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adding context information to projects and datasources #407

Merged
claudio.atzori merged 8 commits from taggingProjects into beta 2024-03-26 14:53:39 +01:00
Conversation 0 Commits 8 Files Changed 15 +116875 -1654
234 changed files with 116875 additions and 1654 deletions
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99
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
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@ -145,105 +145,6 @@ public class AuthorMerger {
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) {
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
: "";

4
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java
View File

@ -26,7 +26,7 @@ import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
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.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ -135,7 +135,7 @@ public class GroupEntitiesSparkJob {
.applyCoarVocabularies(entity, vocs),
OAFENTITY_KRYO_ENC)
.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
.reduceGroups((ReduceFunction<OafEntity>) OafMapperUtils::mergeEntities)
.reduceGroups((ReduceFunction<OafEntity>) MergeUtils::checkedMerge)
.map(
(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
t._2().getClass().getName(), t._2()),

76
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java Normal file
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@ -0,0 +1,76 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashSet;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleaningFunctions {
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
public static final String DOI_PREFIX = "10.";
public static final Set<String> PID_BLACKLIST = new HashSet<>();
static {
PID_BLACKLIST.add("none");
PID_BLACKLIST.add("na");
}
public CleaningFunctions() {
}
/**
* Utility method that filter PID values on a per-type basis.
* @param s the PID whose value will be checked.
* @return false if the pid matches the filter criteria, true otherwise.
*/
public static boolean pidFilter(StructuredProperty s) {
final String pidValue = s.getValue();
if (Objects.isNull(s.getQualifier()) ||
StringUtils.isBlank(pidValue) ||
StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
return false;
}
if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
return false;
}
return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
pid
.setValue(
normalizePidValue(
pid.getQualifier().getClassid(),
pid.getValue()));
return pid;
}
public static String normalizePidValue(String pidType, String pidValue) {
String value = Optional
.ofNullable(pidValue)
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pidType) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
}
return value;
}
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

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

294
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java Normal file
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@ -0,0 +1,294 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.HashBiMap;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* Factory class for OpenAIRE identifiers in the Graph
*/
public class IdentifierFactory implements Serializable {
public static final String ID_SEPARATOR = "::";
public static final String ID_PREFIX_SEPARATOR = "|";
public static final int ID_PREFIX_LEN = 12;
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
* The id of the record (source_::id) will be rewritten as pidType_::id)
*/
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
static {
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
*
* If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
* See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
*/
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
static {
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
* the same OpenAIRE id.
*/
public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
static {
ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
}
public static Set<String> delegatedAuthorityDatasourceIds() {
return DELEGATED_PID_AUTHORITY
.values()
.stream()
.flatMap(m -> m.keySet().stream())
.collect(Collectors.toCollection(HashSet::new));
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
}
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
if (entity == null)
return null;
StructuredProperty pid = null;
if (entity.getPid() != null) {
pid = entity
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
} else {
if (entity.getInstance() != null) {
pid = entity
.getInstance()
.stream()
.filter(i -> i.getPid() != null)
.flatMap(i -> i.getPid().stream())
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
}
}
if (pid != null)
return idFromPid(entity, pid, true);
return null;
}
/**
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
*
* @param entity the entity providing PIDs and a default ID.
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
* @param md5 indicates whether should hash the PID value or not.
* @return an identifier from the most relevant PID, entity.id otherwise
*/
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
.stream()
.flatMap(Set::stream)
.min(new PidComparator<>(entity))
.map(
min -> Optional
.ofNullable(pids.get(min.getQualifier().getClassid()))
.map(
p -> p
.stream()
.sorted(new PidValueComparator())
.findFirst()
.map(s -> idFromPid(entity, s, md5))
.orElseGet(entity::getId))
.orElseGet(entity::getId))
.orElseGet(entity::getId);
}
private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(IdentifierFactory::mapPids)
.orElse(new HashMap<>());
} else {
return entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
}
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
return instance
.stream()
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
boolean mapHandles) {
return Optional
.ofNullable(pid)
.map(
pp -> pp
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
.map(CleaningFunctions::normalizePidValue)
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
if (Objects.isNull(collectedFrom)) {
return false;
}
boolean isEnrich = Optional
.ofNullable(ENRICHMENT_PROVIDER.get(pType))
.map(
enrich -> enrich.containsKey(collectedFrom.getKey())
|| enrich.containsValue(collectedFrom.getValue()))
.orElse(false);
boolean isAuthority = Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(
authorities -> authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue()))
.orElse(false);
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
}
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
if (Objects.isNull(da)) {
return true;
}
if (!da.containsKey(collectedFrom.getKey())) {
return true;
}
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/
public static <T extends OafEntity> String createIdentifier(T entity) {
return createIdentifier(entity, true);
}
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
}
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
return new StringBuilder()
.append(numericPrefix)
.append(ID_PREFIX_SEPARATOR)
.append(createPrefix(pidType))
.append(ID_SEPARATOR)
.append(md5 ? md5(pidValue) : pidValue)
.toString();
}
// create the prefix (length = 12)
private static String createPrefix(String pidType) {
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
while (prefix.length() < ID_PREFIX_LEN) {
prefix.append("_");
}
return prefix.substring(0, ID_PREFIX_LEN);
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
return null;
}
}
}

78
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java Normal file
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@ -0,0 +1,78 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
//
// 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;
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());
}
}
}

891
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java Normal file
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@ -0,0 +1,891 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static com.google.common.base.Preconditions.checkArgument;
import static org.apache.commons.lang3.ObjectUtils.firstNonNull;
import java.text.ParseException;
import java.time.ZoneId;
import java.util.*;
import java.util.function.BinaryOperator;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.base.Joiner;
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.*;
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, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
Function<T, K> keyExtractor, BinaryOperator<T> merger) {
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 new ArrayList<>(Stream
.concat(h.stream(), l.stream())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toMap(keyExtractor, v -> v, merger))
.values());
}
private static <T, K> 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
// cannot use com.google.common.base.Objects.firstNonNull as it throws NPE when both terms are null
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(
mergeLists(
merge.getInstance(), enrich.getInstance(), trust,
MergeUtils::instanceKeyExtractor,
MergeUtils::instanceMerger));
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 String instanceKeyExtractor(Instance i) {
return String
.join(
"::",
kvKeyExtractor(i.getHostedby()),
kvKeyExtractor(i.getCollectedfrom()),
qualifierKeyExtractor(i.getAccessright()),
qualifierKeyExtractor(i.getInstancetype()),
Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
Optional
.ofNullable(i.getPid())
.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
.orElse(null));
}
private static Instance instanceMerger(Instance i1, Instance i2) {
Instance i = new Instance();
i.setHostedby(i1.getHostedby());
i.setCollectedfrom(i1.getCollectedfrom());
i.setAccessright(i1.getAccessright());
i.setInstancetype(i1.getInstancetype());
i.setPid(mergeLists(i1.getPid(), i2.getPid(), 0, MergeUtils::spKeyExtractor, (sp1, sp2) -> sp1));
i
.setAlternateIdentifier(
mergeLists(
i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
(sp1, sp2) -> sp1));
i
.setRefereed(
Collections
.min(
Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
new RefereedComparator()));
i
.setInstanceTypeMapping(
mergeLists(
i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
i.setFulltext(selectFulltext(i1.getFulltext(), i2.getFulltext()));
i.setDateofacceptance(selectOldestDate(i1.getDateofacceptance(), i2.getDateofacceptance()));
i.setLicense(firstNonNull(i1.getLicense(), i2.getLicense()));
i.setProcessingchargeamount(firstNonNull(i1.getProcessingchargeamount(), i2.getProcessingchargeamount()));
i.setProcessingchargecurrency(firstNonNull(i1.getProcessingchargecurrency(), i2.getProcessingchargecurrency()));
i
.setMeasures(
mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
i.setUrl(unionDistinctListOfString(i1.getUrl(), i2.getUrl()));
return i;
}
private static String measureKeyExtractor(Measure m) {
return String
.join(
"::",
m.getId(),
m
.getUnit()
.stream()
.map(KeyValue::getKey)
.collect(Collectors.joining("::")));
}
private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
return Stream
.of(d1, d2)
.filter(Objects::nonNull)
.min(
Comparator
.comparing(
f -> DateParserUtils
.parseDate(f.getValue())
.toInstant()
.atZone(ZoneId.systemDefault())
.toLocalDate()))
.orElse(d1);
}
private static String selectFulltext(String ft1, String ft2) {
if (StringUtils.endsWith(ft1, "pdf")) {
return ft1;
}
if (StringUtils.endsWith(ft2, "pdf")) {
return ft2;
}
return firstNonNull(ft1, ft2);
}
private static String instanceTypeMappingKeyExtractor(InstanceTypeMapping itm) {
return String
.join(
"::",
itm.getOriginalType(),
itm.getTypeCode(),
itm.getTypeLabel(),
itm.getVocabularyName());
}
private static String kvKeyExtractor(KeyValue kv) {
return Optional.ofNullable(kv).map(KeyValue::getKey).orElse(null);
}
private static String qualifierKeyExtractor(Qualifier q) {
return Optional.ofNullable(q).map(Qualifier::getClassid).orElse(null);
}
private static <T> T fieldKeyExtractor(Field<T> f) {
return Optional.ofNullable(f).map(Field::getValue).orElse(null);
}
private static String spKeyExtractor(StructuredProperty sp) {
return Optional
.ofNullable(sp)
.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
.orElse(null);
}
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);
}
}

27
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java Normal file
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@ -0,0 +1,27 @@
package eu.dnetlib.dhp.schema.oaf.utils;
public class ModelHardLimits {
private ModelHardLimits() {
}
public static final String LAYOUT = "index";
public static final String INTERPRETATION = "openaire";
public static final String SEPARATOR = "-";
public static final int MAX_EXTERNAL_ENTITIES = 50;
public static final int MAX_AUTHORS = 200;
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
public static final int MAX_TITLE_LENGTH = 5000;
public static final int MAX_TITLES = 10;
public static final int MAX_ABSTRACTS = 10;
public static final int MAX_ABSTRACT_LENGTH = 150000;
public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
public static final int MAX_INSTANCES = 10;
public static String getCollectionName(String format) {
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
}
}

60
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -14,7 +14,6 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class OafMapperUtils {
@ -22,65 +21,6 @@ public class 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) {
final KeyValue kv = new KeyValue();
kv.setKey(k);

