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Author SHA1 Message Date
Sandro La Bruzzo c8ddb527b3 Added unit test to verify the generation in the OriginalID the old openaire Identifier generated by OAI 2022-07-20 15:33:37 +02:00
Sandro La Bruzzo 27fbc9b385 [DHP Schema refactoring]
- move the business logic from the model class to  dhp-common
2022-07-04 18:22:38 +02:00
Sandro La Bruzzo e517f52e30 Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into doiboost_refactor 2022-06-27 16:24:04 +02:00
Sandro La Bruzzo 8b9f70d977 [DOIBoost Refactor]
- Testing :
    Added common method to retrieve mock vocabulary in test class
    fixed test
- Mapping Crossref:
    Using vocabulary IS to mapping the crossref type instead of a map into the code
2022-06-27 16:23:28 +02:00
50 changed files with 6891 additions and 1874 deletions

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@ -0,0 +1,27 @@
package eu.dnetlib.dhp.common.test;
import org.apache.commons.io.IOUtils;
import java.io.IOException;
import java.util.List;
import java.util.Objects;
public class TestUtils {
public static List<String> getVocabulariesMock() throws IOException {
return IOUtils
.readLines(
Objects
.requireNonNull(
TestUtils.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/terms.txt")));
}
public static List<String> getSynonymsMock() throws IOException {
return IOUtils
.readLines(
Objects
.requireNonNull(
TestUtils.class.getResourceAsStream("/eu/dnetlib/dhp/vocabulary/synonyms.txt")));
}
}

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@ -0,0 +1,74 @@
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;
}
}

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@ -0,0 +1,283 @@
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
*/
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");
}
/**
* 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.
*/
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");
}
/**
* 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 OafEntity> 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 OafEntity> 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(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 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;
}
}
}

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@ -0,0 +1,24 @@
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;
}
}

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@ -26,26 +26,21 @@ public class OafMapperUtils {
if (ModelSupport.isSubClass(left, OafEntity.class)) {
return mergeEntities((OafEntity) left, (OafEntity) right);
} else if (ModelSupport.isSubClass(left, Relation.class)) {
((Relation) left).mergeFrom((Relation) right);
return OafUtils.mergeOAF(left, right);
} else {
throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
}
return left;
}
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)) {
left.mergeFrom(right);
} else if (ModelSupport.isSubClass(left, Organization.class)) {
left.mergeFrom(right);
} else if (ModelSupport.isSubClass(left, Project.class)) {
left.mergeFrom(right);
} else if (ModelSupport.isSubClass(left, Datasource.class) || ModelSupport.isSubClass(left, Organization.class) || ModelSupport.isSubClass(left, Project.class))
{
return OafUtils.mergeOAF(left, right);
} else {
throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
}
return left;
}
public static Result mergeResults(Result left, Result right) {
@ -59,13 +54,11 @@ public class OafMapperUtils {
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
return OafUtils.mergeOAF(left, right);
} else {
right.mergeFrom(left);
return right;
return OafUtils.mergeOAF(right, left);
}
}
@ -251,6 +244,9 @@ public class OafMapperUtils {
return p;
}
public static Journal journal(
final String name,
final String issnPrinted,
@ -416,7 +412,7 @@ public class OafMapperUtils {
public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) {
Measure m = new Measure();
m.setId(id);
m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo)));
m.setUnit(Collections.singletonList(newKeyValueInstance(key, value, dataInfo)));
return m;
}
}

