enrico.ottonello
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merged stable_ids into openorgswf

This commit is contained in:
miconis 2021-03-25 10:44:49 +01:00
parent 5dfb66b0fa 0fe40b08e4
commit 28c1cdd132
284 changed files with 16485 additions and 1635 deletions
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11
dhp-common/pom.xml
View File

@ -29,6 +29,12 @@
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
@ -98,11 +104,6 @@
<artifactId>dnet-pace-core</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>
</project>

35
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
@ -32,27 +33,33 @@ public class AuthorMerger {
}
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
if (pa == pb) {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
} else {
if (sa == sb) {
base = pa > pb ? a : b;
enrich = pa > pb ? b : a;
} else {
base = sa > sb ? a : b;
enrich = sa > sb ? b : a;
}
enrichPidFromList(base, enrich);
enrichPidFromList(base, enrich, threshold);
return base;
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
return mergeAuthor(a, b, THRESHOLD);
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
if (base == null || enrich == null)
return;
// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
final Map<String, Author> basePidAuthorMap = base
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -63,6 +70,7 @@ public class AuthorMerger {
.map(p -> new Tuple2<>(pidToComparableString(p), a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
// <pid, Author> (list of pid that are missing in the other list)
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
@ -83,10 +91,10 @@ public class AuthorMerger {
.max(Comparator.comparing(Tuple2::_1));
if (simAuthor.isPresent()) {
double th = THRESHOLD;
double th = threshold;
// increase the threshold if the surname is too short
if (simAuthor.get()._2().getSurname() != null
&& simAuthor.get()._2().getSurname().length() <= 3)
&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
th = 0.99;
if (simAuthor.get()._1() > th) {
@ -156,7 +164,7 @@ public class AuthorMerger {
}
private static String normalize(final String s) {
return nfd(s)
String[] normalized = nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
@ -166,7 +174,12 @@ public class AuthorMerger {
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
.trim()
.split(" ");
Arrays.sort(normalized);
return String.join(" ", normalized);
}
private static String nfd(final String s) {

110
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java → dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.oa.graph.clean;
package eu.dnetlib.dhp.schema.oaf;
import java.util.*;
import java.util.function.Function;
@ -8,14 +8,16 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.clearspring.analytics.util.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.PidBlacklistProvider;
public class CleaningFunctions {
public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/";
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10.)";
public static final String DOI_PREFIX = "10.";
public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
@ -78,7 +80,7 @@ public class CleaningFunctions {
return value;
}
public static <T extends Oaf> T fixDefaults(T value) {
public static <T extends Oaf> T cleanup(T value) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
@ -86,7 +88,7 @@ public class CleaningFunctions {
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
}
} else if (value instanceof Relation) {
// nothing to clean here
@ -137,28 +139,32 @@ public class CleaningFunctions {
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getPid())) {
r
.setPid(
r
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
.filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(CleaningFunctions::normalizePidValue)
.collect(Collectors.toList()));
r.setPid(processPidCleaning(r.getPid()));
}
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r
.setResourcetype(
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
}
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
final Set<StructuredProperty> pids = Sets.newHashSet(i.getPid());
i
.setAlternateIdentifier(
Optional
.ofNullable(i.getAlternateIdentifier())
.map(
altId -> altId
.stream()
.filter(p -> !pids.contains(p))
.collect(Collectors.toList()))
.orElse(Lists.newArrayList()));
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
i
.setAccessright(
accessRight(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
}
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
@ -169,7 +175,7 @@ public class CleaningFunctions {
}
}
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance());
Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance());
if (Objects.isNull(bestaccessrights)) {
r
.setBestaccessright(
@ -189,7 +195,6 @@ public class CleaningFunctions {
author.setRank(i++);
}
}
for (Author a : r.getAuthor()) {
if (Objects.isNull(a.getPid())) {
a.setPid(Lists.newArrayList());
@ -202,29 +207,14 @@ public class CleaningFunctions {
.filter(p -> Objects.nonNull(p.getQualifier()))
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.map(p -> {
// hack to distinguish orcid from orcid_pending
String pidProvenance = Optional
.ofNullable(p.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
p.getQualifier().setClassid(ModelConstants.ORCID);
} else {
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
}
p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
return p;
})
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect(
Collectors
.toMap(
p -> p.getQualifier().getClassid() + p.getValue(),
Function.identity(),
(p1, p2) -> p1,
StructuredProperty::getValue, Function.identity(), (p1, p2) -> p1,
LinkedHashMap::new))
.values()
.stream()
@ -247,6 +237,19 @@ public class CleaningFunctions {
return value;
}
private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {
return pids
.stream()
.filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
.filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(Collectors.toList());
}
protected static StructuredProperty cleanValue(StructuredProperty s) {
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
return s;
@ -266,12 +269,39 @@ public class CleaningFunctions {
}
}
private static AccessRight accessRight(String classid, String classname, String scheme) {
return OafMapperUtils
.accessRight(
classid, classname, scheme, scheme);
}
private static Qualifier qualifier(String classid, String classname, String scheme) {
return OafMapperUtils
.qualifier(
classid, classname, scheme, scheme);
}
/**
* Utility method that filter PID values on a per-type basis.
* @param s the PID whose value will be checked.
* @return false if the pid matches the filter criteria, true otherwise.
*/
public static boolean pidFilter(StructuredProperty s) {
final String pidValue = s.getValue();
if (Objects.isNull(s.getQualifier()) ||
StringUtils.isBlank(pidValue) ||
StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
return false;
}
if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
return false;
}
if (PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue)) {
return false;
}
return true;
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
@ -286,7 +316,7 @@ public class CleaningFunctions {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, ""));
pid.setValue(value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX));
break;
}
return pid;

22
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ModelHardLimits.java Normal file
View File

@ -0,0 +1,22 @@
package eu.dnetlib.dhp.schema.oaf;
public class ModelHardLimits {
public static final String LAYOUT = "index";
public static final String INTERPRETATION = "openaire";
public static final String SEPARATOR = "-";
public static final int MAX_EXTERNAL_ENTITIES = 50;
public static final int MAX_AUTHORS = 200;
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
public static final int MAX_TITLE_LENGTH = 5000;
public static final int MAX_TITLES = 10;
public static final int MAX_ABSTRACT_LENGTH = 150000;
public static final int MAX_INSTANCES = 10;
public static String getCollectionName(String format) {
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
}
}

