Merge branch 'beta' into oaf_country_beta

This commit is contained in:
Claudio Atzori 2024-03-25 16:13:20 +01:00
commit 538b180fe0
129 changed files with 104313 additions and 1524 deletions

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@ -145,105 +145,6 @@ public class AuthorMerger {
return null; return null;
} }
/**
* This method tries to figure out when two author are the same in the contest
* of ORCID enrichment
*
* @param left Author in the OAF entity
* @param right Author ORCID
* @return based on a heuristic on the names of the authors if they are the same.
*/
public static boolean checkORCIDSimilarity(final Author left, final Author right) {
final Person pl = parse(left);
final Person pr = parse(right);
// If one of them didn't have a surname we verify if they have the fullName not empty
// and verify if the normalized version is equal
if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) &&
pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) {
if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
&& !pr.getFullname().isEmpty()) {
return pl
.getFullname()
.stream()
.anyMatch(
fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
} else {
return false;
}
}
// The Authors have one surname in common
if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
// If one of them has only a surname and is the same we can say that they are the same author
if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
return true;
// The authors have the same initials of Name in common
if (pl
.getName()
.stream()
.anyMatch(
nl -> pr
.getName()
.stream()
.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
return true;
}
// Sometimes we noticed that publication have author wrote in inverse order Surname, Name
// We verify if we have an exact match between name and surname
if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) &&
pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl))))
return true;
else
return false;
}
//
/**
* Method to enrich ORCID information in one list of authors based on another list
*
* @param baseAuthor the Author List in the OAF Entity
* @param orcidAuthor The list of ORCID Author intersected
* @return The Author List of the OAF Entity enriched with the orcid Author
*/
public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
if (baseAuthor == null || baseAuthor.isEmpty())
return orcidAuthor;
if (orcidAuthor == null || orcidAuthor.isEmpty())
return baseAuthor;
if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
return baseAuthor;
final List<Author> oAuthor = new ArrayList<>();
oAuthor.addAll(orcidAuthor);
baseAuthor.forEach(ba -> {
Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
if (aMatch.isPresent()) {
final Author sameAuthor = aMatch.get();
addPid(ba, sameAuthor.getPid());
oAuthor.remove(sameAuthor);
}
});
return baseAuthor;
}
private static void addPid(final Author a, final List<StructuredProperty> pids) {
if (a.getPid() == null) {
a.setPid(new ArrayList<>());
}
a.getPid().addAll(pids);
}
public static String pidToComparableString(StructuredProperty pid) { public static String pidToComparableString(StructuredProperty pid) {
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
: ""; : "";

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@ -1,24 +1,6 @@
package eu.dnetlib.dhp.oa.merge; package eu.dnetlib.dhp.oa.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.when;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ForkJoinPool;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.ReduceFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@ -26,12 +8,29 @@ import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions; import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.ReduceFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Tuple2; import scala.Tuple2;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ForkJoinPool;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.when;
/** /**
* Groups the graph content by entity identifier to ensure ID uniqueness * Groups the graph content by entity identifier to ensure ID uniqueness
*/ */
@ -135,7 +134,7 @@ public class GroupEntitiesSparkJob {
.applyCoarVocabularies(entity, vocs), .applyCoarVocabularies(entity, vocs),
OAFENTITY_KRYO_ENC) OAFENTITY_KRYO_ENC)
.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING()) .groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
.reduceGroups((ReduceFunction<OafEntity>) OafMapperUtils::mergeEntities) .reduceGroups((ReduceFunction<OafEntity>) MergeUtils::checkedMerge)
.map( .map(
(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>( (MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
t._2().getClass().getName(), t._2()), t._2().getClass().getName(), t._2()),

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@ -506,6 +506,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull) .filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(sp.getValue())) .filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.map(GraphCleaningFunctions::cleanValue) .map(GraphCleaningFunctions::cleanValue)
.sorted((s1, s2) -> s2.getValue().length() - s1.getValue().length())
.limit(ModelHardLimits.MAX_ABSTRACTS)
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {

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@ -0,0 +1,79 @@
package eu.dnetlib.dhp.schema.oaf.utils;
//
// Source code recreated from a .class file by IntelliJ IDEA
// (powered by FernFlower decompiler)
//
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
public class MergeComparator implements Comparator<Oaf> {
public MergeComparator() {
}
public int compare(Oaf left, Oaf right) {
// nulls at the end
if (left == null && right == null) {
return 0;
} else if (left == null) {
return -1;
} else if (right == null) {
return 1;
}
// invisible
if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) {
if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) {
return -1;
}
}
// collectedfrom
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
return -1;
} else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
return 1;
}
SubEntityType lClass = SubEntityType.fromClass(left.getClass());
SubEntityType rClass = SubEntityType.fromClass(right.getClass());
return lClass.ordinal() - rClass.ordinal();
}
protected HashSet<String> getCollectedFromIds(Oaf left) {
return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> {
return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}).orElse(new HashSet());
}
enum SubEntityType {
publication, dataset, software, otherresearchproduct, datasource, organization, project;
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends Oaf> SubEntityType fromClass(Class<T> clazz) {
return valueOf(clazz.getSimpleName().toLowerCase());
}
}
}

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@ -0,0 +1,707 @@
package eu.dnetlib.dhp.schema.oaf.utils;
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 java.text.ParseException;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static com.google.common.base.Objects.firstNonNull;
import static com.google.common.base.Preconditions.checkArgument;
public class MergeUtils {
public static <T extends Oaf> T checkedMerge(final T left, final T right) {
return (T) merge(left, right, false);
}
public static Oaf merge(final Oaf left, final Oaf right) {
return merge(left, right, false);
}
public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) {
if (sameClass(left, right, OafEntity.class)) {
return mergeEntities(left, right, checkDelegatedAuthority);
} else if (sameClass(left, right, Relation.class)) {
return mergeRelation((Relation) left, (Relation) right);
} else {
throw new RuntimeException(
String
.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
}
}
private static <T extends Oaf> boolean sameClass(Object left, Object right, Class<T> cls) {
return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass());
}
private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
if (sameClass(left, right, Result.class)) {
if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
return mergeResultsOfDifferentTypes((Result)left, (Result) right);
}
if (sameClass(left, right, Publication.class)) {
return mergePublication((Publication) left, (Publication) right);
}
if (sameClass(left, right, Dataset.class)) {
return mergeDataset((Dataset) left, (Dataset) right);
}
if (sameClass(left, right, OtherResearchProduct.class)) {
return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right);
}
if (sameClass(left, right, Software.class)) {
return mergeSoftware((Software) left, (Software) right);
}
return mergeResult((Result) left, (Result) right);
} else if (sameClass(left, right, Datasource.class)) {
// TODO
final int trust = compareTrust(left, right);
return mergeOafEntityFields((Datasource) left, (Datasource) right, trust);
} else if (sameClass(left, right, Organization.class)) {
return mergeOrganization((Organization) left, (Organization) right);
} else if (sameClass(left, right, Project.class)) {
return mergeProject((Project) left, (Project) right);
} else {
throw new RuntimeException(
String
.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
}
}
/**
* This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority
* https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
* such version.
* <p>
* Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
* and proceeds with the canonical property merging.
*
* @param left
* @param right
* @return
*/
private static <T extends Result> T mergeResultsOfDifferentTypes(T left, T right) {
final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
return left;
}
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
//TODO: raise trust to have preferred fields from one or the other??
if (new ResultTypeComparator().compare(left, right) < 0) {
return mergeResult(left, right);
} else {
return mergeResult(right, left);
}
}
private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) {
if (trust > 0) {
return left;
} else if (trust == 0) {
if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) {
return right;
} else {
return left;
}
} else {
return right;
}
}
private static String chooseString(String left, String right, int trust) {
if (trust > 0) {
return left;
} else if (trust == 0) {
return StringUtils.isNotBlank(left) ? left : right;
} else {
return right;
}
}
private static <T> T chooseReference(T left, T right, int trust) {
if (trust > 0) {
return left;
} else if (trust == 0) {
return left != null ? left : right;
} else {
return right;
}
}
private static Long max(Long left, Long right) {
if (left == null)
return right;
if (right == null)
return left;
return Math.max(left, right);
}
// trust ??
private static Boolean booleanOR(Boolean a, Boolean b) {
if (a == null) {
return b;
} else if (b == null) {
return a;
}
return a || b;
}
private static <T> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
if (left == null) {
return right;
} else if (right == null) {
return left;
}
List<T> h = trust >= 0 ? left : right;
List<T> l = trust >= 0 ? right : left;
return Stream.concat(h.stream(), l.stream())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
private static List<String> unionDistinctListOfString(final List<String> l, final List<String> r) {
if (l == null) {
return r;
} else if (r == null) {
return l;
}
return Stream.concat(l.stream(), r.stream())
.filter(StringUtils::isNotBlank)
.distinct()
.collect(Collectors.toList());
}
//TODO review
private static List<KeyValue> mergeKeyValue(List<KeyValue> left, List<KeyValue> right, int trust) {
if (trust < 0) {
List<KeyValue> s = left;
left = right;
right = s;
}
HashMap<String, KeyValue> values = new HashMap<>();
left.forEach(kv -> values.put(kv.getKey(), kv));
right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv));
return new ArrayList<>(values.values());
}
private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right, int trust) {
if (left == null) {
return right;
} else if (right == null) {
return left;
}
List<StructuredProperty> h = trust >= 0 ? left : right;
List<StructuredProperty> l = trust >= 0 ? right : left;
return Stream.concat(h.stream(), l.stream())
.filter(Objects::isNull)
.distinct()
.collect(Collectors.toList());
}
/**
* Internal utility that merges the common OafEntity fields
*
* @param merged
* @param enrich
* @param <T>
* @return
*/
private static <T extends Oaf> T mergeOafFields(T merged, T enrich, int trust) {
//TODO: union of all values, but what does it mean with KeyValue pairs???
merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust));
merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust));
merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp()));
return merged;
}
/**
* Internal utility that merges the common OafEntity fields
*
* @param original
* @param enrich
* @param <T>
* @return
*/
private static <T extends OafEntity> T mergeOafEntityFields(T original, T enrich, int trust) {
final T merged = mergeOafFields(original, enrich, trust);
merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId()));
merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust));
// dateofcollection mettere today quando si fa merge
merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust));
// setDateoftransformation mettere vuota in dedup, nota per Claudio
merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
// TODO: was missing in OafEntity.merge
merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
//oaiprovenanze da mettere a null quando si genera merge
merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust));
merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust));
return merged;
}
public static <T extends Relation> T mergeRelation(T original, T enrich) {
int trust = compareTrust(original, enrich);
T merge = mergeOafFields(original, enrich, trust);
checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal");
checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal");
checkArgument(
Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
//merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance()));
//TODO: trust ??
merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated()));
try {
merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate()));
} catch (ParseException e) {
throw new IllegalArgumentException(String
.format(
"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
merge.getTarget(),
merge.getValidationDate()));
}
// TODO keyvalue merge
merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust));
return merge;
}
public static <T extends Result> T mergeResult(T original, T enrich) {
final int trust = compareTrust(original, enrich);
T merge = mergeOafEntityFields(original, enrich, trust);
if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
}
// author = usare la stessa logica che in dedup
merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust));
// il primo che mi arriva secondo l'ordinamento per priorita'
merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust));
// gestito come il resulttype perche' e' un subtype
merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust));
// spostiamo nell'instance e qui prendo il primo che arriva
merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust));
// country lasicamo,o cosi' -> parentesi sul datainfo
merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust));
//ok
merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust));
// union per priority quindi vanno in append
merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust));
//ok
merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust));
// prima trust e poi longest list
merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription()));
// trust piu' alto e poi piu' vecchia
merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
// ok, ma publisher va messo ripetibile
merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust));
// ok
merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust));
// ok
merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust));
// ok
merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust));
// ok
merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust));
// ok
merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust));
// prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO
// trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario)
// vedi note
merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype()));
// ok
merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust));
// most open ok
if (enrich.getBestaccessright() != null
&& new AccessRightComparator<>()
.compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) {
merge.setBestaccessright(enrich.getBestaccessright());
}
// TODO merge of datainfo given same id
merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust));
//ok
merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
//instance enrichment or union
// review instance equals => add pid to comparision
if (!isAnEnrichment(merge) && !isAnEnrichment(enrich))
merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust));
else {
final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
: enrich.getInstance();
final List<Instance> enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance()
: merge.getInstance();
if (isAnEnrichment(merge))
merge.setDataInfo(enrich.getDataInfo());
merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances));
}
merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen()));
// OK but should be list of values
merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust));
merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal()));
merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded()));
return merge;
}
private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
int trust = compareTrust(original, enrich);
final T merge = mergeResult(original, enrich);
merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust));
merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust));
merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust));
return merge;
}
private static <T extends Software> T mergeSoftware(T original, T enrich) {
int trust = compareTrust(original, enrich);
final T merge = mergeResult(original, enrich);
merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
return merge;
}
private static <T extends Dataset> T mergeDataset(T original, T enrich) {
int trust = compareTrust(original, enrich);
T merge = mergeResult(original, enrich);
merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust));
merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
return merge;
}
public static <T extends Publication> T mergePublication(T original, T enrich) {
final int trust = compareTrust(original, enrich);
T merged = mergeResult(original, enrich);
merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust));
return merged;
}
private static <T extends Organization> T mergeOrganization(T left, T enrich) {
int trust = compareTrust(left, enrich);
T merged = mergeOafEntityFields(left, enrich, trust);
merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust));
merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust));
return merged;
}
public static <T extends Project> T mergeProject(T original, T enrich) {
int trust = compareTrust(original, enrich);
T merged = mergeOafEntityFields(original, enrich, trust);
merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust));
merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust));
merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust));
merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust));
merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust));
merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust));
merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust));
merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust));
merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust));
merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust));
merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust));
merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust));
merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust));
merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust));
merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust));
merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust));
merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust));
//missin in Project.merge
merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust));
merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust));
// trust ??
if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) {
merged.setH2020topiccode(enrich.getH2020topiccode());
merged.setH2020topicdescription(enrich.getH2020topicdescription());
}
merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
return merged;
}
/**
* 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;
return a.size() >= b.size() ? a : b;
}
/**
* 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;
}
/**
* 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
*/
private 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(MergeUtils::validPid)
.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
if (i.getAlternateIdentifier() != null)
i
.getAlternateIdentifier()
.stream()
.filter(MergeUtils::validPid)
.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
return result.stream();
})
.collect(
Collectors
.toMap(
Pair::getLeft,
Pair::getRight,
(a, b) -> a));
}
private static boolean isFromDelegatedAuthority(Result r) {
return Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.filter(i -> Objects.nonNull(i.getCollectedfrom()))
.map(i -> i.getCollectedfrom().getKey())
.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
.orElse(false);
}
/**
* 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;
}
/**
* Normalize pid string.
*
* @param pid the pid
* @return the string
*/
private 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 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(MergeUtils::extractKeyFromPid)
.map(enrichments::get)
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
/**
* Is an enrichment boolean.
*
* @param e the e
* @return the boolean
*/
private 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 merge the current instance
* @param enrichment the enrichment instance
*/
private static void applyEnrichment(final Instance merge, final Instance enrichment) {
if (merge == null || enrichment == null)
return;
merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense()));
merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright()));
merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype()));
merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping()));
merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
// pid and alternateId are used for matching
merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
}
private static int compareTrust(Oaf a, Oaf b) {
String left = Optional
.ofNullable(a.getDataInfo())
.map(DataInfo::getTrust)
.orElse("0.0");
String right = Optional
.ofNullable(b.getDataInfo())
.map(DataInfo::getTrust)
.orElse("0.0");
return left.compareTo(right);
}
}

View File

@ -14,7 +14,6 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator; import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
public class OafMapperUtils { public class OafMapperUtils {
@ -22,65 +21,6 @@ public class OafMapperUtils {
private OafMapperUtils() { private OafMapperUtils() {
} }
public static Oaf merge(final Oaf left, final Oaf right) {
if (ModelSupport.isSubClass(left, OafEntity.class)) {
return mergeEntities((OafEntity) left, (OafEntity) right);
} else if (ModelSupport.isSubClass(left, Relation.class)) {
((Relation) left).mergeFrom((Relation) right);
} else {
throw new 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 {
throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
}
return left;
}
public static Result mergeResults(Result left, Result right) {
final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
return left;
}
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
} else {
right.mergeFrom(left);
return right;
}
}
private static boolean isFromDelegatedAuthority(Result r) {
return Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.filter(i -> Objects.nonNull(i.getCollectedfrom()))
.map(i -> i.getCollectedfrom().getKey())
.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
.orElse(false);
}
public static KeyValue keyValue(final String k, final String v) { public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue(); final KeyValue kv = new KeyValue();
kv.setKey(k); kv.setKey(k);