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@ -0,0 +1,761 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import com.google.common.base.Preconditions;
import eu.dnetlib.dhp.common.api.zenodo.File;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import static com.google.common.base.Preconditions.checkArgument;
import static com.ibm.icu.text.PluralRules.Operand.e;
import java.text.ParseException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
/**
* The type Oaf utils class groups all
* the utilities method used for OAF Generation
*/
public class OafUtils {
/**
* Normalize pid string.
*
* @param pid the pid
* @return the string
*/
public static String extractKeyFromPid(final StructuredProperty pid) {
if (pid == null)
return null;
final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
}
/**
* This method converts the list of instance enrichments
* into a Map where the key is the normalized identifier
* and the value is the instance itself
*
* @param ri the list of enrichment instances
* @return the result map
*/
public static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
return ri
.stream()
.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
.flatMap(i -> {
final List<Pair<String, Instance>> result = new ArrayList<>();
if (i.getPid() != null)
i.getPid().stream().filter(OafUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
if (i.getAlternateIdentifier() != null)
i.getAlternateIdentifier().stream().filter(OafUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
return result.stream();
}).collect(Collectors.toMap(
Pair::getLeft,
Pair::getRight,
(a, b) -> a
));
}
/**
* Valid pid boolean.
*
* @param p the p
* @return the boolean
*/
private static boolean validPid(final StructuredProperty p) {
return p.getValue()!= null && p.getQualifier()!= null && p.getQualifier().getClassid()!=null;
}
/**
* This utility method finds the list of enrichment instances
* that match one or more PIDs in the input list
*
* @param pids the list of PIDs
* @param enrichments the List of enrichment instances having the same pid
* @return the list
*/
private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
if (pids == null || enrichments == null)
return null;
return pids
.stream()
.map(OafUtils::extractKeyFromPid)
.map(enrichments::get)
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
/**
* Is an enrichment boolean.
*
* @param e the e
* @return the boolean
*/
public static boolean isAnEnrichment(OafEntity e) {
return e.getDataInfo()!= null &&
e.getDataInfo().getProvenanceaction()!= null
&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
}
/**
* This method apply enrichment on a single instance
* The enrichment consists of replacing values on
* single attribute only if in the current instance is missing
* The only repeatable field enriched is measures
*
* @param currentInstance the current instance
* @param enrichment the enrichment instance
*/
private static void applyEnrichment(final Instance currentInstance, final Instance enrichment) {
if (currentInstance == null || enrichment == null)
return;
//ENRICH accessright
if (enrichment.getAccessright()!=null && currentInstance.getAccessright() == null)
currentInstance.setAccessright(enrichment.getAccessright());
//ENRICH license
if (enrichment.getLicense()!=null && currentInstance.getLicense() == null)
currentInstance.setLicense(enrichment.getLicense());
//ENRICH instanceType
if (enrichment.getInstancetype()!=null && currentInstance.getInstancetype() == null)
currentInstance.setInstancetype(enrichment.getInstancetype());
//ENRICH hostedby
if (enrichment.getHostedby()!=null && currentInstance.getHostedby() == null)
currentInstance.setHostedby(enrichment.getHostedby());
//ENRICH distributionlocation
if (enrichment.getDistributionlocation()!=null && currentInstance.getDistributionlocation() == null)
currentInstance.setDistributionlocation(enrichment.getDistributionlocation());
//ENRICH collectedfrom
if (enrichment.getCollectedfrom()!=null && currentInstance.getCollectedfrom() == null)
currentInstance.setCollectedfrom(enrichment.getCollectedfrom());
//ENRICH dateofacceptance
if (enrichment.getDateofacceptance()!=null && currentInstance.getDateofacceptance() == null)
currentInstance.setDateofacceptance(enrichment.getDateofacceptance());
//ENRICH processingchargeamount
if (enrichment.getProcessingchargeamount()!=null && currentInstance.getProcessingchargeamount() == null)
currentInstance.setProcessingchargeamount(enrichment.getProcessingchargeamount());
//ENRICH refereed
if (enrichment.getRefereed()!=null && currentInstance.getRefereed() == null)
currentInstance.setRefereed(enrichment.getRefereed());
//ENRICH measures
if (enrichment.getMeasures()!=null)
if (currentInstance.getMeasures() == null)
currentInstance.setMeasures(enrichment.getMeasures());
else
enrichment.getMeasures().forEach(currentInstance.getMeasures()::add);
}
/**
* This main method apply the enrichment of the instances
*
* @param toEnrichInstances the instances that could be enriched
* @param enrichmentInstances the enrichment instances
* @return list of instances possibly enriched
*/
private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,final List<Instance> enrichmentInstances) {
final List<Instance> enrichmentResult = new ArrayList<>();
if (toEnrichInstances == null) {
return enrichmentResult;
}
if (enrichmentInstances == null) {
return enrichmentResult;
}
Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
toEnrichInstances.forEach(i -> {
final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
if (e!= null && e.size()> 0) {
e.forEach(enr -> applyEnrichment(i, enr));
} else {
final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
if (a!= null && a.size()> 0) {
a.forEach(enr -> applyEnrichment(i, enr));
}
}
enrichmentResult.add(i);
});
return enrichmentResult;
}
/**
* Longest lists list.
*
* @param a the a
* @param b the b
* @return the list
*/
public static List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if (a == null || b == null)
return a == null ? b : a;
if (a.size() == b.size()) {
int msa = a
.stream()
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i != null && i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
return msa > msb ? a : b;
}
return a.size() > b.size() ? a : b;
}
/**
* This method merge two oaf object of the same type
* It should replace the mergeFrom utility inside the oaf
* class.
*
* @param original First object
* @param enrich second object
* @return the merged object
*/
public static <T extends Oaf> T mergeOAF(T original, T enrich) {
if (original == null)
return enrich;
if (enrich == null)
return original;
if (original.getClass() != enrich.getClass())
throw new RuntimeException(String.format("Trying to merge different types of object %s, and %s",
original.getClass().getCanonicalName(),
enrich.getClass().getCanonicalName()));
Oaf result ;
switch (original.getClass().getSimpleName().toLowerCase()) {
case "relation":
result = mergeOAFRelation((Relation) original, (Relation) enrich);
break;
case "publication":
result = mergeOAFPublication((Publication) original, (Publication) enrich);
break;
case "dataset":
result = mergeOAFDataset((Dataset) original, (Dataset) enrich);
break;
case "software":
result = mergeOAFSoftware((Software) original, (Software) enrich);
break;
case "otherresearchproduct":
result = mergeOAFOtherResearchProduct((OtherResearchProduct) original, (OtherResearchProduct) enrich);
break;
case "project":
result = mergeOAFProject((Project) original, (Project)enrich);
break;
case "organization":
result = mergeOAFOrganization((Organization) original, (Organization)enrich);
break;
default:
throw new RuntimeException("Trying to merge an unsupported class");
}
result.setCollectedfrom(
Stream
.concat(
Optional
.ofNullable(original.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(enrich.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals
.collect(Collectors.toList()));
result.setLastupdatetimestamp(
Math
.max(
Optional.ofNullable(original.getLastupdatetimestamp()).orElse(0L),
Optional.ofNullable(enrich.getLastupdatetimestamp()).orElse(0L)));
return (T) result;
}
@SafeVarargs
public static <T> List<T> mergeLists(final List<T>... lists) {
return Arrays
.stream(lists)
.filter(Objects::nonNull)
.flatMap(List::stream)
