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WIP: refactoring model utilities

This commit is contained in:
Claudio Atzori 2023-02-01 16:12:23 +01:00
parent 3f6204ddc0
commit 7b76611955
38 changed files with 3 additions and 2030 deletions
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69
src/main/java/eu/dnetlib/dhp/schema/common/AccessRightComparator.java
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@ -1,69 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class AccessRightComparator<T extends Qualifier> implements Comparator<T> {
@Override
public int compare(T left, T right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals("OPEN SOURCE"))
return -1;
if (rClass.equals("OPEN SOURCE"))
return 1;
if (lClass.equals("OPEN"))
return -1;
if (rClass.equals("OPEN"))
return 1;
if (lClass.equals("6MONTHS"))
return -1;
if (rClass.equals("6MONTHS"))
return 1;
if (lClass.equals("12MONTHS"))
return -1;
if (rClass.equals("12MONTHS"))
return 1;
if (lClass.equals("EMBARGO"))
return -1;
if (rClass.equals("EMBARGO"))
return 1;
if (lClass.equals("RESTRICTED"))
return -1;
if (rClass.equals("RESTRICTED"))
return 1;
if (lClass.equals("CLOSED"))
return -1;
if (rClass.equals("CLOSED"))
return 1;
if (lClass.equals("UNKNOWN"))
return -1;
if (rClass.equals("UNKNOWN"))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

21
src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java
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@ -1,21 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.Entity;
/** Actual entity types in the Graph */
public enum EntityType {
publication, dataset, otherresearchproduct, software, datasource, organization, project;
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends Entity> EntityType fromClass(Class<T> clazz) {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
}
}

7
src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java
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@ -1,7 +0,0 @@
package eu.dnetlib.dhp.schema.common;
/** Main entity types in the Graph */
public enum MainEntityType {
result, datasource, organization, project
}