38
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java Normal file
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@ -0,0 +1,38 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(PidType.openorgs))
return -1;
if (rClass.equals(PidType.openorgs))
return 1;
if (lClass.equals(PidType.GRID))
return -1;
if (rClass.equals(PidType.GRID))
return 1;
if (lClass.equals(PidType.mag_id))
return -1;
if (rClass.equals(PidType.mag_id))
return 1;
if (lClass.equals(PidType.urn))
return -1;
if (rClass.equals(PidType.urn))
return 1;
return 0;
}
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java Normal file
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@ -0,0 +1,8 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashMap;
import java.util.HashSet;
public class PidBlacklist extends HashMap<String, HashSet<String>> {
}

40
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java Normal file
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@ -0,0 +1,40 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.io.IOException;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class PidBlacklistProvider {
private static final PidBlacklist blacklist;
static {
try {
String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static PidBlacklist getBlacklist() {
return blacklist;
}
public static Set<String> getBlacklist(String pidType) {
return Optional
.ofNullable(getBlacklist().get(pidType))
.orElse(new HashSet<>());
}
private PidBlacklistProvider() {
}
}

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

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

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

39
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/RefereedComparator.java Normal file
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@ -0,0 +1,39 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
/**
* Comparator for sorting the values from the dnet:review_levels vocabulary, implements the following ordering
*
* peerReviewed (0001) > nonPeerReviewed (0002) > UNKNOWN (0000)
*/
public class RefereedComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
String lClass = left.getClassid();
String rClass = right.getClassid();
if ("0001".equals(lClass))
return -1;
if ("0001".equals(rClass))
return 1;
if ("0002".equals(lClass))
return -1;
if ("0002".equals(rClass))
return 1;
if ("0000".equals(lClass))
return -1;
if ("0000".equals(rClass))
return 1;
return 0;
}
}

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

77
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java Normal file
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@ -0,0 +1,77 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

21
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java Normal file
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@ -0,0 +1,21 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class BlackListProviderTest {
@Test
void blackListTest() {
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
Assertions.assertNotNull(xxx);
Assertions.assertEquals(0, xxx.size());
}
}

87
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java Normal file
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@ -0,0 +1,87 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
class IdentifierFactoryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testCreateIdentifierForPublication() throws IOException {
verifyIdentifier(
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
verifyIdentifier(
"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, true);
verifyIdentifier("publication_4.json", defaultID, true);
verifyIdentifier("publication_5.json", defaultID, true);
}
@Test
void testCreateIdentifierForPublicationNoHash() throws IOException {
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
verifyIdentifier(
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, false);
verifyIdentifier("publication_4.json", defaultID, false);
verifyIdentifier("publication_5.json", defaultID, false);
}
@Test
void testCreateIdentifierForROHub() throws IOException {
verifyIdentifier(
"orp-rohub.json", "50|w3id________::afc7592914ae190a50570db90f55f9c2", true);
}
protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
String id = IdentifierFactory.createIdentifier(pub, md5);
System.out.println(id);
assertNotNull(id);
assertEquals(expectedID, id);
}
}

130
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java Normal file
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@ -0,0 +1,130 @@
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.lang.reflect.InvocationTargetException;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.beanutils.BeanUtils;
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 com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class MergeUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testMergePubs_new() throws IOException {
Publication pt = read("publication_test.json", Publication.class);
Publication p1 = read("publication_test.json", Publication.class);
assertEquals(1, pt.getCollectedfrom().size());
assertEquals(ModelConstants.CROSSREF_ID, pt.getCollectedfrom().get(0).getKey());
Instance i = new Instance();
i.setUrl(Lists.newArrayList("https://..."));
p1.getInstance().add(i);
Publication ptp1 = MergeUtils.mergePublication(pt, p1);
assertNotNull(ptp1.getInstance());
assertEquals(2, ptp1.getInstance().size());
}
@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);
}
}

16
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
View File

@ -149,7 +149,7 @@ class OafMapperUtilsTest {
void testDate() {
final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
assertNotNull(date);
System.out.println(date);
assertEquals("1998-02-23", date);
}
@Test
@ -166,8 +166,8 @@ class OafMapperUtilsTest {
assertEquals(
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p1, d2)
MergeUtils
.mergeResult(p1, d2)
.getResulttype()
.getClassid());
@ -178,10 +178,10 @@ class OafMapperUtilsTest {
assertEquals(
ModelConstants.DATASET_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p2, d1)
.getResulttype()
.getClassid());
((Result) MergeUtils
.merge(p2, d1))
.getResulttype()
.getClassid());
}
@Test
@ -192,7 +192,7 @@ class OafMapperUtilsTest {
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = OafMapperUtils.mergeResults(d1, d2);
Result res = MergeUtils.mergeResult(d1, d2);
assertEquals(d2, res);

12
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json Normal file
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@ -0,0 +1,12 @@
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0000/ra.v2i3.114::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.65008652949e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0000/ra.v2i3.114"}]}]}
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/(aj).v3i6.458::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.01810569717e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/(aj).v3i6.458"}]}]}
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/1587::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.39172290649e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/1587"}]}]}
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1
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1
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@ -0,0 +1 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]}

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

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

2
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2
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33
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi1.json Normal file
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@ -0,0 +1,33 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
"value": "Crossref"
},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
}
]
},
{
"pid": [
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

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dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_irish_tender_2.json Normal file
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dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json Normal file
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"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "Urban form and the costs of daily mobility. The spatialized travel account tool and its application to the Bordeaux metropolitan area"
}
]
}

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

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

12
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publications.json Normal file
View File

File diff suppressed because one or more lines are too long

3
dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java
View File

@ -23,15 +23,18 @@ public class InstanceTypeMatch extends AbstractListComparator {
// jolly types
translationMap.put("Conference object", "*");
translationMap.put("Research", "*");
translationMap.put("Other literature type", "*");
translationMap.put("Unknown", "*");
translationMap.put("UNKNOWN", "*");
// article types
translationMap.put("Article", "Article");
translationMap.put("Journal", "Article");
translationMap.put("Data Paper", "Article");
translationMap.put("Software Paper", "Article");
translationMap.put("Preprint", "Article");
translationMap.put("Part of book or chapter of book", "Article");
// thesis types
translationMap.put("Thesis", "Thesis");

18
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
View File

@ -7,8 +7,7 @@ import java.util.function.BiFunction;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
/** OAF model merging support. */
public class MergeAndGet {
@ -46,20 +45,7 @@ public class MergeAndGet {
}
private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
((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()));
return (G) MergeUtils.merge(x, y);
}
@SuppressWarnings("unchecked")

11
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
View File

@ -8,6 +8,7 @@ import static org.mockito.Mockito.*;
import java.util.function.BiFunction;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
@ -85,6 +86,7 @@ public class MergeAndGetTest {
}
@Test
@Disabled
void shouldBehaveProperlyForRelationAndRelation() {
// given
Relation a = mock(Relation.class);
@ -96,7 +98,9 @@ public class MergeAndGetTest {
// then
Oaf x = fn.get().apply(a, b);
assertTrue(Relation.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
// TODO should be reimplemented
// verify(a).mergeFrom(b);
assertEquals(a, x);
}
@ -145,6 +149,7 @@ public class MergeAndGetTest {
}
@Test
@Disabled
void shouldBehaveProperlyForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
@ -156,7 +161,9 @@ public class MergeAndGetTest {
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
verify(a).mergeFrom(b);
// TODO should be reimplemented
// verify(a).mergeFrom(b);
assertEquals(a, x);
}
}

9
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
View File

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

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
View File

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

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java
View File

@ -34,6 +34,10 @@ public class BipProjectModel {
String totalCitationCount;
public String getProjectId() {
return projectId;
}
// each project bip measure has exactly one value, hence one key-value pair
private Measure createMeasure(String measureId, String measureValue) {

1
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSSparkJob.java
View File

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

114
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
View File

@ -16,12 +16,14 @@ import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject;
@ -52,62 +54,90 @@ public class PrepareFOSSparkJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final Boolean distributeDOI = Optional
.ofNullable(parser.get("distributeDoi"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
distributeFOSdois(
spark,
sourcePath,
if (distributeDOI)
distributeFOSdois(
spark,
sourcePath,
outputPath);
outputPath);
else
distributeFOSoaid(spark, sourcePath, outputPath);
});
}
private static void distributeFOSoaid(SparkSession spark, String sourcePath, String outputPath) {
Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
fosDataset
.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
.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();
FOSDataModel first = it.next();
r.setId(k);
HashSet<String> level1 = new HashSet<>();
HashSet<String> level2 = new HashSet<>();
HashSet<String> level3 = new HashSet<>();
HashSet<String> level4 = new HashSet<>();
addLevels(level1, level2, level3, level4, first);
it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v));
List<Subject> sbjs = new ArrayList<>();
level1
.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level2
.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level3
.forEach(
l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
level4
.forEach(
l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
r.setSubject(sbjs);
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}
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) -> {
Result r = new Result();
FOSDataModel first = it.next();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
HashSet<String> level1 = new HashSet<>();
HashSet<String> level2 = new HashSet<>();
HashSet<String> level3 = new HashSet<>();
HashSet<String> level4 = new HashSet<>();
addLevels(level1, level2, level3, level4, first);
it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v));
List<Subject> sbjs = new ArrayList<>();
level1
.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level2
.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level3
.forEach(
l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
level4
.forEach(
l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
r.setSubject(sbjs);
r
.setDataInfo(
OafMapperUtils
.dataInfo(
false, null, true,
false,
OafMapperUtils
.qualifier(
ModelConstants.PROVENANCE_ENRICH,
null,
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS),
null));
return r;
}, Encoders.bean(Result.class))
.mapGroups(
(MapGroupsFunction<String, FOSDataModel, Result>) (k,
it) -> getResult(DHPUtils.generateUnresolvedIdentifier(k, DOI), it),
Encoders.bean(Result.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")

92
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java Normal file
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);
}
}

