> ModelConstants.IS_REVIEWED_BY
)
val PidTypeMap: Map[String, String] = Map(
"pbmid" -> "pmid",
"pmcid" -> "pmc",
"pmid" -> "pmid",
"pubmedid" -> "pmid",
"DOI" -> "doi",
"doi" -> "doi"
)
def fixInstance(r:Publication) :Publication = {
val collectedFrom = r.getCollectedfrom.asScala.head
r.getInstance().asScala.foreach(i => i.setCollectedfrom(collectedFrom))
r
}
def fixInstanceDataset(r:Dataset) :Dataset = {
val collectedFrom = r.getCollectedfrom.asScala.head
r.getInstance().asScala.foreach(i => i.setCollectedfrom(collectedFrom))
r
}
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: Dataset =>
val a: AtomicAction[Dataset] = new AtomicAction[Dataset]
a.setClazz(classOf[Dataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def convertClinicalTrial(dataset: DLIDataset): (String, String) = {
val currentId = generateId(dataset.getId)
val pids = dataset.getPid.asScala.filter(p => "clinicaltrials.gov".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => s"50|r3111dacbab5::${DHPUtils.md5(p.getValue.toLowerCase())}")
if (pids.isEmpty)
null
else
(currentId, pids.head)
}
def insertExternalRefs(publication: Publication, externalReferences: List[DLIExternalReference]): Publication = {
val eRefs = externalReferences.map(e => {
val result = new ExternalReference()
result.setSitename(e.sitename)
result.setLabel(e.label)
result.setUrl(e.url)
result.setRefidentifier(e.pid)
result.setDataInfo(generateDataInfo())
result.setQualifier(createQualifier(e.classId, ModelConstants.DNET_EXTERNAL_REFERENCE_TYPE))
result
})
publication.setExternalReference(eRefs.asJava)
publication
}
def filterPid(p: StructuredProperty): Boolean = {
if (expectecdPidType.contains(p.getQualifier.getClassname) && p.getQualifier.getClassname.equalsIgnoreCase("url"))
if (filteredURL.exists(u => p.getValue.contains(u)))
return true
else
return false
expectecdPidType.contains(p.getQualifier.getClassname)
}
def extractTitle(titles: java.util.List[StructuredProperty]): String = {
if (titles == null)
return null
val label = titles.asScala.map(p => p.getValue).find(p => p.nonEmpty)
label.orNull
}
def convertDLIDatasetToExternalReference(dataset: DLIDataset): DLIExternalReference = {
val pids = dataset.getPid.asScala.filter(filterPid)
if (pids == null || pids.isEmpty)
return null
val pid: StructuredProperty = pids.head
pid.getQualifier.getClassname match {
case "uniprot" => DLIExternalReference(generateId(dataset.getId), s"https://www.uniprot.org/uniprot/${pid.getValue}", "UniProt", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "ena" =>
if (pid.getValue != null && pid.getValue.nonEmpty && pid.getValue.length > 7)
DLIExternalReference(generateId(dataset.getId), s"https://www.ebi.ac.uk/ena/data/view/${pid.getValue.substring(0, 8)}", "European Nucleotide Archive", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
else
null
case "chembl" => DLIExternalReference(generateId(dataset.getId), s"https://www.ebi.ac.uk/chembl/compound_report_card/${pid.getValue}", "ChEMBL", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "ncbi-n" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Nucleotide Database", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "ncbi-p" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Nucleotide Database", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "genbank" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "GenBank", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "pdb" => DLIExternalReference(generateId(dataset.getId), s"https://www.ncbi.nlm.nih.gov/nuccore/${pid.getValue}", "Protein Data Bank", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
case "url" => DLIExternalReference(generateId(dataset.getId), pid.getValue, "", extractTitle(dataset.getTitle), pid.getValue, "url")
}
}
def convertDLIPublicationToOAF(inputPublication: DLIPublication): Publication = {
val result = new Publication
val cleanedPids = inputPublication.getPid.asScala.filter(p => PidTypeMap.contains(p.getQualifier.getClassid))
.map(p => {
p.setQualifier(createQualifier(PidTypeMap(p.getQualifier.getClassid), p.getQualifier.getSchemeid))
p
})
if (cleanedPids.isEmpty)
return null
result.setId(generateId(inputPublication.getId))
result.setDataInfo(generateDataInfo(invisible = true))
if (inputPublication.getCollectedfrom == null || inputPublication.getCollectedfrom.size() == 0 || (inputPublication.getCollectedfrom.size() == 1 && inputPublication.getCollectedfrom.get(0) == null))
return null
result.setCollectedfrom(inputPublication.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava)
if(result.getCollectedfrom.isEmpty)
return null
result.setPid(cleanedPids.asJava)
result.setDateofcollection(inputPublication.getDateofcollection)
result.setOriginalId(inputPublication.getPid.asScala.map(p => p.getValue).asJava)
result.setDateoftransformation(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")))
if (inputPublication.getAuthor == null || inputPublication.getAuthor.isEmpty)
return null
result.setAuthor(inputPublication.getAuthor.asScala.map(convertAuthor).asJava)
result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES))
if (inputPublication.getSubject != null)
result.setSubject(inputPublication.getSubject.asScala.map(convertSubject).asJava)
if (inputPublication.getTitle == null || inputPublication.getTitle.isEmpty)
return null
result.setTitle(List(patchTitle(inputPublication.getTitle.get(0))).asJava)
if (inputPublication.getRelevantdate == null || inputPublication.getRelevantdate.size() == 0)
return null
result.setRelevantdate(inputPublication.getRelevantdate.asScala.map(patchRelevantDate).asJava)
result.setDescription(inputPublication.getDescription)
result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue))
result.setPublisher(inputPublication.getPublisher)
result.setSource(inputPublication.getSource)
result.setBestaccessright(createAccessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue)
if (dois.isEmpty)
return null
val i: Instance = createInstance(s"https://dx.doi.org/${dois.head}", firstInstanceOrNull(inputPublication.getInstance()), result.getDateofacceptance)
if (i != null)
result.setInstance(List(i).asJava)
result
}
def convertDLIRelation(r: Relation): Relation = {
val rt = r.getRelType
if (!relationTypeMapping.contains(rt))
return null
r.setRelType(ModelConstants.RESULT_RESULT)
r.setRelClass(relationTypeMapping(rt)._1)
r.setSubRelType(relationTypeMapping(rt)._2)
r.setSource(generateId(r.getSource))
r.setTarget(generateId(r.getTarget))
r
}
def convertDLIDatasetTOOAF(d: DLIDataset): Dataset = {
if (d.getCollectedfrom == null || d.getCollectedfrom.size() == 0 || (d.getCollectedfrom.size() == 1 && d.getCollectedfrom.get(0) == null))
return null
val result: Dataset = new Dataset
result.setId(generateId(d.getId))
result.setDataInfo(generateDataInfo())
result.setCollectedfrom(d.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava)
if(result.getCollectedfrom.isEmpty)
return null
result.setPid(d.getPid)
val fpids = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname) ||
"pdb".equalsIgnoreCase(p.getQualifier.getClassname)
).map(p => p.getValue)
if (fpids == null || fpids.isEmpty)
return null
result.setDateofcollection(d.getDateofcollection)
result.setOriginalId(d.getPid.asScala.map(d => d.getValue).asJava)
result.setDateoftransformation(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")))
if (d.getAuthor == null || d.getAuthor.isEmpty)
return null
result.setAuthor(d.getAuthor.asScala.map(convertAuthor).asJava)
result.setResulttype(createQualifier(d.getResulttype.getClassid, d.getResulttype.getClassname, ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES))
if (d.getSubject != null)
result.setSubject(d.getSubject.asScala.map(convertSubject).asJava)
if (d.getTitle == null || d.getTitle.isEmpty)
return null
result.setTitle(List(patchTitle(d.getTitle.get(0))).asJava)
if (d.getRelevantdate == null || d.getRelevantdate.size() == 0)
return null
result.setRelevantdate(d.getRelevantdate.asScala.map(patchRelevantDate).asJava)
result.setDescription(d.getDescription)
result.setDateofacceptance(asField(d.getRelevantdate.get(0).getValue))
result.setPublisher(d.getPublisher)
result.setSource(d.getSource)
result.setBestaccessright(createAccessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
val instance_urls = if (fpids.head.length < 5) s"https://www.rcsb.org/structure/${fpids.head}" else s"https://dx.doi.org/${fpids.head}"
val i: Instance = createInstance(instance_urls, firstInstanceOrNull(d.getInstance()), result.getDateofacceptance, true)
// Ticket #6281 added pid to Instance
i.setPid(result.getPid)
if (i != null)
result.setInstance(List(i).asJava)
result
}
def firstInstanceOrNull(instances: java.util.List[Instance]): Instance = {
if (instances == null || instances.size() == 0)
return null
instances.get(0)
}
def createInstance(url: String, originalInstance: Instance, doa: Field[String], dataset: Boolean = false): Instance = {
val i = new Instance
i.setUrl(List(url).asJava)
if (dataset)
i.setInstancetype(createQualifier("0021", "Dataset", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
else
i.setInstancetype(createQualifier("0000", "Unknown", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
if (originalInstance != null && originalInstance.getHostedby != null)
i.setHostedby(originalInstance.getHostedby)
i.setAccessright(createAccessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES))
i.setDateofacceptance(doa)
i
}
def patchRelevantDate(d: StructuredProperty): StructuredProperty = {
d.setQualifier(createQualifier(ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE))
d
}
def patchTitle(t: StructuredProperty): StructuredProperty = {
t.setQualifier(ModelConstants.MAIN_TITLE_QUALIFIER)
t
}
def convertSubject(s: StructuredProperty): StructuredProperty = {
s.setQualifier(createQualifier("keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES))
s
}
def convertAuthor(a: Author): Author = {
if (a == null)
return a
val p = new PacePerson(a.getFullname, false)
if (p.isAccurate) {
a.setName(p.getNameString)
a.setSurname(p.getSurnameString)
}
a
}
def generateId(id: String): String = {
val md5 = if (id.contains("::")) StringUtils.substringAfter(id, "::") else StringUtils.substringAfter(id, "|")
s"50|scholix_____::$md5"
}
}

