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dnet-hadoop
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Code Issues 14 Pull Requests 13 Projects 2 Releases 2 Wiki Activity

Merge branch 'master' into graph_cleaning

This commit is contained in:
Claudio Atzori 2020-06-08 15:23:24 +02:00
parent b2349659cf 25a093b1a4
commit 3d871c6651
125 changed files with 10073 additions and 412 deletions
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16
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -58,6 +58,18 @@ public class ModelSupport {
oafTypes.put("relation", Relation.class);
}
public static final Map<Class, String> idPrefixMap = Maps.newHashMap();
static {
idPrefixMap.put(Datasource.class, "10");
idPrefixMap.put(Organization.class, "20");
idPrefixMap.put(Project.class, "40");
idPrefixMap.put(Dataset.class, "50");
idPrefixMap.put(OtherResearchProduct.class, "50");
idPrefixMap.put(Software.class, "50");
idPrefixMap.put(Publication.class, "50");
}
public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
static {
@ -289,6 +301,10 @@ public class ModelSupport {
private ModelSupport() {
}
public static <E extends OafEntity> String getIdPrefix(Class<E> clazz) {
return idPrefixMap.get(clazz);
}
/**
* Checks subclass-superclass relationship.
*

1
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -10,6 +10,7 @@ public class Dataset extends Result implements Serializable {
private Field<String> storagedate;
// candidate for removal
private Field<String> device;
private Field<String> size;

17
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -2,8 +2,10 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
public class Result extends OafEntity implements Serializable {
@ -248,13 +250,24 @@ public class Result extends OafEntity implements Serializable {
StructuredProperty baseMainTitle = null;
if (title != null) {
baseMainTitle = getMainTitle(title);
title.remove(baseMainTitle);
if (baseMainTitle != null) {
final StructuredProperty p = baseMainTitle;
title = title.stream().filter(t -> t != p).collect(Collectors.toList());
}
//
//
// title.remove(baseMainTitle);
}
StructuredProperty newMainTitle = null;
if (r.getTitle() != null) {
newMainTitle = getMainTitle(r.getTitle());
r.getTitle().remove(newMainTitle);
if (newMainTitle != null) {
final StructuredProperty p = newMainTitle;
title = title.stream().filter(t -> t != p).collect(Collectors.toList());
}
// r.getTitle().remove(newMainTitle);
}
if (newMainTitle != null && compareTrust(this, r) < 0)

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -10,8 +10,10 @@ public class Software extends Result implements Serializable {
private List<Field<String>> documentationUrl;
// candidate for removal
private List<StructuredProperty> license;
// candidate for removal
private Field<String> codeRepositoryUrl;
private Qualifier programmingLanguage;

2
dhp-workflows/dhp-broker-events/pom.xml
View File

@ -57,7 +57,7 @@
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaire-broker-common</artifactId>
<version>[2.0.0,3.0.0)</version>
<version>[2.0.1,3.0.0)</version>
</dependency>
</dependencies>

31
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java
View File

@ -12,7 +12,6 @@ import org.apache.commons.codec.digest.DigestUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
@ -37,14 +36,13 @@ public class EventFactory {
final Map<String, Object> map = createMapFromResult(updateInfo);
final String payload = createPayload(updateInfo);
final String eventId =
calculateEventId(updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0), updateInfo.getHighlightValueAsString());
final String eventId = calculateEventId(
updateInfo.getTopicPath(), updateInfo.getTarget().getOriginalId().get(0),
updateInfo.getHighlightValueAsString());
res.setEventId(eventId);
res.setProducerId(PRODUCER_ID);
res.setPayload(payload);
res.setPayload(updateInfo.asBrokerPayload().toJSON());
res.setMap(map);
res.setTopic(updateInfo.getTopicPath());
res.setCreationDate(now);
@ -53,15 +51,6 @@ public class EventFactory {
return res;
}
private static String createPayload(final UpdateInfo<?> updateInfo) {
final OpenAireEventPayload payload = new OpenAireEventPayload();
// TODO : use ConversionUtils
updateInfo.compileHighlight(payload);
return payload.toJSON();
}
private static Map<String, Object> createMapFromResult(final UpdateInfo<?> updateInfo) {
final Map<String, Object> map = new HashMap<>();
@ -92,13 +81,17 @@ public class EventFactory {
final List<StructuredProperty> subjects = target.getSubject();
if (subjects.size() > 0) {
map
.put("target_publication_subject_list", subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
.put(
"target_publication_subject_list",
subjects.stream().map(StructuredProperty::getValue).collect(Collectors.toList()));
}
final List<Author> authors = target.getAuthor();
if (authors.size() > 0) {
map
.put("target_publication_author_list", authors.stream().map(Author::getFullname).collect(Collectors.toList()));
.put(
"target_publication_author_list",
authors.stream().map(Author::getFullname).collect(Collectors.toList()));
}
// PROVENANCE INFO
@ -125,7 +118,9 @@ public class EventFactory {
}
private static long parseDateTolong(final String date) {
if (StringUtils.isBlank(date)) { return -1; }
if (StringUtils.isBlank(date)) {
return -1;
}
try {
return DateUtils.parseDate(date, DATE_PATTERNS).getTime();
} catch (final ParseException e) {

45
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsApplication.java
View File

@ -87,32 +87,25 @@ public class GenerateEventsApplication {
private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMoreSoftware = new EnrichMoreSoftware();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsReferencedBy =
new EnrichMissingPublicationIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsReferencedBy = new EnrichMissingPublicationIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedTo =
new EnrichMissingPublicationIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedBy =
new EnrichMissingPublicationIsSupplementedBy();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedTo = new EnrichMissingPublicationIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedBy = new EnrichMissingPublicationIsSupplementedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMisissingDatasetIsRelatedTo =
new EnrichMissingDatasetIsRelatedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsReferencedBy =
new EnrichMissingDatasetIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetReferences =
new EnrichMissingDatasetReferences();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedTo =
new EnrichMissingDatasetIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedBy =
new EnrichMissingDatasetIsSupplementedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMisissingDatasetIsRelatedTo = new EnrichMissingDatasetIsRelatedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsReferencedBy = new EnrichMissingDatasetIsReferencedBy();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetReferences = new EnrichMissingDatasetReferences();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedTo = new EnrichMissingDatasetIsSupplementedTo();
private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedBy = new EnrichMissingDatasetIsSupplementedBy();
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(GenerateEventsApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
.toString(
GenerateEventsApplication.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
parser.parseArgument(args);
final Boolean isSparkSessionManaged = Optional
@ -156,8 +149,9 @@ public class GenerateEventsApplication {
final String graphPath,
final Class<R> resultClazz) {
final Dataset<R> results = readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<R> results = readPath(
spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), resultClazz)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<Relation> rels = readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
@ -196,15 +190,18 @@ public class GenerateEventsApplication {
return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
}
private static <SRC extends Result, TRG extends OafEntity> JavaRDD<Event> generateRelationEvents(final SparkSession spark,
private static <SRC extends Result, TRG extends OafEntity> JavaRDD<Event> generateRelationEvents(
final SparkSession spark,
final String graphPath,
final Class<SRC> sourceClass,
final Class<TRG> targetClass) {
final Dataset<SRC> sources = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<SRC> sources = readPath(
spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
.filter(r -> r.getDataInfo().getDeletedbyinference());
final Dataset<TRG> targets = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass);
final Dataset<TRG> targets = readPath(
spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass);
final Dataset<Relation> mergedRels = readPath(spark, graphPath + "/relation", Relation.class)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));

3
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMissingProject.java
View File

@ -28,7 +28,8 @@ public class EnrichMissingProject
if (source.getRight().isEmpty()) {
return Arrays.asList();
} else {
return target.getRight()
return target
.getRight()
.stream()
.map(ConversionUtils::oafProjectToBrokerProject)
.map(p -> generateUpdateInfo(p, source, target))

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedProjects/EnrichMoreProject.java
View File

@ -24,12 +24,14 @@ public class EnrichMoreProject extends UpdateMatcher<Pair<Result, List<Project>>
protected List<UpdateInfo<eu.dnetlib.broker.objects.Project>> findUpdates(final Pair<Result, List<Project>> source,
final Pair<Result, List<Project>> target) {
final Set<String> existingProjects = source.getRight()
final Set<String> existingProjects = source
.getRight()
.stream()
.map(Project::getId)
.collect(Collectors.toSet());
return target.getRight()
return target
.getRight()
.stream()
.filter(p -> !existingProjects.contains(p.getId()))
.map(ConversionUtils::oafProjectToBrokerProject)

2
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedPublications/AbstractEnrichMissingPublication.java
View File

@ -39,7 +39,7 @@ public abstract class AbstractEnrichMissingPublication
.getRight()
.stream()
.filter(d -> !existingPublications.contains(d.getId()))
.map(ConversionUtils::oafPublicationToBrokerPublication)
.map(ConversionUtils::oafResultToBrokerPublication)
.map(i -> generateUpdateInfo(i, source, target))
.collect(Collectors.toList());

3
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMissingSoftware.java
View File

@ -29,7 +29,8 @@ public class EnrichMissingSoftware
if (source.getRight().isEmpty()) {
return Arrays.asList();
} else {
return target.getRight()
return target
.getRight()
.stream()
.map(ConversionUtils::oafSoftwareToBrokerSoftware)
.map(p -> generateUpdateInfo(p, source, target))

6
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/relatedSoftware/EnrichMoreSoftware.java
View File

@ -26,12 +26,14 @@ public class EnrichMoreSoftware
final Pair<Result, List<Software>> source,
final Pair<Result, List<Software>> target) {
final Set<String> existingSoftwares = source.getRight()
final Set<String> existingSoftwares = source
.getRight()
.stream()
.map(Software::getId)
.collect(Collectors.toSet());
return target.getRight()
return target
.getRight()
.stream()
.filter(p -> !existingSoftwares.contains(p.getId()))
.map(ConversionUtils::oafSoftwareToBrokerSoftware)

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingOpenAccess.java
View File

@ -28,7 +28,9 @@ public class EnrichMissingOpenAccess extends UpdateMatcher<Result, Instance> {
.filter(right -> right.equals(BrokerConstants.OPEN_ACCESS))
.count();
if (count > 0) { return Arrays.asList(); }
if (count > 0) {
return Arrays.asList();
}
return source
.getInstance()

4
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/BrokerConstants.java
View File

@ -15,7 +15,7 @@ public class BrokerConstants {
public static final String OPEN_ACCESS = "OPEN";
public static final String IS_MERGED_IN_CLASS = "isMergedIn";
public static final List<Class<? extends Result>> RESULT_CLASSES =
Arrays.asList(Publication.class, Dataset.class, Software.class, OtherResearchProduct.class);
public static final List<Class<? extends Result>> RESULT_CLASSES = Arrays
.asList(Publication.class, Dataset.class, Software.class, OtherResearchProduct.class);
}

176
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -5,83 +5,150 @@ import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.broker.objects.Instance;
import eu.dnetlib.broker.objects.Pid;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class ConversionUtils {
public static List<Instance> oafInstanceToBrokerInstances(final eu.dnetlib.dhp.schema.oaf.Instance i) {
private static final Logger log = LoggerFactory.getLogger(ConversionUtils.class);
public static List<eu.dnetlib.broker.objects.Instance> oafInstanceToBrokerInstances(final Instance i) {
return i.getUrl().stream().map(url -> {
final Instance r = new Instance();
r.setUrl(url);
r.setInstancetype(i.getInstancetype().getClassid());
r.setLicense(BrokerConstants.OPEN_ACCESS);
r.setHostedby(i.getHostedby().getValue());
return r;
return new eu.dnetlib.broker.objects.Instance()
.setUrl(url)
.setInstancetype(i.getInstancetype().getClassid())
.setLicense(BrokerConstants.OPEN_ACCESS)
.setHostedby(i.getHostedby().getValue());
}).collect(Collectors.toList());
}
public static Pid oafPidToBrokerPid(final StructuredProperty sp) {
final Pid pid = new Pid();
pid.setValue(sp.getValue());
pid.setType(sp.getQualifier().getClassid());
return pid;
return sp != null ? new Pid()
.setValue(sp.getValue())
.setType(sp.getQualifier().getClassid()) : null;
}
public static final Pair<String, String> oafSubjectToPair(final StructuredProperty sp) {
return Pair.of(sp.getQualifier().getClassid(), sp.getValue());
return sp != null ? Pair.of(sp.getQualifier().getClassid(), sp.getValue()) : null;
}
public static final eu.dnetlib.broker.objects.Dataset oafDatasetToBrokerDataset(final Dataset d) {
final eu.dnetlib.broker.objects.Dataset res = new eu.dnetlib.broker.objects.Dataset();
res.setOriginalId(d.getOriginalId().get(0));
res.setTitles(structPropList(d.getTitle()));
res.setPids(d.getPid().stream().map(ConversionUtils::structeredPropertyToPid).collect(Collectors.toList()));
res.setInstances(d.getInstance().stream().map(ConversionUtils::oafInstanceToBrokerInstances).flatMap(List::stream).collect(Collectors.toList()));
res.setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList()));
return res;
return d != null ? new eu.dnetlib.broker.objects.Dataset()
.setOriginalId(d.getOriginalId().get(0))
.setTitles(structPropList(d.getTitle()))
.setPids(d.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList()))
.setInstances(
d
.getInstance()
.stream()
.map(ConversionUtils::oafInstanceToBrokerInstances)
.flatMap(List::stream)
.collect(Collectors.toList()))
.setCollectedFrom(d.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList()))
: null;
}
public static final eu.dnetlib.broker.objects.Publication oafPublicationToBrokerPublication(final Publication d) {
final eu.dnetlib.broker.objects.Publication res = new eu.dnetlib.broker.objects.Publication();
// TODO This should be reusable
return res;
public static final eu.dnetlib.broker.objects.Publication oafResultToBrokerPublication(final Result result) {
return result != null ? new eu.dnetlib.broker.objects.Publication()
.setOriginalId(result.getOriginalId().get(0))
.setTitles(structPropList(result.getTitle()))
.setAbstracts(fieldList(result.getDescription()))
.setLanguage(result.getLanguage().getClassid())
.setSubjects(structPropList(result.getSubject()))
.setCreators(result.getAuthor().stream().map(Author::getFullname).collect(Collectors.toList()))
.setPublicationdate(result.getDateofcollection())
.setPublisher(fieldValue(result.getPublisher()))
.setEmbargoenddate(fieldValue(result.getEmbargoenddate()))
.setContributor(fieldList(result.getContributor()))
.setJournal(
result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null)
.setCollectedFrom(result.getCollectedfrom().stream().map(KeyValue::getValue).collect(Collectors.toList()))
.setPids(result.getPid().stream().map(ConversionUtils::oafPidToBrokerPid).collect(Collectors.toList()))
.setInstances(
result
.getInstance()
.stream()
.map(ConversionUtils::oafInstanceToBrokerInstances)
.flatMap(List::stream)
.collect(Collectors.toList()))
.setExternalReferences(
result
.getExternalReference()
.stream()
.map(ConversionUtils::oafExtRefToBrokerExtRef)
.collect(Collectors.toList()))
: null;
}
private static eu.dnetlib.broker.objects.Journal oafJournalToBrokerJournal(final Journal journal) {
return journal != null ? new eu.dnetlib.broker.objects.Journal()
.setName(journal.getName())
.setIssn(journal.getIssnPrinted())
.setEissn(journal.getIssnOnline())
.setLissn(journal.getIssnLinking()) : null;
}
private static eu.dnetlib.broker.objects.ExternalReference oafExtRefToBrokerExtRef(final ExternalReference ref) {
return ref != null ? new eu.dnetlib.broker.objects.ExternalReference()
.setRefidentifier(ref.getRefidentifier())
.setSitename(ref.getSitename())
.setType(ref.getQualifier().getClassid())
.setUrl(ref.getUrl())
: null;
}
public static final eu.dnetlib.broker.objects.Project oafProjectToBrokerProject(final Project p) {
final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project();
res.setTitle(fieldValue(p.getTitle()));
res.setAcronym(fieldValue(p.getAcronym()));
res.setCode(fieldValue(p.getCode()));
res.setFunder(null); // TODO
res.setFundingProgram(null); // TODO
res.setJurisdiction(null); // TODO
if (p == null) {
return null;
}
final eu.dnetlib.broker.objects.Project res = new eu.dnetlib.broker.objects.Project()
.setTitle(fieldValue(p.getTitle()))
.setAcronym(fieldValue(p.getAcronym()))
.setCode(fieldValue(p.getCode()));
final String ftree = fieldValue(p.getFundingtree());
if (StringUtils.isNotBlank(ftree)) {
try {
final Document fdoc = DocumentHelper.parseText(ftree);
res.setFunder(fdoc.valueOf("/fundingtree/funder/shortname"));
res.setJurisdiction(fdoc.valueOf("/fundingtree/funder/jurisdiction"));
res.setFundingProgram(fdoc.valueOf("//funding_level_0/name"));
} catch (final DocumentException e) {
log.error("Error in record " + p.getId() + ": invalid fundingtree: " + ftree);
}
}
return res;
}
public static final eu.dnetlib.broker.objects.Software oafSoftwareToBrokerSoftware(final Software sw) {
final eu.dnetlib.broker.objects.Software res = new eu.dnetlib.broker.objects.Software();
res.setName(structPropValue(sw.getTitle()));
res.setDescription(fieldValue(sw.getDescription()));
res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
res.setLandingPage(fieldValue(sw.getDocumentationUrl()));
return res;
}
private static Pid structeredPropertyToPid(final StructuredProperty sp) {
final Pid pid = new Pid();
pid.setValue(sp.getValue());
pid.setType(sp.getQualifier().getClassid());
return pid;
return sw != null ? new eu.dnetlib.broker.objects.Software()
.setName(structPropValue(sw.getTitle()))
.setDescription(fieldValue(sw.getDescription()))
.setRepository(fieldValue(sw.getCodeRepositoryUrl()))
.setLandingPage(fieldValue(sw.getDocumentationUrl()))
: null;
}
private static String fieldValue(final Field<String> f) {
@ -89,14 +156,29 @@ public class ConversionUtils {
}
private static String fieldValue(final List<Field<String>> fl) {
return fl != null && !fl.isEmpty() && fl.get(0) != null ? fl.get(0).getValue() : null;
return fl != null ? fl.stream().map(Field::getValue).filter(StringUtils::isNotBlank).findFirst().orElse(null)
: null;
}
private static String structPropValue(final List<StructuredProperty> props) {
return props != null && !props.isEmpty() && props.get(0) != null ? props.get(0).getValue() : null;
return props != null
? props.stream().map(StructuredProperty::getValue).filter(StringUtils::isNotBlank).findFirst().orElse(null)
: null;
}
private static List<String> fieldList(final List<Field<String>> fl) {
return fl != null
? fl.stream().map(Field::getValue).filter(StringUtils::isNotBlank).collect(Collectors.toList())
: new ArrayList<>();
}
private static List<String> structPropList(final List<StructuredProperty> props) {
return props != null ? props.stream().map(StructuredProperty::getValue).collect(Collectors.toList()) : new ArrayList<>();
return props != null
? props
.stream()
.map(StructuredProperty::getValue)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList())
: new ArrayList<>();
}
}