125
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java
View File

@ -1,11 +1,9 @@
package eu.dnetlib.dhp.schema.oaf;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function;
import java.util.function.Predicate;
@ -13,40 +11,45 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.utils.DHPUtils;
public class OafMapperUtils {
public static Oaf merge(final Oaf o1, final Oaf o2) {
if (ModelSupport.isSubClass(o1, OafEntity.class)) {
if (ModelSupport.isSubClass(o1, Result.class)) {
return mergeResults((Result) o1, (Result) o2);
} else if (ModelSupport.isSubClass(o1, Datasource.class)) {
((Datasource) o1).mergeFrom((Datasource) o2);
} else if (ModelSupport.isSubClass(o1, Organization.class)) {
((Organization) o1).mergeFrom((Organization) o2);
} else if (ModelSupport.isSubClass(o1, Project.class)) {
((Project) o1).mergeFrom((Project) o2);
} else {
throw new RuntimeException("invalid OafEntity subtype:" + o1.getClass().getCanonicalName());
}
} else if (ModelSupport.isSubClass(o1, Relation.class)) {
((Relation) o1).mergeFrom((Relation) o2);
public static Oaf merge(final Oaf left, final Oaf right) {
if (ModelSupport.isSubClass(left, OafEntity.class)) {
return mergeEntities((OafEntity) left, (OafEntity) right);
} else if (ModelSupport.isSubClass(left, Relation.class)) {
((Relation) left).mergeFrom((Relation) right);
} else {
throw new RuntimeException("invalid Oaf type:" + o1.getClass().getCanonicalName());
throw new RuntimeException("invalid Oaf type:" + left.getClass().getCanonicalName());
}
return o1;
return left;
}
public static Result mergeResults(Result r1, Result r2) {
if (new ResultTypeComparator().compare(r1, r2) < 0) {
r1.mergeFrom(r2);
return r1;
public static OafEntity mergeEntities(OafEntity left, OafEntity right) {
if (ModelSupport.isSubClass(left, Result.class)) {
return mergeResults((Result) left, (Result) right);
} else if (ModelSupport.isSubClass(left, Datasource.class)) {
((Datasource) left).mergeFrom((Datasource) right);
} else if (ModelSupport.isSubClass(left, Organization.class)) {
((Organization) left).mergeFrom((Organization) right);
} else if (ModelSupport.isSubClass(left, Project.class)) {
((Project) left).mergeFrom((Project) right);
} else {
r2.mergeFrom(r1);
return r2;
throw new RuntimeException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
}
return left;
}
public static Result mergeResults(Result left, Result right) {
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
} else {
right.mergeFrom(left);
return right;
}
}
@ -102,6 +105,29 @@ public class OafMapperUtils {
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final String schemename) {
return accessRight(classid, classname, schemeid, schemename, null);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final String schemename,
final OpenAccessRoute openAccessRoute) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(classid);
accessRight.setClassname(classname);
accessRight.setSchemeid(schemeid);
accessRight.setSchemename(schemename);
accessRight.setOpenAccessRoute(openAccessRoute);
return accessRight;
}
public static Qualifier qualifier(
final String classid,
final String classname,
@ -115,6 +141,15 @@ public class OafMapperUtils {
return q;
}
public static Qualifier qualifier(final Qualifier qualifier) {
final Qualifier q = new Qualifier();
q.setClassid(qualifier.getClassid());
q.setClassname(qualifier.getClassname());
q.setSchemeid(qualifier.getSchemeid());
q.setSchemename(qualifier.getSchemename());
return q;
}
public static StructuredProperty structuredProperty(
final String value,
final String classid,
@ -294,4 +329,36 @@ public class OafMapperUtils {
final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
}
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<AccessRight> min = instanceList
.stream()
.map(i -> i.getAccessright())
.min(new AccessRightComparator<>());
final Qualifier rights = min.isPresent() ? qualifier(min.get()) : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
}
if (StringUtils.isBlank(rights.getClassname())
|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
rights.setClassname(NOT_AVAILABLE);
}
if (StringUtils.isBlank(rights.getSchemeid())) {
rights.setSchemeid(DNET_ACCESS_MODES);
}
if (StringUtils.isBlank(rights.getSchemename())) {
rights.setSchemename(DNET_ACCESS_MODES);
}
return rights;
}
return null;
}
}

29
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ResultTypeComparator.java
View File

@ -1,7 +1,15 @@
package eu.dnetlib.dhp.schema.oaf;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
@ -17,6 +25,16 @@ public class ResultTypeComparator implements Comparator<Result> {
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
@ -46,4 +64,15 @@ public class ResultTypeComparator implements Comparator<Result> {
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(c -> c.getKey())
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

216
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java Normal file
View File

@ -0,0 +1,216 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.HashBiMap;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.DHPUtils;
/**
* Factory class for OpenAIRE identifiers in the Graph
*/
public class IdentifierFactory implements Serializable {
public static final String ID_SEPARATOR = "::";
public static final String ID_PREFIX_SEPARATOR = "|";
public final static String DOI_REGEX = "(^10\\.[0-9]{4,9}\\/[-._;()\\/:a-zA-Z0-9]+$)|" +
"(^10\\.1002\\/[^\\s]+$)|" +
"(^10\\.1021\\/[a-zA-Z0-9_][a-zA-Z0-9_][0-9]++$)|" +
"(^10\\.1207\\/[a-zA-Z0-9_]+\\&[0-9]+_[0-9]+$)";
public static final int ID_PREFIX_LEN = 12;
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE
*/
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
static {
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom).distinct().collect(Collectors.toList());
}
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
if (entity == null)
return null;
StructuredProperty pid = null;
if (entity.getPid() != null) {
pid = entity
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
} else {
if (entity.getInstance() != null) {
pid = entity
.getInstance()
.stream()
.filter(i -> i.getPid() != null)
.flatMap(i -> i.getPid().stream())
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
}
}
if (pid != null)
return idFromPid(entity, pid, true);
return null;
}
/**
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
*
* @param entity the entity providing PIDs and a default ID.
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
* @param md5 indicates whether should hash the PID value or not.
* @return an identifier from the most relevant PID, entity.id otherwise
*/
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
final Map<String, List<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
.stream()
.flatMap(s -> s.stream())
.min(new PidComparator<>(entity))
.map(
min -> Optional
.ofNullable(pids.get(min.getQualifier().getClassid()))
.map(
p -> p
.stream()
.sorted(new PidValueComparator())
.findFirst()
.map(s -> idFromPid(entity, s, md5))
.orElseGet(entity::getId))
.orElseGet(entity::getId))
.orElseGet(entity::getId);
}
private static <T extends OafEntity> Map<String, List<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(
instance -> mapPids(instance))
.orElse(new HashMap<>());
} else {
return entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toList())));
}
}
private static Map<String, List<StructuredProperty>> mapPids(List<Instance> instance) {
return instance
.stream()
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom()))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toList())));
}
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom) {
return Optional
.ofNullable(pid)
.map(
pp -> pp
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> {
return shouldFilterPid(collectedFrom, p);
})
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPid(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
return pType.equals(PidType.handle) || Optional.ofNullable(collectedFrom).isPresent() &&
Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(authorities -> {
return authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue());
})
.orElse(false);
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/
public static <T extends OafEntity> String createIdentifier(T entity) {
return createIdentifier(entity, true);
}
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
return new StringBuilder()
.append(ModelSupport.getIdPrefix(entity.getClass()))
.append(ID_PREFIX_SEPARATOR)
.append(createPrefix(s.getQualifier().getClassid()))
.append(ID_SEPARATOR)
.append(md5 ? DHPUtils.md5(s.getValue()) : s.getValue())
.toString();
}
// create the prefix (length = 12)
private static String createPrefix(String pidType) {
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
while (prefix.length() < ID_PREFIX_LEN) {
prefix.append("_");
}
return prefix.substring(0, ID_PREFIX_LEN);
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(PidType.GRID))
return -1;
if (rClass.equals(PidType.GRID))
return 1;
if (lClass.equals(PidType.mag_id))
return -1;
if (rClass.equals(PidType.mag_id))
return 1;
if (lClass.equals(PidType.urn))
return -1;
if (rClass.equals(PidType.urn))
return 1;
return 0;
}
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashMap;
import java.util.HashSet;
public class PidBlacklist extends HashMap<String, HashSet<String>> {
}

37
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.io.IOException;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class PidBlacklistProvider {
private static final PidBlacklist blacklist;
static {
try {
String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static PidBlacklist getBlacklist() {
return blacklist;
}
public static Set<String> getBlacklist(String pidType) {
return Optional
.ofNullable(getBlacklist().get(pidType))
.orElse(new HashSet<>());
}
}

48
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
private T entity;
public PidComparator(T entity) {
this.entity = entity;
}
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
if (ModelSupport.isSubClass(entity, Result.class)) {
return compareResultPids(left, right);
}
if (ModelSupport.isSubClass(entity, Organization.class)) {
return compareOrganizationtPids(left, right);
}
// Else (but unlikely), lexicographical ordering will do.
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
}
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
return new ResultPidComparator().compare(left, right);
}
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
return new OrganizationPidComparator().compare(left, right);
}
}

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dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import org.apache.commons.lang3.EnumUtils;
public enum PidType {
// Result
doi, pmid, pmc, handle, arXiv, nct, pdb,
// Organization
GRID, mag_id, urn,
// Used by dedup
undefined, original;
public static boolean isValid(String type) {
return EnumUtils.isValidEnum(PidType.class, type);
}
public static PidType tryValueOf(String s) {
try {
return PidType.valueOf(s);
} catch (Exception e) {
return PidType.original;
}
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.*;
public class PidValueComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
StructuredProperty l = CleaningFunctions.normalizePidValue(left);
StructuredProperty r = CleaningFunctions.normalizePidValue(right);
return Optional
.ofNullable(l.getValue())
.map(
lv -> Optional
.ofNullable(r.getValue())
.map(rv -> lv.compareTo(rv))
.orElse(-1))
.orElse(1);
}
}