View File

@ -0,0 +1,111 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelSupport;
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.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
public class MergeUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testMergePubs() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
Dataset d2 = read("dataset_2.json", Dataset.class);
assertEquals(1, p1.getCollectedfrom().size());
assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
assertEquals(1, d2.getCollectedfrom().size());
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(1, p2.getCollectedfrom().size());
assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(1, d1.getCollectedfrom().size());
assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
final Result p1d2 = MergeUtils.checkedMerge(p1, d2);
assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid());
assertTrue(p1d2 instanceof Publication);
assertEquals(p1.getId(), p1d2.getId());
}
@Test
void testMergePubs_1() throws IOException {
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
final Result p2d1 = MergeUtils.checkedMerge(p2, d1);
assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid());
assertTrue(p2d1 instanceof Dataset);
assertEquals(d1.getId(), p2d1.getId());
assertEquals(2, p2d1.getCollectedfrom().size());
}
@Test
void testMergePubs_2() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Result p1p2 = MergeUtils.checkedMerge(p1, p2);
assertTrue(p1p2 instanceof Publication);
assertEquals(p1.getId(), p1p2.getId());
assertEquals(2, p1p2.getCollectedfrom().size());
}
@Test
void testDelegatedAuthority_1() throws IOException {
Dataset d1 = read("dataset_2.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = (Result) MergeUtils.merge(d1, d2, true);
assertEquals(d2, res);
}
@Test
void testDelegatedAuthority_2() throws IOException {
Dataset p1 = read("publication_1.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = (Result) MergeUtils.merge(p1, d2, true);
assertEquals(d2, res);
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}
protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
return OBJECT_MAPPER.readValue(json, clazz);
}
}

View File

@ -149,7 +149,7 @@ class OafMapperUtilsTest {
void testDate() { void testDate() {
final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998"); final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
assertNotNull(date); assertNotNull(date);
System.out.println(date); assertEquals("1998-02-23", date);
} }
@Test @Test
@ -166,8 +166,8 @@ class OafMapperUtilsTest {
assertEquals( assertEquals(
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
OafMapperUtils MergeUtils
.mergeResults(p1, d2) .mergeResult(p1, d2)
.getResulttype() .getResulttype()
.getClassid()); .getClassid());
@ -178,8 +178,8 @@ class OafMapperUtilsTest {
assertEquals( assertEquals(
ModelConstants.DATASET_RESULTTYPE_CLASSID, ModelConstants.DATASET_RESULTTYPE_CLASSID,
OafMapperUtils MergeUtils
.mergeResults(p2, d1) .mergeResult(p2, d1)
.getResulttype() .getResulttype()
.getClassid()); .getClassid());
} }
@ -192,7 +192,7 @@ class OafMapperUtilsTest {
assertEquals(1, d2.getCollectedfrom().size()); assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID)); assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = OafMapperUtils.mergeResults(d1, d2); Result res = MergeUtils.mergeResult(d1, d2);
assertEquals(d2, res); assertEquals(d2, res);

View File

@ -1,14 +1,13 @@
package eu.dnetlib.dhp.actionmanager.promote; package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import java.util.function.BiFunction; import java.util.function.BiFunction;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
/** OAF model merging support. */ /** OAF model merging support. */
public class MergeAndGet { public class MergeAndGet {
@ -46,20 +45,7 @@ public class MergeAndGet {
} }
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) { private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { return (G) MergeUtils.merge(x, y);
((Relation) x).mergeFrom((Relation) y);
return x;
} else if (isSubClass(x, OafEntity.class)
&& isSubClass(y, OafEntity.class)
&& isSubClass(x, y)) {
((OafEntity) x).mergeFrom((OafEntity) y);
return x;
}
throw new RuntimeException(
String
.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
} }
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")

View File

@ -64,6 +64,9 @@ public class PrepareAffiliationRelations implements Serializable {
final String pubmedInputPath = parser.get("pubmedInputPath"); final String pubmedInputPath = parser.get("pubmedInputPath");
log.info("pubmedInputPath: {}", pubmedInputPath); log.info("pubmedInputPath: {}", pubmedInputPath);
final String openapcInputPath = parser.get("openapcInputPath");
log.info("openapcInputPath: {}", openapcInputPath);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
@ -85,8 +88,14 @@ public class PrepareAffiliationRelations implements Serializable {
JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations( JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
spark, pubmedInputPath, collectedFromPubmed); spark, pubmedInputPath, collectedFromPubmed);
List<KeyValue> collectedFromOpenAPC = OafMapperUtils
.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
spark, openapcInputPath, collectedFromOpenAPC);
crossrefRelations crossrefRelations
.union(pubmedRelations) .union(pubmedRelations)
.union(openAPCRelations)
.saveAsHadoopFile( .saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);

View File

@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> { return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
Project project = new Project(); Project project = new Project();
project.setId(bipProjectScores.getProjectId()); //project.setId(bipProjectScores.getProjectId());
project.setMeasures(bipProjectScores.toMeasures()); project.setMeasures(bipProjectScores.toMeasures());
return project; return project;
}, Encoders.bean(Project.class)) }, Encoders.bean(Project.class))

View File

@ -34,6 +34,11 @@ public class BipProjectModel {
String totalCitationCount; String totalCitationCount;
public String getProjectId() {
return projectId;
}
// each project bip measure has exactly one value, hence one key-value pair // each project bip measure has exactly one value, hence one key-value pair
private Measure createMeasure(String measureId, String measureValue) { private Measure createMeasure(String measureId, String measureValue) {

View File

@ -75,6 +75,7 @@ public class GetFOSSparkJob implements Serializable {
fosData.map((MapFunction<Row, FOSDataModel>) r -> { fosData.map((MapFunction<Row, FOSDataModel>) r -> {
FOSDataModel fosDataModel = new FOSDataModel(); FOSDataModel fosDataModel = new FOSDataModel();
fosDataModel.setDoi(r.getString(0).toLowerCase()); fosDataModel.setDoi(r.getString(0).toLowerCase());
fosDataModel.setOaid(r.getString(1).toLowerCase());
fosDataModel.setLevel1(r.getString(2)); fosDataModel.setLevel1(r.getString(2));
fosDataModel.setLevel2(r.getString(3)); fosDataModel.setLevel2(r.getString(3));
fosDataModel.setLevel3(r.getString(4)); fosDataModel.setLevel3(r.getString(4));

View File

@ -16,12 +16,14 @@ import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel; import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject; import eu.dnetlib.dhp.schema.oaf.Subject;
@ -52,28 +54,46 @@ public class PrepareFOSSparkJob implements Serializable {
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
final Boolean distributeDOI = Optional
.ofNullable(parser.get("distributeDoi"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
if (distributeDOI)
distributeFOSdois( distributeFOSdois(
spark, spark,
sourcePath, sourcePath,
outputPath); outputPath);
else
distributeFOSoaid(spark, sourcePath, outputPath);
}); });
} }
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) { private static void distributeFOSoaid(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class); Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset fosDataset
.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING()) .groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> { .mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it);
}, Encoders.bean(Result.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/fos");
}
@NotNull
private static Result getResult(String k, Iterator<FOSDataModel> it) {
Result r = new Result(); Result r = new Result();
FOSDataModel first = it.next(); FOSDataModel first = it.next();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI)); r.setId(k);
HashSet<String> level1 = new HashSet<>(); HashSet<String> level1 = new HashSet<>();
HashSet<String> level2 = new HashSet<>(); HashSet<String> level2 = new HashSet<>();
@ -107,7 +127,17 @@ public class PrepareFOSSparkJob implements Serializable {
ModelConstants.DNET_PROVENANCE_ACTIONS), ModelConstants.DNET_PROVENANCE_ACTIONS),
null)); null));
return r; return r;
}, Encoders.bean(Result.class)) }
private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset
.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, FOSDataModel, Result>) (k,
it) -> getResult(DHPUtils.generateUnresolvedIdentifier(k, DOI), it),
Encoders.bean(Result.class))
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")

View File

@ -0,0 +1,92 @@
package eu.dnetlib.dhp.actionmanager.fosnodoi;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.*;
import scala.Tuple2;
public class CreateActionSetSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
CreateActionSetSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> createActionSet(spark, inputPath, outputPath));
}
private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
Encoders.bean(Result.class))
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
}
}

View File

@ -22,12 +22,14 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI; import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.*; import eu.dnetlib.dhp.schema.oaf.utils.*;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
@ -37,16 +39,12 @@ public class CreateActionSetSparkJob implements Serializable {
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations"; public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations"; public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
// DOI-to-DOI citations
public static final String COCI = "COCI";
// PMID-to-PMID citations
public static final String POCI = "POCI";
private static final String DOI_PREFIX = "50|doi_________::"; private static final String DOI_PREFIX = "50|doi_________::";
private static final String PMID_PREFIX = "50|pmid________::"; private static final String PMID_PREFIX = "50|pmid________::";
private static final String ARXIV_PREFIX = "50|arXiv_______::";
private static final String PMCID_PREFIX = "50|pmcid_______::";
private static final String TRUST = "0.91"; private static final String TRUST = "0.91";
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
@ -79,38 +77,30 @@ public class CreateActionSetSparkJob implements Serializable {
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath); log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels = Optional
.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels)); spark -> extractContent(spark, inputPath, outputPath));
} }
private static void extractContent(SparkSession spark, String inputPath, String outputPath, private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
boolean shouldDuplicateRels) {
getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI) getTextTextJavaPairRDD(spark, inputPath)
.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI)) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class);
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
} }
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath, private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
boolean shouldDuplicateRels, String prefix) {
return spark return spark
.read() .read()
.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*") .textFile(inputPath)
.map( .map(
(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class), (MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
Encoders.bean(COCI.class)) Encoders.bean(COCI.class))
.flatMap( .flatMap(
(FlatMapFunction<COCI, Relation>) value -> createRelation( (FlatMapFunction<COCI, Relation>) value -> createRelation(
value, shouldDuplicateRels, prefix) value)
.iterator(), .iterator(),
Encoders.bean(Relation.class)) Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) Objects::nonNull) .filter((FilterFunction<Relation>) Objects::nonNull)
@ -121,34 +111,68 @@ public class CreateActionSetSparkJob implements Serializable {
new Text(OBJECT_MAPPER.writeValueAsString(aa)))); new Text(OBJECT_MAPPER.writeValueAsString(aa))));
} }
private static List<Relation> createRelation(COCI value, boolean duplicate, String p) { private static List<Relation> createRelation(COCI value) throws JsonProcessingException {
List<Relation> relationList = new ArrayList<>(); List<Relation> relationList = new ArrayList<>();
String prefix;
String citing; String citing;
String cited; String cited;
switch (p) { switch (value.getCiting_pid()) {
case COCI: case "doi":
prefix = DOI_PREFIX; citing = DOI_PREFIX
citing = prefix
+ IdentifierFactory + IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting())); .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCiting()));
cited = prefix break;
case "pmid":
citing = PMID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
break;
case "arxiv":
citing = ARXIV_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCiting()));
break;
case "pmcid":
citing = PMCID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCiting()));
break;
case "isbn":
case "issn":
return relationList;
default:
throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
}
switch (value.getCited_pid()) {
case "doi":
cited = DOI_PREFIX
+ IdentifierFactory + IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited())); .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
break; break;
case POCI: case "pmid":
prefix = PMID_PREFIX; cited = PMID_PREFIX
citing = prefix
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
cited = prefix
+ IdentifierFactory + IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited())); .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
break; break;
case "arxiv":
cited = ARXIV_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), value.getCited()));
break;
case "pmcid":
cited = PMCID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), value.getCited()));
break;
case "isbn":
case "issn":
return relationList;
default: default:
throw new IllegalStateException("Invalid prefix: " + p); throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
} }
if (!citing.equals(cited)) { if (!citing.equals(cited)) {
@ -157,15 +181,6 @@ public class CreateActionSetSparkJob implements Serializable {
getRelation( getRelation(
citing, citing,
cited, ModelConstants.CITES)); cited, ModelConstants.CITES));
if (duplicate && value.getCiting().endsWith(".refs")) {
citing = prefix + IdentifierFactory
.md5(
CleaningFunctions
.normalizePidValue(
"doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs"))));
relationList.add(getRelation(citing, cited, ModelConstants.CITES));
}
} }
return relationList; return relationList;

View File

@ -12,10 +12,7 @@ import java.util.zip.ZipInputStream;
import org.apache.commons.cli.ParseException; import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream; import org.apache.hadoop.fs.*;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
@ -37,17 +34,17 @@ public class GetOpenCitationsRefs implements Serializable {
parser.parseArgument(args); parser.parseArgument(args);
final String[] inputFile = parser.get("inputFile").split(";"); // final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", Arrays.asList(inputFile)); // log.info("inputFile {}", Arrays.asList(inputFile));
final String workingPath = parser.get("workingPath"); final String inputPath = parser.get("inputPath");
log.info("workingPath {}", workingPath); log.info("inputPath {}", inputPath);
final String hdfsNameNode = parser.get("hdfsNameNode"); final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode); log.info("hdfsNameNode {}", hdfsNameNode);
final String prefix = parser.get("prefix"); final String outputPath = parser.get("outputPath");
log.info("prefix {}", prefix); log.info("outputPath {}", outputPath);
Configuration conf = new Configuration(); Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.defaultFS", hdfsNameNode);
@ -56,20 +53,20 @@ public class GetOpenCitationsRefs implements Serializable {
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs(); GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
for (String file : inputFile) { ocr.doExtract(inputPath, outputPath, fileSystem);
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
}
} }
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix) private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
throws IOException { throws IOException {
final Path path = new Path(inputFile); RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
FSDataInputStream oc_zip = fileSystem.open(path); new Path(inputPath), true);
while (fileStatusListIterator.hasNext()) {
// int count = 1; LocatedFileStatus fileStatus = fileStatusListIterator.next();
// do stuff with the file like ...
FSDataInputStream oc_zip = fileSystem.open(fileStatus.getPath());
try (ZipInputStream zis = new ZipInputStream(oc_zip)) { try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null; ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) { while ((entry = zis.getNextEntry()) != null) {
@ -81,7 +78,7 @@ public class GetOpenCitationsRefs implements Serializable {
// count++; // count++;
try ( try (
FSDataOutputStream out = fileSystem FSDataOutputStream out = fileSystem
.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz")); .create(new Path(outputPath + "/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(zis, gzipOs); IOUtils.copy(zis, gzipOs);
@ -92,6 +89,7 @@ public class GetOpenCitationsRefs implements Serializable {
} }
} }
}
} }

View File

@ -0,0 +1,171 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.Arrays;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import scala.Tuple2;
/**
* @author miriam.baglioni
* @Date 29/02/24
*/
public class MapOCIdsInPids implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
private static final String DELIMITER = ",";
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
MapOCIdsInPids.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final String nameNode = parser.get("nameNode");
log.info("nameNode {}", nameNode);
unzipCorrespondenceFile(inputPath, nameNode);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> mapIdentifiers(spark, inputPath, outputPath));
}
private static void unzipCorrespondenceFile(String inputPath, String hdfsNameNode) throws IOException {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
final Path path = new Path(inputPath + "/correspondence/omid.zip");
FileSystem fileSystem = FileSystem.get(conf);
FSDataInputStream project_zip = fileSystem.open(path);
try (ZipInputStream zis = new ZipInputStream(project_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
byte buffer[] = new byte[1024];
int count;
try (
FSDataOutputStream out = fileSystem
.create(new Path(inputPath + "/correspondence/omid.csv"))) {
while ((count = zis.read(buffer, 0, buffer.length)) != -1)
out.write(buffer, 0, count);
}
}
}
}
}
private static void mapIdentifiers(SparkSession spark, String inputPath, String outputPath) {
Dataset<COCI> coci = spark
.read()
.textFile(inputPath + "/JSON")
.map(
(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
Encoders.bean(COCI.class));
Dataset<Tuple2<String, String>> correspondenceData = spark
.read()
.format("csv")
.option("sep", DELIMITER)
.option("inferSchema", "true")
.option("header", "true")
.option("quotes", "\"")
.load(inputPath + "/correspondence/omid.csv")
.repartition(5000)
.flatMap((FlatMapFunction<Row, Tuple2<String, String>>) r -> {
String ocIdentifier = r.getAs("omid");
String[] correspondentIdentifiers = ((String) r.getAs("id")).split(" ");
return Arrays
.stream(correspondentIdentifiers)
.map(ci -> new Tuple2<String, String>(ocIdentifier, ci))
.collect(Collectors.toList())
.iterator();
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
Dataset<COCI> mappedCitingDataset = coci
.joinWith(correspondenceData, coci.col("citing").equalTo(correspondenceData.col("_1")))
.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
String correspondent = t2._2()._2();
t2._1().setCiting_pid(correspondent.substring(0, correspondent.indexOf(":")));
t2._1().setCiting(correspondent.substring(correspondent.indexOf(":") + 1));
return t2._1();
}, Encoders.bean(COCI.class));
mappedCitingDataset
.joinWith(correspondenceData, mappedCitingDataset.col("cited").equalTo(correspondenceData.col("_1")))
.map((MapFunction<Tuple2<COCI, Tuple2<String, String>>, COCI>) t2 -> {
String correspondent = t2._2()._2();
t2._1().setCited_pid(correspondent.substring(0, correspondent.indexOf(":")));
t2._1().setCited(correspondent.substring(correspondent.indexOf(":") + 1));
return t2._1();
}, Encoders.bean(COCI.class))
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.json(outputPath);
}
}