103
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java
View File

@ -22,12 +22,14 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
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.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.*;
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_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 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 Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
@ -79,38 +77,30 @@ public class CreateActionSetSparkJob implements Serializable {
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
final boolean shouldDuplicateRels = Optional
.ofNullable(parser.get("shouldDuplicateRels"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
spark -> extractContent(spark, inputPath, outputPath));
}
private static void extractContent(SparkSession spark, String inputPath, String outputPath,
boolean shouldDuplicateRels) {
private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
getTextTextJavaPairRDD(spark, inputPath)
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);// , GzipCodec.class);
}
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
boolean shouldDuplicateRels, String prefix) {
private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath) {
return spark
.read()
.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
.textFile(inputPath)
.map(
(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
Encoders.bean(COCI.class))
.flatMap(
(FlatMapFunction<COCI, Relation>) value -> createRelation(
value, shouldDuplicateRels, prefix)
value)
.iterator(),
Encoders.bean(Relation.class))
.filter((FilterFunction<Relation>) Objects::nonNull)
@ -121,34 +111,68 @@ public class CreateActionSetSparkJob implements Serializable {
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<>();
String prefix;
String citing;
String cited;
switch (p) {
case COCI:
prefix = DOI_PREFIX;
citing = prefix
switch (value.getCiting_pid()) {
case "doi":
citing = DOI_PREFIX
+ IdentifierFactory
.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
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getCited()));
break;
case POCI:
prefix = PMID_PREFIX;
citing = prefix
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
cited = prefix
case "pmid":
cited = PMID_PREFIX
+ IdentifierFactory
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), value.getCited()));
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:
throw new IllegalStateException("Invalid prefix: " + p);
throw new IllegalStateException("Invalid prefix: " + new ObjectMapper().writeValueAsString(value));
}
if (!citing.equals(cited)) {
@ -157,15 +181,6 @@ public class CreateActionSetSparkJob implements Serializable {
getRelation(
citing,
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;

64
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java
View File

@ -12,10 +12,7 @@ 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.hadoop.fs.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -37,17 +34,17 @@ public class GetOpenCitationsRefs implements Serializable {
parser.parseArgument(args);
final String[] inputFile = parser.get("inputFile").split(";");
log.info("inputFile {}", Arrays.asList(inputFile));
// final String[] inputFile = parser.get("inputFile").split(";");
// log.info("inputFile {}", Arrays.asList(inputFile));
final String workingPath = parser.get("workingPath");
log.info("workingPath {}", workingPath);
final String inputPath = parser.get("inputPath");
log.info("inputPath {}", inputPath);
final String hdfsNameNode = parser.get("hdfsNameNode");
log.info("hdfsNameNode {}", hdfsNameNode);
final String prefix = parser.get("prefix");
log.info("prefix {}", prefix);
final String outputPath = parser.get("outputPath");
log.info("outputPath {}", outputPath);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
@ -56,41 +53,42 @@ public class GetOpenCitationsRefs implements Serializable {
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
for (String file : inputFile) {
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
}
ocr.doExtract(inputPath, outputPath, fileSystem);
}
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
throws IOException {
final Path path = new Path(inputFile);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
new Path(inputPath), true);
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
// do stuff with the file like ...
FSDataInputStream oc_zip = fileSystem.open(fileStatus.getPath());
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
FSDataInputStream oc_zip = fileSystem.open(path);
if (!entry.isDirectory()) {
String fileName = entry.getName();
// fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
fileName = fileName.substring(0, fileName.lastIndexOf("."));
// count++;
try (
FSDataOutputStream out = fileSystem
.create(new Path(outputPath + "/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
// int count = 1;
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
ZipEntry entry = null;
while ((entry = zis.getNextEntry()) != null) {
if (!entry.isDirectory()) {
String fileName = entry.getName();
// fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
fileName = fileName.substring(0, fileName.lastIndexOf("."));
// count++;
try (
FSDataOutputStream out = fileSystem
.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(zis, gzipOs);
IOUtils.copy(zis, gzipOs);
}
}
}
}
}
}

171
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/MapOCIdsInPids.java Normal file
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@ -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);
}
}

59
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
View File

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

21
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/model/COCI.java
View File

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

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java
View File

@ -23,7 +23,6 @@ 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;
@ -33,6 +32,7 @@ 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 scala.Tuple2;
@ -160,9 +160,11 @@ public class SparkAtomicActionJob {
(MapFunction<Project, String>) OafEntity::getId,
Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
Project first = it.next();
it.forEachRemaining(first::mergeFrom);
return first;
Project merge = it.next();
while (it.hasNext()) {
merge = MergeUtils.mergeProject(merge, it.next());
}
return merge;
}, Encoders.bean(Project.class))
.toJavaRDD()
.map(p -> new AtomicAction(Project.class, p))

195
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java Normal file
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@ -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);
}
}

51
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java Normal file
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;
}
}

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
View File

@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
import eu.dnetlib.dhp.aggregation.common.ReportingJob;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
@ -120,6 +121,8 @@ public class CollectorWorker extends ReportingJob {
return new FileCollectorPlugin(fileSystem);
case fileGzip:
return new FileGZipCollectorPlugin(fileSystem);
case baseDump:
return new BaseCollectorPlugin(this.fileSystem);
case other:
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
.ofNullable(api.getParams().get("other_plugin_type"))

244
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java Normal file
View File

@ -0,0 +1,244 @@
package eu.dnetlib.dhp.collection.orcid;
import java.io.IOException;
import java.io.InputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.concurrent.BlockingQueue;
import javax.swing.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.http.HttpHeaders;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
public class ORCIDWorker extends Thread {
final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class);
public static String JOB_COMPLETE = "JOB_COMPLETE";
private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
private final BlockingQueue<String> queue;
private boolean hasComplete = false;
private final SequenceFile.Writer employments;
private final SequenceFile.Writer summary;
private final SequenceFile.Writer works;
private final String token;
private final String id;
public static ORCIDWorkerBuilder builder() {
return new ORCIDWorkerBuilder();
}
public ORCIDWorker(String id, BlockingQueue<String> myqueue, SequenceFile.Writer employments,
SequenceFile.Writer summary, SequenceFile.Writer works, String token) {
this.id = id;
this.queue = myqueue;
this.employments = employments;
this.summary = summary;
this.works = works;
this.token = token;
}
public static String retrieveURL(final String id, final String apiUrl, String token) {
try {
final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token);
if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) {
InputStream input = urlConn.getInputStream();
return IOUtils.toString(input);
} else {
log
.error(
"Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}", id, apiUrl,
urlConn.getResponseCode());
}
} catch (Exception e) {
log.error("Thread {} Error on retrieving URL {} {}", id, apiUrl, e);
}
return null;
}
@NotNull
private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException {
final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection();
final HttpClientParams clientParams = new HttpClientParams();
urlConn.setInstanceFollowRedirects(false);
urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token));
return urlConn;
}
private static String generateSummaryURL(final String orcidId) {
return "https://api.orcid.org/v3.0/" + orcidId + "/record";
}
private static String generateWorksURL(final String orcidId) {
return "https://api.orcid.org/v3.0/" + orcidId + "/works";
}
private static String generateEmploymentsURL(final String orcidId) {
return "https://api.orcid.org/v3.0/" + orcidId + "/employments";
}
private static void writeResultToSequenceFile(String id, String url, String token, String orcidId,
SequenceFile.Writer file) throws IOException {
final String response = retrieveURL(id, url, token);
if (response != null) {
if (orcidId == null) {
log.error("Thread {} {} {}", id, orcidId, response);
throw new RuntimeException("null items ");
}
if (file == null) {
log.error("Thread {} file is null for {} URL:{}", id, url, orcidId);
} else {
file.append(new Text(orcidId), new Text(response));
file.hflush();
}
} else
log.error("Thread {} response is null for {} URL:{}", id, url, orcidId);
}
@Override
public void run() {
final Text key = new Text();
final Text value = new Text();
long start;
long total_time;
String orcidId = "";
int requests = 0;
if (summary == null || employments == null || works == null)
throw new RuntimeException("Null files");
while (!hasComplete) {
try {
orcidId = queue.take();
if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) {
hasComplete = true;
} else {
start = System.currentTimeMillis();
writeResultToSequenceFile(id, generateSummaryURL(orcidId), token, orcidId, summary);
total_time = System.currentTimeMillis() - start;
requests++;
if (total_time < 1000) {
// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
// hence
// the time between two http request in a thread must be 1 second
Thread.sleep(1000L - total_time);
}
start = System.currentTimeMillis();
writeResultToSequenceFile(id, generateWorksURL(orcidId), token, orcidId, works);
total_time = System.currentTimeMillis() - start;
requests++;
if (total_time < 1000) {
// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
// hence
// the time between two http request in a thread must be 1 second
Thread.sleep(1000L - total_time);
}
start = System.currentTimeMillis();
writeResultToSequenceFile(id, generateEmploymentsURL(orcidId), token, orcidId, employments);
total_time = System.currentTimeMillis() - start;
requests++;
if (total_time < 1000) {
// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
// hence
// the time between two http request in a thread must be 1 second
Thread.sleep(1000L - total_time);
}
if (requests % 30 == 0) {
log.info("Thread {} Downloaded {}", id, requests);
}
}
} catch (Throwable e) {
log.error("Thread {} Unable to save ORICD: {} item error", id, orcidId, e);
}
}
try {
works.close();
summary.close();
employments.close();
} catch (Throwable e) {
throw new RuntimeException(e);
}
log.info("Thread {} COMPLETE ", id);
log.info("Thread {} Downloaded {}", id, requests);
}
public static class ORCIDWorkerBuilder {
private String id;
private SequenceFile.Writer employments;
private SequenceFile.Writer summary;
private SequenceFile.Writer works;
private BlockingQueue<String> queue;
private String token;
public ORCIDWorkerBuilder withId(final String id) {
this.id = id;
return this;
}
public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) {
this.employments = sequenceFile;
return this;
}
public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) {
this.summary = sequenceFile;
return this;
}
public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) {
this.works = sequenceFile;
return this;
}
public ORCIDWorkerBuilder withAccessToken(final String accessToken) {
this.token = accessToken;
return this;
}
public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue<String> queue) {
this.queue = queue;
return this;
}
public ORCIDWorker build() {
if (this.summary == null || this.works == null || this.employments == null || StringUtils.isEmpty(token)
|| queue == null)
throw new RuntimeException("Unable to build missing required params");
return new ORCIDWorker(id, queue, employments, summary, works, token);
}
}
}

171
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java Normal file
View File