53
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class ResultPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(PidType.doi))
return -1;
if (rClass.equals(PidType.doi))
return 1;
if (lClass.equals(PidType.pmid))
return -1;
if (rClass.equals(PidType.pmid))
return 1;
if (lClass.equals(PidType.pmc))
return -1;
if (rClass.equals(PidType.pmc))
return 1;
if (lClass.equals(PidType.handle))
return -1;
if (rClass.equals(PidType.handle))
return 1;
if (lClass.equals(PidType.arXiv))
return -1;
if (rClass.equals(PidType.arXiv))
return 1;
if (lClass.equals(PidType.nct))
return -1;
if (rClass.equals(PidType.nct))
return 1;
if (lClass.equals(PidType.pdb))
return -1;
if (rClass.equals(PidType.pdb))
return 1;
return 0;
}
}

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100
dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java Normal file
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package eu.dnetlib.dhp.oa.merge;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class AuthorMergerTest {
private String publicationsBasePath;
private List<List<Author>> authors;
@BeforeEach
public void setUp() throws Exception {
publicationsBasePath = Paths
.get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI())
.toFile()
.getAbsolutePath();
authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
}
@Test
public void mergeTest() { // used in the dedup: threshold set to 0.95
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = AuthorMerger.merge(authors);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(7, merge.size());
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
public String authorToString(Author a) {
String print = "Fullname = ";
print += a.getFullname() + " pid = [";
if (a.getPid() != null)
for (StructuredProperty sp : a.getPid()) {
print += sp.toComparableString() + " ";
}
print += "]";
return print;
}
}

69
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtilsTest.java Normal file
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package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.jetbrains.annotations.NotNull;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import it.unimi.dsi.fastutil.Hash;
public class OafMapperUtilsTest {
private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
public void testMergePubs() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
Dataset d2 = read("dataset_2.json", Dataset.class);
assertEquals(p1.getCollectedfrom().size(), 1);
assertEquals(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
assertEquals(d2.getCollectedfrom().size(), 1);
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertTrue(
OafMapperUtils
.mergeResults(p1, d2)
.getResulttype()
.getClassid()
.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
assertEquals(p2.getCollectedfrom().size(), 1);
assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(d1.getCollectedfrom().size(), 1);
assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertTrue(
OafMapperUtils
.mergeResults(p2, d1)
.getResulttype()
.getClassid()
.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
}
@NotNull
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(c -> c.getKey()).collect(Collectors.toCollection(HashSet::new));
}
protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
return OBJECT_MAPPER.readValue(json, clazz);
}
}

21
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class BlackListProviderTest {
@Test
public void blackListTest() {
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
Assertions.assertNotNull(xxx);
Assertions.assertEquals(0, xxx.size());
}
}

72
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java Normal file
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package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.utils.DHPUtils;
public class IdentifierFactoryTest {
private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
public void testCreateIdentifierForPublication() throws IOException {
verifyIdentifier(
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, true);
verifyIdentifier("publication_4.json", defaultID, true);
verifyIdentifier("publication_5.json", defaultID, true);
}
@Test
public void testCreateIdentifierForPublicationNoHash() throws IOException {
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
verifyIdentifier(
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, false);
verifyIdentifier("publication_4.json", defaultID, false);
verifyIdentifier("publication_5.json", defaultID, false);
}
protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
String id = IdentifierFactory.createIdentifier(pub, md5);
assertNotNull(id);
assertEquals(expectedID, id);
}
}

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dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json Normal file
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dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/dataset_1.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/dataset_2.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository B"} ]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/publication_1.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resuttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/publication_2.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resuttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository A"} ]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[]}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json Normal file
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{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"}

33
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi1.json Normal file
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{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
"value": "Crossref"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

37
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi2.json Normal file
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@ -0,0 +1,37 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
"value": "Crossref"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

37
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json Normal file
View File

@ -0,0 +1,37 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::1234",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

1
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc1.json Normal file
View File

@ -0,0 +1 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]}

21
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json Normal file
View File

@ -0,0 +1,21 @@
{
"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
"value": "Europe PubMed Central"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier":{"classid":"pmc"},
"value":"21459329"
}
]
}
]
}

23
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json Normal file
View File

@ -0,0 +1,23 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"pid": [
{
"qualifier": {
"classid": "urn"
},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {
"classid": "scp-number"
},
"value": "79953761260"
},
{
"qualifier": {
"classid": "pmcid"
},
"value": "21459329"
}
]
}

5
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java → dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/AccessRightComparator.java
View File

@ -3,12 +3,13 @@ package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class LicenseComparator implements Comparator<Qualifier> {
public class AccessRightComparator<T extends Qualifier> implements Comparator<T> {
@Override
public int compare(Qualifier left, Qualifier right) {
public int compare(T left, T right) {
if (left == null && right == null)
return 0;

18
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -11,13 +11,24 @@ public class ModelConstants {
public static final String ORCID_PENDING = "orcid_pending";
public static final String ORCID_CLASSNAME = "Open Researcher and Contributor ID";
public static final String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
public static final String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
public static final String EUROPE_PUBMED_CENTRAL_ID = "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c";
public static final String PUBMED_CENTRAL_ID = "10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357";
public static final String ARXIV_ID = "10|opendoar____::6f4922f45568161a8cdf4ad2299f6d23";
// VOCABULARY VALUE
public static final String ACCESS_RIGHT_OPEN = "OPEN";
public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies";
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource";
public static final String DNET_ACCESS_MODES = "dnet:access_modes";
public static final String DNET_LANGUAGES = "dnet:languages";
public static final String DNET_PID_TYPES = "dnet:pid_types";
public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date";
public static final String DNET_DATACITE_DATE = "dnet:dataCite_date";
public static final String DNET_DATACITE_TITLE = "dnet:dataCite_title";
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public static final String DNET_COUNTRY_TYPE = "dnet:countries";
@ -105,6 +116,11 @@ public class ModelConstants {
public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
public static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
"main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE);
private static Qualifier qualifier(
final String classid,
final String classname,

27
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
View File

@ -3,6 +3,12 @@ package eu.dnetlib.dhp.schema.common;
import static com.google.common.base.Preconditions.checkArgument;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.time.Instant;
import java.time.format.DateTimeFormatter;
import java.time.temporal.TemporalAccessor;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
@ -375,6 +381,8 @@ public class ModelSupport {
Field.class,
GeoLocation.class,
Instance.class,
AccessRight.class,
OpenAccessRoute.class,
Journal.class,
KeyValue.class,
Oaf.class,
@ -473,4 +481,23 @@ public class ModelSupport {
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
public static String oldest(String dateA, String dateB) throws ParseException {
if (StringUtils.isBlank(dateA)) {
return dateB;
}
if (StringUtils.isBlank(dateB)) {
return dateA;
}
if (StringUtils.isNotBlank(dateA) && StringUtils.isNotBlank(dateB)) {
final Date a = Date.from(Instant.from(DateTimeFormatter.ISO_INSTANT.parse(dateA)));
final Date b = Date.from(Instant.from(DateTimeFormatter.ISO_INSTANT.parse(dateB)));
return a.before(b) ? dateA : dateB;
} else {
return null;
}
}
}

48
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/AccessRight.java Normal file
View File

@ -0,0 +1,48 @@
package eu.dnetlib.dhp.schema.oaf;
import java.util.Optional;
/**
* This class models the access rights of research products.
*/
public class AccessRight extends Qualifier {
private OpenAccessRoute openAccessRoute;
public OpenAccessRoute getOpenAccessRoute() {
return openAccessRoute;
}
public void setOpenAccessRoute(OpenAccessRoute openAccessRoute) {
this.openAccessRoute = openAccessRoute;
}
public String toComparableString() {
String s = super.toComparableString();
return Optional
.ofNullable(getOpenAccessRoute())
.map(x -> s + "::" + x.toString())
.orElse(s);
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Qualifier other = (Qualifier) obj;
return toComparableString().equals(other.toComparableString());
}
}

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

@ -12,6 +12,7 @@ public class Author implements Serializable {
private String surname;
// START WITH 1
private Integer rank;
private List<StructuredProperty> pid;