41
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/UpdateInfo.java
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@ -1,12 +1,16 @@
package eu.dnetlib.dhp.broker.oa.util;
import java.util.List;
import java.util.function.BiConsumer;
import java.util.function.Function;
import eu.dnetlib.broker.objects.OpenAireEventPayload;
import eu.dnetlib.broker.objects.Provenance;
import eu.dnetlib.broker.objects.Publication;
import eu.dnetlib.dhp.broker.model.Topic;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public final class UpdateInfo<T> {
@ -66,12 +70,41 @@ public final class UpdateInfo<T> {
return trust;
}
public void compileHighlight(final OpenAireEventPayload payload) {
compileHighlight.accept(payload.getHighlight(), getHighlightValue());
}
public String getHighlightValueAsString() {
return highlightToString.apply(getHighlightValue());
}
public OpenAireEventPayload asBrokerPayload() {
final Publication p = ConversionUtils.oafResultToBrokerPublication(getSource());
compileHighlight.accept(p, getHighlightValue());
final Publication hl = new Publication();
compileHighlight.accept(hl, getHighlightValue());
final String provId = getSource().getOriginalId().stream().findFirst().orElse(null);
final String provRepo = getSource()
.getCollectedfrom()
.stream()
.map(KeyValue::getValue)
.findFirst()
.orElse(null);
final String provUrl = getSource()
.getInstance()
.stream()
.map(Instance::getUrl)
.flatMap(List::stream)
.findFirst()
.orElse(null);
;
final Provenance provenance = new Provenance().setId(provId).setRepositoryName(provRepo).setUrl(provUrl);
return new OpenAireEventPayload()
.setPublication(p)
.setHighlight(hl)
.setTrust(trust)
.setProvenance(provenance);
}
}

93
dhp-workflows/dhp-doiboost/pom.xml Normal file
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@ -0,0 +1,93 @@
<?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>1.2.2-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-doiboost</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>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
<version>4.3.4</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.cxf</groupId>
<artifactId>cxf-rt-transports-http</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<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>
</dependencies>
</project>

374
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala Normal file
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@ -0,0 +1,374 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
object DoiBoostMappingUtil {
def getUnknownCountry(): Qualifier = {
createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
}
def generateMAGAffiliationId(affId: String): String = {
s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
}
val logger: Logger = LoggerFactory.getLogger(getClass)
//STATIC STRING
val MAG = "microsoft"
val MAG_NAME = "Microsoft Academic Graph"
val ORCID = "ORCID"
val CROSSREF = "Crossref"
val UNPAYWALL = "UnpayWall"
val GRID_AC = "grid.ac"
val WIKPEDIA = "wikpedia"
val doiBoostNSPREFIX = "doiboost____"
val OPENAIRE_PREFIX = "openaire____"
val SEPARATOR = "::"
val DNET_LANGUAGES = "dnet:languages"
val PID_TYPES = "dnet:pid_types"
val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;")
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 organization: Organization =>
val a: AtomicAction[Organization] = new AtomicAction[Organization]
a.setClazz(classOf[Organization])
a.setPayload(organization)
(organization.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 toHostedByItem(input:String): (String, HostedByItemType) = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]]
(c.keys.head, c.values.head)
}
def toISSNPair(publication: Publication) : (String, Publication) = {
val issn = if (publication.getJournal == null) null else publication.getJournal.getIssnPrinted
val eissn =if (publication.getJournal == null) null else publication.getJournal.getIssnOnline
val lissn =if (publication.getJournal == null) null else publication.getJournal.getIssnLinking
if (issn!= null && issn.nonEmpty)
(issn, publication)
else if(eissn!= null && eissn.nonEmpty)
(eissn, publication)
else if(lissn!= null && lissn.nonEmpty)
(lissn, publication)
else
(publication.getId, publication)
}
def generateGridAffiliationId(gridId:String) :String = {
s"20|grid________::${DHPUtils.md5(gridId.toLowerCase().trim())}"
}
def fixResult(result: Dataset) :Dataset = {
val instanceType = result.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty)
if (instanceType.isDefined) {
result.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype))
}
result.getInstance().asScala.foreach(i => {
i.setHostedby(getUbknownHostedBy())
})
result
}
def getUbknownHostedBy():KeyValue = {
val hb = new KeyValue
hb.setValue("Unknown Repository")
hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c")
hb
}
def getOpenAccessQualifier():Qualifier = {
createQualifier("OPEN","Open Access","dnet:access_modes", "dnet:access_modes")
}
def getRestrictedQualifier():Qualifier = {
createQualifier("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes")
}
def fixPublication(input:((String,Publication), (String,HostedByItemType))): Publication = {
val publication = input._1._2
val item = if (input._2 != null) input._2._2 else null
val instanceType = publication.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty)
if (instanceType.isDefined) {
publication.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype))
}
publication.getInstance().asScala.foreach(i => {
val hb = new KeyValue
if (item != null) {
hb.setValue(item.officialname)
hb.setKey(generateDSId(item.id))
if (item.openAccess)
i.setAccessright(getOpenAccessQualifier())
publication.setBestaccessright(getOpenAccessQualifier())
}
else {
hb.setValue("Unknown Repository")
hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c")
}
i.setHostedby(hb)
})
val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid)
if (ar.nonEmpty) {
if(ar.contains("OPEN")){
publication.setBestaccessright(getOpenAccessQualifier())
}
else {
publication.setBestaccessright(getRestrictedQualifier())
}
}
publication
}
def generateDSId(input: String): String = {
val b = StringUtils.substringBefore(input, "::")
val a = StringUtils.substringAfter(input, "::")
s"10|${b}::${DHPUtils.md5(a)}"
}
def generateDataInfo(): DataInfo = {
generateDataInfo("0.9")
}
def filterPublication(publication: Publication): Boolean = {
//Case empty publication
if (publication == null)
return false
//Case publication with no title
if (publication.getTitle == null || publication.getTitle.size == 0)
return false
val s = publication.getTitle.asScala.count(p => p.getValue != null
&& p.getValue.nonEmpty && !p.getValue.equalsIgnoreCase("[NO TITLE AVAILABLE]"))
if (s == 0)
return false
// fixes #4360 (test publisher)
val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null
if (publisher != null && (publisher.equalsIgnoreCase("Test accounts") || publisher.equalsIgnoreCase("CrossRef Test Account"))) {
return false;
}
//Publication with no Author
if (publication.getAuthor == null || publication.getAuthor.size() == 0)
return false
//filter invalid author
val authors = publication.getAuthor.asScala.map(s => {
if (s.getFullname.nonEmpty) {
s.getFullname
}
else
s"${
s.getName
} ${
s.getSurname
}"
})
val c = authors.count(isValidAuthorName)
if (c == 0)
return false
// fixes #4368
if (authors.count(s => s.equalsIgnoreCase("Addie Jackson")) > 0 && "Elsevier BV".equalsIgnoreCase(publication.getPublisher.getValue))
return false
true
}
def isValidAuthorName(fullName: String): Boolean = {
if (fullName == null || fullName.isEmpty)
return false
if (invalidName.contains(fullName.toLowerCase.trim))
return false
true
}
def generateDataInfo(trust: String): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di
}
def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
}
def createCrossrefCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(CROSSREF)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase))
cf
}
def createUnpayWallCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(UNPAYWALL)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase))
cf
}
def createORIDCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(ORCID)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase))
cf
}
def generateIdentifier (oaf: Result, doi: String): String = {
val id = DHPUtils.md5 (doi.toLowerCase)
if (oaf.isInstanceOf[Dataset] )
return s"60|${
doiBoostNSPREFIX
}${
SEPARATOR
}${
id
}"
s"50|${
doiBoostNSPREFIX
}${
SEPARATOR
}${
id
}"
}
def createMAGCollectedFrom(): KeyValue = {
val cf = new KeyValue
cf.setValue(MAG_NAME)
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(MAG))
cf
}
def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = {
val q = new Qualifier
q.setClassid(clsName)
q.setClassname(clsValue)
q.setSchemeid(schName)
q.setSchemename(schValue)
q
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch, sch)
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)
tmp
}
}

80
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala Normal file
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@ -0,0 +1,80 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
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.SparkConf
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkGenerateDOIBoostActionSet {
val logger: Logger = LoggerFactory.getLogger(getClass)
def main(args: Array[String]): Unit = {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
implicit val mapEncoderAS: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
val dbPublicationPath = parser.get("dbPublicationPath")
val dbDatasetPath = parser.get("dbDatasetPath")
val crossRefRelation = parser.get("crossRefRelation")
val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
val dbOrganizationPath = parser.get("dbOrganizationPath")
val workingDirPath = parser.get("targetPath")
spark.read.load(dbDatasetPath).as[OafDataset]
.map(d =>DoiBoostMappingUtil.fixResult(d))
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
spark.read.load(dbPublicationPath).as[Publication]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbOrganizationPath).as[Organization]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(crossRefRelation).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
spark.read.load(dbaffiliationRelationPath).as[Relation]
.map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
.write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
}
}

140
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala Normal file
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@ -0,0 +1,140 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset, Organization}
import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.functions.col
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkGenerateDoiBoost {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
import spark.implicits._
val hostedByMapPath = parser.get("hostedByMapPath")
val workingDirPath = parser.get("workingDirPath")
implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
logger.info("Phase 2) Join Crossref with UnpayWall")
val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p))
val uwPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/uwPublication").as[Publication].map(p => (p.getId, p))
def applyMerge(item:((String, Publication), (String, Publication))) : Publication =
{
val crossrefPub = item._1._2
if (item._2!= null) {
val otherPub = item._2._2
if (otherPub != null) {
crossrefPub.mergeFrom(otherPub)
}
}
crossrefPub
}
crossrefPublication.joinWith(uwPublication, crossrefPublication("_1").equalTo(uwPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/firstJoin")
logger.info("Phase 3) Join Result with ORCID")
val fj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p))
val orcidPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p))
fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/secondJoin")
logger.info("Phase 3) Join Result with MAG")
val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p))
val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p))
sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
val doiBoostPublication: Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
val hostedByDataset : Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left")
.map(DoiBoostMappingUtil.fixPublication)
.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered")
val affiliationPath = parser.get("affiliationPath")
val paperAffiliationPath = parser.get("paperAffiliationPath")
val affiliation = spark.read.load(affiliationPath).select(col("AffiliationId"), col("GridId"), col("OfficialPage"), col("DisplayName"))
val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId"))
val a:Dataset[DoiBoostAffiliation] = paperAffiliation
.joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId")))
.select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
val magPubs:Dataset[(String,Publication)]= spark.read.load(s"$workingDirPath/doiBoostPublicationFiltered").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p))(tupleForJoinEncoder).filter(s =>s._1!= null )
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
val pub:Publication = item._1._2
val affiliation = item._2
val affId:String = if (affiliation.GridId.isDefined) DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId.get) else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
val r:Relation = new Relation
r.setSource(pub.getId)
r.setTarget(affId)
r.setRelType("resultOrganization")
r.setRelClass("hasAuthorInstitution")
r.setSubRelType("affiliation")
r.setDataInfo(pub.getDataInfo)
r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
val r1:Relation = new Relation
r1.setTarget(pub.getId)
r1.setSource(affId)
r1.setRelType("resultOrganization")
r1.setRelClass("isAuthorInstitutionOf")
r1.setSubRelType("affiliation")
r1.setDataInfo(pub.getDataInfo)
r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
List(r, r1)
})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
val affiliation = item._2
if (affiliation.GridId.isEmpty) {
val o = new Organization
o.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
o.setDataInfo(DoiBoostMappingUtil.generateDataInfo())
o.setId(DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString))
o.setOriginalId(List(affiliation.AffiliationId.toString).asJava)
if (affiliation.DisplayName.nonEmpty)
o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
if (affiliation.OfficialPage.isDefined)
o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
o.setCountry(DoiBoostMappingUtil.getUnknownCountry())
o
}
else
null
}).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
}
}