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
private static int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b));
}
private static String extractTrust(Oaf e) {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null)
return "0.0";
return e.getDataInfo().getTrust();
}
private static void mergeOAFDataInfo(Oaf from, Oaf to) {
Optional.ofNullable(to)
.ifPresent(other -> Optional.ofNullable(other.getDataInfo())
.ifPresent(otherDataInfo -> Optional.ofNullable(from.getDataInfo())
.ifPresent(thisDataInfo -> {
if (compareTrust(from, other) < 0 || thisDataInfo.getInvisible()) {
from.setDataInfo(otherDataInfo);
}
})));
}
/**
* Gets main title.
*
* @param titles the titles
* @return the main title
*/
private static StructuredProperty getMainTitle(final List<StructuredProperty> titles) {
// need to check if the list of titles contains more than 1 main title? (in that case, we should chose which
// main title select in the list)
for (StructuredProperty t : titles) {
if (t.getQualifier() != null && t.getQualifier().getClassid() != null)
if (t.getQualifier().getClassid().equals("main title"))
return t;
}
return null;
}
private static OafEntity mergeEntity(final OafEntity original,final OafEntity enrich) {
final OafEntity mergedEntity = original;
mergedEntity.setOriginalId(mergeLists(mergedEntity.getOriginalId(), enrich.getOriginalId()));
mergedEntity.setPid(mergeLists(mergedEntity.getPid(), enrich.getPid()));
if (enrich.getDateofcollection() != null && compareTrust(mergedEntity, enrich) < 0)
mergedEntity.setDateofcollection(enrich.getDateofcollection());
if (enrich.getDateoftransformation() != null && compareTrust(mergedEntity, enrich) < 0)
mergedEntity.setDateoftransformation(enrich.getDateoftransformation());
mergedEntity.setExtraInfo(mergeLists(mergedEntity.getExtraInfo(), enrich.getExtraInfo()));
if (enrich.getOaiprovenance() != null && compareTrust(mergedEntity, enrich) < 0)
mergedEntity.setOaiprovenance(enrich.getOaiprovenance());
return mergedEntity;
}
private static Result mergeOAFResult(final Result original,final Result enrich) {
final Result mergedResult = (Result) mergeEntity(original, enrich);
if(mergedResult.getProcessingchargeamount() == null || StringUtils.isBlank(mergedResult.getProcessingchargeamount().getValue() )){
mergedResult.setProcessingchargeamount(enrich.getProcessingchargeamount());
mergedResult.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
}
mergedResult.setMeasures(mergeLists(mergedResult.getMeasures(), enrich.getMeasures()));
if( !isAnEnrichment(mergedResult) && !isAnEnrichment(enrich))
mergedResult.setInstance(mergeLists(mergedResult.getInstance(), enrich.getInstance()));
else {
final List<Instance> enrichmentInstances = isAnEnrichment(mergedResult) ? mergedResult.getInstance() : enrich.getInstance();
final List<Instance> enrichedInstances= isAnEnrichment(mergedResult) ? enrich.getInstance(): mergedResult.getInstance();
if (isAnEnrichment(mergedResult))
mergedResult.setDataInfo(enrich.getDataInfo());
mergedResult.setInstance(enrichInstances(enrichedInstances,enrichmentInstances));
}
if (enrich.getBestaccessright() != null
&& new AccessRightComparator().compare(enrich.getBestaccessright(), mergedResult.getBestaccessright()) < 0)
mergedResult.setBestaccessright(enrich.getBestaccessright());
if (enrich.getResulttype() != null && compareTrust(mergedResult, enrich) < 0)
mergedResult.setResulttype(enrich.getResulttype());
if (enrich.getLanguage() != null && compareTrust(mergedResult, enrich) < 0)
mergedResult.setLanguage(enrich.getLanguage());
if (Objects.nonNull(enrich.getDateofacceptance())) {
if (Objects.isNull(mergedResult.getDateofacceptance())) {
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
} else if (compareTrust(mergedResult, enrich) < 0) {
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
}
}
mergedResult.setCountry(mergeLists(mergedResult.getCountry(), enrich.getCountry()));
mergedResult.setSubject(mergeLists(mergedResult.getSubject(), enrich.getSubject()));
// merge title lists: main title with higher trust and distinct between the others
StructuredProperty baseMainTitle = null;
if (mergedResult.getTitle() != null) {
baseMainTitle = getMainTitle(mergedResult.getTitle());
if (baseMainTitle != null) {
final StructuredProperty p = baseMainTitle;
mergedResult.setTitle(mergedResult.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
}
}
StructuredProperty newMainTitle = null;
if (enrich.getTitle() != null) {
newMainTitle = getMainTitle(enrich.getTitle());
if (newMainTitle != null) {
final StructuredProperty p = newMainTitle;
enrich.setTitle(enrich.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
}
}
if (newMainTitle != null && compareTrust(mergedResult, enrich) < 0) {
baseMainTitle = newMainTitle;
}
mergedResult.setTitle(mergeLists(mergedResult.getTitle(), enrich.getTitle()));
if (mergedResult.getTitle() != null && baseMainTitle != null) {
mergedResult.getTitle().add(baseMainTitle);
}
mergedResult.setRelevantdate (mergeLists(mergedResult.getRelevantdate(), enrich.getRelevantdate()));
mergedResult.setDescription( longestLists(mergedResult.getDescription(), enrich.getDescription()));
if (enrich.getPublisher() != null && compareTrust(mergedResult, enrich) < 0)
mergedResult.setPublisher(enrich.getPublisher());
if (enrich.getEmbargoenddate() != null && compareTrust(mergedResult, enrich) < 0)
mergedResult.setEmbargoenddate(enrich.getEmbargoenddate());
mergedResult.setSource(mergeLists(mergedResult.getSource(), enrich.getSource()));
mergedResult.setFulltext(mergeLists(mergedResult.getFulltext(), enrich.getFulltext()));
mergedResult.setFormat(mergeLists(mergedResult.getFormat(), enrich.getFormat()));
mergedResult.setContributor(mergeLists(mergedResult.getContributor(), enrich.getContributor()));
if (enrich.getResourcetype() != null)
mergedResult.setResourcetype(enrich.getResourcetype());
mergedResult.setCoverage(mergeLists(mergedResult.getCoverage(), enrich.getCoverage()));
mergedResult.setContext(mergeLists(mergedResult.getContext(), enrich.getContext()));
mergedResult.setExternalReference(mergeLists(mergedResult.getExternalReference(), enrich.getExternalReference()));
return mergedResult;
}
private static OtherResearchProduct mergeOAFOtherResearchProduct(final OtherResearchProduct original,final OtherResearchProduct enrich) {
final OtherResearchProduct mergedORP = (OtherResearchProduct) mergeOAFResult(original, enrich);
mergedORP.setContactperson(mergeLists(mergedORP.getContactperson(), enrich.getContactperson()));
mergedORP.setContactgroup(mergeLists(mergedORP.getContactgroup(), enrich.getContactgroup()));
mergedORP.setTool(mergeLists(mergedORP.getTool(), enrich.getTool()));
mergeOAFDataInfo(mergedORP, enrich);
return mergedORP;
}
private static Software mergeOAFSoftware(final Software original, final Software enrich) {
final Software mergedSoftware = (Software) mergeOAFResult(original, enrich);
mergedSoftware.setDocumentationUrl(mergeLists(mergedSoftware.getDocumentationUrl(), enrich.getDocumentationUrl()));
mergedSoftware.setLicense(mergeLists(mergedSoftware.getLicense(), enrich.getLicense()));
mergedSoftware.setCodeRepositoryUrl(enrich.getCodeRepositoryUrl() != null && compareTrust(mergedSoftware,enrich) < 0
? enrich.getCodeRepositoryUrl()
: mergedSoftware.getCodeRepositoryUrl());
mergedSoftware.setProgrammingLanguage(enrich.getProgrammingLanguage() != null && compareTrust(mergedSoftware, enrich) < 0
? enrich.getProgrammingLanguage()
: mergedSoftware.getProgrammingLanguage());
mergeOAFDataInfo(mergedSoftware, enrich);
return mergedSoftware;
}
private static Dataset mergeOAFDataset(Dataset original, Dataset enrich) {
final Dataset mergedDataset = (Dataset) mergeOAFResult(original, enrich);
mergedDataset.setStoragedate(enrich.getStoragedate() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getStoragedate() : mergedDataset.getStoragedate());
mergedDataset.setDevice(enrich.getDevice() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getDevice() : mergedDataset.getDevice());
mergedDataset.setSize(enrich.getSize() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getSize() : mergedDataset.getSize());
mergedDataset.setVersion(enrich.getVersion() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getVersion() : mergedDataset.getVersion());