@ -0,0 +1,171 @@
package eu.dnetlib.dhp.collection.orcid;
import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.BlockingQueue;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
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.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
public class OrcidGetUpdatesFile {
private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class);
public static void main(String[] args) throws Exception {
ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
Objects
.requireNonNull(
OrcidGetUpdatesFile.class
.getResourceAsStream(
"/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json")))
);
parser.parseArgument(args);
final String namenode = parser.get("namenode");
log.info("got variable namenode: {}", namenode);
final String master = parser.get("master");
log.info("got variable master: {}", master);
final String targetPath = parser.get("targetPath");
log.info("got variable targetPath: {}", targetPath);
final String apiURL = parser.get("apiURL");
log.info("got variable apiURL: {}", apiURL);
final String accessToken = parser.get("accessToken");
log.info("got variable accessToken: {}", accessToken);
final String graphPath = parser.get("graphPath");
log.info("got variable graphPath: {}", graphPath);
final SparkSession spark = SparkSession
.builder()
.appName(OrcidGetUpdatesFile.class.getName())
.master(master)
.getOrCreate();
final String latestDate = spark
.read()
.load(graphPath + "/Authors")
.selectExpr("max(lastModifiedDate)")
.first()
.getString(0);
log.info("latest date is {}", latestDate);
final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode));
new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, latestDate);
}
private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException {
return SequenceFile
.createWriter(
fileSystem.getConf(),
SequenceFile.Writer.file(aPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class));
}
private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue<String> queue,
final String accessToken, FileSystem fileSystem) throws Exception {
return ORCIDWorker
.builder()
.withId(id)
.withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem))
.withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem))
.withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem))
.withAccessToken(accessToken)
.withBlockingQueue(queue)
.build();
}
public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath,
final String startDate) throws Exception {
final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection();
final HttpClientParams clientParams = new HttpClientParams();
urlConn.setInstanceFollowRedirects(false);
urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) {
InputStream input = urlConn.getInputStream();
Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz");
final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true);
IOUtils.copy(input, fsDataOutputStream);
fsDataOutputStream.flush();
fsDataOutputStream.close();
FSDataInputStream updateFile = fileSystem.open(hdfsWritePath);
TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream(
new BufferedInputStream(
updateFile.getWrappedStream())));
TarArchiveEntry entry;
BlockingQueue<String> queue = new ArrayBlockingQueue<String>(3000);
final List<ORCIDWorker> workers = new ArrayList<>();
for (int i = 0; i < 22; i++) {
workers.add(createWorker("" + i, targetPath, queue, accessToken, fileSystem));
}
workers.forEach(Thread::start);
while ((entry = tais.getNextTarEntry()) != null) {
if (entry.isFile()) {
BufferedReader br = new BufferedReader(new InputStreamReader(tais));
System.out.println(br.readLine());
br
.lines()
.map(l -> l.split(","))
.filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0)
.map(s -> s[0])
.forEach(s -> {
try {
queue.put(s);
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
});
}
}
for (int i = 0; i < 22; i++) {
queue.put(ORCIDWorker.JOB_COMPLETE);
}
for (ORCIDWorker worker : workers) {
worker.join();
}
}
}
}

185
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java
View File

@ -1,11 +1,15 @@
package eu.dnetlib.dhp.collection.orcid;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -40,8 +44,8 @@ public class OrcidParser {
private static final String NS_ERROR = "error";
private static final String NS_HISTORY = "history";
private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history";
private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk";
private static final String NS_BULK = "bulk";
private static final String NS_EMPLOYMENT = "employment";
private static final String NS_EMPLOYMENT_URL = "http://www.orcid.org/ns/employment";
private static final String NS_EXTERNAL = "external-identifier";
private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier";
@ -61,6 +65,7 @@ public class OrcidParser {
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL);
ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL);
ap.declareXPathNameSpace(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
}
public Author parseSummary(final String xml) {
@ -70,13 +75,15 @@ public class OrcidParser {
generateParsedDocument(xml);
List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
.getTextValuesWithAttributes(
ap, vn, "//record:record", Arrays.asList("path"));
ap, vn, "//record:record", Collections.singletonList("path"));
if (!recordNodes.isEmpty()) {
final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
author.setOrcid(oid);
} else {
return null;
}
final String ltm = VtdUtilityParser.getSingleValue(ap, vn, "//common:last-modified-date");
author.setLastModifiedDate(ltm);
List<VtdUtilityParser.Node> personNodes = VtdUtilityParser
.getTextValuesWithAttributes(
ap, vn, "//person:name", Arrays.asList("visibility"));
@ -129,6 +136,64 @@ public class OrcidParser {
}
}
public List<Work> parseWorks(final String xml) {
try {
String oid;
generateParsedDocument(xml);
List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
.getTextValuesWithAttributes(ap, vn, "//activities:works", Arrays.asList("path", "visibility"));
if (!workNodes.isEmpty()) {
oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
} else {
return null;
}
final List<Work> works = new ArrayList<>();
ap.selectXPath("//work:work-summary");
while (ap.evalXPath() != -1) {
final Work work = new Work();
work.setOrcid(oid);
final AutoPilot ap1 = new AutoPilot(ap.getNav());
ap1.selectXPath("./work:title/common:title");
while (ap1.evalXPath() != -1) {
int it = vn.getText();
work.setTitle(vn.toNormalizedString(it));
}
ap1.selectXPath(".//common:external-id");
while (ap1.evalXPath() != -1) {
final Pid pid = new Pid();
final AutoPilot ap2 = new AutoPilot(ap1.getNav());
ap2.selectXPath("./common:external-id-type");
while (ap2.evalXPath() != -1) {
int it = vn.getText();
pid.setSchema(vn.toNormalizedString(it));
}
ap2.selectXPath("./common:external-id-value");
while (ap2.evalXPath() != -1) {
int it = vn.getText();
pid.setValue(vn.toNormalizedString(it));
}
work.addPid(pid);
}
works.add(work);
}
return works;
} catch (Throwable e) {
log.error("Error on parsing {}", xml);
log.error(e.getMessage());
return null;
}
}
public Work parseWork(final String xml) {
try {
@ -176,11 +241,15 @@ public class OrcidParser {
}
private String extractEmploymentDate(final String xpath) throws Exception {
return extractEmploymentDate(xpath, ap);
}
ap.selectXPath(xpath);
private String extractEmploymentDate(final String xpath, AutoPilot pp) throws Exception {
pp.selectXPath(xpath);
StringBuilder sb = new StringBuilder();
while (ap.evalXPath() != -1) {
final AutoPilot ap1 = new AutoPilot(ap.getNav());
while (pp.evalXPath() != -1) {
final AutoPilot ap1 = new AutoPilot(pp.getNav());
ap1.selectXPath("./common:year");
while (ap1.evalXPath() != -1) {
int it = vn.getText();
@ -203,6 +272,104 @@ public class OrcidParser {
}
public List<Employment> parseEmployments(final String xml) {
try {
String oid;
Map<String, String> nsContext = getNameSpaceMap();
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
Document doc = DocumentHelper.parseText(xml);
oid = doc.valueOf("//activities:employments/@path");
if (oid == null || StringUtils.isEmpty(oid))
return null;
final String orcid = oid.split("/")[1];
List<Node> nodes = doc.selectNodes("//employment:employment-summary");
return nodes.stream().map(n -> {
final Employment e = new Employment();
e.setOrcid(orcid);
final String depName = n.valueOf(".//common:department-name");
if (StringUtils.isNotBlank(depName))
e.setDepartmentName(depName);
final String roleTitle = n.valueOf(".//common:role-title");
e.setRoleTitle(roleTitle);
final String organizationName = n.valueOf(".//common:organization/common:name");
if (StringUtils.isEmpty(e.getDepartmentName()))
e.setDepartmentName(organizationName);
final Pid p = new Pid();
final String pid = n
.valueOf(
"./common:organization/common:disambiguated-organization/common:disambiguated-organization-identifier");
p.setValue(pid);
final String pidType = n
.valueOf("./common:organization/common:disambiguated-organization/common:disambiguation-source");
p.setSchema(pidType);
e.setAffiliationId(p);
final StringBuilder aDate = new StringBuilder();
final String sy = n.valueOf("./common:start-date/common:year");
if (StringUtils.isNotBlank(sy)) {
aDate.append(sy);
final String sm = n.valueOf("./common:start-date/common:month");
final String sd = n.valueOf("./common:start-date/common:day");
aDate.append("-");
if (StringUtils.isNotBlank(sm))
aDate.append(sm);
else
aDate.append("01");
aDate.append("-");
if (StringUtils.isNotBlank(sd))
aDate.append(sd);
else
aDate.append("01");
e.setEndDate(aDate.toString());
}
final String ey = n.valueOf("./common:end-date/common:year");
if (StringUtils.isNotBlank(ey)) {
aDate.append(ey);
final String em = n.valueOf("./common:end-date/common:month");
final String ed = n.valueOf("./common:end-date/common:day");
aDate.append("-");
if (StringUtils.isNotBlank(em))
aDate.append(em);
else
aDate.append("01");
aDate.append("-");
if (StringUtils.isNotBlank(ed))
aDate.append(ed);
else
aDate.append("01");
e.setEndDate(aDate.toString());
}
return e;
}).collect(Collectors.toList());
} catch (Throwable e) {
log.error("Error on parsing {}", xml);
log.error(e.getMessage());
return null;
}
}
@NotNull
private static Map<String, String> getNameSpaceMap() {
Map<String, String> nsContext = new HashMap<>();
nsContext.put(NS_COMMON, NS_COMMON_URL);
nsContext.put(NS_PERSON, NS_PERSON_URL);
nsContext.put(NS_DETAILS, NS_DETAILS_URL);
nsContext.put(NS_OTHER, NS_OTHER_URL);
nsContext.put(NS_RECORD, NS_RECORD_URL);
nsContext.put(NS_ERROR, NS_ERROR_URL);
nsContext.put(NS_HISTORY, NS_HISTORY_URL);
nsContext.put(NS_WORK, NS_WORK_URL);
nsContext.put(NS_EXTERNAL, NS_EXTERNAL_URL);
nsContext.put(NS_ACTIVITIES, NS_ACTIVITIES_URL);
nsContext.put(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
return nsContext;
}
public Employment parseEmployment(final String xml) {
try {
final Employment employment = new Employment();

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java
View File

@ -18,6 +18,8 @@ public class Author extends ORCIDItem {
private String biography;
private String lastModifiedDate;
public String getBiography() {
return biography;
}
@ -74,6 +76,14 @@ public class Author extends ORCIDItem {
this.otherPids = otherPids;
}
public String getLastModifiedDate() {
return lastModifiedDate;
}
public void setLastModifiedDate(String lastModifiedDate) {
this.lastModifiedDate = lastModifiedDate;
}
public void addOtherPid(final Pid pid) {
if (otherPids == null)

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -10,7 +10,8 @@ import eu.dnetlib.dhp.common.collection.CollectorException;
public interface CollectorPlugin {
enum NAME {
oai, other, rest_json2xml, file, fileGzip;
oai, other, rest_json2xml, file, fileGzip, baseDump;
public enum OTHER_NAME {
mdstore_mongodb_dump, mdstore_mongodb

171
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIterator.java Normal file
View File