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package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.apache.commons.lang.StringUtils
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.util.matching.Regex
case class mappingAffiliation(name: String) {}
case class mappingAuthor(given: Option[String], family: String, ORCID: Option[String], affiliation: Option[mappingAffiliation]) {}
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
case object Crossref2Oaf {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mappingCrossrefType = Map(
"book-section" -> "publication",
"book" -> "publication",
"book-chapter" -> "publication",
"book-part" -> "publication",
"book-series" -> "publication",
"book-set" -> "publication",
"book-track" -> "publication",
"edited-book" -> "publication",
"reference-book" -> "publication",
"monograph" -> "publication",
"journal-article" -> "publication",
"dissertation" -> "publication",
"other" -> "publication",
"peer-review" -> "publication",
"proceedings" -> "publication",
"proceedings-article" -> "publication",
"reference-entry" -> "publication",
"report" -> "publication",
"report-series" -> "publication",
"standard" -> "publication",
"standard-series" -> "publication",
"posted-content" -> "publication",
"dataset" -> "dataset"
)
val mappingCrossrefSubType = Map(
"book-section" -> "0013 Part of book or chapter of book",
"book" -> "0002 Book",
"book-chapter" -> "0013 Part of book or chapter of book",
"book-part" -> "0013 Part of book or chapter of book",
"book-series" -> "0002 Book",
"book-set" -> "0002 Book",
"book-track" -> "0002 Book",
"edited-book" -> "0002 Book",
"reference-book" -> "0002 Book",
"monograph" -> "0002 Book",
"journal-article" -> "0001 Article",
"dissertation" -> "0006 Doctoral thesis",
"other" -> "0038 Other literature type",
"peer-review" -> "0015 Review",
"proceedings" -> "0004 Conference object",
"proceedings-article" -> "0004 Conference object",
"reference-entry" -> "0013 Part of book or chapter of book",
"report" -> "0017 Report",
"report-series" -> "0017 Report",
"standard" -> "0038 Other literature type",
"standard-series" -> "0038 Other literature type",
"dataset" -> "0021 Dataset",
"preprint" -> "0016 Preprint",
"report" -> "0017 Report"
)
def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
//MAPPING Crossref DOI into PID
val doi: String = (json \ "DOI").extract[String]
result.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
//MAPPING Crossref DOI into OriginalId
//and Other Original Identifier of dataset like clinical-trial-number
val clinicalTrialNumbers = for (JString(ctr) <- json \ "clinical-trial-number") yield ctr
val alternativeIds = for (JString(ids) <- json \ "alternative-id") yield ids
val tmp = clinicalTrialNumbers ::: alternativeIds ::: List(doi)
result.setOriginalId(tmp.filter(id => id != null).asJava)
//Set identifier as {50|60} | doiboost____::md5(DOI)
result.setId(generateIdentifier(result, doi))
// Add DataInfo
result.setDataInfo(generateDataInfo())
result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long])
result.setDateofcollection((json \ "indexed" \ "date-time").extract[String])
result.setCollectedfrom(List(createCrossrefCollectedFrom()).asJava)
// Publisher ( Name of work's publisher mapped into Result/Publisher)
val publisher = (json \ "publisher").extractOrElse[String](null)
if (publisher!= null && publisher.nonEmpty)
result.setPublisher(asField(publisher))
// TITLE
val mainTitles = for {JString(title) <- json \ "title" if title.nonEmpty} yield createSP(title, "main title", "dnet:dataCite_title")
val originalTitles = for {JString(title) <- json \ "original-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title")
val shortTitles = for {JString(title) <- json \ "short-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title")
val subtitles = for {JString(title) <- json \ "subtitle" if title.nonEmpty} yield createSP(title, "subtitle", "dnet:dataCite_title")
result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
// DESCRIPTION
val descriptionList = for {JString(description) <- json \ "abstract"} yield asField(description)
result.setDescription(descriptionList.asJava)
// Source
val sourceList = for {JString(source) <- json \ "source" if source!= null && source.nonEmpty} yield asField(source)
result.setSource(sourceList.asJava)
//RELEVANT DATE Mapping
val createdDate = generateDate((json \ "created" \ "date-time").extract[String], (json \ "created" \ "date-parts").extract[List[List[Int]]], "created", "dnet:dataCite_date")
val postedDate = generateDate((json \ "posted" \ "date-time").extractOrElse[String](null), (json \ "posted" \ "date-parts").extract[List[List[Int]]], "available", "dnet:dataCite_date")
val acceptedDate = generateDate((json \ "accepted" \ "date-time").extractOrElse[String](null), (json \ "accepted" \ "date-parts").extract[List[List[Int]]], "accepted", "dnet:dataCite_date")
val publishedPrintDate = generateDate((json \ "published-print" \ "date-time").extractOrElse[String](null), (json \ "published-print" \ "date-parts").extract[List[List[Int]]], "published-print", "dnet:dataCite_date")
val publishedOnlineDate = generateDate((json \ "published-online" \ "date-time").extractOrElse[String](null), (json \ "published-online" \ "date-parts").extract[List[List[Int]]], "published-online", "dnet:dataCite_date")
val issuedDate = extractDate((json \ "issued" \ "date-time").extractOrElse[String](null), (json \ "issued" \ "date-parts").extract[List[List[Int]]])
if (StringUtils.isNotBlank(issuedDate)) {
result.setDateofacceptance(asField(issuedDate))
}
else {
result.setDateofacceptance(asField(createdDate.getValue))
}
result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava)
//Mapping Subject
val subjectList:List[String] = (json \ "subject").extractOrElse[List[String]](List())
if (subjectList.nonEmpty) {
result.setSubject(subjectList.map(s=> createSP(s, "keywords", "dnet:subject_classification_typologies")).asJava)
}
//Mapping Author
val authorList: List[mappingAuthor] = (json \ "author").extractOrElse[List[mappingAuthor]](List())
result.setAuthor(authorList.map(a => generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull)).asJava)
// Mapping instance
val instance = new Instance()
val license = for {
JString(lic) <- json \ "license" \ "URL"
} yield asField(lic)
val l = license.filter(d => StringUtils.isNotBlank(d.getValue))
if (l.nonEmpty)
instance.setLicense(l.head)
val has_review = (json \ "relation" \"has-review" \ "id")
if(has_review != JNothing)
instance.setRefereed(asField("peerReviewed"))
instance.setAccessright(getRestrictedQualifier())
result.setInstance(List(instance).asJava)
instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
result.setResourcetype(createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource"))
instance.setCollectedfrom(createCrossrefCollectedFrom())
if (StringUtils.isNotBlank(issuedDate)) {
instance.setDateofacceptance(asField(issuedDate))
}
val s: String = (json \ "URL").extract[String]
val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct
if (links.nonEmpty)
instance.setUrl(links.asJava)
result
}
def generateAuhtor(given: String, family: String, orcid: String): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
a
}
def convert(input: String): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
var resultList: List[Oaf] = List()
val objectType = (json \ "type").extractOrElse[String](null)
val objectSubType = (json \ "subtype").extractOrElse[String](null)
if (objectType == null)
return resultList
val result = generateItemFromType(objectType, objectSubType)
if (result == null)
return List()
val cOBJCategory = mappingCrossrefSubType.getOrElse(objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type"));
mappingResult(result, json, cOBJCategory)
val funderList: List[mappingFunder] = (json \ "funder").extractOrElse[List[mappingFunder]](List())
if (funderList.nonEmpty) {
resultList = resultList ::: mappingFunderToRelations(funderList, result.getId, createCrossrefCollectedFrom(), result.getDataInfo, result.getLastupdatetimestamp)
}
result match {
case publication: Publication => convertPublication(publication, json, cOBJCategory)
case dataset: Dataset => convertDataset(dataset)
}
resultList = resultList ::: List(result)
resultList
}
def mappingFunderToRelations(funders: List[mappingFunder], sourceId: String, cf: KeyValue, di: DataInfo, ts: Long): List[Relation] = {
val queue = new mutable.Queue[Relation]
def snfRule(award:String): String = {
var tmp1 = StringUtils.substringAfter(award,"_")
val tmp2 = StringUtils.substringBefore(tmp1,"/")
logger.debug(s"From $award to $tmp2")
tmp2
}
def extractECAward(award: String): String = {
val awardECRegex: Regex = "[0-9]{4,9}".r
if (awardECRegex.findAllIn(award).hasNext)
return awardECRegex.findAllIn(award).max
null
}
def generateRelation(sourceId:String, targetId:String, nsPrefix:String) :Relation = {
val r = new Relation
r.setSource(sourceId)
r.setTarget(s"$nsPrefix::$targetId")
r.setRelType("resultProject")
r.setRelClass("isProducedBy")
r.setSubRelType("outcome")
r.setCollectedfrom(List(cf).asJava)
r.setDataInfo(di)
r.setLastupdatetimestamp(ts)
r
}
def generateSimpleRelationFromAward(funder: mappingFunder, nsPrefix: String, extractField: String => String): Unit = {
if (funder.award.isDefined && funder.award.get.nonEmpty)
funder.award.get.map(extractField).filter(a => a!= null && a.nonEmpty).foreach(
award => {
val targetId = DHPUtils.md5(award)
queue += generateRelation(sourceId, targetId, nsPrefix)
}
)
}
if (funders != null)
funders.foreach(funder => {
if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) {
funder.DOI.get match {
case "10.13039/100010663" |
"10.13039/100010661" |
"10.13039/501100007601" |
"10.13039/501100000780" |
"10.13039/100010665" => generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
case "10.13039/100011199" |
"10.13039/100004431" |
"10.13039/501100004963" |
"10.13039/501100000780" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a)
case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a)
case "10.13039/501100001602" => generateSimpleRelationFromAward(funder, "aka_________", a => a.replace("SFI", ""))
case "10.13039/501100000923" => generateSimpleRelationFromAward(funder, "arc_________", a => a)
case "10.13039/501100000038"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "nserc_______" )
case "10.13039/501100000155"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "sshrc_______" )
case "10.13039/501100000024"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "cihr________" )
case "10.13039/501100002848" => generateSimpleRelationFromAward(funder, "conicytf____", a => a)
case "10.13039/501100003448" => generateSimpleRelationFromAward(funder, "gsrt________", extractECAward)
case "10.13039/501100010198" => generateSimpleRelationFromAward(funder, "sgov________", a=>a)
case "10.13039/501100004564" => generateSimpleRelationFromAward(funder, "mestd_______", extractECAward)
case "10.13039/501100003407" => generateSimpleRelationFromAward(funder, "miur________", a=>a)
queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "miur________" )
case "10.13039/501100006588" |
"10.13039/501100004488" => generateSimpleRelationFromAward(funder, "irb_hr______", a=>a.replaceAll("Project No.", "").replaceAll("HRZZ-","") )
case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a)
case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snfRule)
case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a)
case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a)
case "10.13039/100004440"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" )
case _ => logger.debug("no match for "+funder.DOI.get )
}
} else {
funder.name match {
case "European Union’s Horizon 2020 research and innovation program" => generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
case "European Union's" =>
generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward)
generateSimpleRelationFromAward(funder, "corda_______", extractECAward)
case "The French National Research Agency (ANR)" |
"The French National Research Agency" => generateSimpleRelationFromAward(funder, "anr_________", a => a)
case "CONICYT, Programa de Formación de Capital Humano Avanzado" => generateSimpleRelationFromAward(funder, "conicytf____", extractECAward)
case "Wellcome Trust Masters Fellowship" => queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" )
case _ => logger.debug("no match for "+funder.name )
}
}
}
)
queue.toList
}
def convertDataset(dataset: Dataset): Unit = {
// TODO check if there are other info to map into the Dataset
}
def convertPublication(publication: Publication, json: JValue, cobjCategory: String): Unit = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val containerTitles = for {JString(ct) <- json \ "container-title"} yield ct
//Mapping book
if (cobjCategory.toLowerCase.contains("book")) {
val ISBN = for {JString(isbn) <- json \ "ISBN"} yield isbn
if (ISBN.nonEmpty && containerTitles.nonEmpty) {
val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
if (publication.getSource != null) {
val l: List[Field[String]] = publication.getSource.asScala.toList
val ll: List[Field[String]] = l ::: List(asField(source))
publication.setSource(ll.asJava)
}
else
publication.setSource(List(asField(source)).asJava)
}
} else {
// Mapping Journal
val issnInfos = for {JArray(issn_types) <- json \ "issn-type"
JObject(issn_type) <- issn_types
JField("type", JString(tp)) <- issn_type
JField("value", JString(vl)) <- issn_type
} yield Tuple2(tp, vl)
val volume = (json \ "volume").extractOrElse[String](null)
if (containerTitles.nonEmpty) {
val journal = new Journal
journal.setName(containerTitles.head)
if (issnInfos.nonEmpty) {
issnInfos.foreach(tp => {
tp._1 match {
case "electronic" => journal.setIssnOnline(tp._2)
case "print" => journal.setIssnPrinted(tp._2)
}
})
}
journal.setVol(volume)
val page = (json \ "page").extractOrElse[String](null)
if (page != null) {
val pp = page.split("-")
if (pp.nonEmpty)
journal.setSp(pp.head)
if (pp.size > 1)
journal.setEp(pp(1))
}
publication.setJournal(journal)
}
}
}
def extractDate(dt: String, datePart: List[List[Int]]): String = {
if (StringUtils.isNotBlank(dt))
return dt
if (datePart != null && datePart.size == 1) {
val res = datePart.head
if (res.size == 3) {
val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
if (dp.length == 10) {
return dp
}
}
}
null
}
def generateDate(dt: String, datePart: List[List[Int]], classId: String, schemeId: String): StructuredProperty = {
val dp = extractDate(dt, datePart)
if (StringUtils.isNotBlank(dp))
return createSP(dp, classId, schemeId)
null
}
def generateItemFromType(objectType: String, objectSubType: String): Result = {
if (mappingCrossrefType.contains(objectType)) {
if (mappingCrossrefType(objectType).equalsIgnoreCase("publication"))
return new Publication()
if (mappingCrossrefType(objectType).equalsIgnoreCase("dataset"))
return new Dataset()
}
null
}
}

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package eu.dnetlib.doiboost.crossref;
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.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class CrossrefImporter {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
CrossrefImporter.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/import_from_es.json")));
parser.parseArgument(args);
final String hdfsuri = parser.get("namenode");
System.out.println("HDFS URI" + hdfsuri);
Path hdfswritepath = new Path(parser.get("targetPath"));
System.out.println("TargetPath: " + hdfsuri);
final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))
? Long.parseLong(parser.get("timestamp"))
: -1;
if (timestamp > 0)
System.out.println("Timestamp added " + timestamp);
// ====== 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());
ESClient client = timestamp > 0
? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp)
: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfswritepath),
SequenceFile.Writer.keyClass(IntWritable.class),
SequenceFile.Writer.valueClass(Text.class))) {
int i = 0;
long start = System.currentTimeMillis();
long end = 0;
final IntWritable key = new IntWritable(i);
final Text value = new Text();
while (client.hasNext()) {
key.set(i++);
value.set(client.next());
writer.append(key, value);
if (i % 100000 == 0) {
end = System.currentTimeMillis();
final float time = (end - start) / 1000.0F;
System.out
.println(
String.format("Imported %d records last 100000 imported in %f seconds", i, time));
start = System.currentTimeMillis();
}
}
}
}
public 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);
}
byte[] unzippeddata = bos.toByteArray();
decompresser.end();
return new String(unzippeddata);
} catch (Throwable e) {
throw new RuntimeException("Wrong record:" + blob, e);
}
}
}

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package eu.dnetlib.doiboost.crossref;
import java.io.IOException;
import java.util.Iterator;
import java.util.List;
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 org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.jayway.jsonpath.JsonPath;
public class ESClient implements Iterator<String> {
private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
static final String blobPath = "$.hits[*].hits[*]._source.blob";
static final String scrollIdPath = "$._scroll_id";
static final String JSON_NO_TS = "{\"size\":1000}";
static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
private final String scrollId;
private List<String> buffer;
private final String esHost;
public ESClient(final String esHost, final String esIndex) throws IOException {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS);
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body);
}
public ESClient(final String esHost, final String esIndex, final long timestamp)
throws IOException {
this.esHost = esHost;
final String body = getResponse(
String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
String.format(JSON_WITH_TS, timestamp));
scrollId = getJPathString(scrollIdPath, body);
buffer = getBlobs(body);
}
private 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) {
final List<String> res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
return res;
}
@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(JSON_SCROLL, scrollId);
final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
try {
buffer = getBlobs(body);
} catch (Throwable e) {
logger.error("Error on get next page: body:" + body);
}
}
return nextItem;
}
}