408
src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
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@ -1,408 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Function;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*;
/** Oaf model utility methods. */
public class ModelSupport {
/** Defines the mapping between the actual entity type and the main entity type */
private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static {
entityMapping.put(EntityType.publication, MainEntityType.result);
entityMapping.put(EntityType.dataset, MainEntityType.result);
entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result);
entityMapping.put(EntityType.software, MainEntityType.result);
entityMapping.put(EntityType.datasource, MainEntityType.datasource);
entityMapping.put(EntityType.organization, MainEntityType.organization);
entityMapping.put(EntityType.project, MainEntityType.project);
}
/**
* Defines the mapping between the actual entity types and the relative classes implementing them
*/
public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
static {
entityTypes.put(EntityType.datasource, Datasource.class);
entityTypes.put(EntityType.organization, Organization.class);
entityTypes.put(EntityType.project, Project.class);
entityTypes.put(EntityType.dataset, Dataset.class);
entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
entityTypes.put(EntityType.software, Software.class);
entityTypes.put(EntityType.publication, Publication.class);
}
public static final Map<String, Class> oafTypes = Maps.newHashMap();
static {
oafTypes.put("datasource", Datasource.class);
oafTypes.put("organization", Organization.class);
oafTypes.put("project", Project.class);
oafTypes.put("dataset", Dataset.class);
oafTypes.put("otherresearchproduct", OtherResearchProduct.class);
oafTypes.put("software", Software.class);
oafTypes.put("publication", Publication.class);
oafTypes.put("relation", Relation.class);
}
public static final Map<Class, String> idPrefixMap = Maps.newHashMap();
static {
idPrefixMap.put(Datasource.class, "10");
idPrefixMap.put(Organization.class, "20");
idPrefixMap.put(Project.class, "40");
idPrefixMap.put(Dataset.class, "50");
idPrefixMap.put(OtherResearchProduct.class, "50");
idPrefixMap.put(Software.class, "50");
idPrefixMap.put(Publication.class, "50");
}
public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
static {
entityIdPrefix.put("datasource", "10");
entityIdPrefix.put("organization", "20");
entityIdPrefix.put("project", "40");
entityIdPrefix.put("result", "50");
}
public static final Map<String, String> idPrefixEntity = Maps.newHashMap();
static {
idPrefixEntity.put("10", "datasource");
idPrefixEntity.put("20", "organization");
idPrefixEntity.put("40", "project");
idPrefixEntity.put("50", "result");
}
public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
static {
set(relationInverseMap, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, HAS_PARTICIPANT);
set(relationInverseMap, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, HAS_AUTHOR_INSTITUTION);
set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, MERGES);
set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
set(relationInverseMap, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, PRODUCES);
set(relationInverseMap, DATASOURCE_ORGANIZATION, PROVISION, IS_PROVIDED_BY, PROVIDES);
set(relationInverseMap, RESULT_RESULT, SIMILARITY, IS_AMONG_TOP_N_SIMILAR_DOCS, HAS_AMONG_TOP_N_SIMILAR_DOCS);
set(relationInverseMap, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, IS_SUPPLEMENTED_BY);
set(relationInverseMap, RESULT_RESULT, PART, IS_PART_OF, HAS_PART);
set(relationInverseMap, RESULT_RESULT, DEDUP, IS_MERGED_IN, MERGES);
set(relationInverseMap, RESULT_RESULT, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
set(relationInverseMap, RESULT_RESULT, CITATION, IS_CITED_BY, CITES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_IDENTICAL_TO, IS_IDENTICAL_TO);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REFERENCED_BY, REFERENCES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_CONTINUED_BY, CONTINUES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DOCUMENTED_BY, DOCUMENTS);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DERIVED_FROM, IS_SOURCE_OF);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, IS_RELATED_TO);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_COMPILED_BY, COMPILES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DESCRIBED_BY, DESCRIBES);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_METADATA_FOR, IS_METADATA_OF);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, HAS_ASSOCIATION_WITH, HAS_ASSOCIATION_WITH);
set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REQUIRED_BY, REQUIRES);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_PREVIOUS_VERSION_OF, IS_NEW_VERSION_OF);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_VARIANT_FORM_OF, IS_ORIGINAL_FORM_OF);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_OBSOLETED_BY, OBSOLETES);
set(relationInverseMap, RESULT_RESULT, VERSION, IS_VERSION_OF, HAS_VERSION);
set(relationInverseMap, RESULT_RESULT, REVIEW, IS_REVIEWED_BY, REVIEWS);
}
private static void set(Map<String, RelationInverse> relationInverseMap, String relType, String subRelType, String relClass, String inverseRelClass) {