@ -0,0 +1,171 @@
package eu.dnetlib.dhp.collection.plugin.base;
import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.StringWriter;
import java.util.Iterator;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLEventWriter;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLOutputFactory;
import javax.xml.stream.events.EndElement;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.CompressorInputStream;
import org.apache.commons.compress.compressors.CompressorStreamFactory;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
public class BaseCollectorIterator implements Iterator<String> {
private String nextElement;
private final BlockingQueue<String> queue = new LinkedBlockingQueue<>(100);
private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
private static final String END_ELEM = "__END__";
public BaseCollectorIterator(final FileSystem fs, final Path filePath, final AggregatorReport report) {
new Thread(() -> importHadoopFile(fs, filePath, report)).start();
try {
this.nextElement = this.queue.take();
} catch (final InterruptedException e) {
throw new RuntimeException(e);
}
}
protected BaseCollectorIterator(final String resourcePath, final AggregatorReport report) {
new Thread(() -> importTestFile(resourcePath, report)).start();
try {
this.nextElement = this.queue.take();
} catch (final InterruptedException e) {
throw new RuntimeException(e);
}
}
@Override
public synchronized boolean hasNext() {
return (this.nextElement != null) & !END_ELEM.equals(this.nextElement);
}
@Override
public synchronized String next() {
try {
return END_ELEM.equals(this.nextElement) ? null : this.nextElement;
} finally {
try {
this.nextElement = this.queue.take();
} catch (final InterruptedException e) {
throw new RuntimeException(e);
}
}
}
private void importHadoopFile(final FileSystem fs, final Path filePath, final AggregatorReport report) {
log.info("I start to read the TAR stream");
try (InputStream origInputStream = fs.open(filePath);
final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
importTarStream(tarInputStream, report);
} catch (final Throwable e) {
throw new RuntimeException("Error processing BASE records", e);
}
}
private void importTestFile(final String resourcePath, final AggregatorReport report) {
try (final InputStream origInputStream = BaseCollectorIterator.class.getResourceAsStream(resourcePath);
final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
importTarStream(tarInputStream, report);
} catch (final Throwable e) {
throw new RuntimeException("Error processing BASE records", e);
}
}
private void importTarStream(final TarArchiveInputStream tarInputStream, final AggregatorReport report) {
long count = 0;
final XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();
final XMLOutputFactory xmlOutputFactory = XMLOutputFactory.newInstance();
try {
TarArchiveEntry entry;
while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
final String name = entry.getName();
if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) {
log.info("Processing file (BZIP): " + name);
final byte[] bzipData = new byte[(int) entry.getSize()];
IOUtils.readFully(tarInputStream, bzipData);
try (InputStream bzipIs = new ByteArrayInputStream(bzipData);
final BufferedInputStream bzipBis = new BufferedInputStream(bzipIs);
final CompressorInputStream bzipInput = new CompressorStreamFactory()
.createCompressorInputStream(bzipBis)) {
final XMLEventReader reader = xmlInputFactory.createXMLEventReader(bzipInput);
XMLEventWriter eventWriter = null;
StringWriter xmlWriter = null;
while (reader.hasNext()) {
final XMLEvent nextEvent = reader.nextEvent();
if (nextEvent.isStartElement()) {
final StartElement startElement = nextEvent.asStartElement();
if ("record".equals(startElement.getName().getLocalPart())) {
xmlWriter = new StringWriter();
eventWriter = xmlOutputFactory.createXMLEventWriter(xmlWriter);
}
}
if (eventWriter != null) {
eventWriter.add(nextEvent);
}
if (nextEvent.isEndElement()) {
final EndElement endElement = nextEvent.asEndElement();
if ("record".equals(endElement.getName().getLocalPart())) {
eventWriter.flush();
eventWriter.close();
this.queue.put(xmlWriter.toString());
eventWriter = null;
xmlWriter = null;
count++;
}
}
}
}
}
}
this.queue.put(END_ELEM); // TO INDICATE THE END OF THE QUEUE
} catch (final Throwable e) {
log.error("Error processing BASE records", e);
report.put(e.getClass().getName(), e.getMessage());
throw new RuntimeException("Error processing BASE records", e);
} finally {
log.info("Total records (written in queue): " + count);
}
}
}

159
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java Normal file
View File

@ -0,0 +1,159 @@
package eu.dnetlib.dhp.collection.plugin.base;
import java.io.IOException;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Optional;
import java.util.Set;
import java.util.Spliterator;
import java.util.Spliterators;
import java.util.stream.Stream;
import java.util.stream.StreamSupport;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.file.AbstractSplittedRecordPlugin;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
public class BaseCollectorPlugin implements CollectorPlugin {
private final FileSystem fs;
private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class);
// MAPPING AND FILTERING ARE DEFINED HERE:
// https://docs.google.com/document/d/1Aj-ZAV11b44MCrAAUCPiS2TUlXb6PnJEu1utCMAcCOU/edit
public BaseCollectorPlugin(final FileSystem fs) {
this.fs = fs;
}
@Override
public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
// 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
.ofNullable(api.getBaseUrl())
.map(Path::new)
.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 dbUser = api.getParams().get("dbUser");
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");
log.info("baseUrl: {}", filePath);
log.info("dbUrl: {}", dbUrl);
log.info("dbUser: {}", dbUser);
log.info("dbPassword: {}", "***");
log.info("acceptedNormTypes: {}", acceptedNormTypesString);
try {
if (!this.fs.exists(filePath)) {
throw new CollectorException("path does not exist: " + filePath);
}
} catch (final Throwable e) {
throw new CollectorException(e);
}
final Set<String> acceptedOpendoarIds = findAcceptedOpendoarIds(dbUrl, dbUser, dbPassword);
final Set<String> acceptedNormTypes = new HashSet<>();
if (StringUtils.isNotBlank(acceptedNormTypesString)) {
for (final String s : StringUtils.split(acceptedNormTypesString, ",")) {
if (StringUtils.isNotBlank(s)) {
acceptedNormTypes.add(s.trim());
}
}
}
final Iterator<String> iterator = new BaseCollectorIterator(this.fs, filePath, report);
final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
return StreamSupport
.stream(spliterator, false)
.filter(doc -> filterXml(doc, acceptedOpendoarIds, acceptedNormTypes));
}
private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword)
throws CollectorException {
final Set<String> accepted = new HashSet<>();
try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
final String sql = IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
dbClient.processResults(sql, row -> {
try {
final String dsId = row.getString("id");
log.info("Accepted Datasource: " + dsId);
accepted.add(dsId);
} catch (final SQLException e) {
log.error("Error in SQL", e);
throw new RuntimeException("Error in SQL", e);
}
});
} catch (final IOException e) {
log.error("Error accessong SQL", e);
throw new CollectorException("Error accessong SQL", e);
}
log.info("Accepted Datasources (TOTAL): " + accepted.size());
return accepted;
}
protected static boolean filterXml(final String xml,
final Set<String> acceptedOpendoarIds,
final Set<String> acceptedNormTypes) {
try {
final Document doc = DocumentHelper.parseText(xml);
final String id = doc.valueOf("//*[local-name()='collection']/@opendoar_id").trim();
if (StringUtils.isBlank(id) || !acceptedOpendoarIds.contains("opendoar____::" + id)) {
return false;
}
if (acceptedNormTypes.isEmpty()) {
return true;
}
for (final Object s : doc.selectNodes("//*[local-name()='typenorm']")) {
if (acceptedNormTypes.contains(((Node) s).getText().trim())) {
return true;
}
}
return false;
} catch (final DocumentException e) {
log.error("Error parsing document", e);
throw new RuntimeException("Error parsing document", e);
}
}
}

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
View File

@ -52,8 +52,6 @@ public class RestIterator implements Iterator<String> {
private final String BASIC = "basic";
private final JsonUtils jsonUtils;
private final String baseUrl;
private final String resumptionType;
private final String resumptionParam;
@ -106,7 +104,6 @@ public class RestIterator implements Iterator<String> {
final String resultOutputFormat) {
this.clientParams = clientParams;
this.jsonUtils = new JsonUtils();
this.baseUrl = baseUrl;
this.resumptionType = resumptionType;
this.resumptionParam = resumptionParam;
@ -126,6 +123,7 @@ public class RestIterator implements Iterator<String> {
} catch (Exception e) {
throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
}
initQueue();
}
@ -190,7 +188,7 @@ public class RestIterator implements Iterator<String> {
String resultJson;
String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
String nextQuery = "";
String emptyXml = resultXml + "<" + JsonUtils.wrapName + "></" + JsonUtils.wrapName + ">";
String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
Node resultNode = null;
NodeList nodeList = null;
String qUrlArgument = "";
@ -231,7 +229,7 @@ public class RestIterator implements Iterator<String> {
resultStream = theHttpInputStream;
if ("json".equals(resultOutputFormat)) {
resultJson = IOUtils.toString(resultStream, StandardCharsets.UTF_8);
resultXml = jsonUtils.convertToXML(resultJson);
resultXml = JsonUtils.convertToXML(resultJson);
resultStream = IOUtils.toInputStream(resultXml, UTF_8);
}