98
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/SparkMapDumpIntoOAF.scala Normal file
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package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
import org.apache.commons.io.IOUtils
import org.apache.hadoop.io.{IntWritable, Text}
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
case class Reference(author: String, firstPage: String) {}
object SparkMapDumpIntoOAF {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(SparkMapDumpIntoOAF.getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation]
implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
val sc = spark.sparkContext
val targetPath = parser.get("targetPath")
sc.sequenceFile(parser.get("sourcePath"), classOf[IntWritable], classOf[Text])
.map(k => k._2.toString).map(CrossrefImporter.decompressBlob)
.flatMap(k => Crossref2Oaf.convert(k)).saveAsObjectFile(s"${targetPath}/mixObject")
val inputRDD = sc.objectFile[Oaf](s"${targetPath}/mixObject").filter(p=> p!= null)
val distinctPubs:RDD[Publication] = inputRDD.filter(k => k != null && k.isInstanceOf[Publication])
.map(k => k.asInstanceOf[Publication]).map { p: Publication => Tuple2(p.getId, p) }.reduceByKey { case (p1: Publication, p2: Publication) =>
var r = if (p1 == null) p2 else p1
if (p1 != null && p2 != null) {
if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
r = p2
else
r = p1
} else {
r = if (p1.getLastupdatetimestamp == null) p2 else p1
}
}
r
}.map(_._2)
val pubs:Dataset[Publication] = spark.createDataset(distinctPubs)
pubs.write.mode(SaveMode.Overwrite).save(s"${targetPath}/publication")
val distincDatasets:RDD[OafDataset] = inputRDD.filter(k => k != null && k.isInstanceOf[OafDataset])
.map(k => k.asInstanceOf[OafDataset]).map(p => Tuple2(p.getId, p)).reduceByKey { case (p1: OafDataset, p2: OafDataset) =>
var r = if (p1 == null) p2 else p1
if (p1 != null && p2 != null) {
if (p1.getLastupdatetimestamp != null && p2.getLastupdatetimestamp != null) {
if (p1.getLastupdatetimestamp < p2.getLastupdatetimestamp)
r = p2
else
r = p1
} else {
r = if (p1.getLastupdatetimestamp == null) p2 else p1
}
}
r
}.map(_._2)
spark.createDataset(distincDatasets).write.mode(SaveMode.Overwrite).save(s"${targetPath}/dataset")
val distinctRels =inputRDD.filter(k => k != null && k.isInstanceOf[Relation])
.map(k => k.asInstanceOf[Relation]).map(r=> (s"${r.getSource}::${r.getTarget}",r))
.reduceByKey { case (p1: Relation, p2: Relation) =>
if (p1 == null) p2 else p1
}.map(_._2)
val rels: Dataset[Relation] = spark.createDataset(distinctRels)
rels.write.mode(SaveMode.Overwrite).save(s"${targetPath}/relations")
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala Normal file
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package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.util.matching.Regex
case class MagPapers(PaperId: Long, Rank: Integer, Doi: String,
DocType: String, PaperTitle: String, OriginalTitle: String,
BookTitle: String, Year: Option[Integer], Date: Option[java.sql.Timestamp], Publisher: String,
JournalId: Option[Long], ConferenceSeriesId: Option[Long], ConferenceInstanceId: Option[Long],
Volume: String, Issue: String, FirstPage: String, LastPage: String,
ReferenceCount: Option[Long], CitationCount: Option[Long], EstimatedCitation: Option[Long],
OriginalVenue: String, FamilyId: Option[Long], CreatedDate: java.sql.Timestamp) {}
case class MagPaperAbstract(PaperId: Long, IndexedAbstract: String) {}
case class MagAuthor(AuthorId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], LastKnownAffiliationId: Option[Long], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {}
case class MagAffiliation(AffiliationId: Long, Rank: Int, NormalizedName: String, DisplayName: String, GridId: String, OfficialPage: String, WikiPage: String, PaperCount: Long, CitationCount: Long, Latitude: Option[Float], Longitude: Option[Float], CreatedDate: java.sql.Timestamp) {}
case class MagPaperAuthorAffiliation(PaperId: Long, AuthorId: Long, AffiliationId: Option[Long], AuthorSequenceNumber: Int, OriginalAuthor: String, OriginalAffiliation: String) {}
case class MagAuthorAffiliation(author: MagAuthor, affiliation:String)
case class MagPaperWithAuthorList(PaperId: Long, authors: List[MagAuthorAffiliation]) {}
case class MagPaperAuthorDenormalized(PaperId: Long, author: MagAuthor, affiliation:String) {}
case class MagPaperUrl(PaperId: Long, SourceType: Option[Int], SourceUrl: Option[String], LanguageCode: Option[String]) {}
case class MagUrlInstance(SourceUrl:String){}
case class MagUrl(PaperId: Long, instances: List[MagUrlInstance])
case class MagSubject(FieldOfStudyId:Long, DisplayName:String, MainType:Option[String], Score:Float){}
case class MagFieldOfStudy(PaperId:Long, subjects:List[MagSubject]) {}
case class MagJournal(JournalId: Long, Rank: Option[Int], NormalizedName: Option[String], DisplayName: Option[String], Issn: Option[String], Publisher: Option[String], Webpage: Option[String], PaperCount: Option[Long], CitationCount: Option[Long], CreatedDate: Option[java.sql.Timestamp]) {}
case class MagConferenceInstance(ci:Long, DisplayName:Option[String], Location:Option[String], StartDate:Option[java.sql.Timestamp], EndDate:Option[java.sql.Timestamp], PaperId:Long){}
case object ConversionUtil {
def extractMagIdentifier(pids:mutable.Buffer[String]) :String ={
val magIDRegex: Regex = "^[0-9]+$".r
val s =pids.filter(p=> magIDRegex.findAllIn(p).hasNext)
if (s.nonEmpty)
return s.head
null
}
def mergePublication(a: Publication, b:Publication) : Publication = {
if ((a != null) && (b != null)) {
a.mergeFrom(b)
a
} else {
if (a == null) b else a
}
}
def choiceLatestMagArtitcle(p1: MagPapers, p2:MagPapers) :MagPapers = {
var r = if (p1 == null) p2 else p1
if (p1 != null && p2 != null) {
if (p1.CreatedDate != null && p2.CreatedDate != null) {
if (p1.CreatedDate.before(p2.CreatedDate))
r = p2
else
r = p1
} else {
r = if (p1.CreatedDate == null) p2 else p1
}
}
r
}
def updatePubsWithDescription(inputItem:((String, Publication), MagPaperAbstract)) : Publication = {
val pub = inputItem._1._2
val abst = inputItem._2
if (abst != null) {
pub.setDescription(List(asField(abst.IndexedAbstract)).asJava)
}
pub
}
def updatePubsWithConferenceInfo(inputItem:((String, Publication), MagConferenceInstance)) : Publication = {
val publication:Publication= inputItem._1._2
val ci:MagConferenceInstance = inputItem._2
if (ci!= null){
val j:Journal = new Journal
if (ci.Location.isDefined)
j.setConferenceplace(ci.Location.get)
j.setName(ci.DisplayName.get)
if (ci.StartDate.isDefined && ci.EndDate.isDefined)
{
j.setConferencedate(s"${ci.StartDate.get.toString.substring(0,10)} - ${ci.EndDate.get.toString.substring(0,10)}")
}
publication.setJournal(j)
}
publication
}
def updatePubsWithSubject(item:((String, Publication), MagFieldOfStudy)) : Publication = {
val publication = item._1._2
val fieldOfStudy = item._2
if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) {
val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
val s1 = createSP(s.DisplayName, "keywords", "dnet:subject_classification_typologies")
val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
var resList: List[StructuredProperty] = List(s1)
if (s.MainType.isDefined) {
val maintp = s.MainType.get
val s2 = createSP(s.MainType.get, "keywords", "dnet:subject_classification_typologies")
s2.setDataInfo(di)
resList = resList ::: List(s2)
if (maintp.contains(".")) {
val s3 = createSP(maintp.split("\\.").head, "keywords", "dnet:subject_classification_typologies")
s3.setDataInfo(di)
resList = resList ::: List(s3)
}
}
resList
})
publication.setSubject(p.asJava)
}
publication
}
def addInstances(a: (Publication, MagUrl)): Publication = {
val pub = a._1
val urls = a._2
val i = new Instance
if (urls!= null) {
val l:List[String] = urls.instances.filter(k=>k.SourceUrl.nonEmpty).map(k=>k.SourceUrl):::List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}")
i.setUrl(l.asJava)
}
else
i.setUrl(List(s"https://academic.microsoft.com/#/detail/${extractMagIdentifier(pub.getOriginalId.asScala)}").asJava)
i.setCollectedfrom(createMAGCollectedFrom())
pub.setInstance(List(i).asJava)
pub
}
def transformPaperAbstract(input: MagPaperAbstract): MagPaperAbstract = {
MagPaperAbstract(input.PaperId, convertInvertedIndexString(input.IndexedAbstract))
}
def createOAFFromJournalAuthorPaper(inputParams: ((MagPapers, MagJournal), MagPaperWithAuthorList)): Publication = {
val paper = inputParams._1._1
val journal = inputParams._1._2
val authors = inputParams._2
val pub = new Publication
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava)
//Set identifier as {50|60} | doiboost____::md5(DOI)
pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase))
val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title")
val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title")
pub.setTitle(List(mainTitles, originalTitles).asJava)
pub.setSource(List(asField(paper.BookTitle)).asJava)
val authorsOAF = authors.authors.map { f: MagAuthorAffiliation =>
val a: eu.dnetlib.dhp.schema.oaf.Author = new eu.dnetlib.dhp.schema.oaf.Author
a.setFullname(f.author.DisplayName.get)
if(f.affiliation!= null)
a.setAffiliation(List(asField(f.affiliation)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava)
a
}
pub.setAuthor(authorsOAF.asJava)
if (paper.Date != null && paper.Date.isDefined) {
pub.setDateofacceptance(asField(paper.Date.get.toString.substring(0,10)))
}
pub.setPublisher(asField(paper.Publisher))
if (journal != null && journal.DisplayName.isDefined) {
val j = new Journal
j.setName(journal.DisplayName.get)
j.setSp(paper.FirstPage)
j.setEp(paper.LastPage)
if (journal.Publisher.isDefined)
pub.setPublisher(asField(journal.Publisher.get))
if (journal.Issn.isDefined)
j.setIssnPrinted(journal.Issn.get)
pub.setJournal(j)
}
pub.setCollectedfrom(List(createMAGCollectedFrom()).asJava)
pub.setDataInfo(generateDataInfo())
pub
}
def createOAF(inputParams: ((MagPapers, MagPaperWithAuthorList), MagPaperAbstract)): Publication = {
val paper = inputParams._1._1
val authors = inputParams._1._2
val description = inputParams._2
val pub = new Publication
pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", PID_TYPES)).asJava)
pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava)
//Set identifier as {50|60} | doiboost____::md5(DOI)
pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase))
val mainTitles = createSP(paper.PaperTitle, "main title", "dnet:dataCite_title")
val originalTitles = createSP(paper.OriginalTitle, "alternative title", "dnet:dataCite_title")
pub.setTitle(List(mainTitles, originalTitles).asJava)
pub.setSource(List(asField(paper.BookTitle)).asJava)
if (description != null) {
pub.setDescription(List(asField(description.IndexedAbstract)).asJava)
}
val authorsOAF = authors.authors.map { f: MagAuthorAffiliation =>
val a: eu.dnetlib.dhp.schema.oaf.Author = new eu.dnetlib.dhp.schema.oaf.Author
a.setFullname(f.author.DisplayName.get)
if(f.affiliation!= null)
a.setAffiliation(List(asField(f.affiliation)).asJava)
a.setPid(List(createSP(s"https://academic.microsoft.com/#/detail/${f.author.AuthorId}", "URL", PID_TYPES)).asJava)
a
}
if (paper.Date != null) {
pub.setDateofacceptance(asField(paper.Date.toString.substring(0,10)))
}
pub.setAuthor(authorsOAF.asJava)
pub
}
def convertInvertedIndexString(json_input: String): String = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(json_input)
val idl = (json \ "IndexLength").extract[Int]
if (idl > 0) {
val res = Array.ofDim[String](idl)
val iid = (json \ "InvertedIndex").extract[Map[String, List[Int]]]
for {(k: String, v: List[Int]) <- iid} {
v.foreach(item => res(item) = k)
}
(0 until idl).foreach(i => {
if (res(i) == null)
res(i) = ""
})
return res.mkString(" ")
}
""
}
}

92
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkImportMagIntoDataset.scala Normal file
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package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{SaveMode, SparkSession}
import org.apache.spark.sql.types._
import org.slf4j.{Logger, LoggerFactory}
import org.apache.spark.sql.functions._
object SparkImportMagIntoDataset {
val datatypedict = Map(
"int" -> IntegerType,
"uint" -> IntegerType,
"long" -> LongType,
"ulong" -> LongType,
"float" -> FloatType,
"string" -> StringType,
"DateTime" -> DateType
)
val stream = Map(
"Affiliations" -> Tuple2("mag/Affiliations.txt", Seq("AffiliationId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "GridId:string", "OfficialPage:string", "WikiPage:string", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"Authors" -> Tuple2("mag/Authors.txt", Seq("AuthorId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "LastKnownAffiliationId:long?", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"ConferenceInstances" -> Tuple2("mag/ConferenceInstances.txt", Seq("ConferenceInstanceId:long", "NormalizedName:string", "DisplayName:string", "ConferenceSeriesId:long", "Location:string", "OfficialUrl:string", "StartDate:DateTime?", "EndDate:DateTime?", "AbstractRegistrationDate:DateTime?", "SubmissionDeadlineDate:DateTime?", "NotificationDueDate:DateTime?", "FinalVersionDueDate:DateTime?", "PaperCount:long", "CitationCount:long", "Latitude:float?", "Longitude:float?", "CreatedDate:DateTime")),
"ConferenceSeries" -> Tuple2("mag/ConferenceSeries.txt", Seq("ConferenceSeriesId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"EntityRelatedEntities" -> Tuple2("advanced/EntityRelatedEntities.txt", Seq("EntityId:long", "EntityType:string", "RelatedEntityId:long", "RelatedEntityType:string", "RelatedType:int", "Score:float")),
"FieldOfStudyChildren" -> Tuple2("advanced/FieldOfStudyChildren.txt", Seq("FieldOfStudyId:long", "ChildFieldOfStudyId:long")),
"FieldOfStudyExtendedAttributes" -> Tuple2("advanced/FieldOfStudyExtendedAttributes.txt", Seq("FieldOfStudyId:long", "AttributeType:int", "AttributeValue:string")),
"FieldsOfStudy" -> Tuple2("advanced/FieldsOfStudy.txt", Seq("FieldOfStudyId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "MainType:string", "Level:int", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"Journals" -> Tuple2("mag/Journals.txt", Seq("JournalId:long", "Rank:uint", "NormalizedName:string", "DisplayName:string", "Issn:string", "Publisher:string", "Webpage:string", "PaperCount:long", "CitationCount:long", "CreatedDate:DateTime")),
"PaperAbstractsInvertedIndex" -> Tuple2("nlp/PaperAbstractsInvertedIndex.txt.*", Seq("PaperId:long", "IndexedAbstract:string")),
"PaperAuthorAffiliations" -> Tuple2("mag/PaperAuthorAffiliations.txt", Seq("PaperId:long", "AuthorId:long", "AffiliationId:long?", "AuthorSequenceNumber:uint", "OriginalAuthor:string", "OriginalAffiliation:string")),
"PaperCitationContexts" -> Tuple2("nlp/PaperCitationContexts.txt", Seq("PaperId:long", "PaperReferenceId:long", "CitationContext:string")),
"PaperExtendedAttributes" -> Tuple2("mag/PaperExtendedAttributes.txt", Seq("PaperId:long", "AttributeType:int", "AttributeValue:string")),
"PaperFieldsOfStudy" -> Tuple2("advanced/PaperFieldsOfStudy.txt", Seq("PaperId:long", "FieldOfStudyId:long", "Score:float")),
"PaperRecommendations" -> Tuple2("advanced/PaperRecommendations.txt", Seq("PaperId:long", "RecommendedPaperId:long", "Score:float")),
"PaperReferences" -> Tuple2("mag/PaperReferences.txt", Seq("PaperId:long", "PaperReferenceId:long")),
"PaperResources" -> Tuple2("mag/PaperResources.txt", Seq("PaperId:long", "ResourceType:int", "ResourceUrl:string", "SourceUrl:string", "RelationshipType:int")),
"PaperUrls" -> Tuple2("mag/PaperUrls.txt", Seq("PaperId:long", "SourceType:int?", "SourceUrl:string", "LanguageCode:string")),
"Papers" -> Tuple2("mag/Papers.txt", Seq("PaperId:long", "Rank:uint", "Doi:string", "DocType:string", "PaperTitle:string", "OriginalTitle:string", "BookTitle:string", "Year:int?", "Date:DateTime?", "Publisher:string", "JournalId:long?", "ConferenceSeriesId:long?", "ConferenceInstanceId:long?", "Volume:string", "Issue:string", "FirstPage:string", "LastPage:string", "ReferenceCount:long", "CitationCount:long", "EstimatedCitation:long", "OriginalVenue:string", "FamilyId:long?", "CreatedDate:DateTime")),
"RelatedFieldOfStudy" -> Tuple2("advanced/RelatedFieldOfStudy.txt", Seq("FieldOfStudyId1:long", "Type1:string", "FieldOfStudyId2:long", "Type2:string", "Rank:float"))
)
def getSchema(streamName: String): StructType = {
var schema = new StructType()
val d: Seq[String] = stream(streamName)._2
d.foreach { case t =>
val currentType = t.split(":")
val fieldName: String = currentType.head
var fieldType: String = currentType.last
val nullable: Boolean = fieldType.endsWith("?")
if (nullable)
fieldType = fieldType.replace("?", "")
schema = schema.add(StructField(fieldName, datatypedict(fieldType), nullable))
}
schema
}
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
stream.foreach { case (k, v) =>
val s: StructType = getSchema(k)
val df = spark.read
.option("header", "false")
.option("charset", "UTF8")
.option("delimiter", "\t")
.schema(s)
.csv(s"${parser.get("sourcePath")}/${v._1}")
logger.info(s"Converting $k")
df.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/$k")
}
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala Normal file
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package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.functions._
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
object SparkPreProcessMAG {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
import spark.implicits._
implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication]
implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs)
logger.info("Phase 1) make uninque DOI in Papers:")
val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers]
// Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one
val result: RDD[MagPapers] = d.where(col("Doi").isNotNull)
.rdd
.map{ p: MagPapers => Tuple2(p.Doi, p) }
.reduceByKey((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2))
.map(_._2)
val distinctPaper: Dataset[MagPapers] = spark.createDataset(result)
distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct")
logger.info("Phase 6) Enrich Publication with description")
val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract")
logger.info("Phase 3) Group Author by PaperId")
val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor]
val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation]
val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation]
paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId")))
.map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null)) }
.joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left")
.map(s => {
val mpa = s._1._2
val af = s._2
if (af != null) {
MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName)
} else
mpa
}).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors"))
.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors")
logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors")
val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal]
val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers]
val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList]
val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left")
firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left")
.map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) }
.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2")
var magPubs: Dataset[(String, Publication)] =
spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
.select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci")))
.select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]
magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
.map(item => ConversionUtil.updatePubsWithConferenceInfo(item))
.write
.mode(SaveMode.Overwrite)
.save(s"${parser.get("targetPath")}/merge_step_2_conference")
magPubs= spark.read.load(s"${parser.get("targetPath")}/merge_step_2_conference").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl]
logger.info("Phase 5) enrich publication with URL and Instances")
magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left")
.map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) }
.write.mode(SaveMode.Overwrite)
.save(s"${parser.get("targetPath")}/merge_step_3")
// logger.info("Phase 6) Enrich Publication with description")
// val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
// pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract")
val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract]
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left")
.map(item => ConversionUtil.updatePubsWithDescription(item)
).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4")
logger.info("Phase 7) Enrich Publication with FieldOfStudy")
magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication]
.map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]
val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")
val pfos = spark.read.load(s"$sourcePath/PaperFieldsOfStudy")
val paperField = pfos.joinWith(fos, fos("fos").equalTo(pfos("FieldOfStudyId")))
.select($"_1.FieldOfStudyId", $"_2.DisplayName", $"_2.MainType", $"_1.PaperId", $"_1.Score")
.groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects"))
.as[MagFieldOfStudy]
magPubs.joinWith(paperField, col("_1")
.equalTo(paperField("PaperId")), "left")
.map(item => ConversionUtil.updatePubsWithSubject(item))
.write.mode(SaveMode.Overwrite)
.save(s"${parser.get("targetPath")}/mag_publication")
val s:RDD[Publication] = spark.read.load(s"${parser.get("targetPath")}/mag_publication").as[Publication]
.map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
.map(_._2)
spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/mag_publication_u")
}
}