27
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -8,7 +8,7 @@ public class Instance implements Serializable {
private Field<String> license;
private Qualifier accessright;
private AccessRight accessright;
private Qualifier instancetype;
@ -21,6 +21,10 @@ public class Instance implements Serializable {
private KeyValue collectedfrom;
private List<StructuredProperty> pid;
private List<StructuredProperty> alternateIdentifier;
private Field<String> dateofacceptance;
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
@ -41,11 +45,11 @@ public class Instance implements Serializable {
this.license = license;
}
public Qualifier getAccessright() {
public AccessRight getAccessright() {
return accessright;
}
public void setAccessright(Qualifier accessright) {
public void setAccessright(AccessRight accessright) {
this.accessright = accessright;
}
@ -89,6 +93,14 @@ public class Instance implements Serializable {
this.collectedfrom = collectedfrom;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public Field<String> getDateofacceptance() {
return dateofacceptance;
}
@ -97,6 +109,14 @@ public class Instance implements Serializable {
this.dateofacceptance = dateofacceptance;
}
public List<StructuredProperty> getAlternateIdentifier() {
return alternateIdentifier;
}
public void setAlternateIdentifier(List<StructuredProperty> alternateIdentifier) {
this.alternateIdentifier = alternateIdentifier;
}
public Field<String> getProcessingchargeamount() {
return processingchargeamount;
}
@ -149,4 +169,5 @@ public class Instance implements Serializable {
return toComparableString().equals(other.toComparableString());
}
}

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

@ -62,8 +62,6 @@ public abstract class Oaf implements Serializable {
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
mergeOAFDataInfo(o);
setLastupdatetimestamp(
Math
.max(

13
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OpenAccessRoute.java Normal file
View File

@ -0,0 +1,13 @@
package eu.dnetlib.dhp.schema.oaf;
/**
* This Enum models the OpenAccess status, currently including only the values from Unpaywall
*
* https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-
*/
public enum OpenAccessRoute {
gold, green, hybrid, bronze
}

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

@ -351,8 +351,6 @@ public class Project extends OafEntity implements Serializable {
? p.getFundedamount()
: fundedamount;
// programme = mergeLists(programme, p.getProgramme());
h2020classification = mergeLists(h2020classification, p.getH2020classification());
mergeOAFDataInfo(e);

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -3,10 +3,13 @@ package eu.dnetlib.dhp.schema.oaf;
import static com.google.common.base.Preconditions.checkArgument;
import java.text.ParseException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/**
* Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id pointing to
* graph node identifiers and it is further characterised by the semantic of the link through the fields relType,
@ -106,7 +109,7 @@ public class Relation extends Oaf {
}
public Boolean getValidated() {
return validated;
return Objects.nonNull(validated) && validated;
}
public void setValidated(Boolean validated) {
@ -130,6 +133,16 @@ public class Relation extends Oaf {
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setValidated(getValidated() || r.getValidated());
try {
setValidationDate(ModelSupport.oldest(getValidationDate(), r.getValidationDate()));
} catch (ParseException e) {
throw new IllegalArgumentException(String
.format(
"invalid validation date format in relation [s:%s, t:%s]: %s", getSource(), getTarget(),
getValidationDate()));
}
super.mergeFrom(r);
}

11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -2,12 +2,11 @@
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;
import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
public class Result extends OafEntity implements Serializable {
@ -243,12 +242,12 @@ public class Result extends OafEntity implements Serializable {
Result r = (Result) e;
// TODO consider merging also Measures
measures = mergeLists(measures, r.getMeasures());
instance = mergeLists(instance, r.getInstance());
if (r.getBestaccessright() != null
&& new LicenseComparator().compare(r.getBestaccessright(), bestaccessright) < 0)
&& new AccessRightComparator().compare(r.getBestaccessright(), bestaccessright) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0)
@ -323,13 +322,13 @@ public class Result extends OafEntity implements Serializable {
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i.getValue() != null)
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);

14
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/StructuredProperty.java
View File

@ -2,6 +2,13 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Joiner;
public class StructuredProperty implements Serializable {
@ -36,7 +43,12 @@ public class StructuredProperty implements Serializable {
}
public String toComparableString() {
return value != null ? value.toLowerCase() : "";
return Stream
.of(
getQualifier().toComparableString(),
Optional.ofNullable(getValue()).map(String::toLowerCase).orElse(""))
.filter(StringUtils::isNotBlank)
.collect(Collectors.joining("||"));
}
@Override

11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/OafUtils.scala
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dhp.schema.scholexplorer
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
object OafUtils {
@ -39,6 +39,15 @@ object OafUtils {
q
}
def createAccessRight(classId: String, className: String, schemeId: String, schemeName: String): AccessRight = {
val accessRight: AccessRight = new AccessRight
accessRight.setClassid(classId)
accessRight.setClassname(className)
accessRight.setSchemeid(schemeId)
accessRight.setSchemename(schemeName)
accessRight
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]

50
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -63,6 +63,56 @@ public class MergeTest {
assertEquals(3, a.getSubject().size());
}
@Test
public void mergeRelationTest() {
Relation a = createRel(null, null);
Relation b = createRel(null, null);
a.mergeFrom(b);
assertEquals(a, b);
a = createRel(true, null);
b = createRel(null, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(false, null);
a.mergeFrom(b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(true, "2016-04-05T12:41:19.202Z");
a.mergeFrom(b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
a = createRel(true, "2016-05-07T12:41:19.202Z");
b = createRel(true, "2016-04-05T12:41:19.202Z");
a.mergeFrom(b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
}
@Test
public void mergeRelationTestParseException() {
assertThrows(IllegalArgumentException.class, () -> {
Relation a = createRel(true, "2016-04-05");
Relation b = createRel(true, "2016-04-05");
a.mergeFrom(b);
});
}
private Relation createRel(Boolean validated, String validationDate) {
Relation rel = new Relation();
rel.setSource("1");
rel.setTarget("2");
rel.setRelType("reltype");
rel.setSubRelType("subreltype");
rel.setRelClass("relclass");
rel.setValidated(validated);
rel.setValidationDate(validationDate);
return rel;
}
private KeyValue setKV(final String key, final String value) {
KeyValue k = new KeyValue();

13
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -82,7 +82,7 @@ public class ProtoConverter implements Serializable {
private static Instance convertInstance(ResultProtos.Result.Instance ri) {
final Instance i = new Instance();
i.setAccessright(mapQualifier(ri.getAccessright()));
i.setAccessright(mapAccessRight(ri.getAccessright()));
i.setCollectedfrom(mapKV(ri.getCollectedfrom()));
i.setDateofacceptance(mapStringField(ri.getDateofacceptance()));
i.setDistributionlocation(ri.getDistributionlocation());
@ -510,7 +510,7 @@ public class ProtoConverter implements Serializable {
.map(i -> i.getAccessright())
.min(new LicenseComparator());
final Qualifier rights = min.isPresent() ? mapQualifier(min.get()) : new Qualifier();
final Qualifier rights = min.isPresent() ? mapAccessRight(min.get()) : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
@ -579,6 +579,15 @@ public class ProtoConverter implements Serializable {
return qualifier;
}
public static AccessRight mapAccessRight(FieldTypeProtos.Qualifier q) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(q.getClassid());
accessRight.setClassname(q.getClassname());
accessRight.setSchemeid(q.getSchemeid());
accessRight.setSchemename(q.getSchemename());
return accessRight;
}
public static Country mapQualifierAsCountry(FieldTypeProtos.Qualifier q) {
final Country c = new Country();
c.setClassid(q.getClassid());

26
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -68,6 +68,12 @@ public class PromoteActionPayloadForGraphTableJob {
MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
logger.info("strategy: {}", strategy);
Boolean shouldGroupById = Optional
.ofNullable(parser.get("shouldGroupById"))
.map(Boolean::valueOf)
.orElse(true);
logger.info("shouldGroupById: {}", shouldGroupById);
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
@ -89,7 +95,8 @@ public class PromoteActionPayloadForGraphTableJob {
outputGraphTablePath,
strategy,
rowClazz,
actionPayloadClazz);
actionPayloadClazz,
shouldGroupById);
});
}
@ -115,12 +122,12 @@ public class PromoteActionPayloadForGraphTableJob {
String outputGraphTablePath,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
Class<A> actionPayloadClazz, Boolean shouldGroupById) {
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
Dataset<G> result = promoteActionPayloadForGraphTable(
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz, shouldGroupById)
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
saveGraphTable(result, outputGraphTablePath);
@ -174,7 +181,8 @@ public class PromoteActionPayloadForGraphTableJob {
Dataset<A> actionPayloadDS,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
Class<A> actionPayloadClazz,
Boolean shouldGroupById) {
logger
.info(
"Promoting action payload for graph table: payload={}, table={}",
@ -198,9 +206,13 @@ public class PromoteActionPayloadForGraphTableJob {
rowClazz,
actionPayloadClazz);
return PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge(
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
if (shouldGroupById) {
return PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge(
joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
} else {
return joinedAndMerged;
}
}
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json
View File