relationInverseMap
.put(
rel(relType, subRelType, relClass), new RelationInverse()
.setInverseRelClass(inverseRelClass)
.setRelClass(relClass)
.setRelType(relType)
.setSubReltype(subRelType));
if (!relClass.equals(inverseRelClass)) {
relationInverseMap
.put(
rel(relType, subRelType, inverseRelClass), new RelationInverse()
.setInverseRelClass(relClass)
.setRelClass(inverseRelClass)
.setRelType(relType)
.setSubReltype(subRelType));
}
}
/**
* Helper method: lookup relation inverse, given the direct relation encoding (case insensitive)
* @param encoding
* @return the relation inverse descriptor, throws @IllegalArgumentException when not found.
*/
public static RelationInverse findInverse(String encoding) {
return ModelSupport.relationInverseMap
.entrySet()
.stream()
.filter(r -> encoding.equalsIgnoreCase(r.getKey()))
.findFirst()
.map(r -> r.getValue())
.orElseThrow(() -> new IllegalArgumentException("invalid relationship: " + encoding));
}
/**
* Helper method: fina a relation filtering by a relation name
* @param relationName
* @return
*/
public static RelationInverse findRelation(final String relationName) {
return relationInverseMap.values()
.stream()
.filter(r -> relationName.equalsIgnoreCase(r.getRelClass()))
.findFirst()
.orElse(null);
}
/**
* Helper method: combines the relation attributes
* @param relType
* @param subRelType
* @param relClass
* @return
*/
public static String rel(String relType, String subRelType, String relClass) {
return String.format("%s_%s_%s", relType, subRelType, relClass);
}
private static final String schemeTemplate = "dnet:%s_%s_relations";
public static final String DATE_FORMAT = "yyyy-MM-dd";
private ModelSupport() {
}
public static <E extends Entity> String getIdPrefix(Class<E> clazz) {
return idPrefixMap.get(clazz);
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazzObject Subclass object instance
* @param superClazzObject Superclass object instance
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Y superClazzObject) {
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazzObject Subclass object instance
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Class<Y> superClazz) {
return isSubClass(subClazzObject.getClass(), superClazz);
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazz Subclass class
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
Class<X> subClazz, Class<Y> superClazz) {
return superClazz.isAssignableFrom(subClazz);
}
/**
* Lists all the OAF model classes
*
* @param <T>
* @return
*/
public static <T extends Entity> Class<T>[] getOafModelClasses() {
return new Class[] {
AccessRight.class,
Author.class,
AuthorPid.class,
Context.class,
Country.class,
DataInfo.class,
Dataset.class,
Datasource.class,
Entity.class,
EntityDataInfo.class,
EoscIfGuidelines.class,
ExternalReference.class,
ExtraInfo.class,
GeoLocation.class,
H2020Classification.class,
H2020Programme.class,
Instance.class,
Journal.class,
KeyValue.class,
License.class,
Measure.class,
OAIProvenance.class,
OpenAccessRoute.class,
Organization.class,
OriginDescription.class,
OtherResearchProduct.class,
Project.class,
Provenance.class,
Publication.class,
Publisher.class,
Qualifier.class,
Relation.class,
Result.class,
Software.class,
StructuredProperty.class,
Subject.class
};
}
public static String getMainType(final EntityType type) {
return entityMapping.get(type).name();
}
public static boolean isResult(EntityType type) {
return MainEntityType.result.name().equals(getMainType(type));
}
public static String getScheme(final String sourceType, final String targetType) {
return String
.format(
schemeTemplate,
entityMapping.get(EntityType.valueOf(sourceType)).name(),
entityMapping.get(EntityType.valueOf(targetType)).name());
}
public static String tableIdentifier(String dbName, String tableName) {
checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty");
checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty");
return String.format("%s.%s", dbName, tableName);
}
public static <T extends Entity> String tableIdentifier(String dbName, Class<T> clazz) {
checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null");
return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase());
}
private static String idFnForRelation(Relation r) {
return Optional
.ofNullable(r.getSource())
.map(
source -> Optional
.ofNullable(r.getTarget())
.map(
target -> Optional
.ofNullable(r.getRelType())
.map(
relType -> Optional
.ofNullable(r.getSubRelType())
.map(
subRelType -> Optional
.ofNullable(r.getRelClass())
.map(
relClass -> String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(String.join(source, target, relType)))
.orElse(String.join(source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Entity> String idFnForOafEntity(T t) {
return t.getId();
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final NoSuchAlgorithmException e) {
throw new IllegalStateException(e);
}
}
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, md5(originalId));
}
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 = DateParserUtils.parseDate(dateA);
final Date b = DateParserUtils.parseDate(dateB);
if (Objects.nonNull(a) && Objects.nonNull(b)) {
return a.before(b) ? dateA : dateB;
} else {
return null;
}
} else {
return null;
}
}
}