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

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package eu.dnetlib.doiboost.orcid
import java.io.IOException
import eu.dnetlib.dhp.schema.oaf.{Author, Publication}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.apache.commons.lang.StringUtils
import org.codehaus.jackson.map.ObjectMapper
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,errorCode:String){}
case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
object ORCIDToOAF {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper
def isJsonValid(inputStr: String): Boolean = {
import java.io.IOException
try {
mapper.readTree(inputStr)
true
} catch {
case e: IOException =>
false
}
}
def extractValueFromInputString(input: String): (String, String) = {
val i = input.indexOf('[')
if (i <5) {
return null
}
val orcidList = input.substring(i, input.length - 1)
val doi = input.substring(1, i - 1)
if (isJsonValid(orcidList)) {
(doi, orcidList)
} else null
}
def convertTOOAF(input:ORCIDElement) :Publication = {
val doi = input.doi
val pub:Publication = new Publication
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setDataInfo(generateDataInfo())
pub.setId(generateIdentifier(pub, doi.toLowerCase))
try{
pub.setAuthor(input.authors.map(a=> {
generateAuhtor(a.name, a.surname, a.creditName, a.oid)
}).asJava)
pub.setCollectedfrom(List(DoiBoostMappingUtil.createORIDCollectedFrom()).asJava)
pub.setDataInfo(DoiBoostMappingUtil.generateDataInfo())
pub
} catch {
case e: Throwable =>
logger.info(s"ERROR ON GENERATE Publication from $input")
null
}
}
def generateAuhtor(given: String, family: String, fullName:String, orcid: String): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)
if (fullName!= null && fullName.nonEmpty)
a.setFullname(fullName)
else
a.setFullname(s"$given $family")
if (StringUtils.isNotBlank(orcid))
a.setPid(List(createSP(orcid, ORCID, PID_TYPES)).asJava)
a
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidAuthorsDOIsDataGen.java Normal file
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package eu.dnetlib.doiboost.orcid;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.mortbay.log.Log;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidAuthorsDOIsDataGen extends OrcidDSManager {
private String activitiesFileNameTarGz;
private String outputAuthorsDOIsPath;
public static void main(String[] args) throws IOException, Exception {
OrcidAuthorsDOIsDataGen orcidAuthorsDOIsDataGen = new OrcidAuthorsDOIsDataGen();
orcidAuthorsDOIsDataGen.loadArgs(args);
orcidAuthorsDOIsDataGen.generateAuthorsDOIsData();
}
public void generateAuthorsDOIsData() throws Exception {
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(activitiesFileNameTarGz);
Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsDOIsPath));
ActivitiesDecompressor.parseGzActivities(conf, tarGzUri, outputPath);
}
private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
OrcidAuthorsDOIsDataGen.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
Log.info("HDFS URI: " + hdfsServerUri);
hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
Log.info("Default Path: " + hdfsOrcidDefaultPath);
activitiesFileNameTarGz = parser.get("activitiesFileNameTarGz");
Log.info("Activities File Name: " + activitiesFileNameTarGz);
outputAuthorsDOIsPath = parser.get("outputAuthorsDOIsPath");
Log.info("Output Authors DOIs Data: " + outputAuthorsDOIsPath);
}
}

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package eu.dnetlib.doiboost.orcid;
import java.io.IOException;
import java.net.URI;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.mortbay.log.Log;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidDSManager {
protected String hdfsServerUri;
protected String hdfsOrcidDefaultPath;
private String summariesFileNameTarGz;
private String outputAuthorsPath;
public static void main(String[] args) throws IOException, Exception {
OrcidDSManager orcidDSManager = new OrcidDSManager();
orcidDSManager.loadArgs(args);
orcidDSManager.generateAuthors();
}
public void generateAuthors() throws Exception {
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz);
Path outputPath = new Path(
hdfsServerUri
.concat(hdfsOrcidDefaultPath)
.concat(outputAuthorsPath)
.concat("authors.seq"));
SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
}
protected Configuration initConfigurationObject() {
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath));
// 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());
return conf;
}
protected FileSystem initFileSystemObject(Configuration conf) {
// Get the filesystem - HDFS
FileSystem fs = null;
try {
fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return fs;
}
private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
OrcidDSManager.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
Log.info("HDFS URI: " + hdfsServerUri);
hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
Log.info("Default Path: " + hdfsOrcidDefaultPath);
summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
Log.info("Summaries File Name: " + summariesFileNameTarGz);
outputAuthorsPath = parser.get("outputAuthorsPath");
Log.info("Output Authors Data: " + outputAuthorsPath);
}
}

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package eu.dnetlib.doiboost.orcid;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.text.SimpleDateFormat;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import org.apache.commons.io.IOUtils;
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.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
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 org.mortbay.log.Log;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidDownloader extends OrcidDSManager {
static final int REQ_LIMIT = 24;
// static final int REQ_MAX_TEST = 100;
static final int RECORD_PARSED_COUNTER_LOG_INTERVAL = 10000;
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
static final String lastUpdate = "2019-09-30 00:00:00";
private String lambdaFileName;
private String outputPath;
private String token;
public static void main(String[] args) throws IOException, Exception {
OrcidDownloader orcidDownloader = new OrcidDownloader();
orcidDownloader.loadArgs(args);
orcidDownloader.parseLambdaFile();
}
private String downloadRecord(String orcidId) {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization", String.format("Bearer %s", token));
CloseableHttpResponse response = client.execute(httpGet);
if (response.getStatusLine().getStatusCode() != 200) {
Log
.warn(
"Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
return new String("");
}
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
Log.warn("Downloading " + orcidId, e.getMessage());
}
return new String("");
}
public void parseLambdaFile() throws Exception {
int parsedRecordsCounter = 0;
int downloadedRecordsCounter = 0;
int savedRecordsCounter = 0;
long startDownload = 0;
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String lambdaFileUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(lambdaFileName);
Path hdfsreadpath = new Path(lambdaFileUri);
FSDataInputStream lambdaFileStream = fs.open(hdfsreadpath);
Path hdfsoutputPath = new Path(
hdfsServerUri
.concat(hdfsOrcidDefaultPath)
.concat(outputPath)
.concat("orcid_records.seq"));
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(hdfsoutputPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
try (BufferedReader br = new BufferedReader(new InputStreamReader(lambdaFileStream))) {
String line;
int nReqTmp = 0;
startDownload = System.currentTimeMillis();
long startReqTmp = System.currentTimeMillis();
while ((line = br.readLine()) != null) {
parsedRecordsCounter++;
// skip headers line
if (parsedRecordsCounter == 1) {
continue;
}
String[] values = line.split(",");
List<String> recordInfo = Arrays.asList(values);
String orcidId = recordInfo.get(0);
if (isModified(orcidId, recordInfo.get(3))) {
String record = downloadRecord(orcidId);
downloadedRecordsCounter++;
if (!record.isEmpty()) {
String compressRecord = ArgumentApplicationParser.compressArgument(record);
final Text key = new Text(recordInfo.get(0));
final Text value = new Text(compressRecord);
try {
writer.append(key, value);
savedRecordsCounter++;
} catch (IOException e) {
Log.warn("Writing to sequence file: " + e.getMessage());
Log.warn(e);
throw new RuntimeException(e);
}
}
}
long endReq = System.currentTimeMillis();
nReqTmp++;
if (nReqTmp == REQ_LIMIT) {
long reqSessionDuration = endReq - startReqTmp;
if (reqSessionDuration <= 1000) {
Log
.warn(
"\nreqSessionDuration: "
+ reqSessionDuration
+ " nReqTmp: "
+ nReqTmp
+ " wait ....");
Thread.sleep(1000 - reqSessionDuration);
} else {
nReqTmp = 0;
startReqTmp = System.currentTimeMillis();
}
}
// if (parsedRecordsCounter > REQ_MAX_TEST) {
// break;
// }
if ((parsedRecordsCounter % RECORD_PARSED_COUNTER_LOG_INTERVAL) == 0) {
Log
.info(
"Current parsed: "
+ parsedRecordsCounter
+ " downloaded: "
+ downloadedRecordsCounter
+ " saved: "
+ savedRecordsCounter);
// if (parsedRecordsCounter > REQ_MAX_TEST) {
// break;
// }
}
}
long endDownload = System.currentTimeMillis();
long downloadTime = endDownload - startDownload;
Log.info("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
}
}
lambdaFileStream.close();
Log.info("Download started at: " + new Date(startDownload).toString());
Log.info("Parsed Records Counter: " + parsedRecordsCounter);
Log.info("Downloaded Records Counter: " + downloadedRecordsCounter);
Log.info("Saved Records Counter: " + savedRecordsCounter);
}
private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
OrcidDownloader.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/download_orcid_data.json")));
parser.parseArgument(args);
hdfsServerUri = parser.get("hdfsServerUri");
Log.info("HDFS URI: " + hdfsServerUri);
hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
Log.info("Default Path: " + hdfsOrcidDefaultPath);
lambdaFileName = parser.get("lambdaFileName");
Log.info("Lambda File Name: " + lambdaFileName);
outputPath = parser.get("outputPath");
Log.info("Output Data: " + outputPath);
token = parser.get("token");
}
private boolean isModified(String orcidId, String modifiedDate) {
Date modifiedDateDt = null;
Date lastUpdateDt = null;
try {
if (modifiedDate.length() != 19) {
modifiedDate = modifiedDate.substring(0, 19);
}
modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
} catch (Exception e) {
Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage());
return true;
}
return modifiedDateDt.after(lastUpdateDt);
}
}

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package eu.dnetlib.doiboost.orcid
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkConvertORCIDToOAF {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs)
import spark.implicits._
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val dataset:Dataset[ORCIDElement] = spark.read.json(sourcePath).as[ORCIDElement]
logger.info("Converting ORCID to OAF")
val d:RDD[Publication] = dataset.map(o => ORCIDToOAF.convertTOOAF(o)).filter(p=>p!=null).map(p=>(p.getId,p)).rdd.reduceByKey(ConversionUtil.mergePublication)
.map(_._2)
spark.createDataset(d).as[Publication].write.mode(SaveMode.Overwrite).save(targetPath)
}
}

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package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapreduce.Job;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.esotericsoftware.minlog.Log;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.model.WorkData;
import scala.Tuple2;
public class SparkGenerateDoiAuthorList {
public static void main(String[] args) throws IOException, Exception {
Logger logger = LoggerFactory.getLogger(SparkGenerateDoiAuthorList.class);
logger.info("[ SparkGenerateDoiAuthorList STARTED]");
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkGenerateDoiAuthorList.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath);
final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath");
logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaPairRDD<Text, Text> summariesRDD = sc
.sequenceFile(workingPath + "../orcid_summaries/output/authors.seq", Text.class, Text.class);
Dataset<AuthorData> summariesDataset = spark
.createDataset(
summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(AuthorData.class));
JavaPairRDD<Text, Text> activitiesRDD = sc
.sequenceFile(workingPath + "/output/*.seq", Text.class, Text.class);
Dataset<WorkData> activitiesDataset = spark
.createDataset(
activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
Encoders.bean(WorkData.class));
Function<Tuple2<String, AuthorData>, Tuple2<String, List<AuthorData>>> toAuthorListFunction = data -> {
try {
String doi = data._1();
if (doi == null) {
return null;
}
AuthorData author = data._2();
if (author == null) {
return null;
}
List<AuthorData> toAuthorList = Arrays.asList(author);
return new Tuple2<>(doi, toAuthorList);
} catch (Exception e) {
Log.error("toAuthorListFunction ERROR", e);
return null;
}
};
JavaRDD<Tuple2<String, List<AuthorData>>> doisRDD = activitiesDataset
.joinWith(
summariesDataset,
activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
.map(
(MapFunction<Tuple2<WorkData, AuthorData>, Tuple2<String, AuthorData>>) value -> {
WorkData w = value._1;
AuthorData a = value._2;
return new Tuple2<>(w.getDoi(), a);
},
Encoders.tuple(Encoders.STRING(), Encoders.bean(AuthorData.class)))
.filter(Objects::nonNull)
.toJavaRDD()
.map(toAuthorListFunction);
JavaPairRDD
.fromJavaRDD(doisRDD)
.reduceByKey((d1, d2) -> {
try {
if (d1 != null && d2 != null) {
Stream<AuthorData> mergedStream = Stream
.concat(
d1.stream(),
d2.stream());
List<AuthorData> mergedAuthors = mergedStream.collect(Collectors.toList());
return mergedAuthors;
}
if (d1 != null) {
return d1;
}
if (d2 != null) {
return d2;
}
} catch (Exception e) {
Log.error("mergeAuthorsFunction ERROR", e);
return null;
}
return null;
})
.mapToPair(
s -> {
ObjectMapper mapper = new ObjectMapper();
return new Tuple2<>(s._1(), mapper.writeValueAsString(s._2()));
})
.repartition(10)
.saveAsTextFile(workingPath + outputDoiAuthorListPath);
});
}
private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
AuthorData authorData = new AuthorData();
authorData.setOid(orcidId.toString());
JsonElement jElement = new JsonParser().parse(json.toString());
authorData.setName(getJsonValue(jElement, "name"));
authorData.setSurname(getJsonValue(jElement, "surname"));
authorData.setCreditName(getJsonValue(jElement, "creditname"));
return authorData;
}
private static WorkData loadWorkFromJson(Text orcidId, Text json) {
WorkData workData = new WorkData();
workData.setOid(orcidId.toString());
JsonElement jElement = new JsonParser().parse(json.toString());
workData.setDoi(getJsonValue(jElement, "doi"));
return workData;
}
private static String getJsonValue(JsonElement jElement, String property) {
if (jElement.getAsJsonObject().has(property)) {
JsonElement name = null;
name = jElement.getAsJsonObject().get(property);
if (name != null && !name.isJsonNull()) {
return name.getAsString();
}
}
return null;
}
}