175
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala
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@ -1,175 +0,0 @@
package eu.dnetlib.dhp.`export`
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.Text
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.hadoop.mapred.SequenceFileOutputFormat
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions._
import org.apache.spark.sql.expressions.Window
import org.apache.spark.SparkConf
import scala.collection.mutable.ArrayBuffer
object SparkExportContentForOpenAire {
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkExportContentForOpenAire.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val workingPath = parser.get("workingDirPath")
implicit val dliPubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication])
implicit val dliDatEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset])
implicit val pubEncoder: Encoder[Publication] = Encoders.bean(classOf[Publication])
implicit val datEncoder: Encoder[OafDataset] = Encoders.bean(classOf[OafDataset])
implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation])
import spark.implicits._
val dsRel = spark.read.load(s"$workingPath/relation_b").as[Relation]
dsRel.filter(r => r.getDataInfo==null || r.getDataInfo.getDeletedbyinference ==false)
.map(DLIToOAF.convertDLIRelation)
.filter(r => r!= null)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/relationDS")
val dsPubs = spark.read.load(s"$workingPath/publication").as[DLIPublication]
dsPubs
.filter(p=>p.getDataInfo.getDeletedbyinference == false)
.map(DLIToOAF.convertDLIPublicationToOAF)
.filter(p=>p!= null)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/publicationDS")
val dsDataset = spark.read.load(s"$workingPath/dataset").as[DLIDataset]
dsDataset
.filter(p => p.getDataInfo.getDeletedbyinference == false)
.map(DLIToOAF.convertDLIDatasetTOOAF).filter(p=>p!= null)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/datasetDS")
val pubs:Dataset[Publication] = spark.read.load(s"$workingPath/export/publicationDS").as[Publication]
val dats :Dataset[OafDataset] = spark.read.load(s"$workingPath/export/datasetDS").as[OafDataset]
val relDS1 :Dataset[Relation] = spark.read.load(s"$workingPath/export/relationDS").as[Relation]
val pub_id = pubs.select("id").distinct()
val dat_id = dats.select("id").distinct()
pub_id.joinWith(relDS1, pub_id("id").equalTo(relDS1("source"))).map(k => k._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/relationDS_f1")
val relDS2= spark.read.load(s"$workingPath/export/relationDS_f1").as[Relation]
relDS2.joinWith(dat_id, relDS2("target").equalTo(dats("id"))).map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/relationDS_filtered")
val r_source = relDS2.select(relDS2("source")).distinct()
val r_target = relDS2.select(relDS2("target")).distinct()
val w2 = Window.partitionBy("id").orderBy("lastupdatetimestamp")
pubs.joinWith(r_source, pubs("id").equalTo(r_source("source")), "inner").map(k => k._1)
.withColumn("row",row_number.over(w2)).where($"row" === 1).drop("row")
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/publicationDS_filtered")
dats.joinWith(r_target, dats("id").equalTo(r_target("target")), "inner").map(k => k._1)
.withColumn("row",row_number.over(w2)).where($"row" === 1).drop("row")
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/datasetAS")
dsDataset.map(DLIToOAF.convertDLIDatasetToExternalReference).filter(p => p != null).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/externalReference")
val pf = spark.read.load(s"$workingPath/export/publicationDS_filtered").select("id")
val relDS3 = spark.read.load(s"$workingPath/export/relationDS").as[Relation]
val relationTo = pf.joinWith(relDS3, pf("id").equalTo(relDS3("source")),"inner").map(t =>t._2)
val extRef = spark.read.load(s"$workingPath/export/externalReference").as[DLIExternalReference]
spark.createDataset(relationTo.joinWith(extRef, relationTo("target").equalTo(extRef("id")), "inner").map(d => {
val r = d._1
val ext = d._2
(r.getSource, ext)
}).rdd.groupByKey.map(f => {
var dli_ext = ArrayBuffer[DLIExternalReference]()
f._2.foreach(d => if (dli_ext.size < 100) dli_ext += d )
(f._1, dli_ext)
})).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/externalReference_grouped")
val pubf :Dataset[Publication] = spark.read.load(s"$workingPath/export/publicationDS_filtered").as[Publication]
val groupedERf:Dataset[(String, List[DLIExternalReference])]= spark.read.load(s"$workingPath/export/externalReference_grouped").as[(String, List[DLIExternalReference])]
groupedERf.joinWith(pubf,pubf("id").equalTo(groupedERf("_1"))).map(t =>
{
val publication = t._2
if (t._1 != null) {
val eRefs = t._1._2
DLIToOAF.insertExternalRefs(publication, eRefs)
} else
publication
}
).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/publicationAS")
dsDataset
.map(DLIToOAF.convertClinicalTrial)
.filter(p => p != null)
.write.mode(SaveMode.Overwrite).save(s"$workingPath/export/clinicalTrials")
val ct:Dataset[(String,String)] = spark.read.load(s"$workingPath/export/clinicalTrials").as[(String,String)]
val relDS= spark.read.load(s"$workingPath/export/relationDS_f1").as[Relation]
relDS.joinWith(ct, relDS("target").equalTo(ct("_1")), "inner")
.map(k =>{
val currentRel = k._1
currentRel.setTarget(k._2._2)
currentRel
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/clinicalTrialsRels")
val clRels:Dataset[Relation] = spark.read.load(s"$workingPath/export/clinicalTrialsRels").as[Relation]
val rels:Dataset[Relation] = spark.read.load(s"$workingPath/export/relationDS_filtered").as[Relation]
rels.union(clRels).flatMap(r => {
val inverseRel = new Relation
inverseRel.setSource(r.getTarget)
inverseRel.setTarget(r.getSource)
inverseRel.setDataInfo(r.getDataInfo)
inverseRel.setCollectedfrom(r.getCollectedfrom)
inverseRel.setRelType(r.getRelType)
inverseRel.setSubRelType(r.getSubRelType)
inverseRel.setRelClass(DLIToOAF.rel_inverse(r.getRelClass))
List(r, inverseRel)
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/relationAS")
spark.read.load(s"$workingPath/export/publicationAS").as[Publication].map(DLIToOAF.fixInstance).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/publicationAS_fixed")
spark.read.load(s"$workingPath/export/datasetAS").as[OafDataset].map(DLIToOAF.fixInstanceDataset).write.mode(SaveMode.Overwrite).save(s"$workingPath/export/datasetAS_fixed")
val fRels:Dataset[(String,String)] = spark.read.load(s"$workingPath/export/relationAS").as[Relation].map(DLIToOAF.toActionSet)
val fpubs:Dataset[(String,String)] = spark.read.load(s"$workingPath/export/publicationAS_fixed").as[Publication].map(DLIToOAF.toActionSet)
val fdats:Dataset[(String,String)] = spark.read.load(s"$workingPath/export/datasetAS_fixed").as[OafDataset].map(DLIToOAF.toActionSet)
fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

112
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java
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@ -1,112 +0,0 @@
package eu.dnetlib.dhp.export.zenodo;
import java.io.*;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.MakeTarArchive;
public class MakeTar implements Serializable {
private static final Logger log = LoggerFactory.getLogger(MakeTar.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
MakeTar.class
.getResourceAsStream(
"/eu/dnetlib/dhp/export/input_maketar_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String outputPath = parser.get("targetPath");
log.info("hdfsPath: {}", outputPath);
final String hdfsNameNode = parser.get("nameNode");
log.info("nameNode: {}", hdfsNameNode);
final String inputPath = parser.get("sourcePath");
log.info("input path : {}", inputPath);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
MakeTarArchive.tarMaxSize(fileSystem, inputPath, outputPath, "scholix_dump", 25);
}
// public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
//
// RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
//
// while (dir_iterator.hasNext()) {
// LocatedFileStatus fileStatus = dir_iterator.next();
//
// Path p = fileStatus.getPath();
// String p_string = p.toString();
// String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
//
// write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
// }
//
// }
//
// private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
// throws IOException {
//
// Path hdfsWritePath = new Path(outputPath);
// FSDataOutputStream fsDataOutputStream = null;
// if (fileSystem.exists(hdfsWritePath)) {
// fileSystem.delete(hdfsWritePath, true);
//
// }
// fsDataOutputStream = fileSystem.create(hdfsWritePath);
//
// TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
//
// RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
// .listFiles(
// new Path(inputPath), true);
//
// while (fileStatusListIterator.hasNext()) {
// LocatedFileStatus fileStatus = fileStatusListIterator.next();
//
// Path p = fileStatus.getPath();
// String p_string = p.toString();
// if (!p_string.endsWith("_SUCCESS")) {
// String name = p_string.substring(p_string.lastIndexOf("/") + 1);
// TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
// entry.setSize(fileStatus.getLen());
// ar.putArchiveEntry(entry);
//
// InputStream is = fileSystem.open(fileStatus.getPath());
//
// BufferedInputStream bis = new BufferedInputStream(is);
//
// int count;
// byte data[] = new byte[1024];
// while ((count = bis.read(data, 0, data.length)) != -1) {
// ar.write(data, 0, count);
// }
// bis.close();
// ar.closeArchiveEntry();
//
// }
//
// }
//
// ar.close();
// }
}

80
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java
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@ -1,80 +0,0 @@
package eu.dnetlib.dhp.export.zenodo;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
public class SendToZenodoHDFS implements Serializable {
private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class);
public static void main(final String[] args) throws Exception, MissingConceptDoiException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SendToZenodoHDFS.class
.getResourceAsStream(
"/eu/dnetlib/dhp/export/upload_zenodo.json")));
parser.parseArgument(args);
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("nameNode");
final String access_token = parser.get("accessToken");
final String connection_url = parser.get("connectionUrl");
final String metadata = parser.get("metadata");
final Boolean newDeposition = Boolean.valueOf(parser.get("newDeposition"));
final String concept_rec_id = Optional
.ofNullable(parser.get("conceptRecordId"))
.orElse(null);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
new Path(hdfsPath), true);
ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token);
if (newDeposition) {
zenodoApiClient.newDeposition();
} else {
if (concept_rec_id == null) {
throw new MissingConceptDoiException("No concept record id has been provided");
}
zenodoApiClient.newVersion(concept_rec_id);
}
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
Path p = fileStatus.getPath();
String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) {
// String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
log.info("Sending information for community: " + name);
FSDataInputStream inputStream = fileSystem.open(p);
zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
}
}
zenodoApiClient.sendMretadata(metadata);
// zenodoApiClient.publish();
}
}

98
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java
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@ -1,98 +0,0 @@
package eu.dnetlib.dhp.provision;
import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpDelete;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class DropAndCreateESIndex {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
DropAndCreateESIndex.class
.getResourceAsStream(
"/eu/dnetlib/dhp/provision/dropAndCreateIndex.json")));
parser.parseArgument(args);
final String index = parser.get("index");
final String cluster = parser.get("cluster");
final String clusterJson = IOUtils
.toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/cluster.json"));
final Map<String, String> clusterMap = new ObjectMapper().readValue(clusterJson, Map.class);
final String ip = clusterMap.get(cluster).split(",")[0];
System.out.println(ip);
final String url = "http://%s:9200/%s_%s";
CloseableHttpClient client = HttpClients.createDefault();
HttpDelete delete = new HttpDelete(String.format(url, ip, index, "object"));
CloseableHttpResponse response = client.execute(delete);
System.out.println("deleting Index SUMMARY");
System.out.println(response.getStatusLine());
client.close();
client = HttpClients.createDefault();
delete = new HttpDelete(String.format(url, ip, index, "scholix"));
response = client.execute(delete);
System.out.println("deleting Index SCHOLIX");
System.out.println(response.getStatusLine());
client.close();
client = HttpClients.createDefault();
final String summaryConf = IOUtils
.toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/summary_index.json"));
final String scholixConf = IOUtils
.toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/scholix_index.json"));
HttpPut put = new HttpPut(String.format(url, ip, index, "object"));
StringEntity entity = new StringEntity(summaryConf);
put.setEntity(entity);
put.setHeader("Accept", "application/json");
put.setHeader("Content-type", "application/json");
System.out.println("creating First Index SUMMARY");
response = client.execute(put);
client.close();
client = HttpClients.createDefault();
System.out.println(response.getStatusLine());
System.out.println("creating Index SCHOLIX");
put = new HttpPut(String.format(url, ip, index, "scholix"));
entity = new StringEntity(scholixConf);
put.setEntity(entity);
put.setHeader("Accept", "application/json");
put.setHeader("Content-type", "application/json");
response = client.execute(put);
System.out.println(response.getStatusLine());
client.close();
}
}

48
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/ProvisionUtil.java
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@ -1,48 +0,0 @@
package eu.dnetlib.dhp.provision;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.provision.scholix.summary.Typology;
import eu.dnetlib.dhp.utils.DHPUtils;
public class ProvisionUtil {
public static final String deletedByInferenceJPATH = "$.dataInfo.deletedbyinference";
public static final String TARGETJSONPATH = "$.target";
public static final String SOURCEJSONPATH = "$.source";
// public static RelatedItemInfo getItemType(final String item, final String idPath) {
// String targetId = DHPUtils.getJPathString(idPath, item);
// switch (StringUtils.substringBefore(targetId, "|")) {
// case "50":
// return new RelatedItemInfo(null,0,1,0);
// case "60":
// return new RelatedItemInfo(null,1,0,0);
// case "70":
// return new RelatedItemInfo(null,0,0,1);
// default:
// throw new RuntimeException("Unknonw target ID");
//
// }
//
// }
public static Boolean isNotDeleted(final String item) {
return !"true".equalsIgnoreCase(DHPUtils.getJPathString(deletedByInferenceJPATH, item));
}
public static Typology getItemTypeFromId(String id) {
switch (StringUtils.substringBefore(id, "|")) {
case "50":
return Typology.publication;
case "60":
return Typology.dataset;
case "70":
return Typology.unknown;
default:
throw new RuntimeException("Unknonw ID type");
}
}
}

59
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RelatedItemInfo.java
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@ -1,59 +0,0 @@
package eu.dnetlib.dhp.provision;
import java.io.Serializable;
/** This class models the information of related items */
public class RelatedItemInfo implements Serializable {
private String source;
private long relatedDataset = 0;
private long relatedPublication = 0;
private long relatedUnknown = 0;
public RelatedItemInfo() {
}
public RelatedItemInfo(
String source, long relatedDataset, long relatedPublication, long relatedUnknown) {
this.source = source;
this.relatedDataset = relatedDataset;
this.relatedPublication = relatedPublication;
this.relatedUnknown = relatedUnknown;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public long getRelatedDataset() {
return relatedDataset;
}
public void setRelatedDataset(long relatedDataset) {
this.relatedDataset = relatedDataset;
}
public long getRelatedPublication() {
return relatedPublication;
}
public void setRelatedPublication(long relatedPublication) {
this.relatedPublication = relatedPublication;
}
public long getRelatedUnknown() {
return relatedUnknown;
}
public void setRelatedUnknown(int relatedUnknown) {
this.relatedUnknown = relatedUnknown;
}
}

38
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala
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@ -1,38 +0,0 @@
package eu.dnetlib.dhp.provision
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.provision.scholix.Scholix
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.compress.GzipCodec
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
object SparkConvertDatasetToJson {
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertDatasetToJson.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/dataset2Json.json")))
parser.parseArgument(args)
val conf = new SparkConf
val spark = SparkSession.builder.config(conf).appName(SparkConvertDatasetToJson.getClass.getSimpleName).master(parser.get("master")).getOrCreate
implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
val workingPath = parser.get("workingPath")
spark.read.load(s"$workingPath/summary").as[ScholixSummary]
.map(s => new ObjectMapper().writeValueAsString(s))(Encoders.STRING)
.rdd.repartition(500).saveAsTextFile(s"$workingPath/summary_json", classOf[GzipCodec])
spark.read.load(s"$workingPath/scholix").as[Scholix]
.map(s => new ObjectMapper().writeValueAsString(s))(Encoders.STRING)
.rdd.repartition(2000).saveAsTextFile(s"$workingPath/scholix_json", classOf[GzipCodec])
}
}