44
src/main/java/eu/dnetlib/dhp/schema/common/RefereedComparator.java
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@ -1,44 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class RefereedComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
return 1;
if (lClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
return -1;
if (rClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
return 1;
if (lClass.equals(ModelConstants.UNKNOWN))
return -1;
if (rClass.equals(ModelConstants.UNKNOWN))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

46
src/main/java/eu/dnetlib/dhp/schema/common/RelationInverse.java
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@ -1,46 +0,0 @@
package eu.dnetlib.dhp.schema.common;
public class RelationInverse {
private String relClass;
private String inverseRelClass;
private String relType;
private String subReltype;
public String getRelType() {
return relType;
}
public RelationInverse setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubReltype() {
return subReltype;
}
public RelationInverse setSubReltype(String subReltype) {
this.subReltype = subReltype;
return this;
}
public String getRelClass() {
return relClass;
}
public RelationInverse setRelClass(String relClass) {
this.relClass = relClass;
return this;
}
public String getInverseRelClass() {
return inverseRelClass;
}
public RelationInverse setInverseRelClass(String inverseRelClass) {
this.inverseRelClass = inverseRelClass;
return this;
}
}

5
src/main/java/eu/dnetlib/dhp/schema/mdstore/MetadataRecord.java
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@ -3,8 +3,6 @@ package eu.dnetlib.dhp.schema.mdstore;
import java.io.Serializable;
import eu.dnetlib.dhp.schema.common.ModelSupport;
/**
* This class models a record in a Metadata store collection on HDFS
*/
@ -38,6 +36,7 @@ public class MetadataRecord implements Serializable {
}
public MetadataRecord(
String id,
String originalId,
String encoding,
Provenance provenance,
@ -49,7 +48,7 @@ public class MetadataRecord implements Serializable {
this.provenance = provenance;
this.body = body;
this.dateOfCollection = dateOfCollection;
this.id = ModelSupport.generateIdentifier(originalId, this.provenance.getNsPrefix());
this.id = id;
}
public String getId() {

3
src/main/java/eu/dnetlib/dhp/schema/oaf/Entity.java
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@ -14,7 +14,7 @@ public abstract class Entity extends Oaf implements Serializable {
/**
* The list of datasource id/name pairs providing this Oaf.
*/
protected List<KeyValue> collectedfrom;
private List<KeyValue> collectedfrom;
private Long lastupdatetimestamp;
@ -33,7 +33,6 @@ public abstract class Entity extends Oaf implements Serializable {
private EntityDataInfo dataInfo;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}

1
src/main/java/eu/dnetlib/dhp/schema/oaf/EntityDataInfo.java
View File

@ -7,7 +7,6 @@ public class EntityDataInfo extends DataInfo {
private Boolean invisible = false;
private Boolean deletedbyinference = false;
public Boolean getInvisible() {
return invisible;
}

25
src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
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@ -1,16 +1,11 @@
package eu.dnetlib.dhp.schema.oaf;
import static com.google.common.base.Preconditions.checkArgument;
import java.io.Serializable;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
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,
@ -145,26 +140,6 @@ public class Relation extends Oaf implements Serializable {
this.provenance = provenance;
}
public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");
checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal");
checkArgument(
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()));
}
}
@Override
public boolean equals(Object o) {
if (this == o)

74
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java
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@ -1,74 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashSet;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleaningFunctions {
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
public static final String DOI_PREFIX = "10.";
public static final Set<String> PID_BLACKLIST = new HashSet<>();
static {
PID_BLACKLIST.add("none");
PID_BLACKLIST.add("na");
}
public CleaningFunctions() {}
/**
* 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;
}
return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
pid.setValue(
normalizePidValue(
pid.getQualifier().getClassid(),
pid.getValue()));
return pid;
}
public static String normalizePidValue(String pidType, String pidValue) {
String value = Optional
.ofNullable(pidValue)
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pidType) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
}
return value;
}
}