View File

@ -12,11 +12,9 @@ import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.*;
import org.apache.hadoop.fs.LocatedFileStatus;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.RemoteIterator;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*; import org.apache.spark.sql.*;
import org.slf4j.Logger; import org.slf4j.Logger;
@ -42,19 +40,21 @@ public class ReadCOCI implements Serializable {
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
final String[] inputFile = parser.get("inputFile").split(";"); final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("inputFile {}", Arrays.asList(inputFile)); log.info("hdfsNameNode {}", hdfsNameNode);
Boolean isSparkSessionManaged = isSparkSessionManaged(parser); Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String workingPath = parser.get("workingPath"); final String workingPath = parser.get("inputPath");
log.info("workingPath {}", workingPath); log.info("workingPath {}", workingPath);
final String format = parser.get("format");
log.info("format {}", format);
SparkConf sconf = new SparkConf(); SparkConf sconf = new SparkConf();
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
final String delimiter = Optional final String delimiter = Optional
.ofNullable(parser.get("delimiter")) .ofNullable(parser.get("delimiter"))
.orElse(DEFAULT_DELIMITER); .orElse(DEFAULT_DELIMITER);
@ -66,20 +66,21 @@ public class ReadCOCI implements Serializable {
doRead( doRead(
spark, spark,
workingPath, workingPath,
inputFile, fileSystem,
outputPath, outputPath,
delimiter, delimiter);
format);
}); });
} }
private static void doRead(SparkSession spark, String workingPath, String[] inputFiles, private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
String outputPath, String outputPath,
String delimiter, String format) { String delimiter) throws IOException {
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
for (String inputFile : inputFiles) { .listFiles(
String pString = workingPath + "/" + inputFile + ".gz"; new Path(workingPath), true);
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
log.info("extracting file {}", fileStatus.getPath().toString());
Dataset<Row> cociData = spark Dataset<Row> cociData = spark
.read() .read()
.format("csv") .format("csv")
@ -87,26 +88,26 @@ public class ReadCOCI implements Serializable {
.option("inferSchema", "true") .option("inferSchema", "true")
.option("header", "true") .option("header", "true")
.option("quotes", "\"") .option("quotes", "\"")
.load(pString) .load(fileStatus.getPath().toString())
.repartition(100); .repartition(100);
cociData.map((MapFunction<Row, COCI>) row -> { cociData.map((MapFunction<Row, COCI>) row -> {
COCI coci = new COCI(); COCI coci = new COCI();
if (format.equals("COCI")) {
coci.setCiting(row.getString(1)); coci.setCiting(row.getString(1));
coci.setCited(row.getString(2)); coci.setCited(row.getString(2));
} else {
coci.setCiting(String.valueOf(row.getInt(1)));
coci.setCited(String.valueOf(row.getInt(2)));
}
coci.setOci(row.getString(0)); coci.setOci(row.getString(0));
return coci; return coci;
}, Encoders.bean(COCI.class)) }, Encoders.bean(COCI.class))
.filter((FilterFunction<COCI>) c -> c != null)
.write() .write()
.mode(SaveMode.Overwrite) .mode(SaveMode.Append)
.option("compression", "gzip") .option("compression", "gzip")
.json(outputPath + inputFile); .json(outputPath);
fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
} }
} }

View File

@ -9,8 +9,10 @@ public class COCI implements Serializable {
private String oci; private String oci;
private String citing; private String citing;
private String citing_pid;
private String cited; private String cited;
private String cited_pid;
public String getOci() { public String getOci() {
return oci; return oci;
@ -25,6 +27,8 @@ public class COCI implements Serializable {
} }
public void setCiting(String citing) { public void setCiting(String citing) {
if (citing != null && citing.startsWith("omid:"))
citing = citing.substring(5);
this.citing = citing; this.citing = citing;
} }
@ -33,7 +37,24 @@ public class COCI implements Serializable {
} }
public void setCited(String cited) { public void setCited(String cited) {
if (cited != null && cited.startsWith("omid:"))
cited = cited.substring(5);
this.cited = cited; this.cited = cited;
} }
public String getCiting_pid() {
return citing_pid;
}
public void setCiting_pid(String citing_pid) {
this.citing_pid = citing_pid;
}
public String getCited_pid() {
return cited_pid;
}
public void setCited_pid(String cited_pid) {
this.cited_pid = cited_pid;
}
} }

View File

@ -1,12 +1,20 @@
package eu.dnetlib.dhp.actionmanager.project; package eu.dnetlib.dhp.actionmanager.project;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
import java.util.Arrays; import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
import java.util.Objects; import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
import java.util.Optional; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.H2020Classification;
import eu.dnetlib.dhp.schema.oaf.H2020Programme;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@ -18,24 +26,14 @@ import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.H2020Classification;
import eu.dnetlib.dhp.schema.oaf.H2020Programme;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2; import scala.Tuple2;
import java.util.Arrays;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/** /**
* Class that makes the ActionSet. To prepare the AS two joins are needed * Class that makes the ActionSet. To prepare the AS two joins are needed
* *
@ -160,9 +158,11 @@ public class SparkAtomicActionJob {
(MapFunction<Project, String>) OafEntity::getId, (MapFunction<Project, String>) OafEntity::getId,
Encoders.STRING()) Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> { .mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
Project first = it.next(); Project merge = it.next();
it.forEachRemaining(first::mergeFrom); while (it.hasNext()) {
return first; merge = MergeUtils.mergeProject(merge, it.next());
}
return merge;
}, Encoders.bean(Project.class)) }, Encoders.bean(Project.class))
.toJavaRDD() .toJavaRDD()
.map(p -> new AtomicAction(Project.class, p)) .map(p -> new AtomicAction(Project.class, p))

View File

@ -0,0 +1,195 @@
package eu.dnetlib.dhp.actionmanager.transformativeagreement;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.*;
import scala.Tuple2;
public class CreateActionSetSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63";
private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement";
public static void main(final String[] args) throws IOException, ParseException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
CreateActionSetSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json"))));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> createActionSet(spark, inputPath, outputPath));
}
private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
JavaRDD<AtomicAction> relations = spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.flatMap(
(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
value)
.iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) Objects::nonNull)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p));
//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file
spark
.read()
.textFile(inputPath)
.map(
(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
.readValue(value, TransformativeAgreementModel.class),
Encoders.bean(TransformativeAgreementModel.class))
.map(
(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
value),
Encoders.bean(Result.class))
.filter((FilterFunction<Result>) r -> r != null)
.toJavaRDD()
.map(p -> new AtomicAction(p.getClass(), p))
.mapToPair(
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
.saveAsHadoopFile(
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
}
private static Result createResult(TransformativeAgreementModel value) {
Result r = new Result();
r
.setId(
"50|doi_________::"
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())));
r.setTransformativeAgreement(value.getAgreement());
Country country = new Country();
country.setClassid(value.getCountry());
country.setClassname(value.getCountry());
country
.setDataInfo(
OafMapperUtils
.dataInfo(
false, ModelConstants.SYSIMPORT_ACTIONSET, false, false,
OafMapperUtils
.qualifier(
"openapc::transformativeagreement",
"Harvested from Trnasformative Agreement file from OpenAPC",
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
"0.9"));
country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
r.setCountry(Arrays.asList(country));
return r;
}
private static List<Relation> createRelation(TransformativeAgreementModel value) {
List<Relation> relationList = new ArrayList<>();
if (value.getAgreement().startsWith("IReL")) {
String paper;
paper = "50|doi_________::"
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()));
relationList
.add(
getRelation(
paper,
IREL_PROJECT, ModelConstants.IS_PRODUCED_BY));
relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES));
}
return relationList;
}
public static Relation getRelation(
String source,
String target,
String relClass) {
return OafMapperUtils
.getRelation(
source,
target,
ModelConstants.RESULT_PROJECT,
ModelConstants.OUTCOME,
relClass,
Arrays
.asList(
OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)),
OafMapperUtils
.dataInfo(
false, null, false, false,
OafMapperUtils
.qualifier(
TRANSFORMATIVE_AGREEMENT, "Transformative Agreement",
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
"0.9"),
null);
}
}

View File

@ -0,0 +1,51 @@
package eu.dnetlib.dhp.actionmanager.transformativeagreement.model;
import java.io.Serializable;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* @author miriam.baglioni
* @Date 18/12/23
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class TransformativeAgreementModel implements Serializable {
private String institution;
private String doi;
private String agreement;
private String country;
public String getCountry() {
return country;
}
public void setCountry(String country) {
this.country = country;
}
public String getInstitution() {
return institution;
}
public void setInstitution(String institution) {
this.institution = institution;
}
public String getDoi() {
return doi;
}
public void setDoi(String doi) {
this.doi = doi;
}
public String getAgreement() {
return agreement;
}
public void setAgreement(String agreement) {
this.agreement = agreement;
}
}

View File

@ -45,15 +45,22 @@ public class BaseCollectorPlugin implements CollectorPlugin {
@Override @Override
public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException { public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
// get path to file // the path of the dump file on HDFS
// http://oai.base-search.net/initial_load/base_oaipmh_dump-current.tar
// it could be downloaded from iis-cdh5-test-gw.ocean.icm.edu.pl and then copied on HDFS
final Path filePath = Optional final Path filePath = Optional
.ofNullable(api.getBaseUrl()) .ofNullable(api.getBaseUrl())
.map(Path::new) .map(Path::new)
.orElseThrow(() -> new CollectorException("missing baseUrl")); .orElseThrow(() -> new CollectorException("missing baseUrl"));
// get the parameters for the connection to the OpenAIRE database.
// the database is used to obtain the list of the datasources that the plugin will collect
final String dbUrl = api.getParams().get("dbUrl"); final String dbUrl = api.getParams().get("dbUrl");
final String dbUser = api.getParams().get("dbUser"); final String dbUser = api.getParams().get("dbUser");
final String dbPassword = api.getParams().get("dbPassword"); final String dbPassword = api.getParams().get("dbPassword");
// the types(comma separated, empty value for all) that the plugin will collect,
// the types should be expressed in the format of the normalized types of BASE (for example 1,121,...)
final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes"); final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes");
log.info("baseUrl: {}", filePath); log.info("baseUrl: {}", filePath);

View File

@ -48,7 +48,7 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
@Override @Override
public MetadataRecord call(MetadataRecord value) { public MetadataRecord call(MetadataRecord value) {
aggregationCounter.getTotalItems().add(1); aggregationCounter.getTotalItems().add(1);
try {
Processor processor = new Processor(false); Processor processor = new Processor(false);
processor.registerExtensionFunction(cleanFunction); processor.registerExtensionFunction(cleanFunction);
@ -60,11 +60,18 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId())); comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM); QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName())); comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
XsltExecutable xslt = comp XsltExecutable xslt;
XdmNode source;
try {
xslt = comp
.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8))); .compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
XdmNode source = processor source = processor
.newDocumentBuilder() .newDocumentBuilder()
.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8))); .build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
} catch (Throwable e) {
throw new RuntimeException("Error on parsing xslt", e);
}
try {
XsltTransformer trans = xslt.load(); XsltTransformer trans = xslt.load();
trans.setInitialContextNode(source); trans.setInitialContextNode(source);
final StringWriter output = new StringWriter(); final StringWriter output = new StringWriter();

View File

@ -17,6 +17,12 @@
"paramDescription": "the path to get the input data from Pubmed", "paramDescription": "the path to get the input data from Pubmed",
"paramRequired": true "paramRequired": true
}, },
{
"paramName": "oip",
"paramLongName": "openapcInputPath",
"paramDescription": "the path to get the input data from OpenAPC",
"paramRequired": true
},
{ {
"paramName": "o", "paramName": "o",
"paramLongName": "outputPath", "paramLongName": "outputPath",

View File

@ -31,6 +31,7 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
# The following is needed as a property of a workflow # The following is needed as a property of a workflow
oozie.wf.application.path=${oozieTopWfApplicationPath} oozie.wf.application.path=${oozieTopWfApplicationPath}
crossrefInputPath=/data/bip-affiliations/data.json crossrefInputPath=/data/bip-affiliations/crossref-data.json
pubmedInputPath=/data/bip-affiliations/pubmed-data.json pubmedInputPath=/data/bip-affiliations/pubmed-data.json
openapcInputPath=/data/bip-affiliations/openapc-data.json
outputPath=/tmp/crossref-affiliations-output-v5 outputPath=/tmp/crossref-affiliations-output-v5

View File

@ -9,6 +9,10 @@
<name>pubmedInputPath</name> <name>pubmedInputPath</name>
<description>the path where to find the inferred affiliation relations from Pubmed</description> <description>the path where to find the inferred affiliation relations from Pubmed</description>
</property> </property>
<property>
<name>openapcInputPath</name>
<description>the path where to find the inferred affiliation relations from OpenAPC</description>
</property>
<property> <property>
<name>outputPath</name> <name>outputPath</name>
<description>the path where to store the actionset</description> <description>the path where to store the actionset</description>
@ -102,6 +106,7 @@
</spark-opts> </spark-opts>
<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg> <arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg> <arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
<arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg> <arg>--outputPath</arg><arg>${outputPath}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>

View File

@ -16,5 +16,10 @@
"paramLongName": "outputPath", "paramLongName": "outputPath",
"paramDescription": "the path of the new ActionSet", "paramDescription": "the path of the new ActionSet",
"paramRequired": true "paramRequired": true
}, {
"paramName": "fd",
"paramLongName": "distributeDoi",
"paramDescription": "the path of the new ActionSet",
"paramRequired": false
} }
] ]

View File

@ -0,0 +1,20 @@
[
{
"paramName": "sp",
"paramLongName": "sourcePath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
]

View File

@ -0,0 +1,30 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

View File

@ -0,0 +1,153 @@
<workflow-app name="FOS no doi" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>fosPath</name>
<description>the input path of the resources to be extended</description>
</property>
<property>
<name>outputPath</name>
<description>the path where to store the actionset</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="getFOS"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="getFOS">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Gets Data from FOS csv file</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${fosPath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg>
</spark>
<ok to="prepareFos"/>
<error to="Kill"/>
</action>
<action name="prepareFos">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the results from FOS</name>
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/input/fos</arg>
<arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
<arg>--distributeDoi</arg><arg>false</arg>
</spark>
<ok to="produceActionSet"/>
<error to="Kill"/>
</action>
<action name="produceActionSet">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Save the action set grouping results with the same id</name>
<class>eu.dnetlib.dhp.actionmanager.fosnodoi.CreateActionSetSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/prepared/fos</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -1,13 +1,13 @@
[ [
{ {
"paramName": "if", "paramName": "ip",
"paramLongName": "inputFile", "paramLongName": "inputPath",
"paramDescription": "the zipped opencitations file", "paramDescription": "the zipped opencitations file",
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName": "wp", "paramName": "op",
"paramLongName": "workingPath", "paramLongName": "outputPath",
"paramDescription": "the working path", "paramDescription": "the working path",
"paramRequired": true "paramRequired": true
}, },
@ -16,11 +16,5 @@
"paramLongName": "hdfsNameNode", "paramLongName": "hdfsNameNode",
"paramDescription": "the hdfs name node", "paramDescription": "the hdfs name node",
"paramRequired": true "paramRequired": true
},
{
"paramName": "p",
"paramLongName": "prefix",
"paramDescription": "COCI or POCI",
"paramRequired": true
} }
] ]

View File

@ -1,7 +1,7 @@
[ [
{ {
"paramName": "wp", "paramName": "ip",
"paramLongName": "workingPath", "paramLongName": "inputPath",
"paramDescription": "the zipped opencitations file", "paramDescription": "the zipped opencitations file",
"paramRequired": true "paramRequired": true
}, },
@ -24,15 +24,9 @@
"paramLongName": "outputPath", "paramLongName": "outputPath",
"paramDescription": "the hdfs name node", "paramDescription": "the hdfs name node",
"paramRequired": true "paramRequired": true
},
{
"paramName": "if",
"paramLongName": "inputFile",
"paramDescription": "the hdfs name node",
"paramRequired": true
}, { }, {
"paramName": "f", "paramName": "nn",
"paramLongName": "format", "paramLongName": "hdfsNameNode",
"paramDescription": "the hdfs name node", "paramDescription": "the hdfs name node",
"paramRequired": true "paramRequired": true
} }

View File

@ -27,7 +27,9 @@
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case> <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case> <case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
<case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case> <case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed --> <case to="remap">${wf:conf('resumeFrom') eq 'MapContent'}</case>
<case to="create_actionset">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
<default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
</switch> </switch>
</decision> </decision>
@ -35,6 +37,15 @@
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<action name="deleteoutputpath">
<fs>
<delete path='${inputPath}'/>
<mkdir path='${inputPath}'/>
</fs>
<ok to="download"/>
<error to="Kill"/>
</action>
<action name="download"> <action name="download">
<shell xmlns="uri:oozie:shell-action:0.2"> <shell xmlns="uri:oozie:shell-action:0.2">
<job-tracker>${jobTracker}</job-tracker> <job-tracker>${jobTracker}</job-tracker>
@ -47,7 +58,28 @@
</configuration> </configuration>
<exec>download.sh</exec> <exec>download.sh</exec>
<argument>${filelist}</argument> <argument>${filelist}</argument>
<argument>${workingPath}/${prefix}/Original</argument> <argument>${inputPath}/Original</argument>
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
<file>download.sh</file>
<capture-output/>
</shell>
<ok to="download_correspondence"/>
<error to="Kill"/>
</action>
<!-- downloads the correspondence from the omid and the pid (doi, pmid etc)-->
<action name="download_correspondence">
<shell xmlns="uri:oozie:shell-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapred.job.queue.name</name>
<value>${queueName}</value>
</property>
</configuration>
<exec>download_corr.sh</exec>
<argument>${filecorrespondence}</argument>
<argument>${inputPath}/correspondence</argument>
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var> <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
<file>download.sh</file> <file>download.sh</file>
<capture-output/> <capture-output/>
@ -60,9 +92,19 @@
<java> <java>
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class> <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg> <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--inputFile</arg><arg>${inputFile}</arg> <arg>--inputPath</arg><arg>${inputPath}/Original</arg>
<arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg> <arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
<arg>--prefix</arg><arg>${prefix}</arg> </java>
<ok to="read"/>
<error to="Kill"/>
</action>
<action name="extract_correspondence">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
<arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
</java> </java>
<ok to="read"/> <ok to="read"/>
<error to="Kill"/> <error to="Kill"/>
@ -85,11 +127,35 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg> <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
<arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg> <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg> <arg>--delimiter</arg><arg>${delimiter}</arg>
<arg>--inputFile</arg><arg>${inputFileCoci}</arg> <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--format</arg><arg>${prefix}</arg> </spark>
<ok to="remap"/>
<error to="Kill"/>
</action>
<action name="remap">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for OC</name>
<class>eu.dnetlib.dhp.actionmanager.opencitations.MapOCIdsInPids</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${inputPath}</arg>
<arg>--outputPath</arg><arg>${outputPathExtraction}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
</spark> </spark>
<ok to="create_actionset"/> <ok to="create_actionset"/>
<error to="Kill"/> <error to="Kill"/>
@ -112,7 +178,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--inputPath</arg><arg>${workingPath}</arg> <arg>--inputPath</arg><arg>${outputPathExtraction}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg> <arg>--outputPath</arg><arg>${outputPath}</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>