mergedDataset.setLastmetadataupdate(
enrich.getLastmetadataupdate() != null && compareTrust(mergedDataset,enrich) < 0
? enrich.getLastmetadataupdate()
: mergedDataset.getLastmetadataupdate());
mergedDataset.setMetadataversionnumber(
enrich.getMetadataversionnumber() != null && compareTrust(mergedDataset, enrich) < 0
? enrich.getMetadataversionnumber()
: mergedDataset.getMetadataversionnumber());
mergedDataset.setGeolocation(mergeLists(mergedDataset.getGeolocation(), enrich.getGeolocation()));
mergeOAFDataInfo(mergedDataset, enrich);
return mergedDataset;
}
private static Publication mergeOAFPublication(Publication original, Publication enrich) {
final Publication mergedPublication = (Publication) mergeOAFResult(original, enrich);
if (enrich.getJournal() != null && compareTrust(mergedPublication, enrich) < 0)
mergedPublication.setJournal(enrich.getJournal());
mergeOAFDataInfo(mergedPublication, enrich);
return mergedPublication;
}
private static Relation mergeOAFRelation(Relation from, Relation to) {
checkArgument(Objects.equals(from.getSource(), to.getSource()), "source ids must be equal");
checkArgument(Objects.equals(from.getTarget(), to.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(from.getRelType(), to.getRelType()), "relType(s) must be equal");
checkArgument(
Objects.equals(from.getSubRelType(), to.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(from.getRelClass(), to.getRelClass()), "relClass(es) must be equal");
from.setValidated(from.getValidated() || to.getValidated());
try {
from.setValidationDate(ModelSupport.oldest(from.getValidationDate(), to.getValidationDate()));
} catch (ParseException e) {
throw new IllegalArgumentException(String
.format(
"invalid validation date format in relation [s:%s, t:%s]: %s", from.getSource(), from.getTarget(),
from.getValidationDate()));
}
return from;
}
private static Oaf mergeOAFOrganization(Organization original, Organization enrich) {
final Organization mergedOrganization = (Organization) mergeEntity(original, enrich);
int ct = compareTrust(mergedOrganization, enrich);
mergedOrganization.setLegalshortname(enrich.getLegalshortname() != null && ct < 0
? enrich.getLegalshortname()
: mergedOrganization.getLegalname());
mergedOrganization.setLegalname(enrich.getLegalname() != null && ct < 0 ?
enrich.getLegalname()
: mergedOrganization.getLegalname());
mergedOrganization.setAlternativeNames(mergeLists(enrich.getAlternativeNames(), mergedOrganization.getAlternativeNames()));
mergedOrganization.setWebsiteurl(enrich.getWebsiteurl() != null && ct < 0
? enrich.getWebsiteurl()
: mergedOrganization.getWebsiteurl());
mergedOrganization.setLogourl(enrich.getLogourl() != null && ct < 0
? enrich.getLogourl()
: mergedOrganization.getLogourl());
mergedOrganization.setEclegalbody(enrich.getEclegalbody() != null && ct < 0
? enrich.getEclegalbody()
: mergedOrganization.getEclegalbody());
mergedOrganization.setEclegalperson(enrich.getEclegalperson() != null && ct < 0
? enrich.getEclegalperson()
: mergedOrganization.getEclegalperson());
mergedOrganization.setEcnonprofit (enrich.getEcnonprofit() != null && ct< 0
? enrich.getEcnonprofit()
: mergedOrganization.getEcnonprofit());
mergedOrganization.setEcresearchorganization (enrich.getEcresearchorganization() != null && ct < 0
? enrich.getEcresearchorganization()
: mergedOrganization.getEcresearchorganization());
mergedOrganization.setEchighereducation (enrich.getEchighereducation() != null && ct < 0
? enrich.getEchighereducation()
: mergedOrganization.getEchighereducation());
mergedOrganization.setEcinternationalorganizationeurinterests (enrich.getEcinternationalorganizationeurinterests() != null && ct< 0
? enrich.getEcinternationalorganizationeurinterests()
: mergedOrganization.getEcinternationalorganizationeurinterests());
mergedOrganization.setEcinternationalorganization (enrich.getEcinternationalorganization() != null && ct < 0
? enrich.getEcinternationalorganization()
: mergedOrganization.getEcinternationalorganization());
mergedOrganization.setEcenterprise (enrich.getEcenterprise() != null && ct < 0
? enrich.getEcenterprise()
: mergedOrganization.getEcenterprise());
mergedOrganization.setEcsmevalidated (enrich.getEcsmevalidated() != null && ct < 0
? enrich.getEcsmevalidated()
: mergedOrganization.getEcsmevalidated());
mergedOrganization.setEcnutscode( enrich.getEcnutscode() != null && ct < 0
? enrich.getEcnutscode()
: mergedOrganization.getEcnutscode());
mergedOrganization.setCountry (enrich.getCountry() != null && ct < 0 ?
enrich.getCountry()
:mergedOrganization.getCountry());
mergeOAFDataInfo(mergedOrganization, enrich);
return mergedOrganization;
}
private static Oaf mergeOAFProject(Project original, Project enrich) {
final Project mergedProject = (Project) mergeEntity(original, enrich);
int ct = compareTrust(mergedProject, enrich);
mergedProject.setWebsiteurl (enrich.getWebsiteurl() != null && ct < 0
? enrich.getWebsiteurl()
: mergedProject.getWebsiteurl());
mergedProject.setCode(enrich.getCode() != null && ct < 0 ?
enrich.getCode() :
mergedProject.getCode());
mergedProject.setAcronym(enrich.getAcronym() != null && ct < 0
? enrich.getAcronym()
: mergedProject.getAcronym());
mergedProject.setTitle (enrich.getTitle() != null && ct < 0
? enrich.getTitle()
: mergedProject.getTitle());
mergedProject.setStartdate (enrich.getStartdate() != null && ct < 0
? enrich.getStartdate()
: mergedProject.getStartdate());
mergedProject.setEnddate (enrich.getEnddate() != null && ct < 0
? enrich.getEnddate()
: mergedProject.getEnddate());
mergedProject.setCallidentifier ( enrich.getCallidentifier() != null && ct < 0
? enrich.getCallidentifier()
: mergedProject.getCallidentifier());
mergedProject.setKeywords ( enrich.getKeywords() != null && ct < 0
? enrich.getKeywords()
: mergedProject.getKeywords());
mergedProject.setDuration ( enrich.getDuration() != null && ct < 0
? enrich.getDuration()
: mergedProject.getDuration());
mergedProject.setEcsc39 ( enrich.getEcsc39() != null && ct < 0
? enrich.getEcsc39() :
mergedProject.getEcsc39());
mergedProject.setOamandatepublications ( enrich.getOamandatepublications() != null && ct < 0
? enrich.getOamandatepublications()
: mergedProject.getOamandatepublications());
mergedProject.setEcarticle29_3 (enrich.getEcarticle29_3() != null && ct < 0
? enrich.getEcarticle29_3()
: mergedProject.getEcarticle29_3());
mergedProject.setSubjects (mergeLists(mergedProject.getSubjects(), enrich.getSubjects()));
mergedProject.setFundingtree (mergeLists(mergedProject.getFundingtree(), enrich.getFundingtree()));
mergedProject.setContracttype (enrich.getContracttype() != null && ct < 0
? enrich.getContracttype()
: mergedProject.getContracttype());
mergedProject.setOptional1 ( enrich.getOptional1() != null && ct < 0
? enrich.getOptional1()
: mergedProject.getOptional1());
mergedProject.setOptional2 (enrich.getOptional2() != null && ct < 0
? enrich.getOptional2()
: mergedProject.getOptional2());
mergedProject.setJsonextrainfo ( enrich.getJsonextrainfo() != null && ct < 0
? enrich.getJsonextrainfo()
: mergedProject.getJsonextrainfo());
mergedProject.setContactfullname ( enrich.getContactfullname() != null && ct < 0
? enrich.getContactfullname()
: mergedProject.getContactfullname());
mergedProject.setContactfax ( enrich.getContactfax() != null && ct < 0
? enrich.getContactfax()
: mergedProject.getContactfax());
mergedProject.setContactphone (enrich.getContactphone() != null && ct < 0
? enrich.getContactphone()
: mergedProject.getContactphone());
mergedProject.setContactemail ( enrich.getContactemail() != null && ct < 0
? enrich.getContactemail()
: mergedProject.getContactemail());
mergedProject.setSummary ( enrich.getSummary() != null && ct < 0
? enrich.getSummary()
: mergedProject.getSummary());
mergedProject.setCurrency( enrich.getCurrency() != null && ct < 0
? enrich.getCurrency()
: mergedProject.getCurrency());
if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(mergedProject.getH2020topiccode())){
mergedProject.setH2020topiccode(enrich.getH2020topiccode());
mergedProject.setH2020topicdescription(enrich.getH2020topicdescription());
}
mergedProject.setH2020classification (mergeLists(mergedProject.getH2020classification(), enrich.getH2020classification()));
mergeOAFDataInfo(mergedProject, enrich);
return mergedProject;
}
}