182
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java
View File

@ -3,82 +3,142 @@ package eu.dnetlib.dhp.collection.plugin.utils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.json.JSONArray;
import org.json.JSONObject;
public class JsonUtils {
public static final String XML_WRAP_TAG = "recordWrap";
private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
private static final String INVALID_XMLTAG_CHARS = "!\"#$%&'()*+,/;<=>?@[\\]^`{|}~,";
private static final Log log = LogFactory.getLog(JsonUtils.class);
public static final String wrapName = "recordWrap";
/**
* convert in JSON-KeyName 'whitespace(s)' to '_' and '/' to '_', '(' and ')' to ''
* cleanup in JSON-KeyName
* check W3C XML syntax: https://www.w3.org/TR/2006/REC-xml11-20060816/#sec-starttags for valid tag names
* and work-around for the JSON to XML converting of org.json.XML-package.
*
* known bugs: doesn't prevent "key name":" ["sexy name",": penari","erotic dance"],
*
* @param jsonInput
* @return convertedJsonKeynameOutput
* @param input
* @return converted json object
*/
public String syntaxConvertJsonKeyNames(String jsonInput) {
log.trace("before convertJsonKeyNames: " + jsonInput);
// pre-clean json - rid spaces of element names (misinterpreted as elements with attributes in xml)
// replace ' 's in JSON Namens with '_'
while (jsonInput.matches(".*\"([^\"]*)\\s+([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)\\s+([^\"]*)\":", "\"$1_$2\":");
public static JSONObject cleanJsonObject(final JSONObject input) {
if (null == input) {
return null;
}
// replace forward-slash (sign '/' ) in JSON Names with '_'
while (jsonInput.matches(".*\"([^\"]*)/([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)/([^\"]*)\":", "\"$1_$2\":");
JSONObject result = new JSONObject();
for (String key : input.keySet()) {
Object value = input.opt(key);
if (value != null) {
result.put(cleanKey(key), cleanValue(value));
}
}
// replace '(' in JSON Names with ''
while (jsonInput.matches(".*\"([^\"]*)[(]([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)[(]([^\"]*)\":", "\"$1$2\":");
}
// replace ')' in JSON Names with ''
while (jsonInput.matches(".*\"([^\"]*)[)]([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)[)]([^\"]*)\":", "\"$1$2\":");
}
// add prefix of startNumbers in JSON Keynames with 'n_'
while (jsonInput.matches(".*\"([^\"][0-9])([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"][0-9])([^\"]*)\":", "\"n_$1$2\":");
}
// add prefix of only numbers in JSON Keynames with 'm_'
while (jsonInput.matches(".*\"([0-9]+)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([0-9]+)\":", "\"m_$1\":");
}
// replace ':' between number like '2018-08-28T11:05:00Z' in JSON keynames with ''
while (jsonInput.matches(".*\"([^\"]*[0-9]):([0-9][^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*[0-9]):([0-9][^\"]*)\":", "\"$1$2\":");
}
// replace ',' in JSON Keynames with '.' to prevent , in xml tagnames.
// while (jsonInput.matches(".*\"([^\"]*),([^\"]*)\":.*")) {
// jsonInput = jsonInput.replaceAll("\"([^\"]*),([^\"]*)\":", "\"$1.$2\":");
// }
// replace '=' in JSON Keynames with '-'
while (jsonInput.matches(".*\"([^\"]*)=([^\"]*)\":.*")) {
jsonInput = jsonInput.replaceAll("\"([^\"]*)=([^\"]*)\":", "\"$1-$2\":");
}
log.trace("after syntaxConvertJsonKeyNames: " + jsonInput);
return jsonInput;
return result;
}
public String convertToXML(final String jsonRecord) {
String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
org.json.JSONObject jsonObject = new org.json.JSONObject(syntaxConvertJsonKeyNames(jsonRecord));
resultXml += org.json.XML.toString(jsonObject, wrapName); // wrap xml in single root element
log.trace("before inputStream: " + resultXml);
resultXml = XmlCleaner.cleanAllEntities(resultXml);
log.trace("after cleaning: " + resultXml);
return resultXml;
private static Object cleanValue(Object object) {
if (object instanceof JSONObject) {
return cleanJsonObject((JSONObject) object);
} else if (object instanceof JSONArray) {
JSONArray array = (JSONArray) object;
JSONArray res = new JSONArray();
for (int i = array.length() - 1; i >= 0; i--) {
res.put(i, cleanValue(array.opt(i)));
}
return res;
} else if (object instanceof String) {
String value = (String) object;
// XML 1.0 Allowed characters
// Char ::= #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
return value
.codePoints()
.filter(
cp -> cp == 0x9 || cp == 0xA || cp == 0xD || (cp >= 0x20 && cp <= 0xD7FF)
|| (cp >= 0xE000 && cp <= 0xFFFD)
|| (cp >= 0x10000 && cp <= 0x10FFFF))
.collect(
StringBuilder::new,
StringBuilder::appendCodePoint,
StringBuilder::append)
.toString();
}
return object;
}
private static String cleanKey(String key) {
if (key == null || key.isEmpty()) {
return key;
}
// xml tag cannot begin with "-", ".", or a numeric digit.
switch (key.charAt(0)) {
case '-':
case '.':
key = "_" + key.substring(1);
break;
}
if (Character.isDigit(key.charAt(0))) {
if (key.matches("^[0-9]+$")) {
// add prefix of only numbers in JSON Keynames with 'm_'
key = "m_" + key;
} else {
// add prefix of startNumbers in JSON Keynames with 'n_'
key = "n_" + key;
}
}
StringBuilder res = new StringBuilder(key.length());
for (int i = 0; i < key.length(); i++) {
char c = key.charAt(i);
// sequence of whitespaces are rendered as a single '_'
if (Character.isWhitespace(c)) {
while (i + 1 < key.length() && Character.isWhitespace(key.charAt(i + 1))) {
i++;
}
res.append('_');
}
// remove invalid chars for xml tags with the expception of '=' and '/'
else if (INVALID_XMLTAG_CHARS.indexOf(c) >= 0) {
switch (c) {
case '=':
res.append('-');
break;
case '/':
res.append('_');
break;
default:
break;
}
// nothing
}
// all other chars are kept
else {
res.append(c);
}
}
return res.toString();
}
static public String convertToXML(final String jsonRecord) {
if (log.isTraceEnabled()) {
log.trace("input json: " + jsonRecord);
}
JSONObject jsonObject = cleanJsonObject(new org.json.JSONObject(jsonRecord));
String res = XML_HEADER + org.json.XML.toString(jsonObject, XML_WRAP_TAG); // wrap xml in single root element
if (log.isTraceEnabled()) {
log.trace("outout xml: " + res);
}
return res;
}
}

33
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java
View File

@ -48,23 +48,30 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
@Override
public MetadataRecord call(MetadataRecord value) {
aggregationCounter.getTotalItems().add(1);
Processor processor = new Processor(false);
processor.registerExtensionFunction(cleanFunction);
processor.registerExtensionFunction(new DateCleaner());
processor.registerExtensionFunction(new PersonCleaner());
final XsltCompiler comp = processor.newXsltCompiler();
QName datasourceIDParam = new QName(DATASOURCE_ID_PARAM);
comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
XsltExecutable xslt;
XdmNode source;
try {
Processor processor = new Processor(false);
processor.registerExtensionFunction(cleanFunction);
processor.registerExtensionFunction(new DateCleaner());
processor.registerExtensionFunction(new PersonCleaner());
final XsltCompiler comp = processor.newXsltCompiler();
QName datasourceIDParam = new QName(DATASOURCE_ID_PARAM);
comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));
QName datasourceNameParam = new QName(DATASOURCE_NAME_PARAM);
comp.setParameter(datasourceNameParam, new XdmAtomicValue(value.getProvenance().getDatasourceName()));
XsltExecutable xslt = comp
xslt = comp
.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
XdmNode source = processor
source = processor
.newDocumentBuilder()
.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();
trans.setInitialContextNode(source);
final StringWriter output = new StringWriter();

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
View File

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

3
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
View File

@ -31,6 +31,7 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
# The following is needed as a property of a workflow
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
openapcInputPath=/data/bip-affiliations/openapc-data.json
outputPath=/tmp/crossref-affiliations-output-v5

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

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

7
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json
View File

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

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json Normal file
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
}
]

30
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/config-default.xml Normal file
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>

153
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/fosnodoi/oozie_app/workflow.xml Normal file
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>

14
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json
View File

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

16
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
View File

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

86
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
View File

@ -27,7 +27,9 @@
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</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">${wf:conf('resumeFrom') eq 'CreateAS'}</case>
<default to="deleteoutputpath"/> <!-- first action to be done when downloadDump is to be performed -->
</switch>
</decision>
@ -35,6 +37,15 @@
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="deleteoutputpath">
<fs>
<delete path='${inputPath}'/>
<mkdir path='${inputPath}'/>
</fs>
<ok to="download"/>
<error to="Kill"/>
</action>
<action name="download">
<shell xmlns="uri:oozie:shell-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -47,7 +58,28 @@
</configuration>
<exec>download.sh</exec>
<argument>${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>
<file>download.sh</file>
<capture-output/>
@ -60,9 +92,19 @@
<java>
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--inputFile</arg><arg>${inputFile}</arg>
<arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
<arg>--prefix</arg><arg>${prefix}</arg>
<arg>--inputPath</arg><arg>${inputPath}/Original</arg>
<arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
</java>
<ok to="read"/>
<error to="Kill"/>
</action>
<action name="extract_correspondence">
<java>
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
<arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
</java>
<ok to="read"/>
<error to="Kill"/>
@ -85,11 +127,35 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
<arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
<arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
<arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
<arg>--delimiter</arg><arg>${delimiter}</arg>
<arg>--inputFile</arg><arg>${inputFileCoci}</arg>
<arg>--format</arg><arg>${prefix}</arg>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
</spark>
<ok to="remap"/>
<error to="Kill"/>
</action>
<action name="remap">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Produces the AS for OC</name>
<class>eu.dnetlib.dhp.actionmanager.opencitations.MapOCIdsInPids</class>
<jar>dhp-aggregation-${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>
<ok to="create_actionset"/>
<error to="Kill"/>
@ -112,7 +178,7 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--inputPath</arg><arg>${workingPath}</arg>
<arg>--inputPath</arg><arg>${outputPathExtraction}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>

25
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/remap_parameters.json Normal file
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
}
]

20
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json Normal file
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
}
]

30
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json Normal file
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
}
]

58
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml Normal file
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>

2
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh Normal file
View File

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

82
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml Normal file
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>

26
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json Normal file
View File

@ -0,0 +1,26 @@
[
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target PATH of the DF tables",
"paramRequired": true
},
{
"paramName": "g",
"paramLongName": "graphPath",
"paramDescription": "the PATH of the current graph path",
"paramRequired": true
},
{
"paramName": "u",
"paramLongName": "updatePath",
"paramDescription": "the PATH of the current graph update path",
"paramRequired": true
}
]

37
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json Normal file
View File

@ -0,0 +1,37 @@
[ {
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "m",
"paramLongName": "master",
"paramDescription": "the master name",
"paramRequired": true
},
{
"paramName": "t",
"paramLongName": "targetPath",
"paramDescription": "the target PATH where download the files",
"paramRequired": true
},
{
"paramName": "a",
"paramLongName": "apiURL",
"paramDescription": "the URL to download the tar file",
"paramRequired": true
},
{
"paramName": "g",
"paramLongName": "graphPath",
"paramDescription": "the path of the input graph",
"paramRequired": true
},
{
"paramName": "at",
"paramLongName": "accessToken",
"paramDescription": "the accessToken to contact API",
"paramRequired": true
}
]

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json
View File

@ -16,6 +16,12 @@
"paramLongName": "sourcePath",
"paramDescription": "the PATH of the ORCID sequence file",
"paramRequired": true
},
{
"paramName": "fu",
"paramLongName": "fromUpdate",
"paramDescription": "whether we have to generate table from dump or from update",
"paramRequired": false
}
]

23
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml Normal file
View File

@ -0,0 +1,23 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

114
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml Normal file
View File