View File

@ -0,0 +1,25 @@
[
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManged",
"paramDescription": "the hdfs name node",
"paramRequired": false
},{
"paramName": "nn",
"paramLongName": "nameNode",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
]

View File

@ -0,0 +1,20 @@
[
{
"paramName": "ip",
"paramLongName": "inputPath",
"paramDescription": "the zipped opencitations file",
"paramRequired": true
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the working path",
"paramRequired": true
},
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
}
]

View File

@ -0,0 +1,30 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "the hdfs name node",
"paramRequired": false
},
{
"paramName": "d",
"paramLongName": "delimiter",
"paramDescription": "the hdfs name node",
"paramRequired": false
},
{
"paramName": "op",
"paramLongName": "outputPath",
"paramDescription": "the hdfs name node",
"paramRequired": true
},
{
"paramName": "if",
"paramLongName": "inputFile",
"paramDescription": "the hdfs name node",
"paramRequired": true
}
]

View File

@ -0,0 +1,58 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
</configuration>

View File

@ -0,0 +1,2 @@
#!/bin/bash
curl -L $1 | hdfs dfs -put - $2

View File

@ -0,0 +1,82 @@
<workflow-app name="Transfomative Agreement Integration" xmlns="uri:oozie:workflow:0.5">
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="resume_from"/>
<decision name="resume_from">
<switch>
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
</switch>
</decision>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="download">
<shell xmlns="uri:oozie:shell-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapred.job.queue.name</name>
<value>${queueName}</value>
</property>
</configuration>
<exec>download.sh</exec>
<argument>${inputFile}</argument>
<argument>${workingDir}/transformativeagreement/transformativeAgreement.json</argument>
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
<file>download.sh</file>
<capture-output/>
</shell>
<ok to="create_actionset"/>
<error to="Kill"/>
</action>
<action name="create_actionset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for the Transformative Agreement</name>
<class>eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingDir}/transformativeagreement/</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

View File

@ -108,7 +108,7 @@ INSERT INTO dsm_apiparams(
'api_________::openaire____::base_search::dump@@acceptedNormTypes', 'api_________::openaire____::base_search::dump@@acceptedNormTypes',
'api_________::openaire____::base_search::dump', 'api_________::openaire____::base_search::dump',
'acceptedNormTypes', 'acceptedNormTypes',
'' '1,11,111,121,14,15,18,181,182,183,1A,6,7'
); );
COMMIT; COMMIT;

View File

@ -2,6 +2,8 @@ select s.id as id
from dsm_services s from dsm_services s
where collectedfrom = 'openaire____::opendoar' where collectedfrom = 'openaire____::opendoar'
and jurisdiction = 'Institutional' and jurisdiction = 'Institutional'
and s.id not in ( and s.id in (
select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%' or last_collection_total > 0 select service from dsm_api where coalesce(compatibility_override, compatibility) = 'driver' or coalesce(compatibility_override, compatibility) = 'UNKNOWN'
) and s.id not in (
select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%'
); );

View File

@ -66,10 +66,6 @@ dc:language (I used base_dc:lang)
base_dc:link (I used dc:identifier) base_dc:link (I used dc:identifier)
--> -->
<xsl:variable name="varBaseNormType" select="vocabulary:clean(//base_dc:typenorm, 'base:normalized_types')" />
<metadata> <metadata>
<xsl:call-template name="allElements"> <xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:title" /> <xsl:with-param name="sourceElement" select="//dc:title" />
@ -112,9 +108,13 @@ base_dc:link (I used dc:identifier)
<xsl:with-param name="targetElement" select="'dc:format'" /> <xsl:with-param name="targetElement" select="'dc:format'" />
</xsl:call-template> </xsl:call-template>
<xsl:for-each select="//base_dc:typenorm">
<dc:type> <dc:type>
<xsl:value-of select="$varBaseNormType" /> <xsl:value-of select="vocabulary:clean(., 'base:normalized_types')" />
</dc:type> </dc:type>
</xsl:for-each>
<xsl:call-template name="allElements"> <xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:type" /> <xsl:with-param name="sourceElement" select="//dc:type" />
<xsl:with-param name="targetElement" select="'dc:type'" /> <xsl:with-param name="targetElement" select="'dc:type'" />
@ -162,16 +162,150 @@ base_dc:link (I used dc:identifier)
</xsl:if> </xsl:if>
</xsl:for-each> </xsl:for-each>
<dr:CobjCategory> <xsl:choose>
<xsl:variable name="varCobjCategory" select="vocabulary:clean($varBaseNormType, 'dnet:publication_resource')" /> <!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority -->
<xsl:variable name="varSuperType" select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')" />
<xsl:attribute name="type" select="$varSuperType" /> <!-- Book part -->
<xsl:value-of select="$varCobjCategory" /> <xsl:when test="//base_dc:typenorm = '111'">
</dr:CobjCategory> <dr:CobjCategory type="publication">0013</dr:CobjCategory>
</xsl:when>
<!-- Book -->
<xsl:when test="//base_dc:typenorm = '11'">
<dr:CobjCategory type="publication">0002</dr:CobjCategory>
</xsl:when>
<!-- Article contribution -->
<xsl:when test="//base_dc:typenorm = '121'">
<dr:CobjCategory type="publication">0001</dr:CobjCategory>
</xsl:when>
<!-- Journal/Newspaper -->
<xsl:when test="//base_dc:typenorm = '12'">
<dr:CobjCategory type="publication">0043</dr:CobjCategory>
</xsl:when>
<!-- Report -->
<xsl:when test="//base_dc:typenorm = '14'">
<dr:CobjCategory type="publication">0017</dr:CobjCategory>
</xsl:when>
<!-- Review -->
<xsl:when test="//base_dc:typenorm = '15'">
<dr:CobjCategory type="publication">0015</dr:CobjCategory>
</xsl:when>
<!-- Lecture -->
<xsl:when test="//base_dc:typenorm = '17'">
<dr:CobjCategory type="publication">0010</dr:CobjCategory>
</xsl:when>
<!-- Bachelor's thesis -->
<xsl:when test="//base_dc:typenorm = '181'">
<dr:CobjCategory type="publication">0008</dr:CobjCategory>
</xsl:when>
<!-- Master's thesis -->
<xsl:when test="//base_dc:typenorm = '182'">
<dr:CobjCategory type="publication">0007</dr:CobjCategory>
</xsl:when>
<!-- Doctoral and postdoctoral thesis -->
<xsl:when test="//base_dc:typenorm = '183'">
<dr:CobjCategory type="publication">0006</dr:CobjCategory>
</xsl:when>
<!-- Thesis -->
<xsl:when test="//base_dc:typenorm = '18'">
<dr:CobjCategory type="publication">0044</dr:CobjCategory>
</xsl:when>
<!-- Patent -->
<xsl:when test="//base_dc:typenorm = '1A'">
<dr:CobjCategory type="publication">0019</dr:CobjCategory>
</xsl:when>
<!-- Text -->
<xsl:when test="//base_dc:typenorm = '1'">
<dr:CobjCategory type="publication">0001</dr:CobjCategory>
</xsl:when>
<!-- Software -->
<xsl:when test="//base_dc:typenorm = '6'">
<dr:CobjCategory type="software">0029</dr:CobjCategory>
</xsl:when>
<!-- Dataset -->
<xsl:when test="//base_dc:typenorm = '7'">
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
</xsl:when>
<!-- Still image -->
<xsl:when test="//base_dc:typenorm = '51'">
<dr:CobjCategory type="other">0025</dr:CobjCategory>
</xsl:when>
<!-- Moving image/Video -->
<xsl:when test="//base_dc:typenorm = '52'">
<dr:CobjCategory type="other">0024</dr:CobjCategory>
</xsl:when>
<!-- Image/Video -->
<xsl:when test="//base_dc:typenorm = '5'">
<dr:CobjCategory type="other">0033</dr:CobjCategory>
</xsl:when>
<!-- Audio -->
<xsl:when test="//base_dc:typenorm = '4'">
<dr:CobjCategory type="other">0030</dr:CobjCategory>
</xsl:when>
<!-- Musical notation -->
<xsl:when test="//base_dc:typenorm = '2'">
<dr:CobjCategory type="other">0020</dr:CobjCategory>
</xsl:when>
<!-- Map -->
<xsl:when test="//base_dc:typenorm = '3'">
<dr:CobjCategory type="other">0020</dr:CobjCategory>
</xsl:when>
<!-- Other non-article -->
<xsl:when test="//base_dc:typenorm = '122'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Course material -->
<xsl:when test="//base_dc:typenorm = '16'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Manuscript -->
<xsl:when test="//base_dc:typenorm = '19'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Conference object -->
<xsl:when test="//base_dc:typenorm = '13'">
<dr:CobjCategory type="publication">0004</dr:CobjCategory>
</xsl:when>
<!-- Unknown -->
<xsl:when test="//base_dc:typenorm = 'F'">
<dr:CobjCategory type="other">0000</dr:CobjCategory>
</xsl:when>
<xsl:otherwise>
<dr:CobjCategory type="other">0000</dr:CobjCategory>
</xsl:otherwise>
</xsl:choose>
<oaf:accessrights> <oaf:accessrights>
<xsl:choose> <xsl:choose>
<xsl:when test="//base_dc:oa[.='0']">CLOSED</xsl:when>
<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when> <xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
<xsl:when test="//base_dc:oa[.='2']">UNKNOWN</xsl:when>
<xsl:when test="//base_dc:rightsnorm"> <xsl:when test="//base_dc:rightsnorm">
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" /> <xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
</xsl:when> </xsl:when>
@ -208,7 +342,7 @@ base_dc:link (I used dc:identifier)
<oaf:identifier identifierType="oai-original"> <oaf:identifier identifierType="oai-original">
<xsl:value-of <xsl:value-of
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" /> select="//oai:header/oai:identifier" />
</oaf:identifier> </oaf:identifier>
<oaf:hostedBy> <oaf:hostedBy>

View File

@ -51,10 +51,6 @@
base_dc:link (I used dc:identifier) base_dc:link (I used dc:identifier)
--> -->
<xsl:variable name="varBaseNormType" select="vocabulary:clean(//base_dc:typenorm, 'base:normalized_types')" />
<metadata> <metadata>
<datacite:resource> <datacite:resource>
@ -86,14 +82,17 @@
<datacite:identifier alternateIdentifierType="oai-original"> <datacite:identifier alternateIdentifierType="oai-original">
<xsl:value-of <xsl:value-of
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" /> select="//oai:header/oai:identifier" />
</datacite:identifier> </datacite:identifier>
</datacite:alternateIdentifiers> </datacite:alternateIdentifiers>
<datacite:relatedIdentifiers /> <datacite:relatedIdentifiers />
<datacite:resourceType><xsl:value-of select="$varBaseNormType" /></datacite:resourceType> <xsl:for-each select="//base_dc:typenorm">
<datacite:resourceType><xsl:value-of select="vocabulary:clean(., 'base:normalized_types')" /></datacite:resourceType>
</xsl:for-each>
<datacite:titles> <datacite:titles>
<xsl:for-each select="//dc:title"> <xsl:for-each select="//dc:title">
@ -154,13 +153,17 @@
</xsl:for-each> </xsl:for-each>
</datacite:subjects> </datacite:subjects>
<xsl:for-each select="//dc:publisher">
<datacite:publisher> <datacite:publisher>
<xsl:value-of select="normalize-space(//dc:publisher)" /> <xsl:value-of select="normalize-space(.)" />
</datacite:publisher> </datacite:publisher>
</xsl:for-each>
<xsl:for-each select="//base_dc:year">
<datacite:publicationYear> <datacite:publicationYear>
<xsl:value-of select="normalize-space(//base_dc:year)" /> <xsl:value-of select="normalize-space(.)" />
</datacite:publicationYear> </datacite:publicationYear>
</xsl:for-each>
<datacite:formats> <datacite:formats>
<xsl:for-each select="//dc:format"> <xsl:for-each select="//dc:format">
@ -175,6 +178,9 @@
</datacite:language> </datacite:language>
<oaf:accessrights> <oaf:accessrights>
<xsl:if test="//base_dc:oa[.='0']">
<datacite:rights rightsURI="http://purl.org/coar/access_right/c_16ec">restricted access</datacite:rights>
</xsl:if>
<xsl:if test="//base_dc:oa[.='1']"> <xsl:if test="//base_dc:oa[.='1']">
<datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights> <datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
</xsl:if> </xsl:if>
@ -198,16 +204,149 @@
</xsl:if> </xsl:if>
</xsl:for-each> </xsl:for-each>
<dr:CobjCategory> <xsl:choose>
<xsl:variable name="varCobjCategory" select="vocabulary:clean($varBaseNormType, 'dnet:publication_resource')" /> <!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority -->
<xsl:variable name="varSuperType" select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')" />
<xsl:attribute name="type" select="$varSuperType" /> <!-- Book part -->
<xsl:value-of select="$varCobjCategory" /> <xsl:when test="//base_dc:typenorm = '111'">
</dr:CobjCategory> <dr:CobjCategory type="publication">0013</dr:CobjCategory>
</xsl:when>
<!-- Book -->
<xsl:when test="//base_dc:typenorm = '11'">
<dr:CobjCategory type="publication">0002</dr:CobjCategory>
</xsl:when>
<!-- Article contribution -->
<xsl:when test="//base_dc:typenorm = '121'">
<dr:CobjCategory type="publication">0001</dr:CobjCategory>
</xsl:when>
<!-- Journal/Newspaper -->
<xsl:when test="//base_dc:typenorm = '12'">
<dr:CobjCategory type="publication">0043</dr:CobjCategory>
</xsl:when>
<!-- Report -->
<xsl:when test="//base_dc:typenorm = '14'">
<dr:CobjCategory type="publication">0017</dr:CobjCategory>
</xsl:when>
<!-- Review -->
<xsl:when test="//base_dc:typenorm = '15'">
<dr:CobjCategory type="publication">0015</dr:CobjCategory>
</xsl:when>
<!-- Lecture -->
<xsl:when test="//base_dc:typenorm = '17'">
<dr:CobjCategory type="publication">0010</dr:CobjCategory>
</xsl:when>
<!-- Bachelor's thesis -->
<xsl:when test="//base_dc:typenorm = '181'">
<dr:CobjCategory type="publication">0008</dr:CobjCategory>
</xsl:when>
<!-- Master's thesis -->
<xsl:when test="//base_dc:typenorm = '182'">
<dr:CobjCategory type="publication">0007</dr:CobjCategory>
</xsl:when>
<!-- Doctoral and postdoctoral thesis -->
<xsl:when test="//base_dc:typenorm = '183'">
<dr:CobjCategory type="publication">0006</dr:CobjCategory>
</xsl:when>
<!-- Thesis -->
<xsl:when test="//base_dc:typenorm = '18'">
<dr:CobjCategory type="publication">0044</dr:CobjCategory>
</xsl:when>
<!-- Patent -->
<xsl:when test="//base_dc:typenorm = '1A'">
<dr:CobjCategory type="publication">0019</dr:CobjCategory>
</xsl:when>
<!-- Text -->
<xsl:when test="//base_dc:typenorm = '1'">
<dr:CobjCategory type="publication">0001</dr:CobjCategory>
</xsl:when>
<!-- Software -->
<xsl:when test="//base_dc:typenorm = '6'">
<dr:CobjCategory type="software">0029</dr:CobjCategory>
</xsl:when>
<!-- Dataset -->
<xsl:when test="//base_dc:typenorm = '7'">
<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
</xsl:when>
<!-- Still image -->
<xsl:when test="//base_dc:typenorm = '51'">
<dr:CobjCategory type="other">0025</dr:CobjCategory>
</xsl:when>
<!-- Moving image/Video -->
<xsl:when test="//base_dc:typenorm = '52'">
<dr:CobjCategory type="other">0024</dr:CobjCategory>
</xsl:when>
<!-- Image/Video -->
<xsl:when test="//base_dc:typenorm = '5'">
<dr:CobjCategory type="other">0033</dr:CobjCategory>
</xsl:when>
<!-- Audio -->
<xsl:when test="//base_dc:typenorm = '4'">
<dr:CobjCategory type="other">0030</dr:CobjCategory>
</xsl:when>
<!-- Musical notation -->
<xsl:when test="//base_dc:typenorm = '2'">
<dr:CobjCategory type="other">0020</dr:CobjCategory>
</xsl:when>
<!-- Map -->
<xsl:when test="//base_dc:typenorm = '3'">
<dr:CobjCategory type="other">0020</dr:CobjCategory>
</xsl:when>
<!-- Other non-article -->
<xsl:when test="//base_dc:typenorm = '122'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Course material -->
<xsl:when test="//base_dc:typenorm = '16'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Manuscript -->
<xsl:when test="//base_dc:typenorm = '19'">
<dr:CobjCategory type="publication">0038</dr:CobjCategory>
</xsl:when>
<!-- Conference object -->
<xsl:when test="//base_dc:typenorm = '13'">
<dr:CobjCategory type="publication">0004</dr:CobjCategory>
</xsl:when>
<!-- Unknown -->
<xsl:when test="//base_dc:typenorm = 'F'">
<dr:CobjCategory type="other">0000</dr:CobjCategory>
</xsl:when>
<xsl:otherwise>
<dr:CobjCategory type="other">0000</dr:CobjCategory>
</xsl:otherwise>
</xsl:choose>
<oaf:accessrights> <oaf:accessrights>
<xsl:choose> <xsl:choose>
<xsl:when test="//base_dc:oa[.='0']">CLOSED</xsl:when>
<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when> <xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
<xsl:when test="//base_dc:oa[.='2']">UNKNOWN</xsl:when>
<xsl:when test="//base_dc:rightsnorm"> <xsl:when test="//base_dc:rightsnorm">
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" /> <xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
</xsl:when> </xsl:when>
@ -245,7 +384,7 @@
<oaf:identifier identifierType="oai-original"> <oaf:identifier identifierType="oai-original">
<xsl:value-of <xsl:value-of
select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'identifier']" /> select="//oai:header/oai:identifier" />
</oaf:identifier> </oaf:identifier>
<oaf:hostedBy> <oaf:hostedBy>