60
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.scala
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@ -1,60 +0,0 @@
package eu.dnetlib.dhp.provision
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Relation
import org.apache.commons.io.IOUtils
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.functions.{coalesce, col, count, lit}
/**
* SparkExtractRelationCount is a spark job that takes in input relation RDD and retrieve for each item in relation
* which are the number of - Related Dataset - Related Publication - Related Unknown
*/
object SparkExtractRelationCount {
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExtractRelationCount.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_related_entities_parameters.json")))
parser.parseArgument(args)
val spark = SparkSession.builder.appName(SparkExtractRelationCount.getClass.getSimpleName).master(parser.get("master")).getOrCreate
val workingDirPath = parser.get("workingDirPath")
val relationPath = parser.get("relationPath")
implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
val relation = spark.read.load(relationPath).as[Relation].map(r =>r)(Encoders.bean(classOf[Relation]))
val relatedPublication = relation
.where("target like '50%'")
.groupBy("source")
.agg(count("target").as("publication"))
.select(col("source"). alias("p_source"), col("publication"))
val relatedDataset = relation
.where("target like '60%'")
.groupBy("source")
.agg(count("target").as("dataset"))
.select(col("source"). alias("d_source"), col("dataset"))
val relatedUnknown = relation
.where("target like '70%'")
.groupBy("source")
.agg(count("target").as("unknown"))
.select(col("source"). alias("u_source"), col("unknown"))
val firstJoin = relatedPublication
.join(relatedDataset,col("p_source").equalTo(col("d_source")),"full")
.select( coalesce( col("p_source"), col("d_source")).alias("id"),
col("publication"),
col("dataset"))
.join(relatedUnknown, col("u_source").equalTo(col("id")),"full")
.select( coalesce(col("u_source"), col("id")).alias("source"),
coalesce(col("publication"),lit(0)).alias("relatedPublication"),
coalesce(col("dataset"),lit(0)).alias("relatedDataset"),
coalesce(col("unknown"),lit(0)).alias("relatedUnknown")
)
firstJoin.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/relatedItemCount")
}
}

94
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholixIndex.scala
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@ -1,94 +0,0 @@
package eu.dnetlib.dhp.provision
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.provision.scholix.{Scholix, ScholixResource}
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
import eu.dnetlib.dhp.schema.oaf.Relation
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
object SparkGenerateScholixIndex {
def getScholixAggregator(): Aggregator[(String, Scholix), Scholix, Scholix] = new Aggregator[(String, Scholix), Scholix, Scholix]{
override def zero: Scholix = new Scholix()
override def reduce(b: Scholix, a: (String, Scholix)): Scholix = {
b.mergeFrom(a._2)
b
}
override def merge(wx: Scholix, wy: Scholix): Scholix = {
wx.mergeFrom(wy)
wx
}
override def finish(reduction: Scholix): Scholix = reduction
override def bufferEncoder: Encoder[Scholix] =
Encoders.kryo(classOf[Scholix])
override def outputEncoder: Encoder[Scholix] =
Encoders.kryo(classOf[Scholix])
}
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholixIndex.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")))
parser.parseArgument(args)
val conf = new SparkConf
conf.set("spark.sql.shuffle.partitions", "4000")
val spark = SparkSession.builder.config(conf).appName(SparkGenerateScholixIndex.getClass.getSimpleName).master(parser.get("master")).getOrCreate
val graphPath = parser.get("graphPath")
val workingDirPath = parser.get("workingDirPath")
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
implicit val relEncoder:Encoder[Relation] = Encoders.kryo[Relation]
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
implicit val tupleScholix:Encoder[(String,Scholix)]=Encoders.tuple(Encoders.STRING, scholixEncoder)
val scholixSummary:Dataset[(String,ScholixSummary)] = spark.read.load(s"$workingDirPath/summary").as[ScholixSummary]
.map(s => (s.getId, s))(Encoders.tuple(Encoders.STRING, summaryEncoder))
val sourceRelations:Dataset[(String,Relation)]= spark.read.load(s"$graphPath/relation").as[Relation]
.map(r => (r.getSource,r))(Encoders.tuple(Encoders.STRING, relEncoder))
scholixSummary.joinWith(sourceRelations, scholixSummary("_1").equalTo(sourceRelations("_1")), "inner")
.map(r=> {
val summary = r._1._2
val relation = r._2._2
(relation.getTarget, Scholix.generateScholixWithSource(summary,relation))
}).repartition(6000).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/scholix_source")
val sTarget:Dataset[(String,Scholix)] = spark.read.load(s"$workingDirPath/scholix_source").as[(String, Scholix)]
sTarget.joinWith(scholixSummary, sTarget("_1").equalTo(scholixSummary("_1")), "inner").map(i => {
val summary = i._2._2
val scholix = i._1._2
val scholixResource = ScholixResource.fromSummary(summary)
scholix.setTarget(scholixResource)
scholix.generateIdentifier()
scholix.generatelinkPublisher()
scholix
}).repartition(6000).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/scholix_r")
val finalScholix:Dataset[Scholix] = spark.read.load(s"$workingDirPath/scholix_r").as[Scholix]
finalScholix.map(d => (d.getIdentifier, d))(Encoders.tuple(Encoders.STRING, scholixEncoder))
.groupByKey(_._1)(Encoders.STRING)
.agg(getScholixAggregator().toColumn)
.map(p => p._2)
.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/scholix")
}
}

70
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummaryIndex.scala
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@ -1,70 +0,0 @@
package eu.dnetlib.dhp.provision
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
import org.apache.commons.io.IOUtils
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
object SparkGenerateSummaryIndex {
def main(args: Array[String]): Unit = {
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateSummaryIndex.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json")))
parser.parseArgument(args)
val spark = SparkSession.builder.appName(SparkGenerateSummaryIndex.getClass.getSimpleName).master(parser.get("master")).getOrCreate
val graphPath = parser.get("graphPath")
val workingDirPath = parser.get("workingDirPath")
implicit val relatedItemInfoEncoders: Encoder[RelatedItemInfo] = Encoders.bean(classOf[RelatedItemInfo])
implicit val datasetEncoder:Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
implicit val publicationEncoder:Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val oafWithIdEncoder: Encoder[(String, Oaf)] = Encoders.tuple(Encoders.STRING, oafEncoder)
implicit val scholixSummaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
implicit val scholixSummaryEncoderTuple: Encoder[(String,ScholixSummary)] = Encoders.tuple(Encoders.STRING,scholixSummaryEncoder)
val pubs = spark.read.load(s"$graphPath/publication").as[Oaf].map(o => (o.asInstanceOf[DLIPublication].getId, o))
val dats = spark.read.load(s"$graphPath/dataset").as[Oaf].map(o => (o.asInstanceOf[DLIDataset].getId, o))
val ukn = spark.read.load(s"$graphPath/unknown").as[Oaf].map(o => (o.asInstanceOf[DLIUnknown].getId, o))
val summary:Dataset[(String,ScholixSummary)] = pubs.union(dats).union(ukn).map(o =>{
val s = ScholixSummary.fromOAF(o._2)
(s.getId,s)
})
val relatedItemInfoDs:Dataset[RelatedItemInfo] = spark.read.load(s"$workingDirPath/relatedItemCount").as[RelatedItemInfo]
summary.joinWith(relatedItemInfoDs, summary("_1").equalTo(relatedItemInfoDs("source")), "inner")
.map(i => {
val summary = i._1._2
val relatedItemInfo = i._2
summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset)
summary.setRelatedPublications(relatedItemInfo.getRelatedPublication)
summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown)
summary
}).filter(s => s.getLocalIdentifier != null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/summary")
}
}

61
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java
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@ -1,61 +0,0 @@
package eu.dnetlib.dhp.provision;
import java.util.HashMap;
import java.util.Map;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.elasticsearch.spark.rdd.api.java.JavaEsSpark;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class
SparkIndexCollectionOnES {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkIndexCollectionOnES.class
.getResourceAsStream(
"/eu/dnetlib/dhp/provision/index_on_es.json")));
parser.parseArgument(args);
SparkConf conf = new SparkConf()
.setAppName(SparkIndexCollectionOnES.class.getSimpleName())
.setMaster(parser.get("master"));
conf.set("spark.sql.shuffle.partitions", "4000");
final String sourcePath = parser.get("sourcePath");
final String index = parser.get("index");
final String idPath = parser.get("idPath");
final String cluster = parser.get("cluster");
final String clusterJson = IOUtils
.toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/cluster.json"));
final Map<String, String> clusterMap = new ObjectMapper().readValue(clusterJson, Map.class);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<String> inputRdd = sc.textFile(sourcePath);
Map<String, String> esCfg = new HashMap<>();
esCfg.put("es.nodes", clusterMap.get(cluster));
esCfg.put("es.mapping.id", idPath);
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
}
}

286
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java
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@ -1,286 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.DHPUtils;
public class Scholix implements Serializable {
private String publicationDate;
private List<ScholixEntityId> publisher;
private List<ScholixEntityId> linkprovider;
private ScholixRelationship relationship;
private ScholixResource source;
private ScholixResource target;
private String identifier;
public Scholix clone(final ScholixResource t) {
final Scholix clone = new Scholix();
clone.setPublicationDate(publicationDate);
clone.setPublisher(publisher);
clone.setLinkprovider(linkprovider);
clone.setRelationship(relationship);
clone.setSource(source);
clone.setTarget(t);
clone.generatelinkPublisher();
clone.generateIdentifier();
return clone;
}
public static Scholix generateScholixWithSource(
final String sourceSummaryJson, final String relation) {
final ObjectMapper mapper = new ObjectMapper();
try {
ScholixSummary scholixSummary = mapper.readValue(sourceSummaryJson, ScholixSummary.class);
Relation rel = mapper.readValue(relation, Relation.class);
final Scholix s = new Scholix();
if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0)
s.setPublicationDate(scholixSummary.getDate().get(0));
s
.setLinkprovider(
rel
.getCollectedfrom()
.stream()
.map(
cf -> new ScholixEntityId(
cf.getValue(),
Collections
.singletonList(
new ScholixIdentifier(cf.getKey(), "dnet_identifier"))))
.collect(Collectors.toList()));
s.setRelationship(new ScholixRelationship(rel.getRelType(), rel.getRelClass(), null));
s.setSource(ScholixResource.fromSummary(scholixSummary));
return s;
} catch (Throwable e) {
throw new RuntimeException(
String.format("Summary: %s \n relation:%s", sourceSummaryJson, relation), e);
}
}
public static Scholix generateScholixWithSource(
final ScholixSummary scholixSummary, final Relation rel) {
final Scholix s = new Scholix();
if (scholixSummary.getDate() != null && scholixSummary.getDate().size() > 0)
s.setPublicationDate(scholixSummary.getDate().get(0));
s
.setLinkprovider(
rel
.getCollectedfrom()
.stream()
.map(
cf -> new ScholixEntityId(
cf.getValue(),
Collections
.singletonList(
new ScholixIdentifier(cf.getKey(), "dnet_identifier"))))
.collect(Collectors.toList()));
s.setRelationship(new ScholixRelationship(rel.getRelType(), rel.getRelClass(), null));
s.setSource(ScholixResource.fromSummary(scholixSummary));
s.setIdentifier(rel.getTarget());
return s;
}
private List<ScholixEntityId> mergeScholixEntityId(final List<ScholixEntityId> a, final List<ScholixEntityId> b) {
final List<ScholixEntityId> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
if (b != null)
b.forEach(s -> {
if (s != null) {
int tt = (int) m
.stream()
.filter(t -> t != null && t.getName() != null && t.getName().equalsIgnoreCase(s.getName()))
.count();
if (tt == 0) {
m.add(s);
}
}
});
return m;
}
private List<ScholixIdentifier> mergeScholixIdnetifier(final List<ScholixIdentifier> a,
final List<ScholixIdentifier> b) {
final List<ScholixIdentifier> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
if (b != null)
b.forEach(s -> {
int tt = (int) m.stream().filter(t -> t.getIdentifier().equalsIgnoreCase(s.getIdentifier())).count();
if (tt == 0) {
m.add(s);
}
});
return m;
}
private List<ScholixCollectedFrom> mergeScholixCollectedFrom(final List<ScholixCollectedFrom> a,
final List<ScholixCollectedFrom> b) {
final List<ScholixCollectedFrom> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
if (b != null)
b.forEach(s -> {
int tt = (int) m
.stream()
.filter(t -> t.getProvider().getName().equalsIgnoreCase(s.getProvider().getName()))
.count();
if (tt == 0) {
m.add(s);
}
});
return m;
}
private ScholixRelationship mergeRelationships(final ScholixRelationship a, final ScholixRelationship b) {
ScholixRelationship result = new ScholixRelationship();
result.setName(a == null || StringUtils.isEmpty(a.getName()) ? b.getName() : a.getName());
result.setInverse(a == null || StringUtils.isEmpty(a.getInverse()) ? b.getInverse() : a.getInverse());
result.setSchema(a == null || StringUtils.isEmpty(a.getSchema()) ? b.getSchema() : a.getSchema());
return result;
}
private ScholixResource mergeResource(final ScholixResource a, final ScholixResource b) {
if (a == null)
return b;
final ScholixResource result = new ScholixResource();
result.setCollectedFrom(mergeScholixCollectedFrom(a.getCollectedFrom(), b.getCollectedFrom()));
result.setCreator(mergeScholixEntityId(a.getCreator(), b.getCreator()));
result
.setDnetIdentifier(
StringUtils.isBlank(a.getDnetIdentifier()) ? b.getDnetIdentifier() : a.getDnetIdentifier());
result.setIdentifier(mergeScholixIdnetifier(a.getIdentifier(), b.getIdentifier()));
result.setObjectType(StringUtils.isNotBlank(a.getObjectType()) ? a.getObjectType() : b.getObjectType());
result
.setObjectSubType(
StringUtils.isNotBlank(a.getObjectSubType()) ? a.getObjectSubType() : b.getObjectSubType());
result.setPublisher(mergeScholixEntityId(a.getPublisher(), b.getPublisher()));
result
.setPublicationDate(
StringUtils.isNotBlank(a.getPublicationDate()) ? a.getPublicationDate() : b.getPublicationDate());
result.setTitle(StringUtils.isNotBlank(a.getTitle()) ? a.getTitle() : b.getTitle());
return result;
}
public void mergeFrom(final Scholix other) {
linkprovider = mergeScholixEntityId(linkprovider, other.getLinkprovider());
publisher = mergeScholixEntityId(publisher, other.getPublisher());
if (StringUtils.isEmpty(publicationDate))
publicationDate = other.getPublicationDate();
relationship = mergeRelationships(relationship, other.getRelationship());
source = mergeResource(source, other.getSource());
target = mergeResource(target, other.getTarget());
generateIdentifier();
}
public void generatelinkPublisher() {
Set<String> publisher = new HashSet<>();
if (source.getPublisher() != null)
publisher
.addAll(
source
.getPublisher()
.stream()
.map(ScholixEntityId::getName)
.collect(Collectors.toList()));
if (target.getPublisher() != null)
publisher
.addAll(
target
.getPublisher()
.stream()
.map(ScholixEntityId::getName)
.collect(Collectors.toList()));
this.publisher = publisher.stream().map(k -> new ScholixEntityId(k, null)).collect(Collectors.toList());
}
public void generateIdentifier() {
setIdentifier(
DHPUtils
.md5(
String
.format(
"%s::%s::%s",
source.getDnetIdentifier(), relationship.getName(), target.getDnetIdentifier())));
}
public Scholix addTarget(final String targetSummaryJson) {
final ObjectMapper mapper = new ObjectMapper();
try {
ScholixSummary targetSummary = mapper.readValue(targetSummaryJson, ScholixSummary.class);
setTarget(ScholixResource.fromSummary(targetSummary));
generateIdentifier();
return this;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
public String getPublicationDate() {
return publicationDate;
}
public void setPublicationDate(String publicationDate) {
this.publicationDate = publicationDate;
}
public List<ScholixEntityId> getPublisher() {
return publisher;
}
public void setPublisher(List<ScholixEntityId> publisher) {
this.publisher = publisher;
}
public List<ScholixEntityId> getLinkprovider() {
return linkprovider;
}
public void setLinkprovider(List<ScholixEntityId> linkprovider) {
this.linkprovider = linkprovider;
}
public ScholixRelationship getRelationship() {
return relationship;
}
public void setRelationship(ScholixRelationship relationship) {
this.relationship = relationship;
}
public ScholixResource getSource() {
return source;
}
public void setSource(ScholixResource source) {
this.source = source;
}
public ScholixResource getTarget() {
return target;
}
public void setTarget(ScholixResource target) {
this.target = target;
}
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
}