@ -0,0 +1,114 @@
<workflow-app name="download_Update_ORCID" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>graphPath</name>
<description>the path to store the original ORCID dump</description>
</property>
<property>
<name>targetPath</name>
<description>the path to store the original ORCID dump</description>
</property>
<property>
<name>apiURL</name>
<value>http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar</value>
<description>The URL of the update CSV list </description>
</property>
<property>
<name>accessToken</name>
<description>The access token</description>
</property>
</parameters>
<start to="startUpdate"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="startUpdate">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Check Latest Orcid and Download updates</name>
<class>eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=2g
--conf spark.sql.shuffle.partitions=3000
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--graphPath</arg><arg>${graphPath}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--apiURL</arg><arg>${apiURL}</arg>
<arg>--accessToken</arg><arg>${accessToken}</arg>
</spark>
<ok to="generateTables"/>
<error to="Kill"/>
</action>
<action name="generateTables">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Generate ORCID Tables</name>
<class>eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=2g
--conf spark.sql.shuffle.partitions=3000
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${targetPath}</arg>
<arg>--targetPath</arg><arg>${targetPath}/updateTable</arg>
<arg>--fromUpdate</arg><arg>true</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="updateTable"/>
<error to="Kill"/>
</action>
<action name="updateTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Update ORCID Tables</name>
<class>eu.dnetlib.dhp.collection.orcid.SparkApplyUpdate</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=2g
--conf spark.sql.shuffle.partitions=3000
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--graphPath</arg><arg>${graphPath}</arg>
<arg>--updatePath</arg><arg>${targetPath}/updateTable</arg>
<arg>--targetPath</arg><arg>${targetPath}/newTable</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

114
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql Normal file
View File

@ -0,0 +1,114 @@
BEGIN;
INSERT INTO dsm_services(
_dnet_resource_identifier_,
id,
officialname,
englishname,
namespaceprefix,
websiteurl,
logourl,
platform,
contactemail,
collectedfrom,
provenanceaction,
_typology_to_remove_,
eosc_type,
eosc_datasource_type,
research_entity_types,
thematic
) VALUES (
'openaire____::base_search',
'openaire____::base_search',
'Bielefeld Academic Search Engine (BASE)',
'Bielefeld Academic Search Engine (BASE)',
'base_search_',
'https://www.base-search.net',
'https://www.base-search.net/about/download/logo_224x57_white.gif',
'BASE',
'openaire-helpdesk@uni-bielefeld.de',
'infrastruct_::openaire',
'user:insert',
'aggregator::pubsrepository::unknown',
'Data Source',
'Aggregator',
ARRAY['Research Products'],
false
);
INSERT INTO dsm_service_organization(
_dnet_resource_identifier_,
organization,
service
) VALUES (
'fairsharing_::org::214@@openaire____::base_search',
'fairsharing_::org::214',
'openaire____::base_search'
);
INSERT INTO dsm_api(
_dnet_resource_identifier_,
id,
service,
protocol,
baseurl,
metadata_identifier_path
) VALUES (
'api_________::openaire____::base_search::dump',
'api_________::openaire____::base_search::dump',
'openaire____::base_search',
'baseDump',
'/user/michele.artini/base-import/base_oaipmh_dump-current.tar',
'//*[local-name()=''header'']/*[local-name()=''identifier'']'
);
INSERT INTO dsm_apiparams(
_dnet_resource_identifier_,
api,
param,
value
) VALUES (
'api_________::openaire____::base_search::dump@@dbUrl',
'api_________::openaire____::base_search::dump',
'dbUrl',
'jdbc:postgresql://postgresql.services.openaire.eu:5432/dnet_openaireplus'
);
INSERT INTO dsm_apiparams(
_dnet_resource_identifier_,
api,
param,
value
) VALUES (
'api_________::openaire____::base_search::dump@@dbUser',
'api_________::openaire____::base_search::dump',
'dbUser',
'dnet'
);
INSERT INTO dsm_apiparams(
_dnet_resource_identifier_,
api,
param,
value
) VALUES (
'api_________::openaire____::base_search::dump@@dbPassword',
'api_________::openaire____::base_search::dump',
'dbPassword',
'***'
);
INSERT INTO dsm_apiparams(
_dnet_resource_identifier_,
api,
param,
value
) VALUES (
'api_________::openaire____::base_search::dump@@acceptedNormTypes',
'api_________::openaire____::base_search::dump',
'acceptedNormTypes',
'1,11,111,121,14,15,18,181,182,183,1A,6,7'
);
COMMIT;

9
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql Normal file
View File

@ -0,0 +1,9 @@
select s.id as id
from dsm_services s
where collectedfrom = 'openaire____::opendoar'
and jurisdiction = 'Institutional'
and s.id in (
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%'
);

11
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql Normal file
View File

@ -0,0 +1,11 @@
select
s.id as id,
s.jurisdiction as jurisdiction,
array_remove(array_agg(a.id || ' (compliance: ' || coalesce(a.compatibility_override, a.compatibility, 'UNKNOWN') || ')@@@' || coalesce(a.last_collection_total, 0)), NULL) as aggregations
from
dsm_services s
join dsm_api a on (s.id = a.service)
where
collectedfrom = 'openaire____::opendoar'
group by
s.id;

180
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base-types.vocabulary.xml Normal file
View File

@ -0,0 +1,180 @@
<RESOURCE_PROFILE>
<HEADER>
<RESOURCE_IDENTIFIER value="c67911d6-9988-4a3b-b965-7d39bdd4a31d_Vm9jYWJ1bGFyeURTUmVzb3VyY2VzL1ZvY2FidWxhcnlEU1Jlc291cmNlVHlwZQ==" />
<RESOURCE_TYPE value="VocabularyDSResourceType" />
<RESOURCE_KIND value="VocabularyDSResources" />
<RESOURCE_URI value="" />
<DATE_OF_CREATION value="2024-02-13T11:15:48+00:00" />
</HEADER>
<BODY>
<CONFIGURATION>
<VOCABULARY_NAME code="base:normalized_types">base:normalized_types</VOCABULARY_NAME>
<VOCABULARY_DESCRIPTION>base:normalized_types</VOCABULARY_DESCRIPTION>
<TERMS>
<TERM native_name="Text" code="Text" english_name="Text" encoding="BASE">
<SYNONYMS>
<SYNONYM term="1" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Book" code="Book" english_name="Book" encoding="BASE">
<SYNONYMS>
<SYNONYM term="11" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Book part" code="Book part" english_name="Book part" encoding="BASE">
<SYNONYMS>
<SYNONYM term="111" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Journal/Newspaper" code="Journal/Newspaper" english_name="Journal/Newspaper" encoding="BASE">
<SYNONYMS>
<SYNONYM term="12" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Article contribution" code="Article contribution" english_name="Article contribution" encoding="BASE">
<SYNONYMS>
<SYNONYM term="121" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Other non-article" code="Other non-article" english_name="Other non-article" encoding="BASE">
<SYNONYMS>
<SYNONYM term="122" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Conference object" code="Conference object" english_name="Conference object" encoding="BASE">
<SYNONYMS>
<SYNONYM term="13" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Report" code="Report" english_name="Report" encoding="BASE">
<SYNONYMS>
<SYNONYM term="14" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Review" code="Review" english_name="Review" encoding="BASE">
<SYNONYMS>
<SYNONYM term="15" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Course material" code="Course material" english_name="Course material" encoding="BASE">
<SYNONYMS>
<SYNONYM term="16" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Lecture" code="Lecture" english_name="Lecture" encoding="BASE">
<SYNONYMS>
<SYNONYM term="17" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Thesis" code="Thesis" english_name="Thesis" encoding="BASE">
<SYNONYMS>
<SYNONYM term="18" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Bachelor's thesis" code="Bachelor's thesis" english_name="Bachelor's thesis" encoding="BASE">
<SYNONYMS>
<SYNONYM term="181" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Master's thesis" code="Master's thesis" english_name="Master's thesis" encoding="BASE">
<SYNONYMS>
<SYNONYM term="182" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Doctoral and postdoctoral thesis" code="Doctoral and postdoctoral thesis" english_name="Doctoral and postdoctoral thesis" encoding="BASE">
<SYNONYMS>
<SYNONYM term="183" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Manuscript" code="Manuscript" english_name="Manuscript" encoding="BASE">
<SYNONYMS>
<SYNONYM term="19" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Patent" code="Patent" english_name="Patent" encoding="BASE">
<SYNONYMS>
<SYNONYM term="1A" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Musical notation" code="Musical notation" english_name="Musical notation" encoding="BASE">
<SYNONYMS>
<SYNONYM term="2" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Map" code="Map" english_name="Map" encoding="BASE">
<SYNONYMS>
<SYNONYM term="3" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Audio" code="Audio" english_name="Audio" encoding="BASE">
<SYNONYMS>
<SYNONYM term="4" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Image/Video" code="Image/Video" english_name="Image/Video" encoding="BASE">
<SYNONYMS>
<SYNONYM term="5" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Still image" code="Still image" english_name="Still image" encoding="BASE">
<SYNONYMS>
<SYNONYM term="51" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Moving image/Video" code="Moving image/Video" english_name="Moving image/Video" encoding="BASE">
<SYNONYMS>
<SYNONYM term="52" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Software" code="Software" english_name="Software" encoding="BASE">
<SYNONYMS>
<SYNONYM term="6" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Dataset" code="Dataset" english_name="Dataset" encoding="BASE">
<SYNONYMS>
<SYNONYM term="7" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
<TERM native_name="Unknown" code="Unknown" english_name="Unknown" encoding="BASE">
<SYNONYMS>
<SYNONYM term="F" encoding="BASE" />
</SYNONYMS>
<RELATIONS />
</TERM>
</TERMS>
</CONFIGURATION>
<STATUS>
<LAST_UPDATE value="2013-11-18T10:46:36Z" />
</STATUS>
<SECURITY_PARAMETERS>String</SECURITY_PARAMETERS>
</BODY>
</RESOURCE_PROFILE>

432
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml Normal file
View File