View File

@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest {
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json") .getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath(); .getPath();
String pubmedAffiliationRelationsPath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
.getPath();
String outputPath = workingDir.toString() + "/actionSet"; String outputPath = workingDir.toString() + "/actionSet";
PrepareAffiliationRelations PrepareAffiliationRelations
@ -89,7 +85,8 @@ public class PrepareAffiliationRelationsTest {
new String[] { new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-crossrefInputPath", crossrefAffiliationRelationPath, "-crossrefInputPath", crossrefAffiliationRelationPath,
"-pubmedInputPath", pubmedAffiliationRelationsPath, "-pubmedInputPath", crossrefAffiliationRelationPath,
"-openapcInputPath", crossrefAffiliationRelationPath,
"-outputPath", outputPath "-outputPath", outputPath
}); });
@ -106,7 +103,7 @@ public class PrepareAffiliationRelationsTest {
// ); // );
// } // }
// count the number of relations // count the number of relations
assertEquals(40, tmp.count()); assertEquals(60, tmp.count());
Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class)); Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
dataset.createOrReplaceTempView("result"); dataset.createOrReplaceTempView("result");
@ -117,7 +114,7 @@ public class PrepareAffiliationRelationsTest {
// verify that we have equal number of bi-directional relations // verify that we have equal number of bi-directional relations
Assertions Assertions
.assertEquals( .assertEquals(
20, execVerification 30, execVerification
.filter( .filter(
"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'") "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
.collectAsList() .collectAsList()
@ -125,7 +122,7 @@ public class PrepareAffiliationRelationsTest {
Assertions Assertions
.assertEquals( .assertEquals(
20, execVerification 30, execVerification
.filter( .filter(
"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'") "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
.collectAsList() .collectAsList()

View File

@ -0,0 +1,104 @@
package eu.dnetlib.dhp.actionmanager.fosnodoi;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareTest;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
/**
* @author miriam.baglioni
* @Date 13/02/23
*/
public class GetFosTest {
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
private static Path workingDir;
private static SparkSession spark;
private static LocalFileSystem fs;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
fs = FileSystem.getLocal(new Configuration());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(ProduceTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(PrepareTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
@Disabled
void test3() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv")
.getPath();
final String outputPath = workingDir.toString() + "/fos.json";
GetFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", outputPath,
"-delimiter", ","
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<FOSDataModel> tmp = sc
.textFile(outputPath)
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
tmp.foreach(t -> Assertions.assertTrue(t.getOaid() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
}
}

View File

@ -0,0 +1,99 @@
package eu.dnetlib.dhp.actionmanager.fosnodoi;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
import eu.dnetlib.dhp.schema.oaf.Result;
public class PrepareTest {
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
private static Path workingDir;
private static SparkSession spark;
private static LocalFileSystem fs;
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
fs = FileSystem.getLocal(new Configuration());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(ProduceTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(PrepareTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void fosPrepareTest() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json")
.getPath();
PrepareFOSSparkJob
.main(
new String[] {
"--isSparkSessionManaged", Boolean.FALSE.toString(),
"--sourcePath", sourcePath,
"-outputPath", workingDir.toString() + "/work",
"-distributeDoi", Boolean.FALSE.toString()
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Result> tmp = sc
.textFile(workingDir.toString() + "/work/fos")
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
}
}

View File

@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
String inputPath = getClass() String inputPath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI") "/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap/jsonforas")
.getPath(); .getPath();
CreateActionSetSparkJob CreateActionSetSparkJob
@ -84,8 +84,6 @@ public class CreateOpenCitationsASTest {
new String[] { new String[] {
"-isSparkSessionManaged", "-isSparkSessionManaged",
Boolean.FALSE.toString(), Boolean.FALSE.toString(),
"-shouldDuplicateRels",
Boolean.TRUE.toString(),
"-inputPath", "-inputPath",
inputPath, inputPath,
"-outputPath", "-outputPath",
@ -99,9 +97,10 @@ public class CreateOpenCitationsASTest {
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload())); .map(aa -> ((Relation) aa.getPayload()));
assertEquals(31, tmp.count()); Assertions.assertEquals(27, tmp.count());
tmp.foreach(r -> Assertions.assertEquals(1, r.getCollectedfrom().size()));
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
} }

View File

@ -0,0 +1,90 @@
package eu.dnetlib.dhp.actionmanager.opencitations;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocalFileSystem;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
/**
* @author miriam.baglioni
* @Date 07/03/24
*/
public class RemapTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(RemapTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(RemapTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(RemapTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(RemapTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testRemap() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI/inputremap")
.getPath();
MapOCIdsInPids
.main(
new String[] {
"-isSparkSessionManged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/out/",
"-nameNode", "input1;input2;input3;input4;input5"
});
}
}

View File

@ -0,0 +1,324 @@
package eu.dnetlib.dhp.actionmanager.transformativeagreement;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
/**
* @author miriam.baglioni
* @Date 13/02/24
*/
public class CreateTAActionSetTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(CreateOpenCitationsASTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(CreateTAActionSetTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(CreateTAActionSetTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(CreateTAActionSetTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void createActionSet() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json")
.getPath();
eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet1"
});
}
@Test
void testNumberofRelations2() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet2"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
assertEquals(23, tmp.count());
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
@Test
void testRelationsCollectedFrom() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet3"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
});
}
@Test
void testRelationsDataInfo() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet4"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals(false, r.getDataInfo().getInferred());
assertEquals(false, r.getDataInfo().getDeletedbyinference());
assertEquals("0.91", r.getDataInfo().getTrust());
assertEquals(
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSID,
r.getDataInfo().getProvenanceaction().getClassid());
assertEquals(
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME,
r.getDataInfo().getProvenanceaction().getClassname());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
});
}
@Test
void testRelationsSemantics() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet5"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals("citation", r.getSubRelType());
assertEquals("resultResult", r.getRelType());
});
assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
assertEquals(0, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
}
@Test
void testRelationsSourceTargetPrefix() throws Exception {
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet6"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
tmp.foreach(r -> {
assertEquals("50|doi_________::", r.getSource().substring(0, 17));
assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
});
}
@Test
void testRelationsSourceTargetCouple() throws Exception {
final String doi1 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
final String doi2 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
final String doi3 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
final String doi4 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
final String doi5 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
final String doi6 = "50|doi_________::"
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
String inputPath = getClass()
.getResource(
"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
.getPath();
CreateActionSetSparkJob
.main(
new String[] {
"-isSparkSessionManaged",
Boolean.FALSE.toString(),
"-inputPath",
inputPath,
"-outputPath",
workingDir.toString() + "/actionSet7"
});
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
JavaRDD<Relation> tmp = sc
.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
.map(aa -> ((Relation) aa.getPayload()));
JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
assertEquals(5, check.count());
// check.foreach(r -> {
// if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
// r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
// assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
// assertEquals(doi1, r.getTarget());
// }
// });
assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
}
}

View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.collection.plugin.base; package eu.dnetlib.dhp.collection.plugin.base;
import static org.junit.jupiter.api.Assertions.assertThrows;
import java.io.IOException; import java.io.IOException;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
@ -8,7 +10,6 @@ import org.apache.spark.SparkConf;
import org.apache.spark.util.LongAccumulator; import org.apache.spark.util.LongAccumulator;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
@ -20,7 +21,7 @@ import eu.dnetlib.dhp.schema.mdstore.Provenance;
import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction; import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@Disabled // @Disabled
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class BaseTransfomationTest extends AbstractVocabularyTest { public class BaseTransfomationTest extends AbstractVocabularyTest {
@ -64,6 +65,21 @@ public class BaseTransfomationTest extends AbstractVocabularyTest {
System.out.println(result.getBody()); System.out.println(result.getBody());
} }
@Test
void testBase2ODF_wrong_date() throws Exception {
final MetadataRecord mr = new MetadataRecord();
mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record_wrong_1.xml")));
final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml");
assertThrows(NullPointerException.class, () -> {
final MetadataRecord result = tr.call(mr);
System.out.println(result.getBody());
});
}
private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
final String xslt = new SAXReader() final String xslt = new SAXReader()
.read(this.getClass().getResourceAsStream(path)) .read(this.getClass().getResourceAsStream(path))

View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.transformation;
import static eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH; import static eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertThrows;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Path; import java.nio.file.Path;
@ -279,6 +280,19 @@ class TransformationJobTest extends AbstractVocabularyTest {
// TODO Create significant Assert // TODO Create significant Assert
} }
@Test
public void testInvalidXSLT() throws Exception{
final MetadataRecord mr = new MetadataRecord();
mr.setProvenance(new Provenance("openaire____::cnr_explora", "CNR ExploRA", "cnr_________"));
mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_cnr_explora.xml")));
// We Load the XSLT transformation Rule from the classpath
final XSLTTransformationFunction tr = loadTransformationRule("/eu/dnetlib/dhp/transform/invalid.xslt");
assertThrows(RuntimeException.class,()->tr.call(mr));
}
private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception { private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path)); final String trValue = IOUtils.toString(this.getClass().getResourceAsStream(path));
final LongAccumulator la = new LongAccumulator(); final LongAccumulator la = new LongAccumulator();

View File

@ -0,0 +1,19 @@
DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4
N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0
N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0
N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050109 social psychology,05010904 Group processes/Collective identity,0.5589094161987305,0.5166763067245483
N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050105 experimental psychology,05010501 Emotion/Affective science,0.44109055399894714,0.4833236634731293
N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050203 business & management,05020302 Supply chain management/Business terms,0.5459638833999634,0.5460261106491089
N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050211 marketing,05021102 Services marketing/Retailing,0.4540362060070038,0.4539738595485687
N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010504 meteorology & atmospheric sciences,01050407 Geomagnetism/Ionosphere,0.5131047964096069,0.4990350902080536
N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010502 geochemistry & geophysics,01050203 Seismology/Seismology measurement,0.4868951737880707,0.500964879989624
N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022002 Medical imaging/Medical physics,0.5068133473396301,0.10231181626910052
N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,N/A,0.49318668246269226,0.0
N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021702 Aging-associated diseases/Cognitive disorders,0.5134317874908447,0.09614889098529535
N/A,od______3978::6704dcced0fe3dd6fbf985dc2507f61c,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.48656824231147766,0.0
N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,0209 industrial biotechnology,020901 industrial engineering & automation,02090105 Control theory/Advanced driver assistance systems,0.5178514122962952,0.5198937654495239
N/A,dedup_wf_001::b77264819800b90c0328c4d17eea5c1a,02 engineering and technology,"0202 electrical engineering, electronic engineering, information engineering",020201 artificial intelligence & image processing,02020108 Fuzzy logic/Artificial neural networks/Computational neuroscience,0.48214852809906006,0.4801062345504761
N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,03 medical and health sciences,0302 clinical medicine,030217 neurology & neurosurgery,03021708 Neurotrauma/Stroke,0.5014800429344177,0.5109656453132629
N/A,od______2806::a938609e9f36ada6629a1bcc50c88230,02 engineering and technology,0206 medical engineering,020601 biomedical engineering,02060102 Medical terminology/Patient,0.4985199570655823,0.4890343248844147
1 DOI OAID level1 level2 level3 level4 score_for_L3 score_for_L4
2 N/A 78975075580c::e680668c98366c9cd6349afc62486a7f 03 medical and health sciences 0301 basic medicine 030104 developmental biology N/A 0.5 0.0
3 N/A 78975075580c::e680668c98366c9cd6349afc62486a7f 03 medical and health sciences 0303 health sciences 030304 developmental biology N/A 0.5 0.0
4 N/A od______2806::a1da9d2678b12969a9ab5f50b5e71d0a 05 social sciences 0501 psychology and cognitive sciences 050109 social psychology 05010904 Group processes/Collective identity 0.5589094161987305 0.5166763067245483
5 N/A od______2806::a1da9d2678b12969a9ab5f50b5e71d0a 05 social sciences 0501 psychology and cognitive sciences 050105 experimental psychology 05010501 Emotion/Affective science 0.44109055399894714 0.4833236634731293
6 N/A doajarticles::76535d77fd2a5fe9810aefafffb8ef6c 05 social sciences 0502 economics and business 050203 business & management 05020302 Supply chain management/Business terms 0.5459638833999634 0.5460261106491089
7 N/A doajarticles::76535d77fd2a5fe9810aefafffb8ef6c 05 social sciences 0502 economics and business 050211 marketing 05021102 Services marketing/Retailing 0.4540362060070038 0.4539738595485687
8 N/A od_______156::a3a0119c6d9d3a66943f8da042e97a5e 01 natural sciences 0105 earth and related environmental sciences 010504 meteorology & atmospheric sciences 01050407 Geomagnetism/Ionosphere 0.5131047964096069 0.4990350902080536
9 N/A od_______156::a3a0119c6d9d3a66943f8da042e97a5e 01 natural sciences 0105 earth and related environmental sciences 010502 geochemistry & geophysics 01050203 Seismology/Seismology measurement 0.4868951737880707 0.500964879989624
10 N/A od______2806::4b9a664dd6b8b04204cb613e7bc9c873 03 medical and health sciences 0302 clinical medicine 030220 oncology & carcinogenesis 03022002 Medical imaging/Medical physics 0.5068133473396301 0.10231181626910052
11 N/A od______2806::4b9a664dd6b8b04204cb613e7bc9c873 03 medical and health sciences 0302 clinical medicine 030204 cardiovascular system & hematology N/A 0.49318668246269226 0.0
12 N/A od______3341::ef754de29464abf9bc9b99664630ce74 03 medical and health sciences 0302 clinical medicine 030220 oncology & carcinogenesis 03022012 Oncology/Infectious causes of cancer 0.5 0.5
13 N/A od______3341::ef754de29464abf9bc9b99664630ce74 03 medical and health sciences 0302 clinical medicine 030220 oncology & carcinogenesis 03022012 Oncology/Infectious causes of cancer 0.5 0.5
14 N/A od______3978::6704dcced0fe3dd6fbf985dc2507f61c 03 medical and health sciences 0302 clinical medicine 030217 neurology & neurosurgery 03021702 Aging-associated diseases/Cognitive disorders 0.5134317874908447 0.09614889098529535
15 N/A od______3978::6704dcced0fe3dd6fbf985dc2507f61c 03 medical and health sciences 0301 basic medicine 030104 developmental biology N/A 0.48656824231147766 0.0
16 N/A dedup_wf_001::b77264819800b90c0328c4d17eea5c1a 02 engineering and technology 0209 industrial biotechnology 020901 industrial engineering & automation 02090105 Control theory/Advanced driver assistance systems 0.5178514122962952 0.5198937654495239
17 N/A dedup_wf_001::b77264819800b90c0328c4d17eea5c1a 02 engineering and technology 0202 electrical engineering, electronic engineering, information engineering 020201 artificial intelligence & image processing 02020108 Fuzzy logic/Artificial neural networks/Computational neuroscience 0.48214852809906006 0.4801062345504761
18 N/A od______2806::a938609e9f36ada6629a1bcc50c88230 03 medical and health sciences 0302 clinical medicine 030217 neurology & neurosurgery 03021708 Neurotrauma/Stroke 0.5014800429344177 0.5109656453132629
19 N/A od______2806::a938609e9f36ada6629a1bcc50c88230 02 engineering and technology 0206 medical engineering 020601 biomedical engineering 02060102 Medical terminology/Patient 0.4985199570655823 0.4890343248844147