45
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixCollectedFrom.java
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@ -1,45 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
public class ScholixCollectedFrom implements Serializable {
private ScholixEntityId provider;
private String provisionMode;
private String completionStatus;
public ScholixCollectedFrom() {
}
public ScholixCollectedFrom(
ScholixEntityId provider, String provisionMode, String completionStatus) {
this.provider = provider;
this.provisionMode = provisionMode;
this.completionStatus = completionStatus;
}
public ScholixEntityId getProvider() {
return provider;
}
public void setProvider(ScholixEntityId provider) {
this.provider = provider;
}
public String getProvisionMode() {
return provisionMode;
}
public void setProvisionMode(String provisionMode) {
this.provisionMode = provisionMode;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
}

34
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixEntityId.java
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@ -1,34 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
import java.util.List;
public class ScholixEntityId implements Serializable {
private String name;
private List<ScholixIdentifier> identifiers;
public ScholixEntityId() {
}
public ScholixEntityId(String name, List<ScholixIdentifier> identifiers) {
this.name = name;
this.identifiers = identifiers;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public List<ScholixIdentifier> getIdentifiers() {
return identifiers;
}
public void setIdentifiers(List<ScholixIdentifier> identifiers) {
this.identifiers = identifiers;
}
}

33
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixIdentifier.java
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@ -1,33 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
public class ScholixIdentifier implements Serializable {
private String identifier;
private String schema;
public ScholixIdentifier() {
}
public ScholixIdentifier(String identifier, String schema) {
this.identifier = identifier;
this.schema = schema;
}
public String getIdentifier() {
return identifier;
}
public void setIdentifier(String identifier) {
this.identifier = identifier;
}
public String getSchema() {
return schema;
}
public void setSchema(String schema) {
this.schema = schema;
}
}

43
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixRelationship.java
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@ -1,43 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
public class ScholixRelationship implements Serializable {
private String name;
private String schema;
private String inverse;
public ScholixRelationship() {
}
public ScholixRelationship(String name, String schema, String inverse) {
this.name = name;
this.schema = schema;
this.inverse = inverse;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getSchema() {
return schema;
}
public void setSchema(String schema) {
this.schema = schema;
}
public String getInverse() {
return inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
}

151
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java
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@ -1,151 +0,0 @@
package eu.dnetlib.dhp.provision.scholix;
import java.io.Serializable;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
public class ScholixResource implements Serializable {
private List<ScholixIdentifier> identifier;
private String dnetIdentifier;
private String objectType;
private String objectSubType;
private String title;
private List<ScholixEntityId> creator;
private String publicationDate;
private List<ScholixEntityId> publisher;
private List<ScholixCollectedFrom> collectedFrom;
public static ScholixResource fromSummary(ScholixSummary summary) {
final ScholixResource resource = new ScholixResource();
resource.setDnetIdentifier(summary.getId());
resource
.setIdentifier(
summary
.getLocalIdentifier()
.stream()
.map(i -> new ScholixIdentifier(i.getId(), i.getType()))
.collect(Collectors.toList()));
resource.setObjectType(summary.getTypology().toString());
if (summary.getTitle() != null && summary.getTitle().size() > 0)
resource.setTitle(summary.getTitle().get(0));
if (summary.getAuthor() != null)
resource
.setCreator(
summary
.getAuthor()
.stream()
.map(c -> new ScholixEntityId(c, null))
.collect(Collectors.toList()));
if (summary.getDate() != null && summary.getDate().size() > 0)
resource.setPublicationDate(summary.getDate().get(0));
if (summary.getPublisher() != null)
resource
.setPublisher(
summary
.getPublisher()
.stream()
.map(p -> new ScholixEntityId(p, null))
.collect(Collectors.toList()));
if (summary.getDatasources() != null)
resource
.setCollectedFrom(
summary
.getDatasources()
.stream()
.map(
d -> new ScholixCollectedFrom(
new ScholixEntityId(
d.getDatasourceName(),
Collections
.singletonList(
new ScholixIdentifier(d.getDatasourceId(), "dnet_identifier"))),
"collected",
d.getCompletionStatus()))
.collect(Collectors.toList()));
return resource;
}
public List<ScholixIdentifier> getIdentifier() {
return identifier;
}
public void setIdentifier(List<ScholixIdentifier> identifier) {
this.identifier = identifier;
}
public String getDnetIdentifier() {
return dnetIdentifier;
}
public void setDnetIdentifier(String dnetIdentifier) {
this.dnetIdentifier = dnetIdentifier;
}
public String getObjectType() {
return objectType;
}
public void setObjectType(String objectType) {
this.objectType = objectType;
}
public String getObjectSubType() {
return objectSubType;
}
public void setObjectSubType(String objectSubType) {
this.objectSubType = objectSubType;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
public List<ScholixEntityId> getCreator() {
return creator;
}
public void setCreator(List<ScholixEntityId> creator) {
this.creator = creator;
}
public String getPublicationDate() {
return publicationDate;
}
public void setPublicationDate(String publicationDate) {
this.publicationDate = publicationDate;
}
public List<ScholixEntityId> getPublisher() {
return publisher;
}
public void setPublisher(List<ScholixEntityId> publisher) {
this.publisher = publisher;
}
public List<ScholixCollectedFrom> getCollectedFrom() {
return collectedFrom;
}
public void setCollectedFrom(List<ScholixCollectedFrom> collectedFrom) {
this.collectedFrom = collectedFrom;
}
}

44
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/CollectedFromType.java
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@ -1,44 +0,0 @@
package eu.dnetlib.dhp.provision.scholix.summary;
import java.io.Serializable;
public class CollectedFromType implements Serializable {
private String datasourceName;
private String datasourceId;
private String completionStatus;
public CollectedFromType() {
}
public CollectedFromType(String datasourceName, String datasourceId, String completionStatus) {
this.datasourceName = datasourceName;
this.datasourceId = datasourceId;
this.completionStatus = completionStatus;
}
public String getDatasourceName() {
return datasourceName;
}
public void setDatasourceName(String datasourceName) {
this.datasourceName = datasourceName;
}
public String getDatasourceId() {
return datasourceId;
}
public void setDatasourceId(String datasourceId) {
this.datasourceId = datasourceId;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
}

33
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/SchemeValue.java
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@ -1,33 +0,0 @@
package eu.dnetlib.dhp.provision.scholix.summary;
import java.io.Serializable;
public class SchemeValue implements Serializable {
private String scheme;
private String value;
public SchemeValue() {
}
public SchemeValue(String scheme, String value) {
this.scheme = scheme;
this.value = value;
}
public String getScheme() {
return scheme;
}
public void setScheme(String scheme) {
this.scheme = scheme;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