@ -40,5 +40,11 @@
"paramLongName": "mergeAndGetStrategy",
"paramDescription": "strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET",
"paramRequired": true
},
{
"paramName": "sgid",
"paramLongName": "shouldGroupById",
"paramDescription": "indicates whether the promotion operation should group objects in the graph by id or not",
"paramRequired": false
}
]

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
View File

@ -24,6 +24,10 @@
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>shouldGroupById</name>
<description>indicates whether the promotion operation should group objects in the graph by id or not</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -111,6 +115,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/dataset</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForDatasetTable"/>
<error to="Kill"/>
@ -162,6 +167,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/dataset</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

5
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
View File

@ -56,6 +56,11 @@
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>shouldGroupById</name>
<value>false</value>
<description>indicates whether the promotion operation should group objects in the graph by id or not</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
View File

@ -24,6 +24,10 @@
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>shouldGroupById</name>
<description>indicates whether the promotion operation should group objects in the graph by id or not</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -110,6 +114,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForOtherResearchProductTable"/>
<error to="Kill"/>
@ -161,6 +166,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/otherresearchproduct</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
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@ -24,6 +24,10 @@
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>shouldGroupById</name>
<description>indicates whether the promotion operation should group objects in the graph by id or not</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -111,6 +115,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/publication</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForPublicationTable"/>
<error to="Kill"/>
@ -162,6 +167,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/publication</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

6
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
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@ -24,6 +24,10 @@
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>shouldGroupById</name>
<description>indicates whether the promotion operation should group objects in the graph by id or not</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
@ -110,6 +114,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/software</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForSoftwareTable"/>
<error to="Kill"/>
@ -161,6 +166,7 @@
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/software</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>

8
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
View File

@ -101,7 +101,9 @@ public class PromoteActionPayloadForGraphTableJobTest {
"-outputGraphTablePath",
"",
"-mergeAndGetStrategy",
MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name()
MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name(),
"--shouldGroupById",
"true"
}));
// then
@ -141,7 +143,9 @@ public class PromoteActionPayloadForGraphTableJobTest {
"-outputGraphTablePath",
outputGraphTableDir.toString(),
"-mergeAndGetStrategy",
strategy.name()
strategy.name(),
"--shouldGroupById",
"true"
});
// then

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java Normal file
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@ -0,0 +1,28 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
/**
* Class that maps the model of the bipFinder! input data.
* Only needed for deserialization purposes
*/
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
public BipDeserialize() {
super();
}
public List<Score> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipScore.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
/**
* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
*/
public class BipScore implements Serializable {
private String id; // doi
private List<Score> scoreList; // unit as given in the inputfile
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<Score> getScoreList() {
return scoreList;
}
public void setScoreList(List<Score> scoreList) {
this.scoreList = scoreList;
}
}

85
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java Normal file
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@ -0,0 +1,85 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Just collects all the atomic actions produced for the different results and saves them in
* outputpath for the ActionSet
*/
public class CollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
collectAndSave(spark, inputPath, outputPath);
});
}
private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
sc
.sequenceFile(inputPath + "/publication", Text.class, Text.class)
.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
}

26
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java Normal file
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@ -0,0 +1,26 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
public class KeyValue implements Serializable {
private String key;
private String value;
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java Normal file
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@ -0,0 +1,28 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
/**
* Subset of the information of the generic results that are needed to create the atomic action
*/
public class PreparedResult implements Serializable {
private String id; // openaire id
private String value; // doi
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
}

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java Normal file
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@ -0,0 +1,30 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.Serializable;
import java.util.List;
/**
* represents the score in the input file
*/
public class Score implements Serializable {
private String id;
private List<KeyValue> unit;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<KeyValue> getUnit() {
return unit;
}
public void setUnit(List<KeyValue> unit) {
this.unit = unit;
}
}

200
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java Normal file
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@ -0,0 +1,200 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import scala.Tuple2;
/**
* created the Atomic Action for each tipe of results
*/
public class SparkAtomicActionScoreJob implements Serializable {
private static String DOI = "doi";
private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkAtomicActionScoreJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}: ", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}: ", outputPath);
final String bipScorePath = parser.get("bipScorePath");
log.info("bipScorePath: {}", bipScorePath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, outputPath);
prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
});
}
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
.textFile(bipScorePath)
.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
Dataset<BipScore> bipScores = spark
.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
BipScore bs = new BipScore();
bs.setId(key);
bs.setScoreList(entry.get(key));
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
System.out.println(bipScores.count());
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
Dataset<PreparedResult> preparedResult = spark
.sql(
"select pIde.value value, id " +
"from result " +
"lateral view explode (pid) p as pIde " +
"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
.as(Encoders.bean(PreparedResult.class));
bipScores
.joinWith(
preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
"inner")
.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
BipScore ret = value._1();
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());
BipScore first = it.next();
ret.setId(first.getId());
ret.setMeasures(getMeasure(first));
it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
return ret;
}, Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(inputClazz, p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
}
private static List<Measure> getMeasure(BipScore value) {
return value
.getScoreList()
.stream()
.map(score -> {
Measure m = new Measure();
m.setId(score.getId());
m
.setUnit(
score
.getUnit()
.stream()
.map(unit -> {
KeyValue kv = new KeyValue();
kv.setValue(unit.getValue());
kv.setKey(unit.getKey());
kv.setDataInfo(getDataInfo());
return kv;
})
.collect(Collectors.toList()));
return m;
})
.collect(Collectors.toList());
}
private static DataInfo getDataInfo() {
DataInfo di = new DataInfo();
di.setInferred(false);
di.setInvisible(false);
di.setDeletedbyinference(false);
di.setTrust("");
Qualifier qualifier = new Qualifier();
qualifier.setClassid("sysimport:actionset");
qualifier.setClassname("Harvested");
qualifier.setSchemename("dnet:provenanceActions");
qualifier.setSchemeid("dnet:provenanceActions");
di.setProvenanceaction(qualifier);
return di;
}
private static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json Normal file
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@ -0,0 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

32
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json Normal file
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@ -0,0 +1,32 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the URL from where to get the programme file",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "rtn",
"paramLongName": "resultTableName",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
},
{
"paramName": "bsp",
"paramLongName": "bipScorePath",
"paramDescription": "the path of the new ActionSet",
"paramRequired": true
}
]

171
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml Normal file
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@ -0,0 +1,171 @@
<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>inputPath</name>
<description>the input path of the resources to be extended</description>
</property>
<property>
<name>bipScorePath</name>
<description>the path where to find the bipFinder scores</description>
</property>
<property>
<name>outputPath</name>
<description>the path where to store the actionset</description>
</property>
</parameters>
<start to="deleteoutputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="deleteoutputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
<delete path="${workingDir}"/>
<mkdir path="${workingDir}"/>
</fs>
<ok to="atomicactions"/>
<error to="Kill"/>
</action>
<fork name="atomicactions">
<path start="atomicactions_publication"/>
<path start="atomicactions_dataset"/>
<path start="atomicactions_orp"/>
<path start="atomicactions_software"/>
</fork>
<action name="atomicactions_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for publications</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for datasets</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for orp</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<action name="atomicactions_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for software</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/software</arg>
<arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
</spark>
<ok to="join_aa"/>
<error to="Kill"/>
</action>
<join name="join_aa" to="collectandsave"/>
<action name="collectandsave">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>saves all the aa produced for the several types of results in the as output path</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

323
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java Normal file
View File