View File

@ -0,0 +1,18 @@
{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"}
{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0301 basic medicine","level3":"030104 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
{"doi":"n/a","oaid":"od______3341::ef754de29464abf9bc9b99664630ce74","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030220 oncology & carcinogenesis","level4":"03022012 Oncology/Infectious causes of cancer","scoreL3":"0.5","scoreL4":"0.5"}
{"doi":"n/a","oaid":"78975075580c::e680668c98366c9cd6349afc62486a7f","level1":"03 medical and health sciences","level2":"0303 health sciences","level3":"030304 developmental biology","level4":"N/A","scoreL3":"0.5","scoreL4":"0.0"}
{"doi":"n/a","oaid":"od______3978::6704dcced0fe3dd6fbf985dc2507f61c","level1":"03 medical and health sciences","level2":"0302 clinical medicine","level3":"030217 neurology & neurosurgery","level4":"03021702 Aging-associated diseases/Cognitive disorders","scoreL3":"0.5134317874908447","scoreL4":"0.09614889098529535"}
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:dc="http://purl.org/dc/elements/1.1/"
exclude-result-prefixes="xsl vocabulary dateCleaner" version="2.0">
<xsl:param name="varOfficialName" />
<xsl:param name="varDataSourceId" />
<xsl:param name="varFP7" select="'corda_______::'" />
<xsl:param name="varH2020" select="'corda__h2020::'" />
<xsl:param name="repoCode"
select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
<xsl:param name="index" select="0" />
<xsl:param name="transDate" select="current-dateTime()" />
asdf;klamsdof'sdn &
<xsl:template match="/asdfasdf asdf&">
c:format'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:type" />
<xsl:with-param name="targetElement" select="'dc:type'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:source" />
<xsl:with-param name="targetElement" select="'dc:source'" />
</xsl:call-template>
<dc:language>
<xsl:value-of select="vocabulary:clean( //dc:language, 'dnet:languages')" />
</dc:language>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:rights" />
<xsl:with-param name="targetElement" select="'dc:rights'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:relation[not(starts-with(.,'info:cnr-pdr'))]" />
<xsl:with-param name="targetElement" select="'dc:relation'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:identifier[starts-with(., 'http')]" />
<xsl:with-param name="targetElement" select="'dc:identifier'" />
</xsl:call-template>
<xsl:for-each select="//dc:relation">
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
<oaf:projectid>
<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
</oaf:projectid>
</xsl:if>
<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
<oaf:projectid>
<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
</oaf:projectid>
</xsl:if>
</xsl:for-each>
<oaf:accessrights>
<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
</oaf:accessrights>
<xsl:variable name="varCobjCategory" select="vocabulary:clean( //dc:type, 'dnet:publication_resource')" />
<xsl:variable name="varSuperType" select="vocabulary:clean( $varCobjCategory, 'dnet:result_typologies')" />
<dr:CobjCategory type="{$varSuperType}"><xsl:value-of select="$varCobjCategory" /></dr:CobjCategory>
<xsl:variable name="varRefereedConvt" select="for $i in (//dc:type, //dc:description, //oai:setSpec) return vocabulary:clean( normalize-space($i), 'dnet:review_levels')" />
<xsl:variable name="varRefereedIdntf" select="(//*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '(^|.*[\.\-_/\s\(\)%\d#])pre[\.\-_/\s\(\)%\d#]?prints?([\.\-_/\s\(\)%\d#].*)?$')][count(//dc:identifier) = 1]/'0002', //*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '(^|.*[\.\-_/\s\(\)%\d#])refereed([\.\-_/\s\(\)\d%\d#].*)?$')]/'0001', //*[string(node-name(.)) = 'dc:identifier' and matches(lower-case(.), '.*-peer-reviewed-(fulltext-)?article-.*')]/'0001')" />
<xsl:variable name="varRefereedSourc" select="//*[string(node-name(.)) = ('dc:source', 'dc:publisher') and matches(lower-case(.), '^(.*\s)?pre[\s\-_]*prints?([\s\.,].*)?$')]/'0002'" />
<xsl:variable name="varRefereedDescr" select="(//dc:description[matches(lower-case(.), '.*(this\s*book|this\s*volume|it)\s*constitutes\s*the\s*(thoroughly\s*)?refereed') or matches(lower-case(.), '.*peer[\.\-_/\s\(\)]?review\s*under\s*responsibility\s*of.*') or matches(lower-case(.), '(this|a)\s*(article|preprint)\s*(has\s*been\s*)?(peer[\-\s]*)?reviewed\s*and\s*recommended\s*by\s*peer[\-\s]*community')]/'0001', //dc:description[matches(., '^version\s*(préliminaire.*|preliminary.*|0$)')]/'0002')" />
<xsl:variable name="varRefereedTitle" select="(//dc:title[matches(lower-case(.), '.*\[.*peer[\s\-\._]*review\s*:.*\]\s*$')]/'0001', //dc:title[matches(lower-case(.), '.*\(\s*pre[\s\-\._]*prints?\s*\)\s*$')]/'0002')" />
<xsl:variable name="varRefereedSubjt" select="(//dc:subject[matches(lower-case(.), '^\s*refereed\s*$')][//oaf:datasourceprefix = 'narcis______']/'0001', //dc:subject[matches(lower-case(.), '^\s*no[nt].{0,3}refereed\s*$')][//oaf:datasourceprefix = 'narcis______']/'0002')" />
<xsl:variable name="varRefereed" select="($varRefereedConvt, $varRefereedIdntf, $varRefereedSourc, $varRefereedDescr, $varRefereedTitle, $varRefereedSubjt)" />
<xsl:choose>
<xsl:when test="count($varRefereed[. = '0001']) &gt; 0">
<oaf:refereed>
<xsl:value-of select="'0001'" />
</oaf:refereed>
</xsl:when>
<xsl:when test="count($varRefereed[. = '0002']) &gt; 0">
<oaf:refereed>
<xsl:value-of select="'0002'" />
</oaf:refereed>
</xsl:when>
</xsl:choose>
<oaf:dateAccepted>
<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
</oaf:dateAccepted>
<xsl:if test="//dc:relation[starts-with(., 'http')] and //dc:rights[.='info:eu-repo/semantics/openAccess']">
<oaf:fulltext>
<xsl:value-of select="//dc:relation[starts-with(., 'http')]" />
</oaf:fulltext>
</xsl:if>
<oaf:hostedBy name="{$varOfficialName}" id="{$varDataSourceId}" />
<oaf:collectedFrom name="{$varOfficialName}" id="{$varDataSourceId}" />
<xsl:variable name="varKnownFileEndings" select="('.bmp', '.doc', '.docx', '.epub', '.flv', '.jpeg', '.jpg', '.m4v', '.mp4', '.mpg', '.odp', '.pdf', '.png', '.ppt', '.tiv', '.txt', '.xls', '.xlsx', '.zip')" />
<xsl:variable name="varIdDoi" select="distinct-values((//dc:identifier[starts-with(., '10.')][matches(., '(10[.][0-9]{4,}[^\s/&gt;]*/[^\s&gt;]+)')], //dc:identifier[starts-with(., 'http') and (contains(., '://dx.doi.org/10.') or contains(., '://doi.org/10.'))]/substring-after(., 'doi.org/'), //dc:identifier[starts-with(lower-case(.), 'doi:10.')]/substring-after(lower-case(.), 'doi:')))" />
<xsl:for-each select="$varIdDoi">
<oaf:identifier identifierType="doi">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:variable name="varIdHdl" select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))" />
<xsl:for-each select="$varIdHdl" >
<oaf:identifier identifierType="handle">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:variable name="varIdUrn" select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])" />
<xsl:for-each select="$varIdUrn">
<oaf:identifier identifierType="urn">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:variable name="varOrigBaseUrl" select="//*[local-name() = 'about']/*[local-name() = 'provenance']//*[local-name() = 'originDescription' and not(./*[local-name() = 'originDescription'])]/*[local-name() = 'baseURL']" />
<xsl:variable name="varIdLdpg" select="distinct-values(//dc:identifier[(contains(substring-after(., '://'), '/') and contains($varOrigBaseUrl, substring-before(substring-after(., '://'), '/'))) or (contains(substring-after(., '://'), ':') and contains($varOrigBaseUrl, substring-before(substring-after(., '://'), ':')))][not(replace(lower-case(.), '.*(\.[a-z]*)$', '$1') = $varKnownFileEndings)])" />
<xsl:for-each select="$varIdLdpg">
<oaf:identifier identifierType="landingPage">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:variable name="varIdUrl" select="distinct-values(//dc:identifier[starts-with(., 'http')][not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/'))][count(index-of($varIdLdpg, .)) = 0])" />
<xsl:for-each select="$varIdUrl">
<oaf:identifier identifierType="url">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="//oai:setSpec">
<xsl:variable name="rorDsId" select="vocabulary:clean(., 'cnr:institutes')" />
<xsl:if test="contains($rorDsId, '/ror.org/')">
<oaf:relation relType="resultOrganization" subRelType="affiliation" relClass="hasAuthorInstitution">
<xsl:value-of select="concat('ror_________::', $rorDsId)" />
</oaf:relation>
</xsl:if>
</xsl:for-each>
</metadata>
<xsl:copy-of select="//*[local-name() = 'about']" />
</record>
</xsl:template>
<xsl:template name="allElements">
<xsl:param name="sourceElement" />
<xsl:param name="targetElement" />
<xsl:for-each select="$sourceElement">
<xsl:element name="{$targetElement}">
<xsl:value-of select="normalize-space(.)" />
</xsl:element>
</xsl:for-each>
</xsl:template>
<xsl:template match="//*[local-name() = 'header']">
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
<xsl:element name="dr:dateOfTransformation">
<xsl:value-of select="$transDate" />
</xsl:element>
</xsl:copy>
</xsl:template>
<xsl:template match="node()|@*">
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
</xsl:copy>
</xsl:template>
</xsl:stylesheet>

View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.dedup;
import java.util.*; import java.util.*;
import java.util.stream.Stream; import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.beanutils.BeanUtils; import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.FlatMapFunction;
@ -14,6 +15,7 @@ import org.apache.spark.sql.*;
import eu.dnetlib.dhp.oa.dedup.model.Identifier; import eu.dnetlib.dhp.oa.dedup.model.Identifier;
import eu.dnetlib.dhp.oa.merge.AuthorMerger; import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
@ -172,7 +174,7 @@ public class DedupRecordFactory {
entity = swap; entity = swap;
} }
entity.mergeFrom(duplicate); entity = MergeUtils.checkedMerge(entity, duplicate);
if (ModelSupport.isSubClass(duplicate, Result.class)) { if (ModelSupport.isSubClass(duplicate, Result.class)) {
Result re = (Result) entity; Result re = (Result) entity;

View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup;
import static org.apache.spark.sql.functions.col; import static org.apache.spark.sql.functions.col;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
@ -127,10 +128,8 @@ public class SparkPropagateRelation extends AbstractSparkAction {
(MapFunction<Relation, String>) r -> String (MapFunction<Relation, String>) r -> String
.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()), .join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
Encoders.STRING()) Encoders.STRING())
.reduceGroups((ReduceFunction<Relation>) (b, a) -> { .reduceGroups((ReduceFunction<Relation>) MergeUtils::mergeRelation
b.mergeFrom(a); )
return b;
})
.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC); .map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
final String outputRelationPath = graphOutputPath + "/relation"; final String outputRelationPath = graphOutputPath + "/relation";

View File

@ -3,17 +3,18 @@ package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils
import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.doiboost.mag.ConversionUtil import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.functions.col import org.apache.spark.sql.functions.col
import org.apache.spark.sql._ import org.apache.spark.sql._
import org.json4s.DefaultFormats import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse import org.json4s.jackson.JsonMethods.parse
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
object SparkGenerateDoiBoost { object SparkGenerateDoiBoost {
@ -78,8 +79,10 @@ object SparkGenerateDoiBoost {
if (item._2 != null) { if (item._2 != null) {
val otherPub = item._2._2 val otherPub = item._2._2
if (otherPub != null) { if (otherPub != null) {
crossrefPub.mergeFrom(otherPub) val mergedAuthor = AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)
crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)) val res = MergeUtils.mergePublication(crossrefPub, otherPub)
res.setAuthor(mergedAuthor);
return res
} }
} }
crossrefPub crossrefPub
@ -130,14 +133,13 @@ object SparkGenerateDoiBoost {
// So we have to merge // So we have to merge
val b1 = left._2 val b1 = left._2
val b2 = right._2 val b2 = right._2
b1.mergeFrom(b2)
b1.mergeOAFDataInfo(b2)
val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
b1.setAuthor(authors) val merged = MergeUtils.mergePublication(b1, b2);
merged.setAuthor(authors)
if (b2.getId != null && b2.getId.nonEmpty) if (b2.getId != null && b2.getId.nonEmpty)
b1.setId(b2.getId) merged.setId(b2.getId)
//Return publication Merged //Return publication Merged
(b1.getId, b1) (merged.getId, merged)
} }
} else { } else {
// Left is Null so we return right // Left is Null so we return right

View File

@ -1,8 +1,8 @@
package eu.dnetlib.doiboost.mag package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, MergeUtils}
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject} import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, Subject}
import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._ import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.json4s import org.json4s
@ -142,8 +142,7 @@ case object ConversionUtil {
def mergePublication(a: Publication, b: Publication): Publication = { def mergePublication(a: Publication, b: Publication): Publication = {
if ((a != null) && (b != null)) { if ((a != null) && (b != null)) {
a.mergeFrom(b) MergeUtils.mergePublication(a, b)
a
} else { } else {
if (a == null) b else a if (a == null) b else a
} }

View File

@ -0,0 +1,39 @@
package eu.dnetlib.dhp.bulktag.actions;
import java.io.Serializable;
import java.util.List;
/**
* @author miriam.baglioni
* @Date 22/01/24
*/
public class Action implements Serializable {
private String clazz;
private String method;
private List<Parameters> params;
public String getClazz() {
return clazz;
}
public void setClazz(String clazz) {
this.clazz = clazz;
}
public String getMethod() {
return method;
}
public void setMethod(String method) {
this.method = method;
}
public List<Parameters> getParams() {
return params;
}
public void setParams(List<Parameters> params) {
this.params = params;
}
}

View File

@ -0,0 +1,45 @@
package eu.dnetlib.dhp.bulktag.actions;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 19/01/24
*/
public class ExecSubstringAction implements Serializable {
private String value;
private String from;
private String to;
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public String getFrom() {
return from;
}
public void setFrom(String from) {
this.from = from;
}
public String getTo() {
return to;
}
public void setTo(String to) {
this.to = to;
}
public String execSubstring() {
return this.value.substring(Integer.valueOf(this.from), Integer.valueOf(this.to));
}
}

View File

@ -0,0 +1,30 @@
package eu.dnetlib.dhp.bulktag.actions;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 22/01/24
*/
public class MapModel implements Serializable {
private String path;
private Action action;
public String getPath() {
return path;
}
public void setPath(String path) {
this.path = path;
}
public Action getAction() {
return action;
}
public void setAction(Action action) {
this.action = action;
}
}

View File

@ -0,0 +1,29 @@
package eu.dnetlib.dhp.bulktag.actions;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 22/01/24
*/
public class Parameters implements Serializable {
private String paramName;
private String paramValue;
public String getParamName() {
return paramName;
}
public void setParamName(String paramName) {
this.paramName = paramName;
}
public String getParamValue() {
return paramValue;
}
public void setParamValue(String paramValue) {
this.paramValue = paramValue;
}
}

View File

@ -4,7 +4,9 @@ package eu.dnetlib.dhp.bulktag.community;
import java.io.Serializable; import java.io.Serializable;
import java.util.HashMap; import java.util.HashMap;
public class ProtoMap extends HashMap<String, String> implements Serializable { import eu.dnetlib.dhp.bulktag.actions.MapModel;
public class ProtoMap extends HashMap<String, MapModel> implements Serializable {
public ProtoMap() { public ProtoMap() {
super(); super();

View File

@ -5,6 +5,8 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable; import java.io.Serializable;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -15,7 +17,10 @@ import org.slf4j.LoggerFactory;
import com.google.gson.Gson; import com.google.gson.Gson;
import com.jayway.jsonpath.DocumentContext; import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath; import com.jayway.jsonpath.JsonPath;
import com.jayway.jsonpath.PathNotFoundException;
import eu.dnetlib.dhp.bulktag.actions.MapModel;
import eu.dnetlib.dhp.bulktag.actions.Parameters;
import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag; import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ -35,27 +40,59 @@ public class ResultTagger implements Serializable {
return (tmp != clist.size()); return (tmp != clist.size());
} }
private Map<String, List<String>> getParamMap(final Result result, Map<String, String> params) { private Map<String, List<String>> getParamMap(final Result result, Map<String, MapModel> params)
throws NoSuchMethodException, InvocationTargetException {
Map<String, List<String>> param = new HashMap<>(); Map<String, List<String>> param = new HashMap<>();
String json = new Gson().toJson(result, Result.class); String json = new Gson().toJson(result, Result.class);
DocumentContext jsonContext = JsonPath.parse(json); DocumentContext jsonContext = JsonPath.parse(json);
if (params == null) { if (params == null) {
params = new HashMap<>(); params = new HashMap<>();
} }
for (String key : params.keySet()) { for (String key : params.keySet()) {
MapModel mapModel = params.get(key);
try { try {
param.put(key, jsonContext.read(params.get(key))); String path = mapModel.getPath();
} catch (com.jayway.jsonpath.PathNotFoundException e) { Object obj = jsonContext.read(path);
List<String> pathValue;
if (obj instanceof java.lang.String)
pathValue = Arrays.asList((String) obj);
else
pathValue = (List<String>) obj;
if (Optional.ofNullable(mapModel.getAction()).isPresent()) {
Class<?> c = Class.forName(mapModel.getAction().getClazz());
Object class_instance = c.newInstance();
Method setField = c.getMethod("setValue", String.class);
setField.invoke(class_instance, pathValue.get(0));
for (Parameters p : mapModel.getAction().getParams()) {
setField = c.getMethod("set" + p.getParamName(), String.class);
setField.invoke(class_instance, p.getParamValue());
}
param
.put(
key, Arrays
.asList((String) c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance)));
}
else {
param.put(key, pathValue);
}
} catch (PathNotFoundException | ClassNotFoundException | InstantiationException
| IllegalAccessException e) {
param.put(key, new ArrayList<>()); param.put(key, new ArrayList<>());
} }
} }
return param; return param;
} }
public <R extends Result> R enrichContextCriteria( public <R extends Result> R enrichContextCriteria(
final R result, final CommunityConfiguration conf, final Map<String, String> criteria) { final R result, final CommunityConfiguration conf, final Map<String, MapModel> criteria)
throws InvocationTargetException, NoSuchMethodException {
final Map<String, List<String>> param = getParamMap(result, criteria);
// Verify if the entity is deletedbyinference. In case verify if to clean the context list // Verify if the entity is deletedbyinference. In case verify if to clean the context list
// from all the zenodo communities // from all the zenodo communities
@ -64,6 +101,8 @@ public class ResultTagger implements Serializable {
return result; return result;
} }
final Map<String, List<String>> param = getParamMap(result, criteria);
// Execute the EOSCTag for the services // Execute the EOSCTag for the services
switch (result.getResulttype().getClassid()) { switch (result.getResulttype().getClassid()) {
case PUBLICATION_RESULTTYPE_CLASSID: case PUBLICATION_RESULTTYPE_CLASSID:

View File

@ -0,0 +1,34 @@
package eu.dnetlib.dhp.bulktag.criteria;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 11/11/22
*/
@VerbClass("greater_than")
public class GreatThanVerb implements Selection, Serializable {
private String param;
public GreatThanVerb() {
}
public GreatThanVerb(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.compareTo(param) > 0;
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

View File

@ -0,0 +1,34 @@
package eu.dnetlib.dhp.bulktag.criteria;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 11/11/22
*/
@VerbClass("lesser_than")
public class LessThanVerb implements Selection, Serializable {
private String param;
public LessThanVerb() {
}
public LessThanVerb(final String param) {
this.param = param;
}
@Override
public boolean apply(String value) {
return value.compareTo(param) < 0;
}
public String getParam() {
return param;
}
public void setParam(String param) {
this.param = param;
}
}

View File

@ -149,7 +149,7 @@ public class SparkResultToCommunityFromOrganizationJob {
} }
} }
// res.setContext(propagatedContexts); // res.setContext(propagatedContexts);
// ret.mergeFrom(res); // return MergeUtils.mergeResult(ret, res);
} }
return ret; return ret;
}; };

View File

@ -13,6 +13,7 @@ import java.util.List;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
@ -24,8 +25,6 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
import eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Context;
@ -162,7 +161,7 @@ public class SparkResultToCommunityFromProject implements Serializable {
} }
} }
res.setContext(propagatedContexts); res.setContext(propagatedContexts);
ret.mergeFrom(res); return MergeUtils.checkedMerge(ret, res);
} }
return ret; return ret;
}; };

View File

@ -13,6 +13,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row; import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
@ -31,18 +32,26 @@ public class BulkTagJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\"," public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
+ " \"title\" : \"$['title'][*]['value']\"," " \"title\":{\"path\":\"$['title'][*]['value']\"}, " +
+ " \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\"," " \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
+ " \"contributor\" : \"$['contributor'][*]['value']\"," " \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"
+ " \"description\" : \"$['description'][*]['value']\", " +
+ " \"subject\" :\"$['subject'][*]['value']\" , " + "\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," +
"\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," + " \"description\" : {\"path\":\"$['description'][*]['value']\"}," +
"\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," + " \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " +
"\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " + " \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " +
"\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," + "\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," +
"\"publisher\":\"$['publisher'].value\"," + "\"journal\":{\"path\":\"$['journal'].name\"}," +
"\"publicationyear\":\"$['dateofacceptance'].value\"} "; "\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," +
"\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," +
"\"publisher\":{\"path\":\"$['publisher'].value\"}," +
"\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " +
" \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," +
"\"method\":\"execSubstring\"," +
"\"params\":[" +
"{\"paramName\":\"From\", \"paramValue\":0}, " +
"{\"paramName\":\"To\",\"paramValue\":4}]}}}";
private static SparkSession spark; private static SparkSession spark;
@ -1600,4 +1609,94 @@ public class BulkTagJobTest {
Assertions.assertEquals(0, spark.sql(query).count()); Assertions.assertEquals(0, spark.sql(query).count());
} }
@Test
void pubdateTest() throws Exception {
final String pathMap = BulkTagJobTest.pathMap;
SparkBulkTagJob
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(),
"-taggingConf",
IOUtils
.toString(
BulkTagJobTest.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")),
"-outputPath", workingDir.toString() + "/",
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community, MyD.provenanceaction.classid "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
org.apache.spark.sql.Dataset<Row> queryResult = spark.sql(query);
queryResult.show(false);
Assertions.assertEquals(5, queryResult.count());
Assertions
.assertEquals(
1,
queryResult
.filter(
(FilterFunction<Row>) r -> r
.getAs("id")
.equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529"))
.count());
Assertions
.assertEquals(
1,
queryResult
.filter(
(FilterFunction<Row>) r -> r
.getAs("id")
.equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf"))
.count());
Assertions
.assertEquals(
1,
queryResult
.filter(
(FilterFunction<Row>) r -> r
.getAs("id")
.equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177"))
.count());
Assertions
.assertEquals(
1,
queryResult
.filter(
(FilterFunction<Row>) r -> r
.getAs("id")
.equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961"))
.count());
Assertions
.assertEquals(
1,
queryResult
.filter(
(FilterFunction<Row>) r -> r
.getAs("id")
.equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343"))
.count());
}
} }

View File

@ -7,6 +7,7 @@ import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FilterFunction;
@ -24,7 +25,6 @@ import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import scala.Tuple2; import scala.Tuple2;
/** /**
@ -248,11 +248,11 @@ public class MergeGraphTableSparkJob {
private T mergeAndGet(T b, T a) { private T mergeAndGet(T b, T a) {
if (Objects.nonNull(a) && Objects.nonNull(b)) { if (Objects.nonNull(a) && Objects.nonNull(b)) {
if (ModelSupport.isSubClass(a, OafEntity.class) && ModelSupport.isSubClass(b, OafEntity.class)) { if (ModelSupport.isSubClass(a, OafEntity.class) && ModelSupport.isSubClass(b, OafEntity.class)) {
return (T) OafMapperUtils.mergeEntities((OafEntity) b, (OafEntity) a); return (T) MergeUtils.merge(b, a);
} }
if (a instanceof Relation && b instanceof Relation) { if (a instanceof Relation && b instanceof Relation) {
((Relation) a).mergeFrom(b); ((Relation) a).mergeFrom(b);
return a; return (T) MergeUtils.mergeRelation((Relation)a, (Relation) b);
} }
} }
return Objects.isNull(a) ? b : a; return Objects.isNull(a) ? b : a;

View File

@ -1,14 +1,16 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.util.Arrays; import eu.dnetlib.dhp.common.HdfsSupport;
import java.util.List; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import java.util.Objects; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import java.util.Optional; import eu.dnetlib.dhp.schema.common.ModelSupport;
import java.util.stream.Collectors; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
@ -16,27 +18,18 @@ import org.apache.hadoop.io.compress.GzipCodec;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2; import scala.Tuple2;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
public class GenerateEntitiesApplication extends AbstractMigrationApplication { public class GenerateEntitiesApplication extends AbstractMigrationApplication {
private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class);
@ -137,7 +130,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication {
save( save(
inputRdd inputRdd
.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf)) .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
.reduceByKey(OafMapperUtils::merge) .reduceByKey(MergeUtils::merge)
.map(Tuple2::_2), .map(Tuple2::_2),
targetPath); targetPath);
break; break;

View File

@ -12,6 +12,16 @@
<name>targetPath</name> <name>targetPath</name>
<description>the output path of the graph enriched</description> <description>the output path of the graph enriched</description>
</property> </property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
</parameters> </parameters>
<start to="EnrichGraph"/> <start to="EnrichGraph"/>
@ -31,8 +41,8 @@
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=2g --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.sql.shuffle.partitions=3000 --conf spark.sql.shuffle.partitions=5000
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

View File

@ -1,40 +0,0 @@
package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, Publication}
import eu.dnetlib.dhp.schema.sx.OafUtils
import org.apache.spark.sql.Row
import scala.collection.JavaConverters._
object AuthorEnricher extends Serializable {
def createAuthor(givenName: String, familyName: String, orcid: String): Author = {
val a = new Author
a.setName(givenName)
a.setSurname(familyName)
a.setFullname(s"$givenName $familyName")
val pid = OafUtils.createSP(orcid, ModelConstants.ORCID, ModelConstants.ORCID)
pid.setDataInfo(OafUtils.generateDataInfo())
pid.getDataInfo.setProvenanceaction(OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT"))
a.setPid(List(pid).asJava)
a
}
def toOAFAuthor(r: Row): java.util.List[Author] = {
r.getList[Row](1)
.asScala
.map(s => createAuthor(s.getAs[String]("givenName"), s.getAs[String]("familyName"), s.getAs[String]("orcid")))
.toList
.asJava
}
// def enrichAuthor(p:Publication,r:Row): Unit = {
// val k:Map[String, OAuthor] =r.getList[Row](1).asScala.map(s => (s.getAs[String]("orcid"), OAuthor(s.getAs[String]("givenName") ,s.getAs[String]("familyName") ))).groupBy(_._1).mapValues(_.map(_._2).head)
// println(k)
//
//
//
// }
}

View File

@ -0,0 +1,128 @@
package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.OafUtils
import java.util
import scala.beans.BeanProperty
import scala.collection.JavaConverters._
import scala.util.control.Breaks.{break, breakable}
case class ORCIDAuthorEnricherResult(
@BeanProperty var id: String,
@BeanProperty var enriched_author: java.util.List[Author],
@BeanProperty var author_matched: java.util.List[MatchedAuthors],
@BeanProperty var author_unmatched: java.util.List[Author],
@BeanProperty var orcid_unmatched: java.util.List[OrcidAutor]
)
object ORCIDAuthorEnricher extends Serializable {
def enrichOrcid(
id: String,
graph_authors: java.util.List[Author],
orcid_authors: java.util.List[OrcidAutor]
): ORCIDAuthorEnricherResult = {
// Author enriching strategy:
// 1) create a copy of graph author list in unmatched_authors
// 2) find best match in unmatched_authors, remove it from unmatched_authors and enrich it so
// that the enrichment is reflected in graph_authors (they share author instances)
// 3) repeat (2) till the end of the list and then with different matching algorithms that have decreasing
// trust in their output
// At the end unmatched_authors will contain authors not matched with any of the matching algos
val unmatched_authors = new util.ArrayList[Author](graph_authors)
val matches = {
// Look after exact fullname match, reconstruct ORCID fullname as givenName + familyName
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.givenName + " " + orcid.familyName),
"fullName"
) ++
// Look after exact reversed fullname match, reconstruct ORCID fullname as familyName + givenName
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.familyName + " " + orcid.givenName),
"reversedFullName"
) ++
// split author names in tokens, order the tokens, then check for matches of full tokens or abbreviations
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers
.matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName),
"orderedTokens"
) ++
// look after exact matches of ORCID creditName
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) => ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.creditName),
"creditName"
) ++
// look after exact matches in ORCID otherNames
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) =>
orcid.otherNames != null && ORCIDAuthorMatchers.matchOtherNames(author.getFullname, orcid.otherNames.asScala),
"otherNames"
)
}
ORCIDAuthorEnricherResult(id, graph_authors, matches.asJava, unmatched_authors, orcid_authors)
}
private def extractAndEnrichMatches(
graph_authors: java.util.List[Author],
orcid_authors: java.util.List[OrcidAutor],
matchingFunc: (Author, OrcidAutor) => Boolean,
matchName: String
) = {
val matched = scala.collection.mutable.ArrayBuffer.empty[MatchedAuthors]
if (graph_authors != null && !graph_authors.isEmpty) {
val ait = graph_authors.iterator
while (ait.hasNext) {
val author = ait.next()
val oit = orcid_authors.iterator
breakable {
while (oit.hasNext) {
val orcid = oit.next()
if (matchingFunc(author, orcid)) {
ait.remove()
oit.remove()
matched += MatchedAuthors(author, orcid, matchName)
if (author.getPid == null) {
author.setPid(new util.ArrayList[StructuredProperty]())
}
val orcidPID = OafUtils.createSP(orcid.orcid, ModelConstants.ORCID, ModelConstants.ORCID)
orcidPID.setDataInfo(OafUtils.generateDataInfo())
orcidPID.getDataInfo.setProvenanceaction(
OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT")
)
author.getPid.add(orcidPID)
break()
}
}
}
}
}
matched
}
}

View File

@ -0,0 +1,65 @@
package eu.dnetlib.dhp.enrich.orcid
import java.util.Locale
import java.util.regex.Pattern
object ORCIDAuthorMatchers {
val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+")
val WORD_DIFF = 2
def matchEqualsIgnoreCase(a1: String, a2: String): Boolean = {
if (a1 == null || a2 == null)
false
else
a1 == a2 || a1.toLowerCase(Locale.ROOT).equals(a2.toLowerCase(Locale.ROOT))
}
def matchOtherNames(fullName: String, otherNames: Seq[String]): Boolean = {
if (otherNames != null) {
otherNames.exists(matchEqualsIgnoreCase(fullName, _))
} else {
false
}
}
def matchOrderedTokenAndAbbreviations(a1: String, a2: String): Boolean = {
val p1: Array[String] = SPLIT_REGEX.split(a1.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted
val p2: Array[String] = SPLIT_REGEX.split(a2.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted
if (p1.length < 2 || p2.length < 2) return false
if (Math.abs(p1.length - p2.length) > WORD_DIFF) return false // use alternative comparison algo
var p1Idx: Int = 0
var p2Idx: Int = 0
var shortMatches: Int = 0
var longMatches: Int = 0
while (p1Idx < p1.length && p2Idx < p2.length) {
val e1: String = p1(p1Idx)
val c1: Char = e1.charAt(0)
val e2: String = p2(p2Idx)
val c2: Char = e2.charAt(0)
if (c1 < c2) p1Idx += 1
else if (c1 > c2) p2Idx += 1
else {
var res: Boolean = false
if (e1.length != 1 && e2.length != 1) {
res = e1 == e2
longMatches += 1
} else {
res = true
shortMatches += 1
}
if (res) {
p1Idx += 1
p2Idx += 1
} else {
val diff: Int = e1.compareTo(e2)
if (diff < 0) p1Idx += 1
else if (diff > 0) p2Idx += 1
}
}
}
longMatches > 0 && (shortMatches + longMatches) == Math.min(p1.length, p2.length)
}
}