321
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java
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@ -1,321 +0,0 @@
package eu.dnetlib.dhp.provision.scholix.summary;
import java.io.Serializable;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.provision.RelatedItemInfo;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
public class ScholixSummary implements Serializable {
private String id;
private List<TypedIdentifier> localIdentifier;
private Typology typology;
private List<String> title;
private List<String> author;
private List<String> date;
private String description;
private List<SchemeValue> subject;
private List<String> publisher;
private long relatedPublications;
private long relatedDatasets;
private long relatedUnknown;
private List<CollectedFromType> datasources;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<TypedIdentifier> getLocalIdentifier() {
return localIdentifier;
}
public void setLocalIdentifier(List<TypedIdentifier> localIdentifier) {
this.localIdentifier = localIdentifier;
}
public Typology getTypology() {
return typology;
}
public void setTypology(Typology typology) {
this.typology = typology;
}
public List<String> getTitle() {
return title;
}
public void setTitle(List<String> title) {
this.title = title;
}
public List<String> getAuthor() {
return author;
}
public void setAuthor(List<String> author) {
this.author = author;
}
public List<String> getDate() {
return date;
}
public void setDate(List<String> date) {
this.date = date;
}
@JsonProperty("abstract")
public String getDescription() {
return description;
}
@JsonProperty("abstract")
public void setDescription(String description) {
this.description = description;
}
public List<SchemeValue> getSubject() {
return subject;
}
public void setSubject(List<SchemeValue> subject) {
this.subject = subject;
}
public List<String> getPublisher() {
return publisher;
}
public void setPublisher(List<String> publisher) {
this.publisher = publisher;
}
public long getRelatedPublications() {
return relatedPublications;
}
public void setRelatedPublications(long relatedPublications) {
this.relatedPublications = relatedPublications;
}
public long getRelatedDatasets() {
return relatedDatasets;
}
public void setRelatedDatasets(long relatedDatasets) {
this.relatedDatasets = relatedDatasets;
}
public long getRelatedUnknown() {
return relatedUnknown;
}
public void setRelatedUnknown(long relatedUnknown) {
this.relatedUnknown = relatedUnknown;
}
public List<CollectedFromType> getDatasources() {
return datasources;
}
public void setDatasources(List<CollectedFromType> datasources) {
this.datasources = datasources;
}
public static ScholixSummary fromOAF(final Oaf oaf) {
try {
final RelatedItemInfo relatedItemInfo = new RelatedItemInfo();
if (oaf instanceof DLIPublication)
return summaryFromPublication((DLIPublication) oaf, relatedItemInfo);
if (oaf instanceof DLIDataset)
return summaryFromDataset((DLIDataset) oaf, relatedItemInfo);
if (oaf instanceof DLIUnknown)
return summaryFromUnknown((DLIUnknown) oaf, relatedItemInfo);
} catch (Throwable e) {
throw new RuntimeException(e);
}
return null;
}
private static ScholixSummary summaryFromDataset(
final DLIDataset item, final RelatedItemInfo relatedItemInfo) {
ScholixSummary summary = new ScholixSummary();
summary.setId(item.getId());
if (item.getPid() != null)
summary
.setLocalIdentifier(
item
.getPid()
.stream()
.map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid()))
.collect(Collectors.toList()));
summary.setTypology(Typology.dataset);
if (item.getTitle() != null)
summary
.setTitle(
item.getTitle().stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
if (item.getAuthor() != null) {
summary
.setAuthor(
item.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList()));
}
if (item.getRelevantdate() != null)
summary
.setDate(
item
.getRelevantdate()
.stream()
.filter(d -> "date".equalsIgnoreCase(d.getQualifier().getClassname()))
.map(StructuredProperty::getValue)
.collect(Collectors.toList()));
if (item.getDescription() != null && item.getDescription().size() > 0)
summary.setDescription(item.getDescription().get(0).getValue());
if (item.getSubject() != null) {
summary
.setSubject(
item
.getSubject()
.stream()
.map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue()))
.collect(Collectors.toList()));
}
if (item.getPublisher() != null)
summary.setPublisher(Collections.singletonList(item.getPublisher().getValue()));
summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset());
summary.setRelatedPublications(relatedItemInfo.getRelatedPublication());
summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown());
if (item.getDlicollectedfrom() != null)
summary
.setDatasources(
item
.getDlicollectedfrom()
.stream()
.map(c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()))
.collect(Collectors.toList()));
return summary;
}
private static ScholixSummary summaryFromPublication(
final DLIPublication item, final RelatedItemInfo relatedItemInfo) {
ScholixSummary summary = new ScholixSummary();
summary.setId(item.getId());
if (item.getPid() != null)
summary
.setLocalIdentifier(
item
.getPid()
.stream()
.map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid()))
.collect(Collectors.toList()));
summary.setTypology(Typology.publication);
if (item.getTitle() != null)
summary
.setTitle(
item.getTitle().stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
if (item.getAuthor() != null) {
summary
.setAuthor(
item.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList()));
}
if (item.getRelevantdate() != null)
summary
.setDate(
item
.getRelevantdate()
.stream()
.filter(d -> "date".equalsIgnoreCase(d.getQualifier().getClassname()))
.map(StructuredProperty::getValue)
.collect(Collectors.toList()));
if (item.getDescription() != null && item.getDescription().size() > 0)
summary.setDescription(item.getDescription().get(0).getValue());
if (item.getSubject() != null) {
summary
.setSubject(
item
.getSubject()
.stream()
.map(s -> new SchemeValue(s.getQualifier().getClassid(), s.getValue()))
.collect(Collectors.toList()));
}
if (item.getPublisher() != null)
summary.setPublisher(Collections.singletonList(item.getPublisher().getValue()));
summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset());
summary.setRelatedPublications(relatedItemInfo.getRelatedPublication());
summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown());
if (item.getDlicollectedfrom() != null)
summary
.setDatasources(
item
.getDlicollectedfrom()
.stream()
.map(c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()))
.collect(Collectors.toList()));
return summary;
}
private static ScholixSummary summaryFromUnknown(
final DLIUnknown item, final RelatedItemInfo relatedItemInfo) {
ScholixSummary summary = new ScholixSummary();
summary.setId(item.getId());
if (item.getPid() != null)
summary
.setLocalIdentifier(
item
.getPid()
.stream()
.map(p -> new TypedIdentifier(p.getValue(), p.getQualifier().getClassid()))
.collect(Collectors.toList()));
summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset());
summary.setRelatedPublications(relatedItemInfo.getRelatedPublication());
summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown());
summary.setTypology(Typology.unknown);
if (item.getDlicollectedfrom() != null)
summary
.setDatasources(
item
.getDlicollectedfrom()
.stream()
.map(c -> new CollectedFromType(c.getName(), c.getId(), c.getCompletionStatus()))
.collect(Collectors.toList()));
return summary;
}
}

33
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/TypedIdentifier.java
View File

@ -1,33 +0,0 @@
package eu.dnetlib.dhp.provision.scholix.summary;
import java.io.Serializable;
public class TypedIdentifier implements Serializable {
private String id;
private String type;
public TypedIdentifier() {
}
public TypedIdentifier(String id, String type) {
this.id = id;
this.type = type;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
}

8
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/Typology.java
View File

@ -1,8 +0,0 @@
package eu.dnetlib.dhp.provision.scholix.summary;
import java.io.Serializable;
public enum Typology implements Serializable {
dataset, publication, unknown
}

131
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java
View File

@ -1,131 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
import eu.dnetlib.dhp.provision.scholix.ScholixCollectedFrom;
import eu.dnetlib.dhp.provision.scholix.ScholixEntityId;
import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier;
import eu.dnetlib.dhp.provision.scholix.ScholixResource;
import eu.dnetlib.dhp.utils.DHPUtils;
public class CrossRefParserJSON {
private static final List<ScholixCollectedFrom> collectedFrom = generateCrossrefCollectedFrom("complete");
public static ScholixResource parseRecord(final String record) {
if (record == null)
return null;
JsonElement jElement = new JsonParser().parse(record);
JsonElement source = null;
if (jElement.getAsJsonObject().has("_source")) {
source = jElement.getAsJsonObject().get("_source");
if (source == null || !source.isJsonObject())
return null;
} else if (jElement.getAsJsonObject().has("DOI")) {
source = jElement;
} else {
return null;
}
final JsonObject message = source.getAsJsonObject();
ScholixResource currentObject = new ScholixResource();
if (message.get("DOI") != null) {
final String doi = message.get("DOI").getAsString();
currentObject.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi")));
}
if ((!message.get("created").isJsonNull())
&& (message.getAsJsonObject("created").get("date-time") != null)) {
currentObject
.setPublicationDate(
message.getAsJsonObject("created").get("date-time").getAsString());
}
if (message.get("title") != null
&& !message.get("title").isJsonNull()
&& message.get("title").isJsonArray()) {
JsonArray array = message.get("title").getAsJsonArray();
currentObject.setTitle(array.get(0).getAsString());
}
if (message.get("author") != null && !message.get("author").isJsonNull()) {
JsonArray author = message.getAsJsonArray("author");
List<ScholixEntityId> authorList = new ArrayList<>();
for (JsonElement anAuthor : author) {
JsonObject currentAuth = anAuthor.getAsJsonObject();
String family = "";
String given = "";
if (currentAuth != null
&& currentAuth.get("family") != null
&& !currentAuth.get("family").isJsonNull()) {
family = currentAuth.get("family").getAsString();
}
if (currentAuth != null
&& currentAuth.get("given") != null
&& !currentAuth.get("given").isJsonNull()) {
given = currentAuth.get("given").getAsString();
}
authorList.add(new ScholixEntityId(String.format("%s %s", family, given), null));
}
currentObject.setCreator(authorList);
}
if (message.get("publisher") != null && !message.get("publisher").isJsonNull()) {
currentObject
.setPublisher(
Collections
.singletonList(
new ScholixEntityId(message.get("publisher").getAsString(), null)));
}
currentObject.setCollectedFrom(collectedFrom);
currentObject.setObjectType("publication");
currentObject
.setDnetIdentifier(
generateId(message.get("DOI").getAsString(), "doi", "publication"));
return currentObject;
}
private static List<ScholixCollectedFrom> generateCrossrefCollectedFrom(
final String completionStatus) {
final ScholixEntityId scholixEntityId = new ScholixEntityId(
"Crossref",
Collections
.singletonList(
new ScholixIdentifier("dli_________::crossref", "dnet_identifier")));
return Collections
.singletonList(
new ScholixCollectedFrom(scholixEntityId, "resolved", completionStatus));
}
private static String generateId(
final String pid, final String pidType, final String entityType) {
String type;
switch (entityType) {
case "publication":
type = "50|";
break;
case "dataset":
type = "60|";
break;
case "unknown":
type = "70|";
break;
default:
throw new IllegalArgumentException("unexpected value " + entityType);
}
return type
+ DHPUtils
.md5(
String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim()));
}
}

90
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java
View File

@ -1,90 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.io.ByteArrayOutputStream;
import java.util.zip.Inflater;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import eu.dnetlib.dhp.provision.scholix.ScholixResource;
public class CrossrefClient {
private String host;
private String index = "crossref";
private String indexType = "item";
public CrossrefClient(String host) {
this.host = host;
}
public String getHost() {
return host;
}
public void setHost(String host) {
this.host = host;
}
public String getIndex() {
return index;
}
public void setIndex(String index) {
this.index = index;
}
public String getIndexType() {
return indexType;
}
public void setIndexType(String indexType) {
this.indexType = indexType;
}
private static String decompressBlob(final String blob) {
try {
byte[] byteArray = Base64.decodeBase64(blob.getBytes());
final Inflater decompresser = new Inflater();
decompresser.setInput(byteArray);
final ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length);
byte[] buffer = new byte[8192];
while (!decompresser.finished()) {
int size = decompresser.inflate(buffer);
bos.write(buffer, 0, size);
}
decompresser.end();
return bos.toString();
} catch (Throwable e) {
throw new RuntimeException("Wrong record:" + blob, e);
}
}
public ScholixResource getResourceByDOI(final String doi) {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet(
String
.format(
"http://%s:9200/%s/%s/%s", host, index, indexType, doi.replaceAll("/", "%2F")));
CloseableHttpResponse response = client.execute(httpGet);
String json = IOUtils.toString(response.getEntity().getContent());
if (json.contains("blob")) {
JsonParser p = new JsonParser();
final JsonElement root = p.parse(json);
json = decompressBlob(
root.getAsJsonObject().get("_source").getAsJsonObject().get("blob").getAsString());
}
return CrossRefParserJSON.parseRecord(json);
} catch (Throwable e) {
return null;
}
}
}

229
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java
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@ -1,229 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.jayway.jsonpath.JsonPath;
import eu.dnetlib.dhp.provision.scholix.*;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.scholexplorer.relation.RelInfo;
import eu.dnetlib.scholexplorer.relation.RelationMapper;
public class Datacite2Scholix {
private String rootPath = "$.attributes";
final RelationMapper relationMapper;
public Datacite2Scholix(RelationMapper relationMapper) {
this.relationMapper = relationMapper;
}
public List<Scholix> generateScholixFromJson(final String dJson) {
List<Map<String, String>> relIds = getRelatedIendtifiers(dJson);
relIds = relIds != null
? relIds
.stream()
.filter(
m -> m.containsKey("relatedIdentifierType")
&& m.containsKey("relationType")
&& m.containsKey("relatedIdentifier"))
.collect(Collectors.toList())
: null;
if (relIds == null || relIds.size() == 0)
return null;
final String updated = JsonPath.read(dJson, rootPath + ".updated");
ScholixResource resource = generateDataciteScholixResource(dJson);
return relIds
.stream()
.flatMap(
s -> {
try {
final List<Scholix> result = generateScholix(
resource,
"" + s.get("relatedIdentifier"),
s.get("relatedIdentifierType"),
s.get("relationType"),
updated);
return result.stream();
} catch (Throwable e) {
return new ArrayList<Scholix>().stream();
}
})
.collect(Collectors.toList());
}
public String getRootPath() {
return rootPath;
}
public void setRootPath(String rootPath) {
this.rootPath = rootPath;
}
private List<Scholix> generateScholix(
ScholixResource source,
final String pid,
final String pidtype,
final String relType,
final String updated) {
if ("doi".equalsIgnoreCase(pidtype)) {
ScholixResource target = new ScholixResource();
target.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, pidtype)));
final RelInfo relInfo = relationMapper.get(relType.toLowerCase());
final ScholixRelationship rel = new ScholixRelationship(relInfo.getOriginal(), "datacite",
relInfo.getInverse());
final ScholixEntityId provider = source.getCollectedFrom().get(0).getProvider();
final Scholix s = new Scholix();
s.setSource(source);
s.setTarget(target);
s.setLinkprovider(Collections.singletonList(provider));
s.setPublisher(source.getPublisher());
s.setRelationship(rel);
s.setPublicationDate(updated);
return Collections.singletonList(s);
} else {
final List<Scholix> result = new ArrayList<>();
ScholixResource target = new ScholixResource();
target.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, pidtype)));
target.setDnetIdentifier(generateId(pid, pidtype, "unknown"));
target.setObjectType("unknown");
target.setCollectedFrom(generateDataciteCollectedFrom("incomplete"));
final RelInfo relInfo = relationMapper.get(relType.toLowerCase());
final ScholixRelationship rel = new ScholixRelationship(relInfo.getOriginal(), "datacite",
relInfo.getInverse());
final ScholixEntityId provider = source.getCollectedFrom().get(0).getProvider();
final Scholix s = new Scholix();
s.setSource(source);
s.setTarget(target);
s.setLinkprovider(Collections.singletonList(provider));
s.setPublisher(source.getPublisher());
s.setRelationship(rel);
s.setPublicationDate(updated);
s.generateIdentifier();
result.add(s);
final Scholix s2 = new Scholix();
s2.setSource(target);
s2.setTarget(source);
s2.setLinkprovider(Collections.singletonList(provider));
s2.setPublisher(source.getPublisher());
s2
.setRelationship(
new ScholixRelationship(relInfo.getInverse(), "datacite", relInfo.getOriginal()));
s2.setPublicationDate(updated);
s2.generateIdentifier();
result.add(s2);
return result;
}
}
public ScholixResource generateDataciteScholixResource(String dJson) {
ScholixResource resource = new ScholixResource();
String DOI_PATH = rootPath + ".doi";
final String doi = JsonPath.read(dJson, DOI_PATH);
resource.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi")));
resource.setObjectType(getType(dJson));
resource.setDnetIdentifier(generateId(doi, "doi", resource.getObjectType()));
resource.setCollectedFrom(generateDataciteCollectedFrom("complete"));
final String publisher = JsonPath.read(dJson, rootPath + ".publisher");
if (StringUtils.isNotBlank(publisher))
resource.setPublisher(Collections.singletonList(new ScholixEntityId(publisher, null)));
final String date = getDate(dJson);
if (StringUtils.isNotBlank(date))
resource.setPublicationDate(date);
final String title = getTitle(dJson);
if (StringUtils.isNotBlank(title))
resource.setTitle(title);
resource.setCreator(getCreators(dJson));
return resource;
}
private List<ScholixEntityId> getCreators(final String json) {
final List<String> creatorName = JsonPath.read(json, rootPath + ".creators[*].name");
if (creatorName != null && creatorName.size() > 0) {
return creatorName
.stream()
.map(s -> new ScholixEntityId(s, null))
.collect(Collectors.toList());
}
return null;
}
private String getTitle(final String json) {
final List<String> titles = JsonPath.read(json, rootPath + ".titles[*].title");
return titles != null && titles.size() > 0 ? titles.get(0) : null;
}
private String getDate(final String json) {
final List<Map<String, String>> dates = JsonPath.read(json, rootPath + ".dates");
if (dates != null && dates.size() > 0) {
List<Map<String, String>> issued = dates
.stream()
.filter(s -> "issued".equalsIgnoreCase(s.get("dateType")))
.collect(Collectors.toList());
if (issued.size() > 0)
return issued.get(0).get("date");
}
return null;
}
private List<ScholixCollectedFrom> generateDataciteCollectedFrom(final String completionStatus) {
final ScholixEntityId scholixEntityId = new ScholixEntityId(
"Datasets in Datacite",
Collections
.singletonList(
new ScholixIdentifier("dli_________::datacite", "dnet_identifier")));
return Collections
.singletonList(
new ScholixCollectedFrom(scholixEntityId, "collected", completionStatus));
}
private String getType(final String json) {
try {
final String bibtext = JsonPath.read(json, rootPath + ".types.bibtex");
if ("article".equalsIgnoreCase(bibtext)) {
return "publication";
}
return "dataset";
} catch (Throwable e) {
return "dataset";
}
}
private List<Map<String, String>> getRelatedIendtifiers(final String json) {
String REL_IDENTIFIER_PATH = rootPath + ".relatedIdentifiers[*]";
List<Map<String, String>> res = JsonPath.read(json, REL_IDENTIFIER_PATH);
return res;
}
public static String generateId(final String pid, final String pidType, final String entityType) {
String type;
switch (entityType) {
case "publication":
type = "50|";
break;
case "dataset":
type = "60|";
break;
case "unknown":
type = "70|";
break;
default:
throw new IllegalArgumentException("unexpected value " + entityType);
}
return type
+ DHPUtils
.md5(
String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim()));
}
}