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package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
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 org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.Function;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.util.LongAccumulator;
import org.mortbay.log.Log;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.doiboost.orcid.model.DownloadedRecordData;
import scala.Tuple2;
public class SparkOrcidGenerateAuthors {
static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
static final String lastUpdate = "2019-09-30 00:00:00";
public static void main(String[] args) throws IOException, Exception {
Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class);
logger.info("[ SparkOrcidGenerateAuthors STARTED]");
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkOrcidGenerateAuthors.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
logger.info("workingPath: ", workingPath);
final String outputAuthorsPath = parser.get("outputAuthorsPath");
logger.info("outputAuthorsPath: ", outputAuthorsPath);
final String token = parser.get("token");
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
LongAccumulator parsedRecordsAcc = sc.sc().longAccumulator("parsedRecords");
LongAccumulator modifiedRecordsAcc = sc.sc().longAccumulator("modifiedRecords");
LongAccumulator downloadedRecordsAcc = sc.sc().longAccumulator("downloadedRecords");
LongAccumulator alreadyDownloadedRecords = sc.sc().longAccumulator("alreadyDownloadedRecords");
JavaRDD<String> lamdaFileRDD = sc.textFile(workingPath + "lamdafiles");
JavaRDD<String> downloadedRDD = sc.textFile(workingPath + "downloaded");
Function<String, String> getOrcidIdFunction = line -> {
try {
String[] values = line.split(",");
return values[0].substring(1);
} catch (Exception e) {
return new String("");
}
};
List<String> downloadedRecords = downloadedRDD.map(getOrcidIdFunction).collect();
Function<String, Boolean> isModifiedAfterFilter = line -> {
String[] values = line.split(",");
String orcidId = values[0];
parsedRecordsAcc.add(1);
if (isModified(orcidId, values[3])) {
modifiedRecordsAcc.add(1);
return true;
}
return false;
};
Function<String, Boolean> isNotDownloadedFilter = line -> {
String[] values = line.split(",");
String orcidId = values[0];
if (downloadedRecords.contains(orcidId)) {
alreadyDownloadedRecords.add(1);
return false;
}
return true;
};
Function<String, Tuple2<String, String>> downloadRecordFunction = line -> {
String[] values = line.split(",");
String orcidId = values[0];
String modifiedDate = values[3];
return downloadRecord(orcidId, modifiedDate, token, downloadedRecordsAcc);
};
lamdaFileRDD
.filter(isModifiedAfterFilter)
.filter(isNotDownloadedFilter)
.map(downloadRecordFunction)
.rdd()
.saveAsTextFile(workingPath.concat(outputAuthorsPath));
});
}
private static boolean isModified(String orcidId, String modifiedDate) {
Date modifiedDateDt = null;
Date lastUpdateDt = null;
try {
if (modifiedDate.length() != 19) {
modifiedDate = modifiedDate.substring(0, 19);
}
modifiedDateDt = new SimpleDateFormat(DATE_FORMAT).parse(modifiedDate);
lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
} catch (Exception e) {
Log.warn("[" + orcidId + "] Parsing date: ", e.getMessage());
return true;
}
return modifiedDateDt.after(lastUpdateDt);
}
private static Tuple2<String, String> downloadRecord(String orcidId, String modifiedDate, String token,
LongAccumulator downloadedRecordsAcc) {
final DownloadedRecordData data = new DownloadedRecordData();
data.setOrcidId(orcidId);
data.setModifiedDate(modifiedDate);
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization", String.format("Bearer %s", token));
CloseableHttpResponse response = client.execute(httpGet);
int statusCode = response.getStatusLine().getStatusCode();
data.setStatusCode(statusCode);
if (statusCode != 200) {
Log
.warn(
"Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
return data.toTuple2();
}
downloadedRecordsAcc.add(1);
data
.setCompressedData(
ArgumentApplicationParser.compressArgument(IOUtils.toString(response.getEntity().getContent())));
} catch (Throwable e) {
Log.warn("Downloading " + orcidId, e.getMessage());
data.setErrorMessage(e.getMessage());
return data.toTuple2();
}
return data.toTuple2();
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkPartitionLambdaFile.java Normal file
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package eu.dnetlib.doiboost.orcid;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.util.Optional;
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.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class SparkPartitionLambdaFile {
public static void main(String[] args) throws IOException, Exception {
Logger logger = LoggerFactory.getLogger(SparkOrcidGenerateAuthors.class);
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SparkOrcidGenerateAuthors.class
.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
final String workingPath = parser.get("workingPath");
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<String> lamdaFileRDD = sc.textFile(workingPath + "last_modified.csv");
lamdaFileRDD
.repartition(20)
.saveAsTextFile(workingPath.concat("lamdafiles"));
});
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java Normal file
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package eu.dnetlib.doiboost.orcid;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URI;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IOUtils;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.mortbay.log.Log;
import eu.dnetlib.doiboost.orcid.json.JsonWriter;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
public class SummariesDecompressor {
private static final int MAX_XML_RECORDS_PARSED = -1;
public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath)
throws Exception {
String uri = inputUri;
FileSystem fs = FileSystem.get(URI.create(uri), conf);
Path inputPath = new Path(uri);
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodec(inputPath);
if (codec == null) {
System.err.println("No codec found for " + uri);
System.exit(1);
}
CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
InputStream gzipInputStream = null;
try {
gzipInputStream = codec.createInputStream(fs.open(inputPath));
parseTarSummaries(fs, conf, gzipInputStream, outputPath);
} finally {
Log.debug("Closing gzip stream");
IOUtils.closeStream(gzipInputStream);
}
}
private static void parseTarSummaries(
FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
int counter = 0;
int nameFound = 0;
int surnameFound = 0;
int creditNameFound = 0;
int errorFromOrcidFound = 0;
int xmlParserErrorFound = 0;
try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
TarArchiveEntry entry = null;
try (SequenceFile.Writer writer = SequenceFile
.createWriter(
conf,
SequenceFile.Writer.file(outputPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
while ((entry = tais.getNextTarEntry()) != null) {
String filename = entry.getName();
try {
if (entry.isDirectory()) {
Log.debug("Directory entry name: " + entry.getName());
} else {
Log.debug("XML record entry name: " + entry.getName());
counter++;
BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from
// tarInput
String line;
StringBuffer buffer = new StringBuffer();
while ((line = br.readLine()) != null) {
buffer.append(line);
}
AuthorData authorData = XMLRecordParser.VTDParseAuthorData(buffer.toString().getBytes());
if (authorData != null) {
if (authorData.getErrorCode() != null) {
errorFromOrcidFound += 1;
Log
.debug(
"error from Orcid with code "
+ authorData.getErrorCode()
+ " for oid "
+ entry.getName());
continue;
}
String jsonData = JsonWriter.create(authorData);
Log.debug("oid: " + authorData.getOid() + " data: " + jsonData);
final Text key = new Text(authorData.getOid());
final Text value = new Text(jsonData);
try {
writer.append(key, value);
} catch (IOException e) {
Log.debug("Writing to sequence file: " + e.getMessage());
Log.debug(e);
throw new RuntimeException(e);
}
if (authorData.getName() != null) {
nameFound += 1;
}
if (authorData.getSurname() != null) {
surnameFound += 1;
}
if (authorData.getCreditName() != null) {
creditNameFound += 1;
}
} else {
Log.warn("Data not retrievable [" + entry.getName() + "] " + buffer.toString());
xmlParserErrorFound += 1;
}
}
} catch (Exception e) {
Log
.warn(
"Parsing record from tar archive and xml record: "
+ filename
+ " "
+ e.getMessage());
Log.warn(e);
}
if ((counter % 100000) == 0) {
Log.info("Current xml records parsed: " + counter);
}
if ((MAX_XML_RECORDS_PARSED > -1) && (counter > MAX_XML_RECORDS_PARSED)) {
break;
}
}
}
} catch (IOException e) {
Log.warn("Parsing record from gzip archive: " + e.getMessage());
Log.warn(e);
throw new RuntimeException(e);
}
Log.info("Summaries parse completed");
Log.info("Total XML records parsed: " + counter);
Log.info("Name found: " + nameFound);
Log.info("Surname found: " + surnameFound);
Log.info("Credit name found: " + creditNameFound);
Log.info("Error from Orcid found: " + errorFromOrcidFound);
Log.info("Error parsing xml record found: " + xmlParserErrorFound);
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/json/JsonWriter.java Normal file
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package eu.dnetlib.doiboost.orcid.json;
import com.google.gson.JsonObject;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.model.WorkData;
public class JsonWriter {
public static String create(AuthorData authorData) {
JsonObject author = new JsonObject();
author.addProperty("oid", authorData.getOid());
author.addProperty("name", authorData.getName());
author.addProperty("surname", authorData.getSurname());
if (authorData.getCreditName() != null) {
author.addProperty("creditname", authorData.getCreditName());
}
return author.toString();
}
public static String create(WorkData workData) {
JsonObject work = new JsonObject();
work.addProperty("oid", workData.getOid());
work.addProperty("doi", workData.getDoi());
return work.toString();
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/AuthorData.java Normal file
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package eu.dnetlib.doiboost.orcid.model;
import java.io.Serializable;
public class AuthorData implements Serializable {
private String oid;
private String name;
private String surname;
private String creditName;
private String errorCode;
public String getErrorCode() {
return errorCode;
}
public void setErrorCode(String errorCode) {
this.errorCode = errorCode;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getSurname() {
return surname;
}
public void setSurname(String surname) {
this.surname = surname;
}
public String getCreditName() {
return creditName;
}
public void setCreditName(String creditName) {
this.creditName = creditName;
}
public String getOid() {
return oid;
}
public void setOid(String oid) {
this.oid = oid;
}
}

76
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/DownloadedRecordData.java Normal file
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package eu.dnetlib.doiboost.orcid.model;
import java.io.Serializable;
import org.apache.hadoop.io.Text;
import com.google.gson.JsonObject;
import scala.Tuple2;
public class DownloadedRecordData implements Serializable {
private String orcidId;
private String modifiedDate;
private String statusCode;
private String compressedData;
private String errorMessage;
public Tuple2<String, String> toTuple2() {
JsonObject data = new JsonObject();
data.addProperty("statusCode", getStatusCode());
data.addProperty("modifiedDate", getModifiedDate());
if (getCompressedData() != null) {
data.addProperty("compressedData", getCompressedData());
}
if (getErrorMessage() != null) {
data.addProperty("errorMessage", getErrorMessage());
}
return new Tuple2<>(orcidId, data.toString());
}
public String getErrorMessage() {
return errorMessage;
}
public void setErrorMessage(String errorMessage) {
this.errorMessage = errorMessage;
}
public String getOrcidId() {
return orcidId;
}
public void setOrcidId(String orcidId) {
this.orcidId = orcidId;
}
public int getStatusCode() {
try {
return Integer.parseInt(statusCode);
} catch (Exception e) {
return -2;
}
}
public void setStatusCode(int statusCode) {
this.statusCode = Integer.toString(statusCode);
}
public String getCompressedData() {
return compressedData;
}
public void setCompressedData(String compressedData) {
this.compressedData = compressedData;
}
public String getModifiedDate() {
return modifiedDate;
}
public void setModifiedDate(String modifiedDate) {
this.modifiedDate = modifiedDate;
}
}

45
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/model/WorkData.java Normal file
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package eu.dnetlib.doiboost.orcid.model;
import java.io.Serializable;
public class WorkData implements Serializable {
private String oid;
private String doi;
private boolean doiFound = false;
public boolean isDoiFound() {
return doiFound;
}
public void setDoiFound(boolean doiFound) {
this.doiFound = doiFound;
}
public String getOid() {
return oid;
}
public void setOid(String oid) {
this.oid = oid;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public String getErrorCode() {
return errorCode;
}
public void setErrorCode(String errorCode) {
this.errorCode = errorCode;
}
private String errorCode;
}

123
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package eu.dnetlib.doiboost.orcid.xml;
import java.util.Arrays;
import java.util.List;
import com.ximpleware.AutoPilot;
import com.ximpleware.EOFException;
import com.ximpleware.EncodingException;
import com.ximpleware.EntityException;
import com.ximpleware.ParseException;
import com.ximpleware.VTDGen;
import com.ximpleware.VTDNav;
import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.model.WorkData;
public class XMLRecordParser {
private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common";
private static final String NS_COMMON = "common";
private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person";
private static final String NS_PERSON = "person";
private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details";
private static final String NS_DETAILS = "personal-details";
private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name";
private static final String NS_OTHER = "other-name";
private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record";
private static final String NS_RECORD = "record";
private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error";
private static final String NS_WORK = "work";
private static final String NS_WORK_URL = "http://www.orcid.org/ns/work";
private static final String NS_ERROR = "error";
public static AuthorData VTDParseAuthorData(byte[] bytes)
throws VtdException, EncodingException, EOFException, EntityException, ParseException {
final VTDGen vg = new VTDGen();
vg.setDoc(bytes);
vg.parse(true);
final VTDNav vn = vg.getNav();
final AutoPilot ap = new AutoPilot(vn);
ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL);
ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL);
ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL);
ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL);
ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
AuthorData authorData = new AuthorData();
final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
if (!errors.isEmpty()) {
authorData.setErrorCode(errors.get(0));
return authorData;
}
List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
.getTextValuesWithAttributes(
ap, vn, "//record:record", Arrays.asList("path"));
if (!recordNodes.isEmpty()) {
final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
authorData.setOid(oid);
} else {
return null;
}
final List<String> names = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names");
if (!names.isEmpty()) {
authorData.setName(names.get(0));
}
final List<String> surnames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name");
if (!surnames.isEmpty()) {
authorData.setSurname(surnames.get(0));
}
final List<String> creditNames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name");
if (!creditNames.isEmpty()) {
authorData.setCreditName(creditNames.get(0));
}
return authorData;
}
public static WorkData VTDParseWorkData(byte[] bytes)
throws VtdException, EncodingException, EOFException, EntityException, ParseException {
final VTDGen vg = new VTDGen();
vg.setDoc(bytes);
vg.parse(true);
final VTDNav vn = vg.getNav();
final AutoPilot ap = new AutoPilot(vn);
ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
WorkData workData = new WorkData();
final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
if (!errors.isEmpty()) {
workData.setErrorCode(errors.get(0));
return workData;
}
List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
.getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path"));
if (!workNodes.isEmpty()) {
final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
workData.setOid(oid);
} else {
return null;
}
final List<String> dois = VtdUtilityParser
.getTextValue(
ap, vn, "//common:external-id-type[text()=\"doi\"]/../common:external-id-value");
if (!dois.isEmpty()) {
workData.setDoi(dois.get(0));
workData.setDoiFound(true);
}
return workData;
}
}

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dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala Normal file
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package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkMapUnpayWallToOAF {
def main(args: Array[String]): Unit = {
val logger: Logger = LoggerFactory.getLogger(SparkMapDumpIntoOAF.getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkMapDumpIntoOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json")))
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
logger.info("Converting UnpayWall to OAF")
val d:Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
d.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

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package eu.dnetlib.doiboost.uw
import eu.dnetlib.dhp.schema.oaf.{Instance, Publication}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
case class OALocation(evidence:Option[String], host_type:Option[String], is_best:Option[Boolean], license: Option[String], pmh_id:Option[String], updated:Option[String],
url:Option[String], url_for_landing_page:Option[String], url_for_pdf:Option[String], version:Option[String]) {}
object UnpayWallToOAF {
val logger: Logger = LoggerFactory.getLogger(getClass)
def convertToOAF(input:String):Publication = {
val pub = new Publication
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
val doi = (json \"doi").extract[String]
val is_oa = (json\ "is_oa").extract[Boolean]
val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
pub.setPid(List(createSP(doi, "doi", PID_TYPES)).asJava)
pub.setId(generateIdentifier(pub, doi.toLowerCase))
pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
pub.setDataInfo(generateDataInfo())
if (!is_oa)
return null
if(oaLocation== null || oaLocation.url.isEmpty)
return null
val i :Instance= new Instance()
i.setCollectedfrom(createUnpayWallCollectedFrom())
i.setAccessright(getOpenAccessQualifier())
i.setUrl(List(oaLocation.url.get).asJava)
if (oaLocation.license.isDefined)
i.setLicense(asField(oaLocation.license.get))
pub.setInstance(List(i).asJava)
pub
}
}