@ -0,0 +1,323 @@
package eu.dnetlib.dhp.actionmanager.bipfinder;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class SparkAtomicActionScoreJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(SparkAtomicActionScoreJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void matchOne() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 1);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(2, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0));
}
@Test
public void matchOneWithTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 1);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
execVerification.select("oaid").collectAsList().get(0).getString(0));
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
List<Row> tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList();
String tmp_influence = tmp_ds.get(0).getString(0);
Assertions
.assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
tmp_influence = tmp_ds.get(1).getString(0);
Assertions
.assertTrue(
"1.47565045883e-08".equals(tmp_influence) ||
"1.98956540239e-08".equals(tmp_influence));
Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0)));
}
@Test
public void matchTwo() throws Exception {
String bipScoresPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
.getPath();
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json")
.getPath();
SparkAtomicActionScoreJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-bipScorePath",
bipScoresPath,
"-resultTableName",
"eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath",
workingDir.toString() + "/actionSet"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Publication> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Publication) aa.getPayload()));
Assertions.assertTrue(tmp.count() == 2);
Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
verificationDataset.createOrReplaceTempView("publication");
Dataset<Row> execVerification = spark
.sql(
"Select p.id oaid, mes.id, mUnit.value from publication p " +
"lateral view explode(measures) m as mes " +
"lateral view explode(mes.unit) u as mUnit ");
Assertions.assertEquals(4, execVerification.count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count());
Assertions
.assertEquals(
2,
execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'influence'").count());
Assertions
.assertEquals(
2,
execVerification.filter("id = 'popularity'").count());
Assertions
.assertEquals(
"1.47565045883e-08",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"1.98956540239e-08",
execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'influence'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.282046161584",
execVerification
.filter(
"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
Assertions
.assertEquals(
"0.227515392",
execVerification
.filter(
"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
"and id = 'popularity'")
.select("value")
.collectAsList()
.get(0)
.getString(0));
}
}

1101
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json Normal file
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18
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json Normal file
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7
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/CheckDuplictedIdsJob.java
View File

@ -32,15 +32,15 @@ public class CheckDuplictedIdsJob {
IOUtils
.toString(
CheckDuplictedIdsJob.class
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/check_duplicates.json")));
parser.parseArgument(args);
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String countPath = parser.get("workingPath") + "/counts";
final String countPath = parser.get("outputDir") + "/counts";
log.info("countPath: {}", countPath);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
@ -59,6 +59,7 @@ public class CheckDuplictedIdsJob {
.map(o -> ClusterUtils.incrementAccumulator(o, total), Encoders.tuple(Encoders.STRING(), Encoders.LONG()))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(countPath);
;

13
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateEventsJob.java
View File

@ -44,10 +44,10 @@ public class GenerateEventsJob {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String eventsPath = workingPath + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final Set<String> dsIdWhitelist = ClusterUtils.parseParamAsList(parser, "datasourceIdWhitelist");
@ -59,6 +59,9 @@ public class GenerateEventsJob {
final Set<String> dsIdBlacklist = ClusterUtils.parseParamAsList(parser, "datasourceIdBlacklist");
log.info("datasourceIdBlacklist: {}", StringUtils.join(dsIdBlacklist, ","));
final Set<String> topicWhitelist = ClusterUtils.parseParamAsList(parser, "topicWhitelist");
log.info("topicWhitelist: {}", StringUtils.join(topicWhitelist, ","));
final SparkConf conf = new SparkConf();
runWithSparkSession(conf, isSparkSessionManaged, spark -> {
@ -70,12 +73,12 @@ public class GenerateEventsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_events");
final Dataset<ResultGroup> groups = ClusterUtils
.readPath(spark, workingPath + "/duplicates", ResultGroup.class);
.readPath(spark, workingDir + "/duplicates", ResultGroup.class);
final Dataset<Event> dataset = groups
.map(
g -> EventFinder
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, accumulators),
.generateEvents(g, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist, topicWhitelist, accumulators),
Encoders
.bean(EventGroup.class))
.flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class));

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

@ -46,7 +46,7 @@ public class GenerateStatsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String dbUrl = parser.get("dbUrl");

22
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java
View File

@ -46,7 +46,7 @@ public class IndexEventSubsetJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -55,6 +55,18 @@ public class IndexEventSubsetJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic"));
log.info("maxEventsForTopic: {}", maxEventsForTopic);
@ -86,10 +98,10 @@ public class IndexEventSubsetJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

22
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java
View File

@ -54,7 +54,7 @@ public class IndexNotificationsJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -63,6 +63,18 @@ public class IndexNotificationsJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl");
log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl);
@ -92,10 +104,10 @@ public class IndexNotificationsJob {
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
log.info("*** Start indexing");
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);

24
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java
View File

@ -36,7 +36,7 @@ public class IndexOnESJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String index = parser.get("index");
@ -45,6 +45,18 @@ public class IndexOnESJob {
final String indexHost = parser.get("esHost");
log.info("indexHost: {}", indexHost);
final String esBatchWriteRetryCount = parser.get("esBatchWriteRetryCount");
log.info("esBatchWriteRetryCount: {}", esBatchWriteRetryCount);
final String esBatchWriteRetryWait = parser.get("esBatchWriteRetryWait");
log.info("esBatchWriteRetryWait: {}", esBatchWriteRetryWait);
final String esBatchSizeEntries = parser.get("esBatchSizeEntries");
log.info("esBatchSizeEntries: {}", esBatchSizeEntries);
final String esNodesWanOnly = parser.get("esNodesWanOnly");
log.info("esNodesWanOnly: {}", esNodesWanOnly);
final SparkSession spark = SparkSession.builder().config(conf).getOrCreate();
final JavaRDD<String> inputRdd = ClusterUtils
@ -53,15 +65,13 @@ public class IndexOnESJob {
.javaRDD();
final Map<String, String> esCfg = new HashMap<>();
// esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54");
esCfg.put("es.index.auto.create", "false");
esCfg.put("es.nodes", indexHost);
esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY
esCfg.put("es.batch.write.retry.count", "8");
esCfg.put("es.batch.write.retry.wait", "60s");
esCfg.put("es.batch.size.entries", "200");
esCfg.put("es.nodes.wan.only", "true");
esCfg.put("es.batch.write.retry.count", esBatchWriteRetryCount);
esCfg.put("es.batch.write.retry.wait", esBatchWriteRetryWait);
esCfg.put("es.batch.size.entries", esBatchSizeEntries);
esCfg.put("es.nodes.wan.only", esNodesWanOnly);
JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg);
}

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep0Job.java
View File

@ -42,10 +42,10 @@ public class JoinStep0Job {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step0";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -57,10 +57,10 @@ public class JoinStep0Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/simpleEntities", OaBrokerMainEntity.class);
final Dataset<RelatedDatasource> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
.readPath(spark, workingDir + "/relatedDatasources", RelatedDatasource.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep1Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep1Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step1";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step1";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep1Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step0", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step0", OaBrokerMainEntity.class);
final Dataset<RelatedProject> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedProjects", RelatedProject.class);
.readPath(spark, workingDir + "/relatedProjects", RelatedProject.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedProject>, OaBrokerMainEntity> aggr = new RelatedProjectAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep2Job.java
View File

@ -39,10 +39,10 @@ public class JoinStep2Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step2";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step2";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -54,10 +54,10 @@ public class JoinStep2Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step1", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step1", OaBrokerMainEntity.class);
final Dataset<RelatedSoftware> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedSoftwares", RelatedSoftware.class);
.readPath(spark, workingDir + "/relatedSoftwares", RelatedSoftware.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedSoftware>, OaBrokerMainEntity> aggr = new RelatedSoftwareAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep3Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep3Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step3";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step3";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep3Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step2", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step2", OaBrokerMainEntity.class);
final Dataset<RelatedDataset> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedDatasets", RelatedDataset.class);
.readPath(spark, workingDir + "/relatedDatasets", RelatedDataset.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDataset>, OaBrokerMainEntity> aggr = new RelatedDatasetAggregator()
.toColumn();

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/JoinStep4Job.java
View File

@ -40,10 +40,10 @@ public class JoinStep4Job {
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String joinedEntitiesPath = workingPath + "/joinedEntities_step4";
final String joinedEntitiesPath = workingDir + "/joinedEntities_step4";
log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
final SparkConf conf = new SparkConf();
@ -55,10 +55,10 @@ public class JoinStep4Job {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
final Dataset<OaBrokerMainEntity> sources = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step3", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step3", OaBrokerMainEntity.class);
final Dataset<RelatedPublication> typedRels = ClusterUtils
.readPath(spark, workingPath + "/relatedPublications", RelatedPublication.class);
.readPath(spark, workingDir + "/relatedPublications", RelatedPublication.class);
final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedPublication>, OaBrokerMainEntity> aggr = new RelatedPublicationAggregator()
.toColumn();

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PartitionEventsByDsIdJob.java
View File