75
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java
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@ -1,75 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import eu.dnetlib.dhp.provision.scholix.ScholixResource;
public class DataciteClient {
private String host;
private String index = "datacite";
private String indexType = "dump";
private final Datacite2Scholix d2s;
public DataciteClient(String host) {
this.host = host;
d2s = new Datacite2Scholix(null);
d2s.setRootPath("$._source.attributes");
}
public Iterable<String> getDatasetsFromTs(final Long timestamp) {
return () -> {
try {
return new DataciteClientIterator(host, index, timestamp);
} catch (IOException e) {
throw new RuntimeException(e);
}
};
}
public String getHost() {
return host;
}
public void setHost(String host) {
this.host = host;
}
public String getIndex() {
return index;
}
public void setIndex(String index) {
this.index = index;
}
public String getIndexType() {
return indexType;
}
public void setIndexType(String indexType) {
this.indexType = indexType;
}
public ScholixResource getDatasetByDOI(final String doi) {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet(
String
.format(
"http://%s:9200/%s/%s/%s", host, index, indexType, doi.replaceAll("/", "%2F")));
CloseableHttpResponse response = client.execute(httpGet);
final String json = IOUtils.toString(response.getEntity().getContent());
return d2s.generateDataciteScholixResource(json);
} catch (Throwable e) {
return null;
}
}
}

120
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java
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@ -1,120 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
public class DataciteClientIterator implements Iterator<String> {
static final String blobPath = "$.hits.hits[*]._source";
static final String scrollIdPath = "$._scroll_id";
String scrollId;
List<String> buffer;
final String esHost;
final String esIndex;
final ObjectMapper mapper = new ObjectMapper();
public DataciteClientIterator(final String esHost, final String esIndex, long timestamp)
throws IOException {
this.esHost = esHost;
this.esIndex = esIndex;
// THIS FIX IS NECESSARY to avoid different timezone
timestamp -= (60 * 60 * 2);
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
String
.format(
"{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}", timestamp));
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body);
}
public String getResponse(final String url, final String json) {
CloseableHttpClient client = HttpClients.createDefault();
try {
HttpPost httpPost = new HttpPost(url);
if (json != null) {
StringEntity entity = new StringEntity(json);
httpPost.setEntity(entity);
httpPost.setHeader("Accept", "application/json");
httpPost.setHeader("Content-type", "application/json");
}
CloseableHttpResponse response = client.execute(httpPost);
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
throw new RuntimeException("Error on executing request ", e);
} finally {
try {
client.close();
} catch (IOException e) {
throw new RuntimeException("Unable to close client ", e);
}
}
}
private String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);
if (o instanceof String)
return (String) o;
return null;
} catch (Exception e) {
return "";
}
}
private List<String> getBlobs(final String body) {
JSONArray array = JsonPath.read(body, blobPath);
return array
.stream()
.map(
o -> {
try {
return mapper.writeValueAsString(o);
} catch (Throwable e) {
throw new RuntimeException(e);
}
})
.collect(Collectors.toList());
}
@Override
public boolean hasNext() {
return (buffer != null && !buffer.isEmpty());
}
@Override
public String next() {
final String nextItem = buffer.remove(0);
if (buffer.isEmpty()) {
final String json_param = String.format("{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}", scrollId);
final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
try {
buffer = getBlobs(body);
} catch (Throwable e) {
System.out.println(body);
}
}
return nextItem;
}
}

72
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java
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@ -1,72 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.net.URI;
import java.util.List;
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.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.provision.scholix.Scholix;
import eu.dnetlib.scholexplorer.relation.RelationMapper;
public class RetrieveUpdateFromDatacite {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
RetrieveUpdateFromDatacite.class
.getResourceAsStream(
"/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json")));
parser.parseArgument(args);
final String hdfsuri = parser.get("namenode");
Path hdfswritepath = new Path(parser.get("targetPath"));
final long timestamp = Long.parseLong(parser.get("timestamp"));
final String host = parser.get("indexHost");
final String index = parser.get("indexName");
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsuri);
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
FileSystem.get(URI.create(hdfsuri), conf);
final Datacite2Scholix d2s = new Datacite2Scholix(RelationMapper.load());
final ObjectMapper mapper = new ObjectMapper();
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
final Text value = new Text();
final IntWritable key = new IntWritable();
int i = 0;
for (String dataset : new DataciteClient(host).getDatasetsFromTs(timestamp)) {
i++;
List<Scholix> scholix = d2s.generateScholixFromJson(dataset);
if (scholix != null)
for (Scholix s : scholix) {
key.set(i);
value.set(mapper.writeValueAsString(s));
writer.append(key, value);
if (i % 10000 == 0) {
System.out.println("wrote " + i);
}
}
}
}
}
}

184
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java
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@ -1,184 +0,0 @@
package eu.dnetlib.dhp.provision.update;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.provision.scholix.Scholix;
import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier;
import eu.dnetlib.dhp.provision.scholix.ScholixRelationship;
import eu.dnetlib.dhp.provision.scholix.ScholixResource;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;
public class SparkResolveScholixTarget {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkResolveScholixTarget.class
.getResourceAsStream(
"/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json")));
parser.parseArgument(args);
final SparkConf conf = new SparkConf();
final String master = parser.get("master");
final String sourcePath = parser.get("sourcePath");
final String workingDirPath = parser.get("workingDirPath");
final String indexHost = parser.get("indexHost");
try (SparkSession spark = getSession(conf, master)) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
spark
.createDataset(
sc
.sequenceFile(sourcePath, IntWritable.class, Text.class)
.map(Tuple2::_2)
.map(s -> new ObjectMapper().readValue(s.toString(), Scholix.class))
.rdd(),
Encoders.bean(Scholix.class))
.write()
.save(workingDirPath + "/stepA");
Dataset<Scholix> s1 = spark.read().load(workingDirPath + "/stepA").as(Encoders.bean(Scholix.class));
s1
.where(s1.col("target.dnetIdentifier").isNull())
.select(s1.col("target.identifier"))
.distinct()
.map(
(MapFunction<Row, ScholixResource>) f -> {
final String pid = ((Row) f.getList(0).get(0)).getString(0);
ScholixResource publication = new CrossrefClient(indexHost).getResourceByDOI(pid);
if (publication != null) {
return publication;
}
ScholixResource dataset = new DataciteClient(indexHost).getDatasetByDOI(pid);
if (dataset != null) {
return dataset;
}
ScholixResource r = new ScholixResource();
r.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, "doi")));
r.setObjectType("unknown");
r
.setDnetIdentifier(
"70|" + DHPUtils.md5(String.format("%s::doi", pid.toLowerCase().trim())));
return r;
},
Encoders.bean(ScholixResource.class))
.write()
.mode(SaveMode.Overwrite)
.save(workingDirPath + "/stepB");
Dataset<ScholixResource> s2 = spark
.read()
.load(workingDirPath + "/stepB")
.as(Encoders.bean(ScholixResource.class));
s1
.joinWith(
s2,
s1.col("target.identifier.identifier").equalTo(s2.col("identifier.identifier")),
"left")
.flatMap(
(FlatMapFunction<Tuple2<Scholix, ScholixResource>, Scholix>) f -> {
final List<Scholix> res = new ArrayList<>();
final Scholix s = f._1();
final ScholixResource target = f._2();
if (StringUtils.isNotBlank(s.getIdentifier()))
res.add(s);
else if (target == null) {
ScholixResource currentTarget = s.getTarget();
currentTarget.setObjectType("unknown");
currentTarget
.setDnetIdentifier(
Datacite2Scholix
.generateId(
currentTarget.getIdentifier().get(0).getIdentifier(),
currentTarget.getIdentifier().get(0).getSchema(),
currentTarget.getObjectType()));
s.generateIdentifier();
res.add(s);
final Scholix inverse = new Scholix();
inverse.setTarget(s.getSource());
inverse.setSource(s.getTarget());
inverse.setLinkprovider(s.getLinkprovider());
inverse.setPublicationDate(s.getPublicationDate());
inverse.setPublisher(s.getPublisher());
inverse
.setRelationship(
new ScholixRelationship(
s.getRelationship().getInverse(),
s.getRelationship().getSchema(),
s.getRelationship().getName()));
inverse.generateIdentifier();
res.add(inverse);
} else {
target
.setIdentifier(
target
.getIdentifier()
.stream()
.map(
d -> new ScholixIdentifier(
d.getIdentifier().toLowerCase(),
d.getSchema().toLowerCase()))
.collect(Collectors.toList()));
s.setTarget(target);
s.generateIdentifier();
res.add(s);
final Scholix inverse = new Scholix();
inverse.setTarget(s.getSource());
inverse.setSource(s.getTarget());
inverse.setLinkprovider(s.getLinkprovider());
inverse.setPublicationDate(s.getPublicationDate());
inverse.setPublisher(s.getPublisher());
inverse
.setRelationship(
new ScholixRelationship(
s.getRelationship().getInverse(),
s.getRelationship().getSchema(),
s.getRelationship().getName()));
inverse.generateIdentifier();
res.add(inverse);
}
return res.iterator();
},
Encoders.bean(Scholix.class))
.javaRDD()
.map(s -> new ObjectMapper().writeValueAsString(s))
.saveAsTextFile(workingDirPath + "/resolved_json");
}
}
private static SparkSession getSession(SparkConf conf, String master) {
return SparkSession
.builder()
.config(conf)
.appName(SparkResolveScholixTarget.class.getSimpleName())
.master(master)
.getOrCreate();
}
}

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_export_content_parameters.json
View File

@ -1,14 +0,0 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingDirPath",
"paramDescription": "the working path where generated files",
"paramRequired": true
}
]

20
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_maketar_parameters.json
View File

@ -1,20 +0,0 @@
[
{
"paramName": "n",
"paramLongName": "nameNode",
"paramDescription": "the Name Node",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source path",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target path",
"paramRequired": true
}
]