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_params.json Normal file
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[
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
]

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json Normal file
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[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
]

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/create_orcid_authors_dois_data.json Normal file
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[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"activitiesFileNameTarGz", "paramDescription": "the name of the activities orcid file", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputAuthorsDOIsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
]

42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/config-default.xml Normal file
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<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.launcher.mapreduce.user.classpath.first</name>
<value>true</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>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/oozie_app/workflow.xml Normal file
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<workflow-app name="import Crossref from index into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base 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>number of cores used by single executor</description>
</property>
<property>
<name>timestamp</name>
<description>Timestamp for incremental Harvesting</description>
</property>
</parameters>
<start to="ExtractCrossrefToOAF"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}/input/crossref/index_dump'/>
<!-- <mkdir path='${workingPath}/input/crossref'/>-->
</fs>
<ok to="ImportCrossRef"/>
<error to="Kill"/>
</action>
<action name="ImportCrossRef">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
<arg>-t</arg><arg>${workingPath}/input/crossref/index_dump</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-ts</arg><arg>${timestamp}</arg>
</java>
<ok to="ExtractCrossrefToOAF"/>
<error to="Kill"/>
</action>
<action name="ExtractCrossrefToOAF">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ExtractCrossrefToOAF</name>
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/index_dump,${workingPath}/crossref/index_dump</arg>
<arg>--targetPath</arg><arg>${workingPath}/input/crossref</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

7
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_orcid_data.json Normal file
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[
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
{"paramName":"f", "paramLongName":"lambdaFileName", "paramDescription": "the name of the lambda file", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true},
{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true}
]

3
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json Normal file
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[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputDoiAuthorListPath", "paramDescription": "the relative folder of the sequencial file to write the data", "paramRequired": true}
]

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/gen_orcid_authors_parameters.json Normal file
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[{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path", "paramRequired": true},
{"paramName":"t", "paramLongName":"token", "paramDescription": "token to grant access", "paramRequired": true},
{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write the authors data", "paramRequired": true}
]

9
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json Normal file
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[
{"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true},
{"paramName": "dp", "paramLongName":"dbPublicationPath", "paramDescription": "the Crossref Publication Path", "paramRequired": true},
{"paramName": "dd", "paramLongName":"dbDatasetPath", "paramDescription": "the Crossref Dataset Path", "paramRequired": true},
{"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
{"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}
]

7
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json Normal file
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[
{"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true},
{"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true},
{"paramName": "w", "paramLongName":"workingDirPath", "paramDescription": "the Working Path", "paramRequired": true}
]

5
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json Normal file
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[
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the sequencial file to write", "paramRequired": true},
{"paramName":"n", "paramLongName":"namenode", "paramDescription": "the hive metastore uris", "paramRequired": true},
{"paramName":"ts", "paramLongName":"timestamp", "paramDescription": "timestamp", "paramRequired": false}
]

38
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/config-default.xml Normal file
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<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>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>

103
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml Normal file
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<workflow-app name="Create DOIBoostActionSet" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>hostedByMapPath</name>
<description>the Hosted By Map Path</description>
</property>
<property>
<name>affiliationPath</name>
<description>the Affliation Path</description>
</property>
<property>
<name>paperAffiliationPath</name>
<description>the paperAffiliation Path</description>
</property>
<property>
<name>workingDirPath</name>
<description>the Working 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>number of cores used by single executor</description>
</property>
</parameters>
<start to="GenerateActionSet"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingDirPath}'/>
<mkdir path='${workingDirPath}'/>
</fs>
<ok to="CreateDOIBoost"/>
<error to="Kill"/>
</action>
<action name="CreateDOIBoost">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Create DOIBoost Infospace</name>
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
<arg>--affiliationPath</arg><arg>${affiliationPath}</arg>
<arg>--paperAffiliationPath</arg><arg>${paperAffiliationPath}</arg>
<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="GenerateActionSet"/>
<error to="Kill"/>
</action>
<action name="GenerateActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Generate DOIBoost ActionSet</name>
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--dbPublicationPath</arg><arg>${workingDirPath}/doiBoostPublicationFiltered</arg>
<arg>--dbDatasetPath</arg><arg>${workingDirPath}/crossrefDataset</arg>
<arg>--crossRefRelation</arg><arg>/data/doiboost/input/crossref/relations</arg>
<arg>--dbaffiliationRelationPath</arg><arg>${workingDirPath}/doiBoostPublicationAffiliation</arg>
<arg>-do</arg><arg>${workingDirPath}/doiBoostOrganization</arg>
<arg>--targetPath</arg><arg>${workingDirPath}/actionDataSet</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/convert_mag_to_oaf_params.json Normal file
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[
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
]

42
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/config-default.xml Normal file
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<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>

87
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/oozie_app/workflow.xml Normal file
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<workflow-app name="import MAG into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base 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>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${targetPath}'/>
<mkdir path='${targetPath}'/>
</fs>
<ok to="PreprocessMag"/>
<error to="Kill"/>
</action>
<action name="ConvertMagToDataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="PreprocessMag">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert Mag to Dataset</name>
<class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json Normal file
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[
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the base path of MAG input", "paramRequired": true},
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the working dir path", "paramRequired": true},
{"paramName":"m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true}
]

22
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.action.sharelib.for.java</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
</configuration>

41
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml Normal file
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<workflow-app name="import Orcid" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base path</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath}/output'/>
<mkdir path='${workingPath}/output'/>
</fs>
<ok to="ImportOrcidSummary"/>
<error to="Kill"/>
</action>
<action name="ImportOrcidSummary">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
<arg>-d</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
<arg>-o</arg><arg>output/</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

22
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.action.sharelib.for.java</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
</configuration>

505
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_authors_dois_data/oozie_app/workflow.xml Normal file
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<workflow-app name="Gen Orcid Authors DOIs" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath_activities</name>
<description>the working dir base path</description>
</property>
<property>
<name>shell_cmd_0</name>
<value>wget -O /tmp/ORCID_2019_activites_0.tar.gz https://orcid.figshare.com/ndownloader/files/18017660 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_0.tar.gz /data/orcid_activities/ORCID_2019_activites_0.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 0</description>
</property>
<property>
<name>shell_cmd_1</name>
<value>wget -O /tmp/ORCID_2019_activites_1.tar.gz https://orcid.figshare.com/ndownloader/files/18017675 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_1.tar.gz /data/orcid_activities/ORCID_2019_activites_1.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 1</description>
</property>
<property>
<name>shell_cmd_2</name>
<value>wget -O /tmp/ORCID_2019_activites_2.tar.gz https://orcid.figshare.com/ndownloader/files/18017717 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_2.tar.gz /data/orcid_activities/ORCID_2019_activites_2.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 2</description>
</property>
<property>
<name>shell_cmd_3</name>
<value>wget -O /tmp/ORCID_2019_activites_3.tar.gz https://orcid.figshare.com/ndownloader/files/18017765 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_3.tar.gz /data/orcid_activities/ORCID_2019_activites_3.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 3</description>
</property>
<property>
<name>shell_cmd_4</name>
<value>wget -O /tmp/ORCID_2019_activites_4.tar.gz https://orcid.figshare.com/ndownloader/files/18017831 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_4.tar.gz /data/orcid_activities/ORCID_2019_activites_4.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 4</description>
</property>
<property>
<name>shell_cmd_5</name>
<value>wget -O /tmp/ORCID_2019_activites_5.tar.gz https://orcid.figshare.com/ndownloader/files/18017987 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_5.tar.gz /data/orcid_activities/ORCID_2019_activites_5.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 5</description>
</property>
<property>
<name>shell_cmd_6</name>
<value>wget -O /tmp/ORCID_2019_activites_6.tar.gz https://orcid.figshare.com/ndownloader/files/18018053 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_6.tar.gz /data/orcid_activities/ORCID_2019_activites_6.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 6</description>
</property>
<property>
<name>shell_cmd_7</name>
<value>wget -O /tmp/ORCID_2019_activites_7.tar.gz https://orcid.figshare.com/ndownloader/files/18018023 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_7.tar.gz /data/orcid_activities/ORCID_2019_activites_7.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 7</description>
</property>
<property>
<name>shell_cmd_8</name>
<value>wget -O /tmp/ORCID_2019_activites_8.tar.gz https://orcid.figshare.com/ndownloader/files/18018248 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_8.tar.gz /data/orcid_activities/ORCID_2019_activites_8.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 8</description>
</property>
<property>
<name>shell_cmd_9</name>
<value>wget -O /tmp/ORCID_2019_activites_9.tar.gz https://orcid.figshare.com/ndownloader/files/18018029 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_9.tar.gz /data/orcid_activities/ORCID_2019_activites_9.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file 9</description>
</property>
<property>
<name>shell_cmd_X</name>
<value>wget -O /tmp/ORCID_2019_activites_X.tar.gz https://orcid.figshare.com/ndownloader/files/18018182 ; hdfs dfs -copyFromLocal /tmp/ORCID_2019_activites_X.tar.gz /data/orcid_activities/ORCID_2019_activites_X.tar.gz
</value>
<description>the shell command that downloads and puts to hdfs orcid activity file X</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath_activities}/output'/>
<mkdir path='${workingPath_activities}/output'/>
</fs>
<ok to="fork_gen_orcid_authors_dois"/>
<error to="Kill"/>
</action>
<fork name = "fork_gen_orcid_authors_dois">
<path start = "check_exist_on_hdfs_activities_0"/>
<path start = "check_exist_on_hdfs_activities_1"/>
<path start = "check_exist_on_hdfs_activities_2"/>
<path start = "check_exist_on_hdfs_activities_3"/>
<path start = "check_exist_on_hdfs_activities_4"/>
<path start = "check_exist_on_hdfs_activities_5"/>
<path start = "check_exist_on_hdfs_activities_6"/>
<path start = "check_exist_on_hdfs_activities_7"/>
<path start = "check_exist_on_hdfs_activities_8"/>
<path start = "check_exist_on_hdfs_activities_9"/>
<path start = "check_exist_on_hdfs_activities_X"/>
</fork>
<decision name="check_exist_on_hdfs_activities_0">
<switch>
<case to="Gen_Orcid_Authors_DOIs_0">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_0.tar.gz'))}
</case>
<default to="Download_0" />
</switch>
</decision>
<action name="Download_0">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_0}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_0"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_0">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_0.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_0.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_1">
<switch>
<case to="Gen_Orcid_Authors_DOIs_1">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_1.tar.gz'))}
</case>
<default to="Download_1" />
</switch>
</decision>
<action name="Download_1">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_1}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_1"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_1">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_1.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_1.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_2">
<switch>
<case to="Gen_Orcid_Authors_DOIs_2">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_2.tar.gz'))}
</case>
<default to="Download_2" />
</switch>
</decision>
<action name="Download_2">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_2}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_2"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_2">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_2.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_2.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_3">
<switch>
<case to="Gen_Orcid_Authors_DOIs_3">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_3.tar.gz'))}
</case>
<default to="Download_3" />
</switch>
</decision>
<action name="Download_3">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_3}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_3"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_3">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_3.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_3.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_4">
<switch>
<case to="Gen_Orcid_Authors_DOIs_4">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_4.tar.gz'))}
</case>
<default to="Download_4" />
</switch>
</decision>
<action name="Download_4">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_4}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_4"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_4">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_4.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_4.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_5">
<switch>
<case to="Gen_Orcid_Authors_DOIs_5">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_5.tar.gz'))}
</case>
<default to="Download_5" />
</switch>
</decision>
<action name="Download_5">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_5}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_5"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_5">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_5.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_5.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_6">
<switch>
<case to="Gen_Orcid_Authors_DOIs_6">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_6.tar.gz'))}
</case>
<default to="Download_6" />
</switch>
</decision>
<action name="Download_6">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_6}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_6"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_6">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_6.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_6.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_7">
<switch>
<case to="Gen_Orcid_Authors_DOIs_7">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_7.tar.gz'))}
</case>
<default to="Download_7" />
</switch>
</decision>
<action name="Download_7">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_7}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_7"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_7">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_7.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_7.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_8">
<switch>
<case to="Gen_Orcid_Authors_DOIs_8">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_8.tar.gz'))}
</case>
<default to="Download_8" />
</switch>
</decision>
<action name="Download_8">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_8}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_8"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_8">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_8.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_8.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_9">
<switch>
<case to="Gen_Orcid_Authors_DOIs_9">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_9.tar.gz'))}
</case>
<default to="Download_9" />
</switch>
</decision>
<action name="Download_9">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_9}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_9"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_9">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_9.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_9.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<decision name="check_exist_on_hdfs_activities_X">
<switch>
<case to="Gen_Orcid_Authors_DOIs_X">
${fs:exists(concat(workingPath_activities,'/ORCID_2019_activites_X.tar.gz'))}
</case>
<default to="Download_X" />
</switch>
</decision>
<action name="Download_X">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>bash</exec>
<argument>-c</argument>
<argument>${shell_cmd_X}</argument>
<capture-output/>
</shell>
<ok to="Gen_Orcid_Authors_DOIs_X"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors_DOIs_X">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidAuthorsDOIsDataGen</main-class>
<arg>-d</arg><arg>${workingPath_activities}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_activites_X.tar.gz</arg>
<arg>-o</arg><arg>output/authors_dois_X.seq</arg>
</java>
<ok to="join_node"/>
<error to="Kill"/>
</action>
<join name = "join_node" to = "End"/>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
</property>
<property>
<name>queueName</name>
<value>default</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

55
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_doi_author_list/oozie_app/workflow.xml Normal file
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<workflow-app name="Gen_Doi_Author_List_WF" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base 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>number of cores used by single executor</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath_activities}/doi_author_list'/>
</fs>
<ok to="Gen_Doi_Author_List"/>
<error to="Kill"/>
</action>
<action name="Gen_Doi_Author_List">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn</master>
<mode>cluster</mode>
<name>Gen_Doi_Author_List</name>
<class>eu.dnetlib.doiboost.orcid.SparkGenerateDoiAuthorList</class>
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 10 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
</spark-opts>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-o</arg><arg>doi_author_list/</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.action.sharelib.for.java</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
</configuration>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_download/oozie_app/workflow.xml Normal file
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<workflow-app name="Orcid Download" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPathOrcid</name>
<description>the working dir base path</description>
</property>
<property>
<name>token</name>
<description>access token</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPathOrcid}/download'/>
<mkdir path='${workingPathOrcid}/download'/>
</fs>
<ok to="DownloadOrcidData"/>
<error to="Kill"/>
</action>
<action name="DownloadOrcidData">
<java>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.doiboost.orcid.OrcidDownloader</main-class>
<arg>-d</arg><arg>${workingPathOrcid}/</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>last_modified.csv</arg>
<arg>-o</arg><arg>download/</arg>
<arg>-t</arg><arg>${token}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

22
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>hadoop-rm3.garr-pa1.d4science.org:8032</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://hadoop-rm1.garr-pa1.d4science.org:8020</value>
</property>
<property>
<name>queueName</name>
<value>default</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_gen_authors/oozie_app/workflow.xml Normal file
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<workflow-app name="Gen Orcid Authors" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>workingPath</name>
<description>the working dir base path</description>
</property>
<property>
<name>token</name>
<description>access token</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>number of cores used by single executor</description>
</property>
<property>
<name>outputPath</name>
<description>the working dir base path</description>
</property>
</parameters>
<start to="ResetWorkingPath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResetWorkingPath">
<fs>
<delete path='${workingPath_activities}/authors'/>
</fs>
<ok to="Gen_Orcid_Authors"/>
<error to="Kill"/>
</action>
<action name="Split_Lambda_File">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn</master>
<mode>cluster</mode>
<name>Split_Lambda_File</name>
<class>eu.dnetlib.doiboost.orcid.SparkPartitionLambdaFile</class>
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 24 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
</spark-opts>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-o</arg><arg>authors/</arg>
<arg>-t</arg><arg>${token}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="Gen_Orcid_Authors">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn</master>
<mode>cluster</mode>
<name>Gen_Orcid_Authors</name>
<class>eu.dnetlib.doiboost.orcid.SparkOrcidGenerateAuthors</class>
<jar>dhp-doiboost-1.2.1-SNAPSHOT.jar</jar>
<spark-opts>--num-executors 20 --conf spark.yarn.jars=&quot;hdfs://hadoop-rm1.garr-pa1.d4science.org:8020/user/oozie/share/lib/lib_20180405103059/spark2&quot; --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory}
</spark-opts>
<arg>-w</arg><arg>${workingPath}/</arg>
<arg>-o</arg><arg>authors/</arg>
<arg>-t</arg><arg>${token}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/config-default.xml Normal file
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<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>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>