@ -36,7 +36,7 @@ import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
public class PartitionEventsByDsIdJob {
private static final Logger log = LoggerFactory.getLogger(PartitionEventsByDsIdJob.class);
private static final String OPENDOAR_NSPREFIX = "10|opendoar____::";
private static final String OPENDOAR_NSPREFIX = "opendoar____::";
public static void main(final String[] args) throws Exception {
@ -55,10 +55,10 @@ public class PartitionEventsByDsIdJob {
final SparkConf conf = new SparkConf();
final String eventsPath = parser.get("workingPath") + "/events";
final String eventsPath = parser.get("outputDir") + "/events";
log.info("eventsPath: {}", eventsPath);
final String partitionPath = parser.get("workingPath") + "/eventsByOpendoarId";
final String partitionPath = parser.get("outputDir") + "/eventsByOpendoarId";
log.info("partitionPath: {}", partitionPath);
final String opendoarIds = parser.get("opendoarIds");
@ -91,6 +91,7 @@ public class PartitionEventsByDsIdJob {
.write()
.partitionBy("group")
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(partitionPath);
});
@ -122,6 +123,7 @@ public class PartitionEventsByDsIdJob {
final ShortEventMessageWithGroupId res = new ShortEventMessageWithGroupId();
res.setEventId(e.getEventId());
res.setOriginalId(payload.getResult().getOriginalId());
res.setTitle(payload.getResult().getTitles().stream().filter(StringUtils::isNotBlank).findFirst().orElse(null));
res.setTopic(e.getTopic());

10
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareGroupsJob.java
View File

@ -45,10 +45,10 @@ public class PrepareGroupsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String groupsPath = workingPath + "/duplicates";
final String groupsPath = workingDir + "/duplicates";
log.info("groupsPath: {}", groupsPath);
final SparkConf conf = new SparkConf();
@ -60,10 +60,10 @@ public class PrepareGroupsJob {
final LongAccumulator total = spark.sparkContext().longAccumulator("total_groups");
final Dataset<OaBrokerMainEntity> results = ClusterUtils
.readPath(spark, workingPath + "/joinedEntities_step4", OaBrokerMainEntity.class);
.readPath(spark, workingDir + "/joinedEntities_step4", OaBrokerMainEntity.class);
final Dataset<Relation> mergedRels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
final TypedColumn<Tuple2<OaBrokerMainEntity, Relation>, ResultGroup> aggr = new ResultAggregator()

11
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedDatasetsJob.java
View File

@ -42,10 +42,10 @@ public class PrepareRelatedDatasetsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasets";
final String relsPath = workingDir + "/relatedDatasets";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -62,7 +62,7 @@ public class PrepareRelatedDatasetsJob {
.map(ConversionUtils::oafDatasetToBrokerDataset, Encoders.bean(OaBrokerRelatedDataset.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -72,7 +72,8 @@ public class PrepareRelatedDatasetsJob {
final Dataset<RelatedDataset> dataset = rels
.joinWith(datasets, datasets.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedDataset rel = new RelatedDataset(t._1.getSource(), t._2);
final RelatedDataset rel = new RelatedDataset(t._1.getSource(),
t._2);
rel.getRelDataset().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedDataset.class));

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

@ -48,10 +48,10 @@ public class PrepareRelatedDatasourcesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedDatasources";
final String relsPath = workingDir + "/relatedDatasources";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
View File

@ -44,10 +44,10 @@ public class PrepareRelatedProjectsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedProjects";
final String relsPath = workingDir + "/relatedProjects";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedProjectsJob {
.map(ConversionUtils::oafProjectToBrokerProject, Encoders.bean(OaBrokerProject.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

11
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedPublicationsJob.java
View File

@ -43,10 +43,10 @@ public class PrepareRelatedPublicationsJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedPublications";
final String relsPath = workingDir + "/relatedPublications";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -65,7 +65,7 @@ public class PrepareRelatedPublicationsJob {
Encoders.bean(OaBrokerRelatedPublication.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> ClusterUtils.isValidResultResultClass(r.getRelClass()))
@ -75,7 +75,8 @@ public class PrepareRelatedPublicationsJob {
final Dataset<RelatedPublication> dataset = rels
.joinWith(pubs, pubs.col("openaireId").equalTo(rels.col("target")), "inner")
.map(t -> {
final RelatedPublication rel = new RelatedPublication(t._1.getSource(), t._2);
final RelatedPublication rel = new RelatedPublication(
t._1.getSource(), t._2);
rel.getRelPublication().setRelType(t._1.getRelClass());
return rel;
}, Encoders.bean(RelatedPublication.class));

8
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedSoftwaresJob.java
View File

@ -44,10 +44,10 @@ public class PrepareRelatedSoftwaresJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String relsPath = workingPath + "/relatedSoftwares";
final String relsPath = workingDir + "/relatedSoftwares";
log.info("relsPath: {}", relsPath);
final SparkConf conf = new SparkConf();
@ -64,7 +64,7 @@ public class PrepareRelatedSoftwaresJob {
.map(ConversionUtils::oafSoftwareToBrokerSoftware, Encoders.bean(OaBrokerRelatedSoftware.class));
final Dataset<Relation> rels = ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.loadRelations(graphPath, spark)
.filter(r -> r.getDataInfo().getDeletedbyinference())
.filter(r -> r.getRelType().equals(ModelConstants.RESULT_RESULT))
.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))

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

@ -44,10 +44,10 @@ public class PrepareSimpleEntititiesJob {
final String graphPath = parser.get("graphPath");
log.info("graphPath: {}", graphPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
final String workingDir = parser.get("workingDir");
log.info("workingDir: {}", workingDir);
final String simpleEntitiesPath = workingPath + "/simpleEntities";
final String simpleEntitiesPath = workingDir + "/simpleEntities";
log.info("simpleEntitiesPath: {}", simpleEntitiesPath);
final SparkConf conf = new SparkConf();

19
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingSubject.java
View File

@ -16,7 +16,24 @@ public class EnrichMissingSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMissingSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MISSING/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MISSING_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MISSING_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MISSING_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MISSING_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MISSING_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MISSING_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

19
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
View File

@ -16,7 +16,24 @@ public class EnrichMoreSubject extends UpdateMatcher<OaBrokerTypedValue> {
public EnrichMoreSubject() {
super(20,
s -> Topic.fromPath("ENRICH/MORE/SUBJECT/" + s.getType()),
s -> {
switch (s.getType().toLowerCase()) {
case "acm":
return Topic.ENRICH_MORE_SUBJECT_ACM;
case "arxiv":
return Topic.ENRICH_MORE_SUBJECT_ARXIV;
case "ddc":
return Topic.ENRICH_MORE_SUBJECT_DDC;
case "jel":
return Topic.ENRICH_MORE_SUBJECT_JEL;
case "mesh":
return Topic.ENRICH_MORE_SUBJECT_MESHEUROPMC;
case "rvk":
return Topic.ENRICH_MORE_SUBJECT_RVK;
default:
return null;
}
},
(p, s) -> p.getSubjects().add(s),
s -> subjectAsString(s));
}

12
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ClusterUtils.java
View File

@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class ClusterUtils {
@ -30,6 +31,16 @@ public class ClusterUtils {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static Dataset<Relation> loadRelations(final String graphPath, final SparkSession spark) {
return ClusterUtils
.readPath(spark, graphPath + "/relation", Relation.class)
.map(r -> {
r.setSource(ConversionUtils.cleanOpenaireId(r.getSource()));
r.setTarget(ConversionUtils.cleanOpenaireId(r.getTarget()));
return r;
}, Encoders.bean(Relation.class));
}
public static <R> Dataset<R> readPath(
final SparkSession spark,
final String inputPath,
@ -67,6 +78,7 @@ public class ClusterUtils {
.map(o -> ClusterUtils.incrementAccumulator(o, acc), Encoders.bean(clazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(path);
}