292
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
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@ -1,292 +0,0 @@
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.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.codec.binary.Hex;
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.*;
/**
* 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 static final int ID_PREFIX_LEN = 12;
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
* The id of the record (source_::id) will be rewritten as pidType_::id)
*/
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.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
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");
PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
*
* If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
* See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
*/
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
static {
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
* the same OpenAIRE id.
*/
public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
static {
ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
}
public static Set<String> delegatedAuthorityDatasourceIds() {
return DELEGATED_PID_AUTHORITY.values()
.stream()
.flatMap(m -> m.keySet().stream())
.collect(Collectors.toCollection(HashSet::new));
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom, true).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 Entity> String createIdentifier(T entity, boolean md5) {
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
.stream()
.flatMap(Set::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 Entity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(IdentifierFactory::mapPids)
.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.toCollection(HashSet::new))));
}
}
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
return instance
.stream()
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
boolean mapHandles) {
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 -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
.map(CleaningFunctions::normalizePidValue)
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
if (Objects.isNull(collectedFrom)) {
return false;
}
boolean isEnrich = Optional
.ofNullable(ENRICHMENT_PROVIDER.get(pType))
.map(enrich -> enrich.containsKey(collectedFrom.getKey())
|| enrich.containsValue(collectedFrom.getValue()))
.orElse(false);
boolean isAuthority = Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(authorities -> authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue()))
.orElse(false);
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
}
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
if (Objects.isNull(da)) {
return true;
}
if (!da.containsKey(collectedFrom.getKey())) {
return true;
}
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
}
/**
* @see {@link IdentifierFactory#createIdentifier(Entity, boolean)}
*/
public static <T extends Entity> String createIdentifier(T entity) {
return createIdentifier(entity, true);
}
private static <T extends Entity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
}
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
return new StringBuilder()
.append(numericPrefix)
.append(ID_PREFIX_SEPARATOR)
.append(createPrefix(pidType))
.append(ID_SEPARATOR)
.append(md5 ? md5(pidValue) : pidValue)
.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);
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
return null;
}
}
}

24
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
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@ -1,24 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
public class ModelHardLimits {
private 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;
}
}

38
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java
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@ -1,38 +0,0 @@
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.openorgs))
return -1;
if (rClass.equals(PidType.openorgs))
return 1;
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
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java
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@ -1,8 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashMap;
import java.util.HashSet;
public class PidBlacklist extends HashMap<String, HashSet<String>> {
}

39
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java
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@ -1,39 +0,0 @@
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<>());
}
private PidBlacklistProvider() {}
}

48
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java
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@ -1,48 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Entity;
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 Entity> implements Comparator<StructuredProperty> {
private final 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);
}
}

79
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java
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@ -1,79 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import org.apache.commons.lang3.EnumUtils;
public enum PidType {
/**
* The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
*
* There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
*
* The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
* of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
* defined for an application by the ISO 26324 Registration Authority.
*
*
* DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
* These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
* distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
* resolution system.
*
* Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
* unique string assigned to a registrant.
*
* DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
* Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
* or it might incorporate an identifier generated from or based on another system used by the registrant
* (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
* specified, as in Example 1).
*
* Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
*/
doi,
/**
* PubMed Unique Identifier (PMID)
*
* This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
* accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
*
* Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
* (e.g., 21804956.2). All citations are considered version 1 until replaced. The extended PMID is not displayed
* on the MEDLINE format.
*
* View the citation in abstract format in PubMed to access additional versions when available (see the article in
* the Jan-Feb 2012 NLM Technical Bulletin).
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
*/
pmid,
/**
* This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
* prefix PMC.
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
*/
pmc, handle, arXiv, nct, pdb, w3id,
// Organization
openorgs, corda, corda_h2020, 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
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java
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@ -1,33 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java
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@ -1,53 +0,0 @@
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;
}
}

77
src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java
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@ -1,77 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
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 eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
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();
String rClass = right.getResulttype();
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
// 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(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

5
src/main/resources/eu/dnetlib/dhp/schema/oaf/utils/pid_blacklist.json
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File diff suppressed because one or more lines are too long