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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.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;
}
}

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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>> {
}

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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<>());
}
private PidBlacklistProvider() {}
}

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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 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);
}
}

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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,
// 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;
}
}
}

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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.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);
}
}

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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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@ -0,0 +1,77 @@
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().getClassid();
String rClass = right.getResulttype().getClassid();
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<>());
}
}

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@ -7,9 +7,14 @@ import java.security.MessageDigest;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@ -32,6 +37,9 @@ import net.minidev.json.JSONArray;
import scala.collection.JavaConverters;
import scala.collection.Seq;
/**
* The type Dhp utils.
*/
public class DHPUtils {
private static final Logger log = LoggerFactory.getLogger(DHPUtils.class);
@ -39,10 +47,22 @@ public class DHPUtils {
private DHPUtils() {
}
/**
* To seq seq.
*
* @param list the list
* @return the seq
*/
public static Seq<String> toSeq(List<String> list) {
return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
}
/**
* Md 5 string.
*
* @param s the s
* @return the string
*/
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
@ -54,14 +74,71 @@ public class DHPUtils {
}
}
private static Pair<Qualifier, Qualifier> searchTypeInVocabularies(final String aType, final VocabularyGroup vocabularies) {
if (StringUtils.isNotBlank(aType)) {
final Qualifier typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, aType);
if (typeQualifier != null)
return new ImmutablePair<>(typeQualifier, vocabularies.getSynonymAsQualifier(
ModelConstants.DNET_RESULT_TYPOLOGIES,
typeQualifier.getClassid()
));
}
return null;
}
/**
* Retrieve oaf type from vocabulary pair.
*
* This method tries to find the correct oaf type general and instance type from
* vocabularies giving this order:
* 1 - search a vocabulary synonym from subResourceType
* 2 - search a vocabulary synonym from otherResourceType
*
*
*
* @param resourceTypeGeneral the resource type general
* @param subResourceType the sub resource type
* @param otherResourceType the other resource type
* @param vocabularies the vocabularies
* @return the pair
*/
public static Pair<Qualifier, Qualifier> retrieveOAFTypeFromVocabulary(final String resourceTypeGeneral , final String subResourceType, final String otherResourceType, final VocabularyGroup vocabularies ) {
if (StringUtils.isNotBlank(subResourceType)) {
Pair<Qualifier, Qualifier> result = searchTypeInVocabularies(subResourceType, vocabularies);
if (result!= null)
return result;
}
if (StringUtils.isNotBlank(otherResourceType)) {
Pair<Qualifier, Qualifier> result = searchTypeInVocabularies(otherResourceType, vocabularies);
if (result!= null)
return result;
}
if (StringUtils.isNotBlank(resourceTypeGeneral)) {
Pair<Qualifier, Qualifier> result = searchTypeInVocabularies(resourceTypeGeneral, vocabularies);
return result;
}
return null;
}
/**
* Retrieves from the metadata store manager application the list of paths associated with mdstores characterized
* by he given format, layout, interpretation
*
* @param mdstoreManagerUrl the URL of the mdstore manager service
* @param format the mdstore format
* @param layout the mdstore layout
* @param interpretation the mdstore interpretation
* @param includeEmpty include Empty mdstores
* @param format the mdstore format
* @param layout the mdstore layout
* @param interpretation the mdstore interpretation
* @param includeEmpty include Empty mdstores
* @return the set of hdfs paths
* @throws IOException in case of HTTP communication issues
*/
@ -93,10 +170,24 @@ public class DHPUtils {
}
}
/**
* Generate identifier string.
*
* @param originalId the original id
* @param nsPrefix the ns prefix
* @return the string
*/
public static String generateIdentifier(final String originalId, final String nsPrefix) {
return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
}
/**
* Generate unresolved identifier string.
*
* @param pid the pid
* @param pidType the pid type
* @return the string
*/
public static String generateUnresolvedIdentifier(final String pid, final String pidType) {
final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid);
@ -104,6 +195,13 @@ public class DHPUtils {
return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim());
}
/**
* Gets j path string.
*
* @param jsonPath the json path
* @param json the json
* @return the j path string
*/
public static String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);
@ -117,8 +215,19 @@ public class DHPUtils {
}
}
/**
* The constant MAPPER.
*/
public static final ObjectMapper MAPPER = new ObjectMapper();
/**
* Write hdfs file.
*
* @param conf the conf
* @param content the content
* @param path the path
* @throws IOException the io exception
*/
public static void writeHdfsFile(final Configuration conf, final String content, final String path)
throws IOException {
@ -130,6 +239,14 @@ public class DHPUtils {
}
}
/**
* Read hdfs file string.
*
* @param conf the conf
* @param path the path
* @return the string
* @throws IOException the io exception
*/
public static String readHdfsFile(Configuration conf, String path) throws IOException {
log.info("reading file {}", path);
@ -142,10 +259,27 @@ public class DHPUtils {
}
}
/**
* Read hdfs file as t.
*
* @param <T> the type parameter
* @param conf the conf
* @param path the path
* @param clazz the clazz
* @return the t
* @throws IOException the io exception
*/
public static <T> T readHdfsFileAs(Configuration conf, String path, Class<T> clazz) throws IOException {
return MAPPER.readValue(readHdfsFile(conf, path), clazz);
}
/**
* Save dataset.
*
* @param <T> the type parameter
* @param mdstore the mdstore
* @param targetPath the target path
*/
public static <T> void saveDataset(final Dataset<T> mdstore, final String targetPath) {
log.info("saving dataset in: {}", targetPath);
mdstore
@ -155,6 +289,12 @@ public class DHPUtils {
.save(targetPath);
}
/**
* Gets hadoop configuration.
*
* @param nameNode the name node
* @return the hadoop configuration
*/
public static Configuration getHadoopConfiguration(String nameNode) {
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
@ -168,6 +308,12 @@ public class DHPUtils {
return conf;
}
/**
* Populate oozie env.
*
* @param report the report
* @throws IOException the io exception
*/
public static void populateOOZIEEnv(final Map<String, String> report) throws IOException {
File file = new File(System.getProperty("oozie.action.output.properties"));
Properties props = new Properties();
@ -178,6 +324,13 @@ public class DHPUtils {
}
}
/**
* Populate oozie env.
*
* @param paramName the param name
* @param value the value
* @throws IOException the io exception
*/
public static void populateOOZIEEnv(final String paramName, String value) throws IOException {
Map<String, String> report = Maps.newHashMap();
report.put(paramName, value);