16
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -74,7 +74,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedDataset res = new OaBrokerRelatedDataset();
res.setOpenaireId(d.getId());
res.setOpenaireId(cleanOpenaireId(d.getId()));
res.setOriginalId(first(d.getOriginalId()));
res.setTitle(structPropValue(d.getTitle()));
res.setPids(mappedList(d.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -89,7 +89,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedPublication res = new OaBrokerRelatedPublication();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setOriginalId(first(p.getOriginalId()));
res.setTitle(structPropValue(p.getTitle()));
res.setPids(mappedList(p.getPid(), ConversionUtils::oafPidToBrokerPid));
@ -106,7 +106,7 @@ public class ConversionUtils {
final OaBrokerMainEntity res = new OaBrokerMainEntity();
res.setOpenaireId(result.getId());
res.setOpenaireId(cleanOpenaireId(result.getId()));
res.setOriginalId(first(result.getOriginalId()));
res.setTypology(classId(result.getResulttype()));
res.setTitles(structPropList(result.getTitle()));
@ -129,6 +129,10 @@ public class ConversionUtils {
return res;
}
public static String cleanOpenaireId(final String id) {
return id.contains("|") ? StringUtils.substringAfter(id, "|") : id;
}
private static OaBrokerAuthor oafAuthorToBrokerAuthor(final Author author) {
if (author == null) {
return null;
@ -188,7 +192,7 @@ public class ConversionUtils {
}
final OaBrokerProject res = new OaBrokerProject();
res.setOpenaireId(p.getId());
res.setOpenaireId(cleanOpenaireId(p.getId()));
res.setTitle(fieldValue(p.getTitle()));
res.setAcronym(fieldValue(p.getAcronym()));
res.setCode(fieldValue(p.getCode()));
@ -214,7 +218,7 @@ public class ConversionUtils {
}
final OaBrokerRelatedSoftware res = new OaBrokerRelatedSoftware();
res.setOpenaireId(sw.getId());
res.setOpenaireId(cleanOpenaireId(sw.getId()));
res.setName(structPropValue(sw.getTitle()));
res.setDescription(fieldValue(sw.getDescription()));
res.setRepository(fieldValue(sw.getCodeRepositoryUrl()));
@ -230,7 +234,7 @@ public class ConversionUtils {
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
res.setOpenaireId(ds.getId());
res.setOpenaireId(cleanOpenaireId(ds.getId()));
res.setType(classId(ds.getDatasourcetype()));
return res;
}

13
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/DatasourceRelationsAccumulator.java
View File

@ -59,9 +59,18 @@ public class DatasourceRelationsAccumulator implements Serializable {
final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
collectedFromSet
.stream()
.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.COLLECTED_FROM_REL))
.forEach(res::addTuple);
hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
hostedBySet
.stream()
.map(
s -> new Tuple3<>(ConversionUtils.cleanOpenaireId(r.getId()), ConversionUtils.cleanOpenaireId(s),
BrokerConstants.HOSTED_BY_REL))
.forEach(res::addTuple);
return res;
}

9
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/EventFinder.java
View File

@ -76,6 +76,7 @@ public class EventFinder {
final Set<String> dsIdWhitelist,
final Set<String> dsIdBlacklist,
final Set<String> dsTypeWhitelist,
final Set<String> topicWhitelist,
final Map<String, LongAccumulator> accumulators) {
final List<UpdateInfo<?>> list = new ArrayList<>();
@ -84,7 +85,13 @@ public class EventFinder {
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
for (final UpdateMatcher<?> matcher : matchers) {
list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
for (final UpdateInfo<?> info : matcher
.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators)) {
if (topicWhitelist == null || topicWhitelist.isEmpty()
|| topicWhitelist.contains(info.getTopic().getPath())) {
list.add(info);
}
}
}
}
}

9
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/check_duplicates.json Normal file
View File

@ -0,0 +1,9 @@
[
{
"paramName": "o",
"paramLongName": "outputDir",
"paramDescription": "the path where the data are stored",
"paramRequired": true
}
]

2
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/common_params.json
View File

@ -7,7 +7,7 @@
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data will be stored",
"paramRequired": true
}

137
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
View File

@ -6,7 +6,7 @@
<description>the path where the graph is stored</description>
</property>
<property>
<name>workingPath</name>
<name>outputDir</name>
<description>the path where the the generated data will be stored</description>
</property>
<property>
@ -24,6 +24,11 @@
<value>-</value>
<description>a black list (comma separeted, - for empty list) of datasource ids</description>
</property>
<property>
<name>topicWhitelist</name>
<value>*</value>
<description>a white list (comma separeted, * for all) of topics</description>
</property>
<property>
<name>esEventIndexName</name>
<description>the elasticsearch index name for events</description>
@ -36,6 +41,26 @@
<name>esIndexHost</name>
<description>the elasticsearch host</description>
</property>
<property>
<name>esBatchWriteRetryCount</name>
<value>8</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchWriteRetryWait</name>
<value>60s</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esBatchSizeEntries</name>
<value>200</value>
<description>an ES configuration property</description>
</property>
<property>
<name>esNodesWanOnly</name>
<value>true</value>
<description>an ES configuration property</description>
</property>
<property>
<name>maxIndexedEventsForDsAndTopic</name>
<description>the max number of events for each couple (ds/topic)</description>
@ -111,15 +136,25 @@
</configuration>
</global>
<start to="ensure_working_path"/>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="ensure_output_dir">${wf:conf('resumeFrom') eq 'ensure_output_dir'}</case>
<case to="index_event_subset">${wf:conf('resumeFrom') eq 'index_event_subset'}</case>
<case to="stats">${wf:conf('resumeFrom') eq 'stats'}</case>
<case to="index_notifications">${wf:conf('resumeFrom') eq 'index_notifications'}</case>
<default to="ensure_output_dir"/>
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ensure_working_path">
<action name="ensure_output_dir">
<fs>
<mkdir path='${workingPath}'/>
<mkdir path='${outputDir}'/>
</fs>
<ok to="start_entities_and_rels"/>
<error to="Kill"/>
@ -152,7 +187,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -176,7 +211,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -201,7 +236,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -225,7 +260,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -249,7 +284,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -273,7 +308,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="wait_entities_and_rels"/>
<error to="Kill"/>
@ -299,7 +334,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step1"/>
<error to="Kill"/>
@ -323,7 +358,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step2"/>
<error to="Kill"/>
@ -347,7 +382,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step3"/>
<error to="Kill"/>
@ -371,7 +406,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="join_entities_step4"/>
<error to="Kill"/>
@ -395,7 +430,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="prepare_groups"/>
<error to="Kill"/>
@ -419,7 +454,7 @@
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
</spark>
<ok to="generate_events"/>
<error to="Kill"/>
@ -442,10 +477,12 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--workingDir</arg><arg>${workingDir}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
<arg>--topicWhitelist</arg><arg>${topicWhitelist}</arg>
</spark>
<ok to="index_event_subset"/>
<error to="Kill"/>
@ -468,38 +505,16 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esEventIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--maxEventsForTopic</arg><arg>${maxIndexedEventsForDsAndTopic}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="index_notifications"/>
<error to="Kill"/>
</action>
<action name="index_notifications">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexNotificationsOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="stats"/>
<error to="Kill"/>
</action>
@ -521,16 +536,46 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}</arg>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--dbUrl</arg><arg>${brokerDbUrl}</arg>
<arg>--dbUser</arg><arg>${brokerDbUser}</arg>
<arg>--dbPassword</arg><arg>${brokerDbPassword}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="index_notifications"/>
<error to="Kill"/>
</action>
<action name="index_notifications">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>IndexNotificationsOnESJob</name>
<class>eu.dnetlib.dhp.broker.oa.IndexNotificationsJob</class>
<jar>dhp-broker-events-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.dynamicAllocation.maxExecutors="8"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--outputDir</arg><arg>${outputDir}</arg>
<arg>--index</arg><arg>${esNotificationsIndexName}</arg>
<arg>--esHost</arg><arg>${esIndexHost}</arg>
<arg>--esBatchWriteRetryCount</arg><arg>${esBatchWriteRetryCount}</arg>
<arg>--esBatchWriteRetryWait</arg><arg>${esBatchWriteRetryWait}</arg>
<arg>--esBatchSizeEntries</arg><arg>${esBatchSizeEntries}</arg>
<arg>--esNodesWanOnly</arg><arg>${esNodesWanOnly}</arg>
<arg>--brokerApiBaseUrl</arg><arg>${brokerApiBaseUrl}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

14
dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_events.json
View File

@ -1,7 +1,13 @@
[
{
"paramName": "wp",
"paramLongName": "workingDir",
"paramDescription": "the path where the temporary data are stored",
"paramRequired": true
},
{
"paramName": "o",
"paramLongName": "workingPath",
"paramLongName": "outputDir",
"paramDescription": "the path where the generated events will be stored",
"paramRequired": true
},
@ -22,5 +28,11 @@
"paramLongName": "datasourceIdBlacklist",
"paramDescription": "a black list (comma separeted, - for empty list) of datasource ids",
"paramRequired": true
},
{
"paramName": "topicWhitelist",
"paramLongName": "topicWhitelist",
"paramDescription": "a white list (comma separeted, * for all) of topics",
"paramRequired": true
}
]

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