55
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid_oaf/oozie_app/workflow.xml Normal file
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<workflow-app name="import ORCID into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base 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>number of cores used by single executor</description>
</property>
</parameters>
<start to="PreprocessORCID"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PreprocessORCID">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert ORCID to Dataset</name>
<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/config-default.xml Normal file
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<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>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>

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dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/unpaywall/oozie_app/workflow.xml Normal file
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<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the working dir base path</description>
</property>
<property>
<name>targetPath</name>
<description>the working dir base 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>number of cores used by single executor</description>
</property>
</parameters>
<start to="PreprocessUW"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PreprocessUW">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>Convert UnpayWall to Dataset</name>
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
<jar>dhp-doiboost-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.sql.shuffle.partitions=3840
${sparkExtraOPT}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/uw_extracted</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala Normal file
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package eu.dnetlib.dhp.doiboost
import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType}
import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass
import eu.dnetlib.doiboost.mag.ConversionUtil
import eu.dnetlib.doiboost.orcid.ORCIDElement
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import scala.io.Source
class DoiBoostHostedByMapTest {
// @Test
// def testMerge():Unit = {
// val conf: SparkConf = new SparkConf()
// val spark: SparkSession =
// SparkSession
// .builder()
// .config(conf)
// .appName(getClass.getSimpleName)
// .master("local[*]").getOrCreate()
//
//
//
// implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
// implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
// implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
//
//
// import spark.implicits._
// val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz")
//
//
// val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem))
//
//
// hbMap.show()
//
//
//
//
//
//
//
//
//
//
// }
@Test
def idDSGeneration():Unit = {
val s ="doajarticles::0066-782X"
println(DoiBoostMappingUtil.generateDSId(s))
}
}

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package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
import scala.util.matching.Regex
class CrossrefMappingTest {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper()
@Test
def testFunderRelationshipsMapping(): Unit = {
val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
val funder_doi = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
val funder_name = Source.fromInputStream(getClass.getResourceAsStream("funder_doi")).mkString
for (line <- funder_doi.lines) {
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
checkRelation(resultList)
}
for (line <- funder_name.lines) {
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
checkRelation(resultList)
}
}
def checkRelation(generatedOAF: List[Oaf]): Unit = {
val rels: List[Relation] = generatedOAF.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
assertFalse(rels.isEmpty)
rels.foreach(relation => {
val relJson = mapper.writeValueAsString(relation)
assertNotNull(relation.getSource, s"Source of relation null $relJson")
assertNotNull(relation.getTarget, s"Target of relation null $relJson")
assertFalse(relation.getTarget.isEmpty, s"Target is empty: $relJson")
assertFalse(relation.getRelClass.isEmpty, s"RelClass is empty: $relJson")
assertFalse(relation.getRelType.isEmpty, s"RelType is empty: $relJson")
assertFalse(relation.getSubRelType.isEmpty, s"SubRelType is empty: $relJson")
})
}
@Test
def testEmptyTitle() :Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Result])
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
items.foreach(p => println(mapper.writeValueAsString(p)))
}
@Test
def testPeerReviewed(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("prwTest.json")).mkString
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Result])
items.foreach(p => logger.info(mapper.writeValueAsString(p)))
}
def extractECAward(award: String): String = {
val awardECRegex: Regex = "[0-9]{4,9}".r
if (awardECRegex.findAllIn(award).hasNext)
return awardECRegex.findAllIn(award).max
null
}
@Test
def extractECTest(): Unit = {
val s = "FP7/2007-2013"
val awardExtracted = extractECAward(s)
println(awardExtracted)
println(DHPUtils.md5(awardExtracted))
}
@Test
def testJournalRelation(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("awardTest.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val rels:List[Relation] = resultList.filter(p => p.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation])
rels.foreach(s => logger.info(s.getTarget))
assertEquals(rels.size, 3 )
}
@Test
def testConvertBookFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("book.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Result])
assert(items.nonEmpty)
assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Result]
assertNotNull(result)
logger.info(mapper.writeValueAsString(result));
assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
assertNotNull(
result.getDataInfo.getProvenanceaction,
"DataInfo/Provenance test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
"DataInfo/Provenance/classId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
"DataInfo/Provenance/className test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
"DataInfo/Provenance/SchemeId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
"DataInfo/Provenance/SchemeName test not null Failed");
assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
assertFalse(result.getCollectedfrom.isEmpty);
val collectedFromList = result.getCollectedfrom.asScala
assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
val relevantDates = result.getRelevantdate.asScala
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-online")), "Missing relevant date of type published-online")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-print")), "Missing relevant date of type published-print")
val rels = resultList.filter(p => p.isInstanceOf[Relation])
assert(rels.isEmpty)
}
@Test
def testConvertPreprintFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("preprint.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Publication])
assert(items.nonEmpty)
assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Publication]
assertNotNull(result)
logger.info(mapper.writeValueAsString(result));
assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
assertNotNull(
result.getDataInfo.getProvenanceaction,
"DataInfo/Provenance test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
"DataInfo/Provenance/classId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
"DataInfo/Provenance/className test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
"DataInfo/Provenance/SchemeId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
"DataInfo/Provenance/SchemeName test not null Failed");
assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
assertFalse(result.getCollectedfrom.isEmpty);
val collectedFromList = result.getCollectedfrom.asScala
assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
val relevantDates = result.getRelevantdate.asScala
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("available")), "Missing relevant date of type available")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("accepted")), "Missing relevant date of type accepted")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-online")), "Missing relevant date of type published-online")
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("published-print")), "Missing relevant date of type published-print")
val rels = resultList.filter(p => p.isInstanceOf[Relation])
assert(rels.isEmpty)
}
@Test
def testConvertDatasetFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("dataset.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Dataset])
assert(items.nonEmpty)
assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Dataset]
assertNotNull(result)
logger.info(mapper.writeValueAsString(result));
assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
assertNotNull(
result.getDataInfo.getProvenanceaction,
"DataInfo/Provenance test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
"DataInfo/Provenance/classId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
"DataInfo/Provenance/className test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
"DataInfo/Provenance/SchemeId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
"DataInfo/Provenance/SchemeName test not null Failed");
assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
assertFalse(result.getCollectedfrom.isEmpty);
}
@Test
def testConvertArticleFromCrossRef2Oaf(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Publication])
assert(items.nonEmpty)
assert(items.size == 1)
val result: Result = items.head.asInstanceOf[Publication]
assertNotNull(result)
logger.info(mapper.writeValueAsString(result));
assertNotNull(result.getDataInfo, "Datainfo test not null Failed");
assertNotNull(
result.getDataInfo.getProvenanceaction,
"DataInfo/Provenance test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassid.isEmpty,
"DataInfo/Provenance/classId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getClassname.isEmpty,
"DataInfo/Provenance/className test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemeid.isEmpty,
"DataInfo/Provenance/SchemeId test not null Failed");
assertFalse(
result.getDataInfo.getProvenanceaction.getSchemename.isEmpty,
"DataInfo/Provenance/SchemeName test not null Failed");
assertNotNull(result.getCollectedfrom, "CollectedFrom test not null Failed");
assertFalse(result.getCollectedfrom.isEmpty);
val collectedFromList = result.getCollectedfrom.asScala
assert(collectedFromList.exists(c => c.getKey.equalsIgnoreCase("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")), "Wrong collected from assertion")
assert(collectedFromList.exists(c => c.getValue.equalsIgnoreCase("crossref")), "Wrong collected from assertion")
val relevantDates = result.getRelevantdate.asScala
assert(relevantDates.exists(d => d.getQualifier.getClassid.equalsIgnoreCase("created")), "Missing relevant date of type created")
val rels = resultList.filter(p => p.isInstanceOf[Relation]).asInstanceOf[List[Relation]]
assertFalse(rels.isEmpty)
rels.foreach(relation => {
assertNotNull(relation)
assertFalse(relation.getSource.isEmpty)
assertFalse(relation.getTarget.isEmpty)
assertFalse(relation.getRelClass.isEmpty)
assertFalse(relation.getRelType.isEmpty)
assertFalse(relation.getSubRelType.isEmpty)
})
}
}

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala Normal file
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package eu.dnetlib.doiboost.mag
import java.sql.Timestamp
import eu.dnetlib.dhp.schema.oaf.Publication
import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature
import org.apache.spark.SparkConf
import org.apache.spark.api.java.function.MapFunction
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import org.junit.jupiter.api.Assertions._
import org.apache.spark.sql.functions._
import scala.collection.JavaConverters._
import scala.io.Source
import scala.reflect.ClassTag
import scala.util.matching.Regex
class MAGMappingTest {
val logger: Logger = LoggerFactory.getLogger(getClass)
val mapper = new ObjectMapper()
@Test
def testSplitter():Unit = {
val s = "sports.team"
if (s.contains(".")) {
println(s.split("\\.")head)
}
}
@Test
def testDate() :Unit = {
val p:Timestamp = Timestamp.valueOf("2011-10-02 00:00:00")
println(p.toString.substring(0,10))
}
@Test
def buildInvertedIndexTest(): Unit = {
val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString
val description = ConversionUtil.convertInvertedIndexString(json_input)
assertNotNull(description)
assertTrue(description.nonEmpty)
logger.debug(description)
}
}

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/ElasticSearchTest.java Normal file
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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala Normal file
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package eu.dnetlib.doiboost.orcid
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
import org.junit.jupiter.api.Assertions._
import scala.io.Source
class MappingORCIDToOAFTest {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper()
@Test
def testExtractData():Unit ={
val json = Source.fromInputStream(getClass.getResourceAsStream("dataOutput")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
json.lines.foreach(s => {
assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
})
}
}

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/OrcidClientTest.java Normal file
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package eu.dnetlib.doiboost.orcid;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
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 org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidClientTest {
final String orcidId = "0000-0001-7291-3210";
final int REQ_LIMIT = 24;
final int REQ_MAX_TEST = 100;
final int RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL = 10;
final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
final String toRetrieveDate = "2020-05-06 23:59:46.031145";
String toNotRetrieveDate = "2019-09-29 23:59:59.000000";
String lastUpdate = "2019-09-30 00:00:00";
String shortDate = "2020-05-06 16:06:11";
// curl -i -H "Accept: application/vnd.orcid+xml"
// -H 'Authorization: Bearer 78fdb232-7105-4086-8570-e153f4198e3d'
// 'https://api.orcid.org/v3.0/0000-0001-7291-3210/record'
public String testDownloadRecord(String orcidId) throws Exception {
try (CloseableHttpClient client = HttpClients.createDefault()) {
HttpGet httpGet = new HttpGet("https://api.orcid.org/v3.0/" + orcidId + "/record");
httpGet.addHeader("Accept", "application/vnd.orcid+xml");
httpGet.addHeader("Authorization", "Bearer 78fdb232-7105-4086-8570-e153f4198e3d");
CloseableHttpResponse response = client.execute(httpGet);
if (response.getStatusLine().getStatusCode() != 200) {
System.out
.println("Downloading " + orcidId + " status code: " + response.getStatusLine().getStatusCode());
}
return IOUtils.toString(response.getEntity().getContent());
} catch (Throwable e) {
e.printStackTrace();
}
return new String("");
}
// @Test
public void testLambdaFileParser() throws Exception {
try (BufferedReader br = new BufferedReader(
new InputStreamReader(this.getClass().getResourceAsStream("last_modified.csv")))) {
String line;
int counter = 0;
int nReqTmp = 0;
long startDownload = System.currentTimeMillis();
long startReqTmp = System.currentTimeMillis();
while ((line = br.readLine()) != null) {
counter++;
// skip headers line
if (counter == 1) {
continue;
}
String[] values = line.split(",");
List<String> recordInfo = Arrays.asList(values);
testDownloadRecord(recordInfo.get(0));
long endReq = System.currentTimeMillis();
nReqTmp++;
if (nReqTmp == REQ_LIMIT) {
long reqSessionDuration = endReq - startReqTmp;
if (reqSessionDuration <= 1000) {
System.out
.println(
"\nreqSessionDuration: " + reqSessionDuration + " nReqTmp: " + nReqTmp + " wait ....");
Thread.sleep(1000 - reqSessionDuration);
} else {
nReqTmp = 0;
startReqTmp = System.currentTimeMillis();
}
}
if (counter > REQ_MAX_TEST) {
break;
}
if ((counter % RECORD_DOWNLOADED_COUNTER_LOG_INTERVAL) == 0) {
System.out.println("Current record downloaded: " + counter);
}
}
long endDownload = System.currentTimeMillis();
long downloadTime = endDownload - startDownload;
System.out.println("Download time: " + ((downloadTime / 1000) / 60) + " minutes");
}
}
// @Test
public void getRecordDatestamp() throws ParseException {
Date toRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toRetrieveDate);
Date toNotRetrieveDateDt = new SimpleDateFormat(DATE_FORMAT).parse(toNotRetrieveDate);
Date lastUpdateDt = new SimpleDateFormat(DATE_FORMAT).parse(lastUpdate);
assertTrue(toRetrieveDateDt.after(lastUpdateDt));
assertTrue(!toNotRetrieveDateDt.after(lastUpdateDt));
}
public void testDate(String value) throws ParseException {
System.out.println(value.toString());
if (value.length() != 19) {
value = value.substring(0, 19);
}
Date valueDt = new SimpleDateFormat(DATE_FORMAT).parse(value);
System.out.println(valueDt.toString());
}
// @Test
public void testModifiedDate() throws ParseException {
testDate(toRetrieveDate);
testDate(toNotRetrieveDate);
testDate(shortDate);
}
// @Test
public void testReadBase64CompressedRecord() throws Exception {
final String base64CompressedRecord = IOUtils
.toString(getClass().getResourceAsStream("0000-0001-6645-509X.compressed.base64"));
final String recordFromSeqFile = ArgumentApplicationParser.decompressValue(base64CompressedRecord);
System.out.println(recordFromSeqFile);
final String downloadedRecord = testDownloadRecord("0000-0001-6645-509X");
assertTrue(recordFromSeqFile.equals(downloadedRecord));
}
}

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java Normal file
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package eu.dnetlib.doiboost.orcid.xml;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.model.WorkData;
public class XMLRecordParserTest {
@Test
public void testOrcidAuthorDataXMLParser() throws Exception {
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
XMLRecordParser p = new XMLRecordParser();
AuthorData authorData = p.VTDParseAuthorData(xml.getBytes());
assertNotNull(authorData);
assertNotNull(authorData.getName());
System.out.println("name: " + authorData.getName());
assertNotNull(authorData.getSurname());
System.out.println("surname: " + authorData.getSurname());
}
@Test
public void testOrcidXMLErrorRecordParser() throws Exception {
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml"));
XMLRecordParser p = new XMLRecordParser();
AuthorData authorData = p.VTDParseAuthorData(xml.getBytes());
assertNotNull(authorData);
assertNotNull(authorData.getErrorCode());
System.out.println("error: " + authorData.getErrorCode());
}
@Test
public void testOrcidWorkDataXMLParser() throws Exception {
String xml = IOUtils
.toString(
this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml"));
XMLRecordParser p = new XMLRecordParser();
WorkData workData = p.VTDParseWorkData(xml.getBytes());
assertNotNull(workData);
assertNotNull(workData.getOid());
System.out.println("oid: " + workData.getOid());
assertNotNull(workData.getDoi());
System.out.println("doi: " + workData.getDoi());
}
}

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dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala Normal file
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package eu.dnetlib.doiboost.uw
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Test
import scala.io.Source
import org.junit.jupiter.api.Assertions._
import org.slf4j.{Logger, LoggerFactory}
class UnpayWallMappingTest {
val logger: Logger = LoggerFactory.getLogger(getClass)
val mapper = new ObjectMapper()
@Test
def testMappingToOAF():Unit ={
val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString
for (line <-Ilist.lines) {
val p = UnpayWallToOAF.convertToOAF(line)
if(p!= null) {
assertTrue(p.getPid.size()==1)
logger.info(p.getId)
}
assertNotNull(line)
assertTrue(line.nonEmpty)
}
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
val l = Ilist.lines.next()
logger.info(mapper.writeValueAsString(UnpayWallToOAF.convertToOAF(l)))
}
}

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dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publicationInput.json Normal file
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dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/publication_merge Normal file
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dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article.json Normal file
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{
"DOI": "10.26850/1678-4618eqj.v35.1.2010.p41-46",
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