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@ -1,4 +1,4 @@
package eu.dnetlib.dhp.datacite
package eu.dnetlib.dhp.client
import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig

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

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@ -0,0 +1,80 @@
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;
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);
}
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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@ -0,0 +1,617 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.io.InputStream;
import java.time.format.DateTimeParseException;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.*;
/**
* The type Merge test.
*/
class MergeTest {
/**
* The Oaf.
*/
OafEntity oaf;
/**
* Sets up.
*/
@BeforeEach
public void setUp() {
oaf = new Publication();
}
/**
* Merge lists test.
*/
@Test
@SuppressWarnings("unchecked")
void mergeListsTest() {
// string list merge test
List<String> a = Arrays.asList("a", "b", "c", "e");
List<String> b = Arrays.asList("a", "b", "c", "d");
List<String> c = null;
System.out.println("merge result 1 = " + OafUtils.mergeLists(a, b));
System.out.println("merge result 2 = " + OafUtils.mergeLists(a, c));
System.out.println("merge result 3 = " + OafUtils.mergeLists(c, c));
}
/**
* Merge publication collected from test.
*/
@Test
void mergePublicationCollectedFromTest() {
Publication a = publication();
Publication b = publication();
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
a = OafUtils.mergeOAF(a, b);
assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size());
}
/**
* Load resource result list.
*
* @param <T> the type parameter
* @param path the path
* @param clazz the clazz
* @return the list
* @throws Exception the exception
*/
private <T extends Result> List<T> loadResourceResult(final String path, final Class<T> clazz ) throws Exception {
final ObjectMapper mapper = new ObjectMapper();
final InputStream str = Objects.requireNonNull(getClass().getResourceAsStream(path));
// LOAD test publications
return IOUtils.readLines(str).stream().map(s -> {
try {
return mapper.readValue(s, clazz);
} catch (IOException e) {
return null;
}
}).filter(Objects::nonNull).collect(Collectors.toList());
}
/**
* Apply to any test list result the same pid of the enrichment instance
*
* @param source the source
* @param enrichment the enrichment
* @param overrideAlternateIdentifier the override alternate identifier
*/
private <T extends Result> void updatePidIntoPublicationInstance(final List<T> source, final List<T>enrichment, final boolean overrideAlternateIdentifier) {
for(int i = 0 ; i< source.size(); i++) {
final Result currentPub = source.get(i);
final Result currentEnrichment = enrichment.get(i);
final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
if (overrideAlternateIdentifier)
currentInstance.setAlternateIdentifier(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
else
currentInstance.setPid(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
}
}
private <T extends Result> void applyAndVerifyEnrichment(final List<T> l1, final List<T> l2) {
// Apply Merge and verify that enrichments works
for(int i = 0 ; i< l1.size(); i++) {
final Result currentPub = l2.get(i);
final Result currentEnrichment = l1.get(i);
final Result result = OafUtils.mergeOAF(currentPub, currentEnrichment);
assertEquals(1, result.getInstance().size());
final Instance currentInstance = Objects.requireNonNull(result.getInstance()).get(0);
assertNotNull(currentInstance.getMeasures());
assertNotNull(result.getTitle());
assertFalse(OafUtils.isAnEnrichment(result));
}
}
/**
* Test the merge of the APC at the level of the result and the instance.
*
* @throws Exception the exception
*/
@Test
void testAPCMerge() throws Exception {
List<Publication> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc.json", Publication.class);
System.out.println(publications.size());
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
publications.forEach(p -> assertTrue(p.getProcessingchargeamount() != null ));
publications.forEach(p -> assertTrue(p.getProcessingchargecurrency() != null ));
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargeamount().getValue() )));
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargecurrency().getValue() )));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(i.getProcessingchargeamount() != null)));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(i.getProcessingchargecurrency() != null)));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargeamount().getValue()))));
publications.forEach(p -> p.getInstance().stream()
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargecurrency().getValue()))));
Result p1 = publications.get(0);
Result p2 = publications.get(1);
p1 = OafUtils.mergeOAF(p1, p2);
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
assertEquals(2 , p1.getInstance().size());
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargeamount() != null));
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargecurrency() != null));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("2000.47"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("1721.47"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("EUR"));
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("USD"));
System.out.println(new ObjectMapper().writeValueAsString(p1));
}
@Test
void testAPCMerge2() throws Exception {
List<Publication> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc2.json", Publication.class);
System.out.println(publications.size());
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
assertTrue(publications.get(0).getProcessingchargeamount() != null );
assertTrue(publications.get(0).getProcessingchargecurrency() != null );
assertTrue(publications.get(1).getProcessingchargeamount() == null );
Result p1 = publications.get(1);
Result p2 = publications.get(0);
//merge visible record with OpenAPC
p1 = (Result) OafUtils.mergeOAF(p1, p2);
assertFalse(p1.getDataInfo().getInvisible());
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
assertEquals(2 , p1.getInstance().size());
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
assertEquals("1721.47", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
assertEquals("EUR", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
assertFalse(p1.getDataInfo().getInvisible());
System.out.println(new ObjectMapper().writeValueAsString(p1));
//merge OpenAPC with visible record
p2 = (Result) OafUtils.mergeOAF(p2, p1);
assertFalse(p2.getDataInfo().getInvisible());
assertEquals("1721.47", p2.getProcessingchargeamount().getValue());
assertEquals("EUR", p2.getProcessingchargecurrency().getValue());
assertEquals(2 , p2.getInstance().size());
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
assertEquals("1721.47", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
assertEquals("EUR", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
}
/**
* Test enrichment function.
*
* @throws Exception the exception
*/
@Test
void testEnrichment() throws Exception {
// 1 TEST UPDATING PID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
// LOAD test publications
List<Publication> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
// Assert that each publication has only one instance and inside that all the measure field is empty
publications.forEach(p -> {
assertEquals(1, p.getInstance().size());
final Instance currentInstance = Objects.requireNonNull(p.getInstance()).get(0);
assertNull(currentInstance.getMeasures());
});
// LOAD test enrichments
List<Publication> enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Publication.class);
updatePidIntoPublicationInstance(publications, enrichment, false);
applyAndVerifyEnrichment(publications, enrichment);
// 2 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Publication.class);
updatePidIntoPublicationInstance(publications, enrichment, true);
applyAndVerifyEnrichment(publications, enrichment);
// 3 TEST UPDATING PID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Publication.class);
updatePidIntoPublicationInstance(publications, enrichment, false);
applyAndVerifyEnrichment( enrichment, publications);
// 4 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Publication.class);
updatePidIntoPublicationInstance(publications, enrichment, true);
applyAndVerifyEnrichment( enrichment, publications);
}
/**
* Merge publication date of acceptance test both present.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent() {
Publication a = publication();
Publication b = publication();
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test both present 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent_1() {
Publication a = publication("0.8");
Publication b = publication("0.9");
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test both present 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_bothPresent_2() {
Publication a = publication("0.9");
Publication b = publication("0.8");
a.setDateofacceptance(field("2021-06-18"));
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing() {
Publication a = publication();
Publication b = publication();
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing_1() {
Publication a = publication("0.9");
Publication b = publication("0.8");
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test left missing 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_leftMissing_2() {
Publication a = publication("0.8");
Publication b = publication("0.9");
b.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing() {
Publication a = publication();
Publication b = publication();
a.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing 1.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing_1() {
Publication a = publication("0.8");
Publication b = publication("0.9");
a.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication date of acceptance test right missing 2.
*/
@Test
void mergePublicationDateOfAcceptanceTest_rightMissing_2() {
Publication a = publication("0.9");
Publication b = publication("0.8");
a.setDateofacceptance(field("2021-06-19"));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getDateofacceptance());
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
}
/**
* Merge publication subject test.
*/
@Test
void mergePublicationSubjectTest() {
Publication a = publication();
Publication b = publication();
a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "open", "classe")));
b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe")));
a = OafUtils.mergeOAF(a,b);
assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size());
}
/**
* Merge relation test.
*/
@Test
void mergeRelationTest() {
Relation a = createRel(null, null);
Relation b = createRel(null, null);
a = OafUtils.mergeOAF(a,b);
assertEquals(a, b);
a = createRel(true, null);
b = createRel(null, null);
a = OafUtils.mergeOAF(a,b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(false, null);
a = OafUtils.mergeOAF(a,b);
assertEquals(true, a.getValidated());
a = createRel(true, null);
b = createRel(true, "2016-04-05T12:41:19.202Z");
a = OafUtils.mergeOAF(a,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 = OafUtils.mergeOAF(a,b);
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
a = createRel(true, "2020-09-10 11:08:52");
b = createRel(true, "2021-09-10 11:08:52");
a = OafUtils.mergeOAF(a,b);
assertEquals("2020-09-10 11:08:52", a.getValidationDate());
a = createRel(true, "2021-03-16T10:32:42Z");
b = createRel(true, "2020-03-16T10:32:42Z");
a = OafUtils.mergeOAF(a,b);
assertEquals("2020-03-16T10:32:42Z", a.getValidationDate());
}
/**
* Merge relation test parse exception.
*/
@Test
void mergeRelationTestParseException() {
assertThrows(DateTimeParseException.class, () -> {
Relation a = createRel(true, "Once upon a time ...");
Relation b = createRel(true, "... in a far away land");
a = OafUtils.mergeOAF(a,b);
});
}
/**
* Create rel relation.
*
* @param validated the validated
* @param validationDate the validation date
* @return the relation
*/
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;
}
/**
* Sets kv.
*
* @param key the key
* @param value the value
* @return the kv
*/
private KeyValue setKV(final String key, final String value) {
KeyValue k = new KeyValue();
k.setKey(key);
k.setValue(value);
return k;
}
/**
* Sets sp.
*
* @param value the value
* @param schema the schema
* @param classname the classname
* @return the sp
*/
private StructuredProperty setSP(
final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty();
s.setValue(value);
Qualifier q = new Qualifier();
q.setClassname(classname);
q.setClassid(classname);
q.setSchemename(schema);
q.setSchemeid(schema);
s.setQualifier(q);
return s;
}
/**
* Field field.
*
* @param <T> the type parameter
* @param value the value
* @return the field
*/
private <T> Field<T> field(T value) {
Field<T> f = new Field();
f.setValue(value);
return f;
}
/**
* Publication publication.
*
* @return the publication
*/
private Publication publication() {
Publication p = new Publication();
p.setDataInfo(df("0.9"));
return p;
}
/**
* Publication publication.
*
* @param trust the trust
* @return the publication
*/
private Publication publication(String trust) {
Publication p = new Publication();
p.setDataInfo(df(trust));
return p;
}
/**
* Df data info.
*
* @param trust the trust
* @return the data info
*/
private DataInfo df(String trust) {
DataInfo d = new DataInfo();
d.setTrust(trust);
return d;
}
}

View File

@ -1,140 +1 @@
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@ -0,0 +1 @@
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{
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]
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},
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},
{
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},
{
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}
],
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}
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@ -0,0 +1,23 @@
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@ -1,5 +1,6 @@
package eu.dnetlib.dhp.datacite
import eu.dnetlib.dhp.client.AbstractRestClient
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import org.json4s.{DefaultFormats, JValue}

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@ -511,7 +511,7 @@ object DoiBoostMappingUtil {
if (!ret.startsWith(DOI_PREFIX))
return null
return ret
ret
}

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@ -0,0 +1,50 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo}
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import org.apache.commons.lang.StringUtils
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
import scala.collection.JavaConverters._
object DoiBoostTransformationUtils {
val TRUST = "0.9"
def generateDataInfo(): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)
di.setInferred(false)
di.setInvisible(false)
di.setTrust(TRUST)
di.setProvenanceaction(
OafMapperUtils.qualifier(
ModelConstants.SYSIMPORT_ACTIONSET,
ModelConstants.SYSIMPORT_ACTIONSET,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS
)
)
di
}
def generateOAFAuthor(given: String, family: String, orcid: String, index: Int): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)
a.setFullname(s"$given $family")
a.setRank(index + 1)
if (StringUtils.isNotBlank(orcid))
a.setPid(
List(
structuredProperty(orcid, qualifier(ModelConstants.ORCID_PENDING,ModelConstants.ORCID_PENDING,ModelConstants.DNET_PID_TYPES,ModelConstants.DNET_PID_TYPES), generateDataInfo)
).asJava
)
a
}
}