53
src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java
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@ -1,53 +0,0 @@
package eu.dnetlib.dhp.schema.common;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.Entity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ModelSupportTest {
@Nested
class IsSubClass {
@Test
void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Relation.class, Entity.class);
// then
assertFalse(result);
}
@Test
void shouldReturnTrueWhenSubClassExtendsSuperClass() {
// when
Boolean result = ModelSupport.isSubClass(Result.class, Entity.class);
// then
assertTrue(result);
}
}
@Nested
class InverseRelation {
@Test
void findRelations() throws IOException {
assertNotNull(ModelSupport.findRelation("isMetadataFor"));
assertNotNull(ModelSupport.findRelation("ismetadatafor"));
assertNotNull(ModelSupport.findRelation("ISMETADATAFOR"));
assertNotNull(ModelSupport.findRelation("isRelatedTo"));
}
}
}

21
src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java
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@ -1,21 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class BlackListProviderTest {
@Test
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());
}
}

87
src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
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@ -1,87 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
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;
class IdentifierFactoryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
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_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
verifyIdentifier(
"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", 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
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);
}
@Test
void testCreateIdentifierForROHub() throws IOException {
verifyIdentifier(
"orp-rohub.json", "50|w3id________::afc7592914ae190a50570db90f55f9c2", true);
}
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);
System.out.println(id);
assertNotNull(id);
assertEquals(expectedID, id);
}
}

197
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/orp-rohub.json
View File

@ -1,197 +0,0 @@
{
"collectedfrom": [
{
"key": "10|fairsharing_::1b69ebedb522700034547abc5652ffac",
"value": "ROHub",
"dataInfo": null
}
],
"dataInfo": {
"invisible": false,
"inferred": false,
"deletedbyinference": false,
"trust": "0.9",
"inferenceprovenance": null,
"provenanceaction": {
"classid": "sysimport:crosswalk:repository",
"classname": "sysimport:crosswalk:repository",
"schemeid": "dnet:provenanceActions"
}
},
"lastupdatetimestamp": 1663926081966,
"id": "50|w3id________::afc7592914ae190a50570db90f55f9c2",
"originalId": [
"50|fsh_____4119::afc7592914ae190a50570db90f55f9c2",
"https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca"
],
"pid": [
{
"value": "https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca",
"qualifier": {
"classid": "w3id",
"classname": "w3id.org",
"schemeid": "dnet:pid_types"
}
}
],
"dateofcollection": "2019-03-27T15:15:22.22Z",
"dateoftransformation": "2019-04-17T16:04:20.586Z",
"extraInfo": [],
"oaiprovenance": null,
"processingchargeamount": null,
"processingchargecurrency": null,
"measures": null,
"author": [
{
"fullname": "CNR-ISMAR",
"name": "",
"surname": "",
"rank": 1,
"pid": []
}
],
"resulttype": "other",
"language": {
"classid": "UNKNOWN",
"classname": "Unknown",
"schemeid": "dnet:languages"
},
"country": [],
"subject": [
{
"value": "Ecology",
"qualifier": {
"classid": "",
"classname": "",
"schemeid": ""
},
"dataInfo": {
"inferred": false,
"trust": "0.9",
"inferenceprovenance": null,
"provenanceaction": {
"classid": "sysimport:crosswalk:repository",
"classname": "sysimport:crosswalk:repository",
"schemeid": "dnet:provenanceActions"
}
}
},
{
"value": "EOSC::RO-crate",
"qualifier": {
"classid": "",
"classname": "",
"schemeid": ""
},
"dataInfo": {
"inferred": false,
"trust": "0.9",
"inferenceprovenance": null,
"provenanceaction": {
"classid": "sysimport:crosswalk:repository",
"classname": "sysimport:crosswalk:repository",
"schemeid": "dnet:provenanceActions"
}
}
}
],
"title": [
{
"value": "Using biological effects tools to define Good Environmental Status under the European Union Marine Strategy Framework Directive",
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title"
}
}
],
"relevantdate": [
{
"value": "2018-06-20T11:21:46Z",
"qualifier": {
"classid": "UNKNOWN",
"classname": "UNKNOWN",
"schemeid": "dnet:dataCite_date"
}
}
],
"description": [
"The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status (GES), such as demonstrating that \"Concentrations of contaminants are at levels not giving rise to pollution effects\" (GES Descriptor 8). This paper discusses the combined approach of monitoring chemical contaminant levels, along side biological effect measurements relating to the effect of pollutants, for undertaking assessments of GES across European marine regions. We outline the minimum standards that biological effects tools should meet if they are to be used for defining GES in relation to Descriptor 8 and describe the current international initiatives underway to develop assessment criteria for these biological effects techniques. Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserved."
],
"dateofacceptance": null,
"publisher": {
"name": "Poznań Supercomputing and Networking Center"
},
"embargoenddate": null,
"source": [],
"fulltext": [],
"format": [],
"contributor": [
"Generation Service"
],
"resourcetype": {
"classid": "RO-crate",
"classname": "RO-crate",
"schemeid": "dnet:dataCite_resource",
"schemename": "dnet:dataCite_resource"
},
"coverage": [],
"bestaccessright": {
"classid": "OPEN",
"classname": "Open Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"context": [],
"externalReference": [],
"instance": [
{
"license": null,
"accessright": {
"classid": "OPEN",
"classname": "Open Access",
"schemeid": "dnet:access_modes",
"openAccessRoute": null
},
"instancetype": {
"classid": "other research product",
"classname": "other research product",
"schemeid": "dnet:publication_resource"
},
"hostedby": {
"key": "10|fairsharing_::1b69ebedb522700034547abc5652ffac",
"value": "ROHub"
},
"url": null,
"distributionlocation": null,
"collectedfrom": {
"key": "10|fairsharing_::1b69ebedb522700034547abc5652ffac",
"value": "ROHub"
},
"pid": [
{
"value": "https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca",
"qualifier": {
"classid": "w3id",
"classname": "w3id.org",
"schemeid": "dnet:pid_types"
}
}
],
"alternateIdentifier": [],
"dateofacceptance": null,
"processingchargeamount": null,
"processingchargecurrency": null,
"refereed": {
"classid": "UNKNOWN",
"classname": "Unknown",
"schemeid": "dnet:review_levels"
},
"measures": null
}
],
"eoscifguidelines": null,
"contactperson": [],
"contactgroup": [],
"tool": []
}