View File

@ -1,14 +1,39 @@
package eu.dnetlib.dhp.enrich.orcid package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.application.AbstractScalaApplication import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.common.ModelSupport import eu.dnetlib.dhp.schema.common.ModelSupport
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software} import eu.dnetlib.dhp.schema.oaf._
import org.apache.spark.sql.functions._
import org.apache.spark.sql._ import org.apache.spark.sql._
import org.apache.spark.sql.functions._
import org.slf4j.{Logger, LoggerFactory} import org.slf4j.{Logger, LoggerFactory}
import scala.beans.BeanProperty
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
case class OrcidAutor(
@BeanProperty var orcid: String,
@BeanProperty var familyName: String,
@BeanProperty var givenName: String,
@BeanProperty var creditName: String,
@BeanProperty var otherNames: java.util.List[String]
) {
def this() = this("null", "null", "null", "null", null)
}
case class MatchData(
@BeanProperty var id: String,
@BeanProperty var graph_authors: java.util.List[Author],
@BeanProperty var orcid_authors: java.util.List[OrcidAutor]
) {
def this() = this("null", null, null)
}
case class MatchedAuthors(
@BeanProperty var author: Author,
@BeanProperty var orcid: OrcidAutor,
@BeanProperty var `type`: String
)
class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) { extends AbstractScalaApplication(propertyPath, args, log: Logger) {
@ -22,107 +47,132 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String]
log.info(s"orcidPath is '$orcidPath'") log.info(s"orcidPath is '$orcidPath'")
val targetPath = parser.get("targetPath") val targetPath = parser.get("targetPath")
log.info(s"targetPath is '$targetPath'") log.info(s"targetPath is '$targetPath'")
val orcidPublication: Dataset[Row] = generateOrcidTable(spark, orcidPath)
// ModelSupport.entityTypes.entrySet().asScala.filter(k => k.getKey.getClass isInstance(Result))
enrichResult( createTemporaryData(graphPath, orcidPath, targetPath)
spark, analisys(targetPath)
s"$graphPath/publication", generateGraph(graphPath, targetPath)
orcidPublication,
s"$targetPath/publication",
Encoders.bean(classOf[Publication])
)
enrichResult(
spark,
s"$graphPath/dataset",
orcidPublication,
s"$targetPath/dataset",
Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset])
)
enrichResult(
spark,
s"$graphPath/software",
orcidPublication,
s"$targetPath/software",
Encoders.bean(classOf[Software])
)
enrichResult(
spark,
s"$graphPath/otherresearchproduct",
orcidPublication,
s"$targetPath/otherresearchproduct",
Encoders.bean(classOf[OtherResearchProduct])
)
} }
private def enrichResult[T <: Result]( private def generateGraph(graphPath: String, targetPath: String): Unit = {
spark: SparkSession,
graphPath: String,
orcidPublication: Dataset[Row],
outputPath: String,
enc: Encoder[T]
): Unit = {
val entities = spark.read ModelSupport.entityTypes.asScala
.filter(e => ModelSupport.isResult(e._1))
.foreach(e => {
val resultType = e._1.name()
val enc = Encoders.bean(e._2)
val matched = spark.read
.schema(Encoders.bean(classOf[ORCIDAuthorEnricherResult]).schema)
.parquet(s"${targetPath}/${resultType}_matched")
.selectExpr("id", "enriched_author")
spark.read
.schema(enc.schema) .schema(enc.schema)
.json(graphPath) .json(s"$graphPath/$resultType")
.join(matched, Seq("id"), "left")
.withColumn(
"author",
when(size(col("enriched_author")).gt(0), col("enriched_author"))
.otherwise(col("author"))
)
.drop("enriched_author")
.write
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(s"${targetPath}/${resultType}")
})
}
private def createTemporaryData(graphPath: String, orcidPath: String, targetPath: String): Unit = {
val orcidAuthors =
spark.read.load(s"$orcidPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames")
val orcidWorks = spark.read
.load(s"$orcidPath/Works")
.select(col("orcid"), explode(col("pids")).alias("identifier"))
.where(
"identifier.schema IN('doi','pmid','pmc','arxiv','handle')" // scopus eid ?
)
val orcidWorksWithAuthors = orcidAuthors
.join(orcidWorks, Seq("orcid"))
.select(
lower(col("identifier.schema")).alias("pid_schema"),
lower(col("identifier.value")).alias("pid_value"),
struct(
col("orcid"),
col("givenName"),
col("familyName"),
col("creditName"),
col("otherNames")
).alias("author")
)
.cache()
ModelSupport.entityTypes.asScala
.filter(e => ModelSupport.isResult(e._1))
.foreach(e => {
val resultType = e._1.name()
val enc = Encoders.bean(e._2)
val oaEntities = spark.read
.schema(enc.schema)
.json(s"$graphPath/$resultType")
.select(col("id"), col("datainfo"), col("instance")) .select(col("id"), col("datainfo"), col("instance"))
.where("datainfo.deletedbyinference != true") .where("datainfo.deletedbyinference != true")
.drop("datainfo") .drop("datainfo")
.withColumn("instances", explode(col("instance"))) .withColumn("instances", explode(col("instance")))
.withColumn("pids", explode(col("instances.pid"))) .withColumn("pids", explode(col("instances.pid")))
.select( .select(
col("pids.qualifier.classid").alias("pid_schema"), lower(col("pids.qualifier.classid")).alias("pid_schema"),
col("pids.value").alias("pid_value"), lower(col("pids.value")).alias("pid_value"),
col("id").alias("dnet_id") col("id")
) )
val orcidDnet = orcidPublication val orcidDnet = orcidWorksWithAuthors
.join( .join(
entities, oaEntities,
lower(col("schema")).equalTo(lower(col("pid_schema"))) && Seq("pid_schema", "pid_value"),
lower(col("value")).equalTo(lower(col("pid_value"))),
"inner" "inner"
) )
.groupBy(col("dnet_id")) .groupBy(col("id"))
.agg(collect_set(orcidPublication("author")).alias("orcid_authors")) .agg(collect_set(col("author")).alias("orcid_authors"))
.select("dnet_id", "orcid_authors") .select("id", "orcid_authors")
.cache()
orcidDnet.count() val result =
val result = spark.read.schema(enc.schema).json(graphPath).as[T](enc) spark.read.schema(enc.schema).json(s"$graphPath/$resultType").selectExpr("id", "author as graph_authors")
result result
.joinWith(orcidDnet, result("id").equalTo(orcidDnet("dnet_id")), "left") .join(orcidDnet, Seq("id"))
.map {
case (r: T, null) =>
r
case (p: T, r: Row) =>
p.setAuthor(AuthorMerger.enrichOrcid(p.getAuthor, AuthorEnricher.toOAFAuthor(r)))
p
}(enc)
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)
.option("compression", "gzip") .option("compression", "gzip")
.json(outputPath) .parquet(s"$targetPath/${resultType}_unmatched")
})
orcidWorksWithAuthors.unpersist()
} }
private def generateOrcidTable(spark: SparkSession, inputPath: String): Dataset[Row] = { private def analisys(targetPath: String): Unit = {
val orcidAuthors = ModelSupport.entityTypes.asScala
spark.read.load(s"$inputPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") .filter(e => ModelSupport.isResult(e._1))
val orcidWorks = spark.read .foreach(e => {
.load(s"$inputPath/Works") val resultType = e._1.name()
.select(col("orcid"), explode(col("pids")).alias("identifier"))
.where( spark.read
"identifier.schema IN('doi','pmid','pmc','arxiv','handle')" .parquet(s"$targetPath/${resultType}_unmatched")
) .where("size(graph_authors) > 0")
val orcidPublication = orcidAuthors .as[MatchData](Encoders.bean(classOf[MatchData]))
.join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) .map(md => {
.select( ORCIDAuthorEnricher.enrichOrcid(md.id, md.graph_authors, md.orcid_authors)
col("identifier.schema").alias("schema"), })(Encoders.bean(classOf[ORCIDAuthorEnricherResult]))
col("identifier.value").alias("value"), .write
struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") .option("compression", "gzip")
) .mode("overwrite")
orcidPublication.cache() .parquet(s"$targetPath/${resultType}_matched")
})
} }
} }

View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.graph.resolution
import com.fasterxml.jackson.databind.ObjectMapper import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.common.EntityType import eu.dnetlib.dhp.schema.common.EntityType
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.hadoop.fs.{FileSystem, Path} import org.apache.hadoop.fs.{FileSystem, Path}
@ -118,15 +119,12 @@ object SparkResolveEntities {
currentEntityDataset currentEntityDataset
.joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left") .joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left")
.map(k => { .map(k => {
val a = k._1 val a = k._1
val b = k._2 val b = k._2
if (b == null) if (b == null)
a._2 a._2
else { else
a._2.mergeFrom(b._2) MergeUtils.mergeResult(a._2, b._2)
a._2
}
}) })
.map(r => mapper.writeValueAsString(r))(Encoders.STRING) .map(r => mapper.writeValueAsString(r))(Encoders.STRING)
.write .write

View File

@ -1,6 +1,7 @@
package eu.dnetlib.dhp.sx.graph package eu.dnetlib.dhp.sx.graph
import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _} import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import org.apache.commons.io.IOUtils import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf import org.apache.spark.SparkConf
@ -130,10 +131,7 @@ object SparkCreateInputGraph {
val ds: Dataset[T] = spark.read.load(sourcePath).as[T] val ds: Dataset[T] = spark.read.load(sourcePath).as[T]
ds.groupByKey(_.getId) ds.groupByKey(_.getId)
.reduceGroups { (x: T, y: T) => .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] }
x.mergeFrom(y)
x
}
.map(_._2) .map(_._2)
.write .write
.mode(SaveMode.Overwrite) .mode(SaveMode.Overwrite)

View File

@ -1,10 +1,9 @@
package eu.dnetlib.oa.merge; package eu.dnetlib.dhp.enrich.orcid;
import static org.junit.jupiter.api.Assertions.*;
import java.io.BufferedReader; import java.io.BufferedReader;
import java.io.InputStreamReader; import java.io.InputStreamReader;
import java.util.Collections;
import java.util.List; import java.util.List;
import java.util.Objects; import java.util.Objects;
@ -14,10 +13,9 @@ import org.junit.platform.commons.util.StringUtils;
import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Author;
public class AuthorMergerTest { public class ORCIDAuthorEnricherTest {
@Test @Test
public void testEnrcichAuthor() throws Exception { public void testEnrcichAuthor() throws Exception {
@ -26,12 +24,13 @@ public class AuthorMergerTest {
BufferedReader pr = new BufferedReader(new InputStreamReader( BufferedReader pr = new BufferedReader(new InputStreamReader(
Objects Objects
.requireNonNull( .requireNonNull(
AuthorMergerTest.class ORCIDAuthorEnricherTest.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); .getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_publication_sample.json"))));
BufferedReader or = new BufferedReader(new InputStreamReader( BufferedReader or = new BufferedReader(new InputStreamReader(
Objects Objects
.requireNonNull( .requireNonNull(
AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); ORCIDAuthorEnricherTest.class
.getResourceAsStream("/eu/dnetlib/dhp/enrich/orcid/authors_orcid_sample.json"))));
TypeReference<List<Author>> aclass = new TypeReference<List<Author>>() { TypeReference<List<Author>> aclass = new TypeReference<List<Author>>() {
}; };
@ -67,7 +66,8 @@ public class AuthorMergerTest {
long start = System.currentTimeMillis(); long start = System.currentTimeMillis();
// final List<Author> enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); // final List<Author> enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors);
final List<Author> enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); final List<Author> enrichedList = Collections.emptyList(); // SparkEnrichGraphWithOrcidAuthors.enrichOrcid(publicationAuthors,
// orcidAuthors);
long enrichedAuthorWithPid = enrichedList long enrichedAuthorWithPid = enrichedList
.stream() .stream()
@ -91,24 +91,4 @@ public class AuthorMergerTest {
} }
} }
@Test
public void checkSimilarityTest() {
final Author left = new Author();
left.setName("Anand");
left.setSurname("Rachna");
left.setFullname("Anand, Rachna");
System.out.println(AuthorMerger.normalizeFullName(left.getFullname()));
final Author right = new Author();
right.setName("Rachna");
right.setSurname("Anand");
right.setFullname("Rachna, Anand");
// System.out.println(AuthorMerger.normalize(right.getFullname()));
boolean same = AuthorMerger.checkORCIDSimilarity(left, right);
assertTrue(same);
}
} }

View File

@ -1,13 +1,12 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertEquals; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import static org.junit.jupiter.api.Assertions.assertTrue; import eu.dnetlib.dhp.schema.common.ModelConstants;
import static org.mockito.Mockito.lenient; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
import java.io.IOException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import java.util.List; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
@ -16,13 +15,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import java.io.IOException;
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; import java.util.List;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import static org.junit.jupiter.api.Assertions.assertEquals;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import static org.junit.jupiter.api.Assertions.assertTrue;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import static org.mockito.Mockito.lenient;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
class GenerateEntitiesApplicationTest { class GenerateEntitiesApplicationTest {
@ -72,7 +70,7 @@ class GenerateEntitiesApplicationTest {
protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz, protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz,
String resultType) { String resultType) {
final Result merge = OafMapperUtils.mergeResults(publication, dataset); final Result merge = MergeUtils.mergeResult(publication, dataset);
assertTrue(clazz.isAssignableFrom(merge.getClass())); assertTrue(clazz.isAssignableFrom(merge.getClass()));
assertEquals(resultType, merge.getResulttype().getClassid()); assertEquals(resultType, merge.getResulttype().getClassid());
} }

View File

@ -0,0 +1,35 @@
package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.enrich.orcid.ORCIDAuthorMatchers.matchOrderedTokenAndAbbreviations
import org.junit.jupiter.api.Assertions.{assertFalse, assertTrue}
import org.junit.jupiter.api.Test
class ORCIDAuthorMatchersTest {
@Test def testShortNames(): Unit = {
assertTrue(matchOrderedTokenAndAbbreviations("Lasagni Mariozzi Federico", "Lasagni F. Mariozzi"))
}
@Test def testInvertedNames(): Unit = {
assertTrue(matchOrderedTokenAndAbbreviations("Andrea, Paolo Marcello", "Marcello Paolo, Andrea"))
}
@Test def testHomonymy(): Unit = {
assertTrue(matchOrderedTokenAndAbbreviations("Jang Myung Lee", "J Lee"))
}
@Test def testAmbiguousShortNames(): Unit = {
assertFalse(matchOrderedTokenAndAbbreviations("P. Mariozzi", "M. Paolozzi"))
}
@Test def testNonMatches(): Unit = {
assertFalse(matchOrderedTokenAndAbbreviations("Giovanni Paolozzi", "Francesco Paolozzi"))
assertFalse(matchOrderedTokenAndAbbreviations("G. Paolozzi", "F. Paolozzi"))
}
@Test def testChineseNames(): Unit = {
assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin"))
// assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented
}
}

View File

@ -0,0 +1,52 @@
/*
* Copyright (c) 2024.
* SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
* SPDX-License-Identifier: AGPL-3.0-or-later
*/
package eu.dnetlib.dhp.oa.provision;
import java.io.StringReader;
import java.io.StringWriter;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
public abstract class AbstractSolrRecordTransformJob {
protected static String toIndexRecord(Transformer tr, final String xmlRecord) {
final StreamResult res = new StreamResult(new StringWriter());
try {
tr.transform(new StreamSource(new StringReader(xmlRecord)), res);
return res.getWriter().toString();
} catch (TransformerException e) {
throw new IllegalArgumentException("XPathException on record: \n" + xmlRecord, e);
}
}
/**
* Creates the XSLT responsible for building the index xml records.
*
* @param format Metadata format name (DMF|TMF)
* @param xslt xslt for building the index record transformer
* @param fields the list of fields
* @return the javax.xml.transform.Transformer
* @throws TransformerException could happen
*/
protected static String getLayoutTransformer(String format, String fields, String xslt)
throws TransformerException {
final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt);
final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter());
layoutTransformer.setParameter("format", format);
layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt);
return layoutToXsltXslt.getWriter().toString();
}
}

View File

@ -27,14 +27,7 @@ import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper; import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits; import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
import scala.Tuple2; import scala.Tuple2;
@ -156,10 +149,33 @@ public class CreateRelatedEntitiesJob_phase1 {
case software: case software:
final Result result = (Result) entity; final Result result = (Result) entity;
if (result.getTitle() != null && !result.getTitle().isEmpty()) { if (Objects.nonNull(result.getTitle()) && !result.getTitle().isEmpty()) {
final StructuredProperty title = result.getTitle().stream().findFirst().get(); result
title.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH)); .getTitle()
re.setTitle(title); .stream()
.findFirst()
.map(StructuredProperty::getValue)
.ifPresent(
title -> re.getTitle().setValue(StringUtils.left(title, ModelHardLimits.MAX_TITLE_LENGTH)));
}
if (Objects.nonNull(result.getDescription()) && !result.getDescription().isEmpty()) {
result
.getDescription()
.stream()
.findFirst()
.map(Field::getValue)
.ifPresent(
d -> re.setDescription(StringUtils.left(d, ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH)));
}
if (Objects.nonNull(result.getAuthor()) && !result.getAuthor().isEmpty()) {
re
.setAuthor(
result
.getAuthor()
.stream()
.map(Author::getFullname)
.filter(StringUtils::isNotBlank)
.collect(Collectors.toList()));
} }
re.setDateofacceptance(getValue(result.getDateofacceptance())); re.setDateofacceptance(getValue(result.getDateofacceptance()));

View File

@ -0,0 +1,144 @@
package eu.dnetlib.dhp.oa.provision;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Optional;
import javax.xml.transform.TransformerException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoder;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
private static final Logger log = LoggerFactory.getLogger(SolrRecordDumpJob.class);
private static final Integer DEFAULT_BATCH_SIZE = 1000;
private final String inputPath;
private final String format;
private final String outputPath;
private final SparkSession spark;
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SolrRecordDumpJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("inputPath");
log.info("inputPath: {}", inputPath);
final String format = parser.get("format");
log.info("format: {}", format);
final String outputPath = Optional
.ofNullable(parser.get("outputPath"))
.map(StringUtils::trim)
.orElse(null);
log.info("outputPath: {}", outputPath);
final Integer batchSize = Optional
.ofNullable(parser.get("batchSize"))
.map(Integer::valueOf)
.orElse(DEFAULT_BATCH_SIZE);
log.info("batchSize: {}", batchSize);
final boolean shouldIndex = Optional
.ofNullable(parser.get("shouldIndex"))
.map(Boolean::valueOf)
.orElse(false);
log.info("shouldIndex: {}", shouldIndex);
final SparkConf conf = new SparkConf();
conf.registerKryoClasses(new Class[] {
SerializableSolrInputDocument.class
});
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
new SolrRecordDumpJob(spark, inputPath, format, outputPath).run(isLookup);
});
}
public SolrRecordDumpJob(SparkSession spark, String inputPath, String format, String outputPath) {
this.spark = spark;
this.inputPath = inputPath;
this.format = format;
this.outputPath = outputPath;
}
public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
final String fields = isLookup.getLayoutSource(format);
log.info("fields: {}", fields);
final String xslt = isLookup.getLayoutTransformer();
final String dsId = isLookup.getDsId(format);
log.info("dsId: {}", dsId);
final String indexRecordXslt = getLayoutTransformer(format, fields, xslt);
log.info("indexRecordTransformer {}", indexRecordXslt);
final Encoder<TupleWrapper> encoder = Encoders.bean(TupleWrapper.class);
spark
.read()
.schema(encoder.schema())
.json(inputPath)
.as(encoder)
.map(
(MapFunction<TupleWrapper, TupleWrapper>) t -> new TupleWrapper(
toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()),
t.getJson()),
Encoders.bean(TupleWrapper.class))
.map(
(MapFunction<TupleWrapper, SerializableSolrInputDocument>) t -> {
SolrInputDocument s = new StreamingInputDocumentFactory()
.parseDocument(t.getXml(), t.getJson());
return new SerializableSolrInputDocument(s);
},
Encoders.kryo(SerializableSolrInputDocument.class))
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);
}
}

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