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@ -1,18 +1,21 @@
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.apache.commons.lang.StringUtils
import org.apache.commons.lang3.tuple
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.JsonAST._
import org.json4s.jackson.JsonMethods._
import org.slf4j.{Logger, LoggerFactory}
import eu.dnetlib.doiboost.DoiBoostTransformationUtils._
import java.util
import scala.collection.JavaConverters._
import scala.collection.mutable
@ -32,63 +35,10 @@ case class mappingAuthor(
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
case object Crossref2Oaf {
object Crossref2Oaf {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mappingCrossrefType = Map(
"book-section" -> "publication",
"book" -> "publication",
"book-chapter" -> "publication",
"book-part" -> "publication",
"book-series" -> "publication",
"book-set" -> "publication",
"book-track" -> "publication",
"edited-book" -> "publication",
"reference-book" -> "publication",
"monograph" -> "publication",
"journal-article" -> "publication",
"dissertation" -> "publication",
"other" -> "publication",
"peer-review" -> "publication",
"proceedings" -> "publication",
"proceedings-article" -> "publication",
"reference-entry" -> "publication",
"report" -> "publication",
"report-series" -> "publication",
"standard" -> "publication",
"standard-series" -> "publication",
"posted-content" -> "publication",
"dataset" -> "dataset"
)
val mappingCrossrefSubType = Map(
"book-section" -> "0013 Part of book or chapter of book",
"book" -> "0002 Book",
"book-chapter" -> "0013 Part of book or chapter of book",
"book-part" -> "0013 Part of book or chapter of book",
"book-series" -> "0002 Book",
"book-set" -> "0002 Book",
"book-track" -> "0002 Book",
"edited-book" -> "0002 Book",
"reference-book" -> "0002 Book",
"monograph" -> "0002 Book",
"journal-article" -> "0001 Article",
"dissertation" -> "0044 Thesis",
"other" -> "0038 Other literature type",
"peer-review" -> "0015 Review",
"proceedings" -> "0004 Conference object",
"proceedings-article" -> "0004 Conference object",
"reference-entry" -> "0013 Part of book or chapter of book",
"report" -> "0017 Report",
"report-series" -> "0017 Report",
"standard" -> "0038 Other literature type",
"standard-series" -> "0038 Other literature type",
"dataset" -> "0021 Dataset",
"preprint" -> "0016 Preprint",
"report" -> "0017 Report"
)
def mappingResult(result: Result, json: JValue, cobjCategory: String): Result = {
def mappingResult(result: Result, json: JValue, resourceType:Qualifier, instanceType: Qualifier): Result = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
//MAPPING Crossref DOI into PID
@ -214,7 +164,7 @@ case object Crossref2Oaf {
)
result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull, index)
generateOAFAuthor(a.given.orNull, a.family, a.ORCID.orNull, index)
}.asJava)
// Mapping instance
@ -256,22 +206,8 @@ case object Crossref2Oaf {
instance.setAccessright(
decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)
)
instance.setInstancetype(
OafMapperUtils.qualifier(
cobjCategory.substring(0, 4),
cobjCategory.substring(5),
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
result.setResourcetype(
OafMapperUtils.qualifier(
cobjCategory.substring(0, 4),
cobjCategory.substring(5),
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE
)
)
instance.setInstancetype(instanceType)
result.setResourcetype(resourceType)
instance.setCollectedfrom(createCrossrefCollectedFrom())
if (StringUtils.isNotBlank(issuedDate)) {
@ -280,10 +216,7 @@ case object Crossref2Oaf {
instance.setDateofacceptance(asField(createdDate.getValue))
}
val s: List[String] = List("https://doi.org/" + doi)
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
// if (links.nonEmpty) {
// instance.setUrl(links.asJava)
// }
if (s.nonEmpty) {
instance.setUrl(s.asJava)
}
@ -309,28 +242,9 @@ case object Crossref2Oaf {
result
}
def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
val a = new Author
a.setName(given)
a.setSurname(family)
a.setFullname(s"$given $family")
a.setRank(index + 1)
if (StringUtils.isNotBlank(orcid))
a.setPid(
List(
createSP(
orcid,
ModelConstants.ORCID_PENDING,
ModelConstants.DNET_PID_TYPES,
generateDataInfo()
)
).asJava
)
a
}
def convert(input: String): List[Oaf] = {
def convert(input: String, vocabularies: VocabularyGroup): List[Oaf] = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
@ -341,14 +255,14 @@ case object Crossref2Oaf {
if (objectType == null)
return resultList
val result = generateItemFromType(objectType, objectSubType)
val result = generateItemFromType(objectType, objectSubType, vocabularies)
if (result == null)
return List()
val cOBJCategory = mappingCrossrefSubType.getOrElse(
objectType,
mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type")
)
mappingResult(result, json, cOBJCategory)
val (resourceType, instanceType) =getTypeQualifier(objectType, objectSubType, vocabularies)
mappingResult(result, json, resourceType, instanceType)
if (result == null || result.getId == null)
return List()
@ -366,7 +280,7 @@ case object Crossref2Oaf {
}
result match {
case publication: Publication => convertPublication(publication, json, cOBJCategory)
case publication: Publication => convertPublication(publication, json)
case dataset: Dataset => convertDataset(dataset)
}
@ -521,12 +435,14 @@ case object Crossref2Oaf {
// TODO check if there are other info to map into the Dataset
}
def convertPublication(publication: Publication, json: JValue, cobjCategory: String): Unit = {
def convertPublication(publication: Publication, json: JValue): Unit = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val containerTitles = for { JString(ct) <- json \ "container-title" } yield ct
val className = publication.getInstance().asScala.map(i => i.getInstancetype.getClassname).head
//Mapping book
if (cobjCategory.toLowerCase.contains("book")) {
if ("book".equalsIgnoreCase(className)) {
val ISBN = for { JString(isbn) <- json \ "ISBN" } yield isbn
if (ISBN.nonEmpty && containerTitles.nonEmpty) {
val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
@ -607,14 +523,29 @@ case object Crossref2Oaf {
null
}
def generateItemFromType(objectType: String, objectSubType: String): Result = {
if (mappingCrossrefType.contains(objectType)) {
if (mappingCrossrefType(objectType).equalsIgnoreCase("publication"))
return new Publication()
if (mappingCrossrefType(objectType).equalsIgnoreCase("dataset"))
return new Dataset()
}
null
def getTypeQualifier(objectType: String, objectSubType:String, vocabularies: VocabularyGroup):(Qualifier,Qualifier) = {
val result: tuple.Pair[Qualifier, Qualifier] = DHPUtils.retrieveOAFTypeFromVocabulary(objectType, objectSubType,null, vocabularies)
if (result!= null)
(result.getValue, result.getKey)
else
null
}
def generateItemFromType(objectType: String, objectSubType:String, vocabularies: VocabularyGroup): Result = {
val result =getTypeQualifier(objectType, objectSubType, vocabularies)
if (result != null)
{
if ("publication".equalsIgnoreCase(result._1.getClassname)) {
return new Publication
}
if ("dataset".equalsIgnoreCase(result._1.getClassname))
return new Dataset
}
null
}
}

View File

@ -0,0 +1,37 @@
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.client.AbstractRestClient
import org.json4s.{DefaultFormats, JValue}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
class CrossrefFunderRetriever(var cursor:String = "*") extends AbstractRestClient{
override def extractInfo(input: String): Unit = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
buffer = (json \\ "items").extract[List[JValue]].map(s => compact(render(s)))
cursor = (json \ "message" \ "next-cursor").extractOrElse[String](null)
if (cursor.isEmpty)
complete = true
current_index = 0
}
def get_url(): String = {
println(s"cursor is $cursor")
s"https://api.crossref.org/funders?rows=1000&cursor=$cursor"
}
override def getBufferData(): Unit = {
if (!complete) {
val response =
if (scroll_value.isDefined) doHTTPGETRequest(scroll_value.get)
else doHTTPGETRequest(get_url())
extractInfo(response)
}
}
}