1
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json
View File

@ -1 +0,0 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]}

1
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json
View File

@ -1 +0,0 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[]}

1
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json
View File

@ -1 +0,0 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"}

33
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi1.json
View File

@ -1,33 +0,0 @@
{
"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
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi2.json
View File

@ -1,37 +0,0 @@
{
"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
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
View File

@ -1,37 +0,0 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"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"
}
]
}
]
}

37
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi4.json
View File

@ -1,37 +0,0 @@
{
"id": "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
]
},
{
"collectedfrom": {
"key": "10|opendoar____::2852",
"value": "Digital library of Brno University of Technology"
},
"pid": [
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
},
{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
]
}
]
}

37
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi5.json
View File

@ -1,37 +0,0 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.5281/zenodo.5121485"
}
]
},
{
"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"
}
]
}
]
}

31
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_openapc.json
View File

@ -1,31 +0,0 @@
{
"id": "50|openapc_____::000023f9cb6e3a247c764daec4273cbc",
"resuttype": {
"classid": "publication"
},
"instance": [
{
"collectedfrom": {
"key": "10|apc_________::e2b1600b229fc30663c8a1f662debddf",
"value": "OpenAPC Global Initiative"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
},
{
"qualifier": {"classid": "pmid"},
"value": "25811027"
}
],
"url":["https://doi.org/10.1155/2015/439379"]
}
]
}

17
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc1.json
View File

@ -1,17 +0,0 @@
{
"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
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
View File

@ -1,21 +0,0 @@
{
"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
src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json
View File

@ -1,23 +0,0 @@
{
"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"
}
]
}