45
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/upload_zenodo.json
View File

@ -1,45 +0,0 @@
[
{
"paramName":"nd",
"paramLongName":"newDeposition",
"paramDescription": "if it is a new deposition (true) or a new version (false)",
"paramRequired": true
},
{
"paramName":"cri",
"paramLongName":"conceptRecordId",
"paramDescription": "The id of the concept record for a new version",
"paramRequired": false
},
{
"paramName":"hdfsp",
"paramLongName":"hdfsPath",
"paramDescription": "the path of the folder tofind files to send to Zenodo",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "nameNode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "at",
"paramLongName": "accessToken",
"paramDescription": "the access token for the deposition",
"paramRequired": false
},
{
"paramName":"cu",
"paramLongName":"connectionUrl",
"paramDescription": "the url to connect to deposit",
"paramRequired": false
},
{
"paramName":"m",
"paramLongName":"metadata",
"paramDescription": "metadata associated to the deposition",
"paramRequired": false
}
]

4
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/cluster.json
View File

@ -1,4 +0,0 @@
{
"cluster1": "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54",
"cluster2": "10.19.65.55, 10.19.65.56, 10.19.65.57, 10.19.65.58"
}

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dataset2Json.json
View File

@ -1,14 +0,0 @@
[
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "master should be local or yarn",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingPath",
"paramDescription": "the working path",
"paramRequired": true
}
]

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dropAndCreateIndex.json
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@ -1,14 +0,0 @@
[
{
"paramName": "c",
"paramLongName": "cluster",
"paramDescription": "should be cluster1 or cluster2",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "index",
"paramDescription": "index name",
"paramRequired": true
}
]

33
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json
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@ -1,33 +0,0 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the working path where generated files",
"paramRequired": true
},
{
"paramName": "i",
"paramLongName": "index",
"paramDescription": "the index name",
"paramRequired": true
},
{
"paramName": "c",
"paramLongName": "cluster",
"paramDescription": "the index cluster",
"paramRequired": true
},
{
"paramName": "id",
"paramLongName": "idPath",
"paramDescription": "the identifier field name",
"paramRequired": true
}
]

20
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json
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@ -1,20 +0,0 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingDirPath",
"paramDescription": "the working path where generated files",
"paramRequired": true
},
{
"paramName": "g",
"paramLongName": "graphPath",
"paramDescription": "the relationPath path ",
"paramRequired": true
}
]

20
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_related_entities_parameters.json
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@ -1,20 +0,0 @@
[
{
"paramName": "mt",
"paramLongName": "master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingDirPath",
"paramDescription": "the working path where generated files",
"paramRequired": true
},
{
"paramName": "r",
"paramLongName": "relationPath",
"paramDescription": "the relationPath path ",
"paramRequired": true
}
]

26
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json
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@ -1,26 +0,0 @@
[
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "s",
"paramLongName": "sourcePath",
"paramDescription": "the source path",
"paramRequired": true
},
{
"paramName": "w",
"paramLongName": "workingDirPath",
"paramDescription": "the working Dir Path",
"paramRequired": true
},
{
"paramName": "h",
"paramLongName": "indexHost",
"paramDescription": "the working Dir Path",
"paramRequired": true
}
]

33
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json
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@ -1,33 +0,0 @@
[
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the working path where generated files",
"paramRequired": true
},
{
"paramName": "ts",
"paramLongName": "timestamp",
"paramDescription": "the timestamp for incremental harvesting",
"paramRequired": true
},
{
"paramName": "ih",
"paramLongName": "indexHost",
"paramDescription": "the ip name of the index",
"paramRequired": true
},
{
"paramName": "in",
"paramLongName": "indexName",
"paramDescription": "the name of the index",
"paramRequired": true
}
]

331
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/scholix_index.json
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@ -1,331 +0,0 @@
{
"mappings": {
"properties": {
"identifier": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"linkprovider": {
"type": "nested",
"properties": {
"identifiers": {
"properties": {
"identifier": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"name": {
"type": "keyword"
}
}
},
"publicationDate": {
"type": "keyword"
},
"relationship": {
"properties": {
"name": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"source": {
"type": "nested",
"properties": {
"collectedFrom": {
"properties": {
"completionStatus": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"provider": {
"properties": {
"identifiers": {
"properties": {
"identifier": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"name": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"provisionMode": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"creator": {
"properties": {
"name": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"dnetIdentifier": {
"type": "keyword"
},
"identifier": {
"type": "nested",
"properties": {
"identifier": {
"type": "keyword"
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"type": {
"type": "keyword"
}
}
},
"objectType": {
"type": "keyword"
},
"publicationDate": {
"type": "keyword"
},
"publisher": {
"type": "nested",
"properties": {
"name": {
"type": "keyword"
}
}
},
"title": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"target": {
"type": "nested",
"properties": {
"collectedFrom": {
"properties": {
"completionStatus": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"provider": {
"properties": {
"identifiers": {
"properties": {
"identifier": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"name": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"provisionMode": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"creator": {
"properties": {
"name": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"dnetIdentifier": {
"type": "keyword"
},
"identifier": {
"type": "nested",
"properties": {
"identifier": {
"type": "keyword"
},
"schema": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"type": {
"type": "keyword"
}
}
},
"objectType": {
"type": "keyword"
},
"publicationDate": {
"type": "keyword"
},
"publisher": {
"type": "nested",
"properties": {
"name": {
"type": "keyword"
}
}
},
"title": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
}
}
},
"settings": {
"index": {
"refresh_interval": "600s",
"number_of_shards": "48",
"translog": {
"sync_interval": "15s",
"durability": "ASYNC"
},
"analysis": {
"analyzer": {
"analyzer_keyword": {
"filter": "lowercase",
"tokenizer": "keyword"
}
}
},
"number_of_replicas": "0"
}
}
}

132
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/summary_index.json
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@ -1,132 +0,0 @@
{
"mappings": {
"properties": {
"abstract": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"author": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"datasources": {
"type": "nested",
"properties": {
"completionStatus": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"datasourceId": {
"type": "keyword"
},
"datasourceName": {
"type": "keyword"
}
}
},
"date": {
"type": "keyword"
},
"id": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"localIdentifier": {
"type": "nested",
"properties": {
"id": {
"type": "keyword"
},
"type": {
"type": "keyword"
}
}
},
"publisher": {
"type": "keyword"
},
"relatedDatasets": {
"type": "long"
},
"relatedPublications": {
"type": "long"
},
"relatedUnknown": {
"type": "long"
},
"subject": {
"properties": {
"scheme": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"value": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
}
}
},
"title": {
"type": "text",
"fields": {
"keyword": {
"type": "keyword",
"ignore_above": 256
}
}
},
"typology": {
"type": "keyword"
}
}
},
"settings": {
"index": {
"refresh_interval": "600s",
"number_of_shards": "48",
"translog": {
"sync_interval": "15s",
"durability": "ASYNC"
},
"analysis": {
"analyzer": {
"analyzer_keyword": {
"filter": "lowercase",
"tokenizer": "keyword"
}
}
},
"number_of_replicas": "0"
}
}
}

42
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/config-default.xml
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@ -1,42 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.wf.rerun.failnodes</name>
<value>false</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
</configuration>

49
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/export/oozie_app/workflow.xml
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@ -1,49 +0,0 @@
<workflow-app name="Export Scholexplorer Graph to OpenAIRE" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingDirPath</name>
<description>the source path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>memory for individual executor</description>
</property>
</parameters>
<start to="ExtractOAF"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ExtractOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractOAF</name>
<class>eu.dnetlib.dhp.export.SparkExportContentForOpenAire</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/config-default.xml
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@ -1,14 +0,0 @@
<configuration>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

86
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml
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@ -1,86 +0,0 @@
<workflow-app name="Materialize and Index graph to ElasticSearch" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingDirPath</name>
<description>the source path</description>
</property>
<property>
<name>index</name>
<description>the index name</description>
</property>
<property>
<name>esCluster</name>
<description>the Index cluster</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
</parameters>
<start to="DropAndCreateIndex"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DropAndCreateIndex">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.provision.DropAndCreateESIndex</main-class>
<arg>-i</arg><arg>${index}</arg>
<arg>-c</arg><arg>${esCluster}</arg>
</java>
<ok to="indexSummary"/>
<error to="Kill"/>
</action>
<action name="indexSummary">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>index summary</name>
<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingDirPath}/summary_json</arg>
<arg>--index</arg><arg>${index}_object</arg>
<arg>--idPath</arg><arg>id</arg>
<arg>--cluster</arg><arg>${esCluster}</arg>
</spark>
<ok to="indexScholix"/>
<error to="Kill"/>
</action>
<action name="indexScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>index scholix</name>
<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>
<arg>--index</arg><arg>${index}_scholix</arg>
<arg>--idPath</arg><arg>identifier</arg>
<arg>--cluster</arg><arg>${esCluster}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/config-default.xml
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@ -1,14 +0,0 @@
<configuration>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

116
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml
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@ -1,116 +0,0 @@
<workflow-app name="Materialize and Index graph to ElasticSearch" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingDirPath</name>
<description>the source path</description>
</property>
<property>
<name>graphPath</name>
<description>the graph path</description>
</property>
<property>
<name>index</name>
<description>the index name</description>
</property>
<property>
<name>esCluster</name>
<description>the Index cluster</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
</parameters>
<start to="DeleteTargetPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="DeleteTargetPath">
<fs>
<delete path='${workingDirPath}'/>
<mkdir path='${workingDirPath}'/>
</fs>
<ok to="CalculateRelatedItem"/>
<error to="Kill"/>
</action>
<action name="CalculateRelatedItem">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>calculate for each ID the number of related Dataset, publication and Unknown</name>
<class>eu.dnetlib.dhp.provision.SparkExtractRelationCount</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--relationPath</arg><arg>${graphPath}/relation</arg>
</spark>
<ok to="generateSummary"/>
<error to="Kill"/>
</action>
<action name="generateSummary">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>generate Summary</name>
<class>eu.dnetlib.dhp.provision.SparkGenerateSummaryIndex</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--graphPath</arg><arg>${graphPath}</arg>
</spark>
<ok to="generateScholix"/>
<error to="Kill"/>
</action>
<action name="generateScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>generate Scholix</name>
<class>eu.dnetlib.dhp.provision.SparkGenerateScholixIndex</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT}</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--graphPath</arg><arg>${graphPath}</arg>
</spark>
<ok to="datasetToJson"/>
<error to="Kill"/>
</action>
<action name="datasetToJson">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>generate Scholix</name>
<class>eu.dnetlib.dhp.provision.SparkConvertDatasetToJson</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT}</spark-opts>
<arg>-m</arg> <arg>yarn-cluster</arg>
<arg>--workingPath</arg><arg>${workingDirPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

14
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/config-default.xml
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@ -1,14 +0,0 @@
<configuration>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

97
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/workflow.xml
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@ -1,97 +0,0 @@
<workflow-app name="Keep On Synch datacite" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingDirPath</name>
<description>the source path</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>index</name>
<description>index name</description>
</property>
<property>
<name>timestamp</name>
<description>timestamp from incremental harvesting</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingDirPath}/synch'/>
<mkdir path='${workingDirPath}/synch'/>
</fs>
<ok to="ImportDataciteUpdate"/>
<error to="Kill"/>
</action>
<action name="ImportDataciteUpdate">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.provision.update.RetrieveUpdateFromDatacite</main-class>
<arg>-t</arg><arg>${workingDirPath}/synch/input_json</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-ts</arg><arg>${timestamp}</arg>
<arg>-ih</arg><arg>ip-90-147-167-25.ct1.garrservices.it</arg>
<arg>-in</arg><arg>datacite</arg>
</java>
<ok to="resolveScholix"/>
<error to="Kill"/>
</action>
<action name="resolveScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>resolve and generate Scholix</name>
<class>eu.dnetlib.dhp.provision.update.SparkResolveScholixTarget</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>
<arg>-m</arg> <arg>yarn-cluster</arg>
<arg>-s</arg><arg>${workingDirPath}/synch/input_json</arg>
<arg>-w</arg><arg>${workingDirPath}/synch</arg>
<arg>-h</arg><arg>ip-90-147-167-25.ct1.garrservices.it</arg>
</spark>
<ok to="indexScholix"/>
<error to="Kill"/>
</action>
<action name="indexScholix">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>index scholix</name>
<class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
<jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${workingDirPath}/synch/resolved_json</arg>
<arg>--index</arg><arg>${index}_scholix</arg>
<arg>--idPath</arg><arg>identifier</arg>
<arg>--type</arg><arg>scholix</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

48
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/config-default.xml
View File

@ -1,48 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.wf.rerun.failnodes</name>
<value>false</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