View File

@ -1,9 +1,9 @@
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.application.{AbstractScalaApplication, ArgumentApplicationParser, SparkScalaApplication}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.{SparkConf, SparkContext}
import org.json4s
import org.json4s.DefaultFormats
@ -12,59 +12,103 @@ import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object GenerateCrossrefDataset {
val log: Logger = LoggerFactory.getLogger(GenerateCrossrefDataset.getClass)
class SparkGenerateCrossrefDataset (propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
def crossrefElement(meta: String): CrossrefDT = {
/**
* This method convert the Json crossoref to CrossrefDT class
*
* @param metadata the json metadata
* @return the CrossrefDT
*/
def crossrefElement(metadata: String): CrossrefDT = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(meta)
lazy val json: json4s.JValue = parse(metadata)
val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String])
val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long]
CrossrefDT(doi, meta, timestamp)
CrossrefDT(doi, metadata, timestamp)
}
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(
Source
.fromInputStream(
getClass.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json"
)
)
.mkString
)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val targetPath = parser.get("targetPath")
val spark: SparkSession = SparkSession
.builder()
.config(conf)
.appName(UnpackCrtossrefEntries.getClass.getSimpleName)
.master(master)
.getOrCreate()
val sc: SparkContext = spark.sparkContext
def convertDataset(spark:SparkSession, sourcePath:String, targetPath:String):Unit = {
import spark.implicits._
val tmp: RDD[String] = sc.textFile(sourcePath, 6000)
spark
.createDataset(tmp)
.map(entry => crossrefElement(entry))
spark.read.text(sourcePath).as[String].map(entry => crossrefElement(entry))
.write
.mode(SaveMode.Overwrite)
.save(targetPath)
// .map(meta => crossrefElement(meta))
// .toDS.as[CrossrefDT]
// .write.mode(SaveMode.Overwrite).save(targetPath)
}
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
override def run(): Unit = {
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath is $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath is $targetPath")
convertDataset(spark, sourcePath, targetPath)
}
}
//object GenerateCrossrefDataset {
//
// val log: Logger = LoggerFactory.getLogger(GenerateCrossrefDataset.getClass)
//
// implicit val mrEncoder: Encoder[CrossrefDT] = Encoders.kryo[CrossrefDT]
//
//
//
// def main(args: Array[String]): Unit = {
// val conf = new SparkConf
// val parser = new ArgumentApplicationParser(
// Source
// .fromInputStream(
// getClass.getResourceAsStream(
// "/eu/dnetlib/dhp/doiboost/crossref_dump_reader/generate_dataset_params.json"
// )
// )
// .mkString
// )
// parser.parseArgument(args)
// val master = parser.get("master")
// val sourcePath = parser.get("sourcePath")
// val targetPath = parser.get("targetPath")
//
// val spark: SparkSession = SparkSession
// .builder()
// .config(conf)
// .appName(UnpackCrtossrefEntries.getClass.getSimpleName)
// .master(master)
// .getOrCreate()
// val sc: SparkContext = spark.sparkContext
//
// import spark.implicits._
//
// val tmp: RDD[String] = sc.textFile(sourcePath, 6000)
//
// spark
// .createDataset(tmp)
// .map(entry => crossrefElement(entry))
// .write
// .mode(SaveMode.Overwrite)
// .save(targetPath)
// }
//
//}

View File

@ -1,8 +1,10 @@
package eu.dnetlib.doiboost.crossref
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql._
@ -39,12 +41,19 @@ object SparkMapDumpIntoOAF {
implicit val mapEncoderRelatons: Encoder[Relation] = Encoders.kryo[Relation]
implicit val mapEncoderDatasets: Encoder[oaf.Dataset] = Encoders.kryo[OafDataset]
val isLookupUrl: String = parser.get("isLookupUrl")
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
require(vocabularies != null)
val targetPath = parser.get("targetPath")
spark.read
.load(parser.get("sourcePath"))
.as[CrossrefDT]
.flatMap(k => Crossref2Oaf.convert(k.json))
.flatMap(k => Crossref2Oaf.convert(k.json,vocabularies))
.filter(o => o != null)
.write
.mode(SaveMode.Overwrite)

View File

@ -0,0 +1,42 @@
package eu.dnetlib.doiboost;
import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.common.test.TestUtils;
import org.apache.commons.io.IOUtils;
import org.mockito.Mock;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public abstract class AbstractVocabularyTest {
@Mock
protected ISLookUpService isLookUpService;
protected VocabularyGroup vocabularies;
public void setUpVocabulary() throws ISLookUpException, IOException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms());
vocabularies = VocabularyGroup.loadVocsFromIS(isLookUpService);
}
private static List<String> vocs() throws IOException {
return TestUtils.getVocabulariesMock();
}
private static List<String> synonyms() throws IOException {
return TestUtils.getSynonymsMock();
}
}

View File

@ -0,0 +1,62 @@
package eu.dnetlib.dhp.doiboost.crossref
import eu.dnetlib.doiboost.crossref.CrossrefFunderRetriever
import org.json4s.DefaultFormats
import org.json4s.JsonAST.JString
import org.json4s.jackson.JsonMethods.parse
import org.junit.jupiter.api.Test
import java.io.PrintWriter
class CrossrefFunderTest {
def parse_funder(input:String):(String, String, List[String]) = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
val l:List[String] = for { JString(desc) <- json \ "descendants" } yield desc
((json \ "name").extract[String],(json \ "uri").extract[String], l)
}
@Test
def testFunderRelationshipsMapping(): Unit = {
val cf = new CrossrefFunderRetriever()
var i = 0
val w =new PrintWriter("/tmp/funder_names")
cf.map(s=>parse_funder(s)).foreach(s=> w.write(s"${s._1} \t${s._2} \t${s._3.mkString("--")}\t\n"))
w.close()
// cf.foreach{_ =>
//
// i = i+1
//
// if (i % 1000 == 0)
// println(s"get $i documents")
//
// }
//
//
//
//
// println(s"Total item $i")
}
}

View File

@ -2,21 +2,32 @@ package eu.dnetlib.dhp.doiboost.crossref
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.AbstractVocabularyTest
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.{BeforeAll, BeforeEach, Test}
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.junit.jupiter.MockitoExtension
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
import scala.io.Source
import scala.util.matching.Regex
class CrossrefMappingTest {
@ExtendWith(Array(classOf[MockitoExtension]))
class CrossrefMappingTest extends AbstractVocabularyTest {
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
val mapper = new ObjectMapper()
@BeforeEach
def setUp(): Unit = {
setUpVocabulary()
}
@Test
def testFunderRelationshipsMapping(): Unit = {
val template = Source
@ -33,13 +44,13 @@ class CrossrefMappingTest {
for (line <- funder_doi.lines) {
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json, vocabularies)
assertTrue(resultList.nonEmpty)
checkRelation(resultList)
}
for (line <- funder_name.lines) {
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json, vocabularies)
assertTrue(resultList.nonEmpty)
checkRelation(resultList)
}
@ -79,7 +90,7 @@ class CrossrefMappingTest {
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Result])
@ -98,7 +109,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -120,7 +131,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -141,7 +152,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -177,7 +188,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
val rels: List[Relation] =
@ -197,7 +208,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -273,7 +284,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -357,7 +368,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -405,7 +416,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -485,7 +496,7 @@ class CrossrefMappingTest {
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -508,7 +519,7 @@ class CrossrefMappingTest {
val line: String =
"\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}],"
val json = template.replace("%s", line)
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Publication])
val result: Result = items.head.asInstanceOf[Publication]
@ -527,7 +538,7 @@ class CrossrefMappingTest {
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article.json"))
.mkString
val resultList: List[Oaf] = Crossref2Oaf.convert(template)
val resultList: List[Oaf] = Crossref2Oaf.convert(template, vocabularies)
assertTrue(resultList.nonEmpty)
val items = resultList.filter(p => p.isInstanceOf[Publication])
val result: Result = items.head.asInstanceOf[Publication]
@ -551,7 +562,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -581,7 +592,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -616,7 +627,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -651,7 +662,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -686,7 +697,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)
@ -719,7 +730,7 @@ class CrossrefMappingTest {
assertNotNull(json)
assertFalse(json.isEmpty);
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
val resultList: List[Oaf] = Crossref2Oaf.convert(json,vocabularies)
assertTrue(resultList.nonEmpty)

View File

@ -801,7 +801,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.12.0]</dhp-schemas.version>
<dhp-schemas.version>2.12.1-DOIBOOST_REFACTOR-SNAPSHOT</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>