53
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml
View File

@ -1,53 +0,0 @@
<workflow-app name="Send Dump to Zenodo" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>targetPath</name>
<description>the target path</description>
</property>
<!-- <property>-->
<!-- <name>metadata</name>-->
<!-- <description>the metadata</description>-->
<!-- </property>-->
</parameters>
<start to="send_zenodo"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="MakeTar">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.export.zenodo.MakeTar</main-class>
<arg>-t</arg><arg>${targetPath}</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-s</arg><arg>${sourcePath}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<!-- <action name="send_zenodo">-->
<!-- <java>-->
<!-- <main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class>-->
<!-- <arg>&#45;&#45;hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg>-->
<!-- <arg>&#45;&#45;nameNode</arg><arg>${nameNode}</arg>-->
<!-- <arg>&#45;&#45;accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg>-->
<!-- <arg>&#45;&#45;connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg>-->
<!-- <arg>&#45;&#45;metadata</arg><arg>${metadata}</arg>-->
<!-- <arg>&#45;&#45;conceptRecordId</arg><arg>1200252</arg>-->
<!-- <arg>&#45;&#45;newDeposition</arg><arg>false</arg>-->
<!-- </java>-->
<!-- <ok to="End"/>-->
<!-- <error to="Kill"/>-->
<!-- </action>-->
<end name="End"/>
</workflow-app>

102
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala
View File

@ -1,102 +0,0 @@
package eu.dnetlib.dhp.export
import java.time.LocalDateTime
import java.time.format.DateTimeFormatter
import eu.dnetlib.dhp.provision.scholix.Scholix
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
import eu.dnetlib.dhp.schema.oaf.Relation
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import scala.io.Source
import scala.collection.JavaConverters._
class ExportDLITOOAFTest {
val mapper = new ObjectMapper()
@Test
def testDate():Unit = {
println(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")))
}
def extractDatasources(s:Scholix):List[String]= {
s.getTarget.getCollectedFrom.asScala.map(c => c.getProvider.getName)(collection.breakOut)
}
def extractDatasources(s:ScholixSummary):List[String] = {
s.getDatasources.asScala.map(c => c.getDatasourceName)(collection.breakOut)
}
@Test
def testMappingRele():Unit = {
val r:Relation = new Relation
r.setSource("60|fbff1d424e045eecf24151a5fe3aa738")
r.setTarget("50|dedup_wf_001::ec409f09e63347d4e834087fe1483877")
r.setRelType("IsReferencedBy")
val r1 =DLIToOAF.convertDLIRelation(r)
println(r1.getSource, r1.getTarget)
}
@Test
def testPublicationMapping():Unit = {
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val json = Source.fromInputStream(getClass.getResourceAsStream("publication.json")).mkString
val oaf =DLIToOAF.convertDLIPublicationToOAF(mapper.readValue(json, classOf[DLIPublication]))
println(mapper.writeValueAsString(oaf))
}
@Test
def testExternalReferenceMapping():Unit = {
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString
val oaf =DLIToOAF.convertDLIDatasetToExternalReference(mapper.readValue(json, classOf[DLIDataset]))
println(oaf)
}
@Test
def testRelationMapping():Unit = {
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val json = Source.fromInputStream(getClass.getResourceAsStream("relation.json")).mkString
val oaf =mapper.readValue(json, classOf[Relation])
println(mapper.writeValueAsString(oaf))
}
}

50
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java
View File

@ -1,50 +0,0 @@
package eu.dnetlib.dhp.provision;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.provision.scholix.Scholix;
import eu.dnetlib.dhp.provision.scholix.ScholixResource;
import eu.dnetlib.dhp.provision.update.*;
import eu.dnetlib.scholexplorer.relation.RelationMapper;
public class DataciteClientTest {
@Test
public void dataciteSCholixTest() throws Exception {
final String json = IOUtils.toString(getClass().getResourceAsStream("datacite.json"));
final RelationMapper mapper = RelationMapper.load();
Datacite2Scholix ds = new Datacite2Scholix(mapper);
final List<Scholix> s = ds.generateScholixFromJson(json);
System.out.println(new ObjectMapper().writeValueAsString(s));
}
// public void testS() throws Exception {
// RetrieveUpdateFromDatacite.main(new String[]{
// "-n", "file:///data/new_s2.txt",
// "-t", "/data/new_s2.txt",
// "-ts", "1586974078",
// "-ih", "ip-90-147-167-25.ct1.garrservices.it",
// "-in", "datacite",
// });
//
// }
public void testResolveDataset() throws Exception {
DataciteClient dc = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it");
ScholixResource datasetByDOI = dc.getDatasetByDOI("10.17182/hepdata.15392.v1/t5");
Assertions.assertNotNull(datasetByDOI);
System.out.println(new ObjectMapper().writeValueAsString(datasetByDOI));
CrossrefClient cr = new CrossrefClient("ip-90-147-167-25.ct1.garrservices.it");
ScholixResource crossrefByDOI = cr.getResourceByDOI("10.26850/1678-4618eqj.v35.1.2010.p41-46");
Assertions.assertNotNull(crossrefByDOI);
System.out.println(new ObjectMapper().writeValueAsString(crossrefByDOI));
}
}

13
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DropAndCreateESIndexTest.java
View File

@ -1,13 +0,0 @@
package eu.dnetlib.dhp.provision;
import org.junit.jupiter.api.Test;
public class DropAndCreateESIndexTest {
public void testDropAndCreate() throws Exception {
DropAndCreateESIndex.main("-c localhost -i dli_shadow".split(" "));
}
}

30
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/ExtractInfoTest.java
View File

@ -1,30 +0,0 @@
package eu.dnetlib.dhp.provision;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.provision.scholix.Scholix;
import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary;
public class ExtractInfoTest {
@Test
public void testSerialization() throws Exception {
ScholixSummary summary = new ScholixSummary();
summary.setDescription("descrizione");
ObjectMapper mapper = new ObjectMapper();
String json = mapper.writeValueAsString(summary);
System.out.println(json);
System.out.println(mapper.readValue(json, ScholixSummary.class).getDescription());
}
@Test
public void testScholix() throws Exception {
final String jsonSummary = IOUtils.toString(getClass().getResourceAsStream("summary.json"));
final String jsonRelation = IOUtils.toString(getClass().getResourceAsStream("relation.json"));
Scholix.generateScholixWithSource(jsonSummary, jsonRelation);
}
}

101
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/dataset.json
View File

@ -1,101 +0,0 @@
{
"dataInfo": {
"invisible": false,
"inferred": null,
"deletedbyinference": false,
"trust": "0.9",
"inferenceprovenance": null,
"provenanceaction": null
},
"lastupdatetimestamp": null,
"id": "60|719f19e5a996de1b87cddf93871bf2d4",
"originalId": [
"a0a3p2gws9::uniprot"
],
"collectedfrom": [
{
"key": "dli_________::europe_pmc__",
"value": "Europe PMC",
"dataInfo": null
}
],
"pid": [
{
"value": "acc63471",
"qualifier": {
"classid": "ena",
"classname": "ena",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"dataInfo": null
}
],
"dateofcollection": "2019-07-05T12:47:11.545+02:00",
"dateoftransformation": null,
"extraInfo": null,
"oaiprovenance": null,
"author": null,
"resulttype": {
"classid": "dataset",
"classname": "dataset",
"schemeid": "dataset",
"schemename": "dataset"
},
"language": null,
"country": null,
"subject": [],
"title": [
{
"value": "CMD domain-containing protein",
"qualifier": null,
"dataInfo": null
}
],
"relevantdate": [
{
"value": "2019-07-15T16:14:28.636",
"qualifier": {
"classid": "resolvedDate",
"classname": "resolvedDate",
"schemeid": "dnet::date",
"schemename": "dnet::date"
},
"dataInfo": null
}
],
"description": null,
"dateofacceptance": null,
"publisher": {
"value": "UniProt",
"dataInfo": null
},
"embargoenddate": null,
"source": null,
"fulltext": null,
"format": null,
"contributor": null,
"resourcetype": null,
"coverage": null,
"bestaccessright": null,
"context": null,
"externalReference": null,
"instance": [],
"storagedate": null,
"device": null,
"size": null,
"version": null,
"lastmetadataupdate": null,
"metadataversionnumber": null,
"geolocation": null,
"originalObjIdentifier": "europe_pmc__::719f19e5a996de1b87cddf93871bf2d4",
"dlicollectedfrom": [
{
"id": "dli_________::europe_pmc__",
"name": "Europe PMC",
"completionStatus": "complete",
"collectionMode": null
}
],
"completionStatus": "complete"
}

128
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/publication.json
View File

@ -1,128 +0,0 @@
{
"dataInfo": {
"invisible": false,
"inferred": null,
"deletedbyinference": false,
"trust": "0.9",
"inferenceprovenance": null,
"provenanceaction": null
},
"lastupdatetimestamp": null,
"id": "50|9e117414be07bf03cbce8889d22d661a",
"originalId": [
"9e117414be07bf03cbce8889d22d661a"
],
"collectedfrom": [
{
"key": "dli_________::crossref",
"value": "Crossref",
"dataInfo": null
}
],
"pid": [
{
"value": "10.1007/978-94-017-3490-5_15",
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"dataInfo": null
}
],
"dateofcollection": "2020-06-08T07:28:55.731Z",
"dateoftransformation": null,
"extraInfo": null,
"oaiprovenance": null,
"author": [
{
"fullname": "Calcaterra Domenico",
"name": null,
"surname": null,
"rank": null,
"pid": null,
"affiliation": null
},
{
"fullname": "Parise Mario",
"name": null,
"surname": null,
"rank": null,
"pid": null,
"affiliation": null
}
],
"resulttype": {
"classid": "publication",
"classname": "publication",
"schemeid": "publication",
"schemename": "publication"
},
"language": null,
"country": null,
"subject":[
{
"value":"Strain-linked information about bacterial and archaeal biodiversity",
"qualifier":{
"classid":"dnet:subject",
"classname":"dnet:subject",
"schemeid":"",
"schemename":""
},
"dataInfo":null
}
],
"title": [
{
"value": "The Contribution of Historical Information in the Assessment of Landslide Hazard",
"qualifier": null,
"dataInfo": null
}
],
"relevantdate": [
{
"value": "2013-01-29T16:50:44Z",
"qualifier": {
"classid": "date",
"classname": "date",
"schemeid": "dnet::date",
"schemename": "dnet::date"
},
"dataInfo": null
}
],
"description": [
{
"value": null,
"dataInfo": null
}
],
"dateofacceptance": null,
"publisher": {
"value": "Springer Netherlands",
"dataInfo": null
},
"embargoenddate": null,
"source": null,
"fulltext": null,
"format": null,
"contributor": null,
"resourcetype": null,
"coverage": null,
"bestaccessright": null,
"context": null,
"externalReference": null,
"instance": [],
"journal": null,
"originalObjIdentifier": "dli_resolver::9e117414be07bf03cbce8889d22d661a",
"dlicollectedfrom": [
{
"id": "dli_________::crossref",
"name": "Crossref",
"completionStatus": "complete",
"collectionMode": "resolved"
}
],
"completionStatus": "complete"
}

23
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json
View File

@ -1,23 +0,0 @@
{
"subRelType": null,
"relClass": "datacite",
"dataInfo": {
"deletedbyinference": false,
"provenanceaction": null,
"inferred": null,
"inferenceprovenance": null,
"invisible": false,
"trust": "0.9"
},
"target": "50|00062410e2a15322480277d063c181bb",
"lastupdatetimestamp": null,
"relType": "IsReferencedBy",
"source": "60|4ee78ab329b49416b45c3774c132f244",
"collectedfrom": [
{
"dataInfo": null,
"value": "Europe PMC",
"key": "dli_________::europe_pmc__"
}
]
}

136
dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/provision/datacite.json
View File

@ -1,136 +0,0 @@
{
"relationships": {
"client": {
"data": {
"type": "clients",
"id": "crossref.citations"
}
}
},
"attributes": {
"contributors": [
],
"titles": [
{
"title": "UV-visible spectroscopy in the interpretation of the tautomeric equilibrium of N,N′(bis-3,5-di-bromo-salicyliden)-1,2-diaminobenzene and the redox activity of its Co(II) complex. A quantum chemical approach."
}
],
"descriptions": [
],
"referenceCount": 0,
"subjects": [
],
"container": {
"title": "Journal of Molecular Structure: THEOCHEM",
"firstPage": "97",
"volume": "367",
"lastPage": "110",
"identifierType": "ISSN",
"identifier": "0166-1280",
"type": "Journal"
},
"state": "findable",
"created": "2020-03-26T13:31:57.000Z",
"source": "levriero",
"metadataVersion": 0,
"version": null,
"isActive": true,
"contentUrl": null,
"geoLocations": [
],
"updated": "2020-03-26T13:31:58.000Z",
"fundingReferences": [
],
"viewCount": 0,
"registered": "2020-03-26T13:31:58.000Z",
"published": "1996",
"dates": [
{
"date": "1996-09",
"dateType": "Issued"
},
{
"date": "2019-04-17T13:58:25Z",
"dateType": "Updated"
}
],
"relatedIdentifiers": [
{
"relationType": "IsPartOf",
"relatedIdentifier": "0166-1280",
"relatedIdentifierType": "ISSN",
"resourceTypeGeneral": "Collection"
}
],
"reason": null,
"rightsList": [
{
"rightsUri": "https://www.elsevier.com/tdm/userlicense/1.0"
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