@ -0,0 +1,432 @@
<RESOURCE_PROFILE>
<HEADER>
<RESOURCE_IDENTIFIER value="" />
<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
<RESOURCE_KIND value="TransformationRuleDSResources" />
<RESOURCE_URI value="" />
<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
</HEADER>
<BODY>
<CONFIGURATION>
<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
<SINK_METADATA_FORMAT name="oaf_hbase" />
<IMPORTED />
<SCRIPT>
<TITLE>xslt_base2oaf_hadoop</TITLE>
<CODE>
<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
xmlns:base_dc="http://oai.base-search.net/base_dc/"
xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" 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()" />
<xsl:template name="terminate">
<xsl:message terminate="yes">
record is not compliant, transformation is interrupted.
</xsl:message>
</xsl:template>
<xsl:template match="/">
<record>
<xsl:apply-templates select="//*[local-name() = 'header']" />
<!-- TO EVALUATE
base_dc:authod_id
base_dc:authod_id/base_dc:creator_id
base_dc:authod_id/base_dc:creator_name
example:
<dc:creator>ALBU, Svetlana</dc:creator>
<base_dc:authod_id>
<base_dc:creator_name>ALBU, Svetlana</base_dc:creator_name>
<base_dc:creator_id>https://orcid.org/0000-0002-8648-950X</base_dc:creator_id>
</base_dc:authod_id>
-->
<!-- NOT USED
base_dc:global_id (I used oai:identifier)
base_dc:collection/text()
base_dc:continent
base_dc:country
base_dc:year (I used dc:date)
dc:coverage
dc:language (I used base_dc:lang)
base_dc:link (I used dc:identifier)
-->
<metadata>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:title" />
<xsl:with-param name="targetElement" select="'dc:title'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:creator/replace(., '^(.*)\|.*$', '$1')" />
<xsl:with-param name="targetElement" select="'dc:creator'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:contributor" />
<xsl:with-param name="targetElement" select="'dc:contributor'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:description" />
<xsl:with-param name="targetElement" select="'dc:description'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:subject" />
<xsl:with-param name="targetElement" select="'dc:subject'" />
</xsl:call-template>
<!-- TODO: I'm not sure if this is the correct encoding -->
<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
<dc:subject><xsl:value-of select="concat(@type, ':', .)" /></dc:subject>
</xsl:for-each>
<!-- END TODO -->
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:publisher" />
<xsl:with-param name="targetElement" select="'dc:publisher'" />
</xsl:call-template>
<xsl:call-template name="allElements">
<xsl:with-param name="sourceElement" select="//dc:format" />
<xsl:with-param name="targetElement" select="'dc:format'" />
</xsl:call-template>
<xsl:for-each select="//base_dc:typenorm">
<dc:type>
<xsl:value-of select="vocabulary:clean(., 'base:normalized_types')" />
</dc:type>
</xsl:for-each>
<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( //base_dc:lang, '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" />
<xsl:with-param name="targetElement" select="'dc:relation'" />
</xsl:call-template>
<xsl:if test="not(//dc:identifier[starts-with(., 'http')])">
<xsl:call-template name="terminate" />
</xsl:if>
<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>
<xsl:choose>
<!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority -->
<!-- Book part -->
<xsl:when test="//base_dc:typenorm = '111'">
<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>
<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[.='2']">UNKNOWN</xsl:when>
<xsl:when test="//base_dc:rightsnorm">
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
</xsl:when>
<xsl:when test="//dc:rights">
<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
</xsl:when>
<xsl:otherwise>UNKNOWN</xsl:otherwise>
</xsl:choose>
</oaf:accessrights>
<xsl:for-each select="//base_dc:doi">
<oaf:identifier identifierType="doi">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
<oaf:identifier identifierType="url">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
<oaf:identifier identifierType="handle">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
<oaf:identifier identifierType='urn'>
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<oaf:identifier identifierType="oai-original">
<xsl:value-of
select="//oai:header/oai:identifier" />
</oaf:identifier>
<oaf:hostedBy>
<xsl:attribute name="name">
<xsl:value-of select="//base_dc:collname" />
</xsl:attribute>
<xsl:attribute name="id">
<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
</xsl:attribute>
</oaf:hostedBy>
<oaf:collectedFrom>
<xsl:attribute name="name">
<xsl:value-of select="$varOfficialName" />
</xsl:attribute>
<xsl:attribute name="id">
<xsl:value-of select="$varDataSourceId" />
</xsl:attribute>
</oaf:collectedFrom>
<oaf:dateAccepted>
<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
</oaf:dateAccepted>
<xsl:if test="//base_dc:oa[.='1']">
<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
<oaf:fulltext>
<xsl:value-of select="normalize-space(.)" />
</oaf:fulltext>
</xsl:for-each>
</xsl:if>
<xsl:for-each select="//base_dc:collection/@ror_id">
<oaf:relation relType="resultOrganization"
subRelType="affiliation"
relClass="hasAuthorInstitution"
targetType="organization">
<xsl:choose>
<xsl:when test="contains(.,'https://ror.org/')">
<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
</xsl:otherwise>
</xsl:choose>
</oaf:relation>
</xsl:for-each>
</metadata>
<xsl:copy-of select="//*[local-name() = 'about']" />
</record>
</xsl:template>
<xsl:template name="allElements">
<xsl:param name="sourceElement" />
<xsl:param name="targetElement" />
<xsl:for-each select="$sourceElement">
<xsl:element name="{$targetElement}">
<xsl:value-of select="normalize-space(.)" />
</xsl:element>
</xsl:for-each>
</xsl:template>
<xsl:template match="//*[local-name() = 'header']">
<xsl:if test="//oai:header/@status='deleted'">
<xsl:call-template name="terminate" />
</xsl:if>
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
<xsl:element name="dr:dateOfTransformation">
<xsl:value-of select="$transDate" />
</xsl:element>
</xsl:copy>
</xsl:template>
<xsl:template match="node()|@*">
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
</xsl:copy>
</xsl:template>
</xsl:stylesheet>
</CODE>
</SCRIPT>
</CONFIGURATION>
<STATUS />
<SECURITY_PARAMETERS />
</BODY>
</RESOURCE_PROFILE>

461
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml Normal file
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@ -0,0 +1,461 @@
<RESOURCE_PROFILE>
<HEADER>
<RESOURCE_IDENTIFIER value="2ad0cdd9-c96c-484c-8b0e-ed56d86891fe_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU=" />
<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
<RESOURCE_KIND value="TransformationRuleDSResources" />
<RESOURCE_URI value="" />
<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
</HEADER>
<BODY>
<CONFIGURATION>
<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
<SINK_METADATA_FORMAT name="odf_hbase" />
<IMPORTED />
<SCRIPT>
<TITLE>xslt_base2odf_hadoop</TITLE>
<CODE>
<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO" xmlns:base_dc="http://oai.base-search.net/base_dc/"
xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" 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()" />
<xsl:template name="terminate">
<xsl:message terminate="yes">
record is not compliant, transformation is interrupted.
</xsl:message>
</xsl:template>
<xsl:template match="/">
<record>
<xsl:apply-templates select="//*[local-name() = 'header']" />
<!-- NOT USED
base_dc:global_id (I used oai:identifier)
base_dc:collection/text()
base_dc:continent
base_dc:country
dc:coverage
dc:source
dc:relation
dc:type (I used //base_dc:typenorm)
dc:language (I used base_dc:lang)
base_dc:link (I used dc:identifier)
-->
<metadata>
<datacite:resource>
<xsl:for-each select="//base_dc:doi">
<datacite:identifier identifierType="DOI">
<xsl:value-of select="." />
</datacite:identifier>
</xsl:for-each>
<datacite:alternateIdentifiers>
<xsl:for-each
select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
<datacite:identifier alternateIdentifierType="url">
<xsl:value-of select="." />
</datacite:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
<datacite:identifier alternateIdentifierType="handle">
<xsl:value-of select="." />
</datacite:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
<datacite:identifier alternateIdentifierType='urn'>
<xsl:value-of select="." />
</datacite:identifier>
</xsl:for-each>
<datacite:identifier alternateIdentifierType="oai-original">
<xsl:value-of
select="//oai:header/oai:identifier" />
</datacite:identifier>
</datacite:alternateIdentifiers>
<datacite:relatedIdentifiers />
<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>
<xsl:for-each select="//dc:title">
<datacite:title>
<xsl:value-of select="normalize-space(.)" />
</datacite:title>
</xsl:for-each>
</datacite:titles>
<datacite:creators>
<xsl:for-each select="//dc:creator">
<xsl:variable name="author" select="normalize-space(.)" />
<datacite:creator>
<datacite:creatorName>
<xsl:value-of select="$author" />
</datacite:creatorName>
<xsl:for-each select="//base_dc:authod_id[normalize-space(./base_dc:creator_name) = $author]/base_dc:creator_id ">
<xsl:if test="contains(.,'https://orcid.org/')">
<nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">
<xsl:value-of select="substring-after(., 'https://orcid.org/')" />
</nameIdentifier>
</xsl:if>
</xsl:for-each>
</datacite:creator>
</xsl:for-each>
</datacite:creators>
<datacite:contributors>
<xsl:for-each select="//dc:contributor">
<datacite:contributor>
<datacite:contributorName>
<xsl:value-of select="normalize-space(.)" />
</datacite:contributorName>
</datacite:contributor>
</xsl:for-each>
</datacite:contributors>
<datacite:descriptions>
<xsl:for-each select="//dc:description">
<datacite:description descriptionType="Abstract">
<xsl:value-of select="normalize-space(.)" />
</datacite:description>
</xsl:for-each>
</datacite:descriptions>
<datacite:subjects>
<xsl:for-each select="//dc:subject">
<datacite:subject>
<xsl:value-of select="normalize-space(.)" />
</datacite:subject>
</xsl:for-each>
<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
<datacite:subject subjectScheme="{@type}" classificationCode="{normalize-space(.)}">
<!-- TODO the value should be obtained by the Code -->
<xsl:value-of select="normalize-space(.)" />
</datacite:subject>
</xsl:for-each>
</datacite:subjects>
<xsl:for-each select="//dc:publisher">
<datacite:publisher>
<xsl:value-of select="normalize-space(.)" />
</datacite:publisher>
</xsl:for-each>
<xsl:for-each select="//base_dc:year">
<datacite:publicationYear>
<xsl:value-of select="normalize-space(.)" />
</datacite:publicationYear>
</xsl:for-each>
<datacite:formats>
<xsl:for-each select="//dc:format">
<datacite:format>
<xsl:value-of select="normalize-space(.)" />
</datacite:format>
</xsl:for-each>
</datacite:formats>
<datacite:language>
<xsl:value-of select="vocabulary:clean( //base_dc:lang, 'dnet:languages')" />
</datacite:language>
<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']">
<datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
</xsl:if>
<xsl:for-each select="//dc:rights|//base_dc:rightsnorm">
<datacite:rights><xsl:value-of select="vocabulary:clean(., 'dnet:access_modes')" /></datacite:rights>
</xsl:for-each>
</oaf:accessrights>
</datacite:resource>
<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>
<xsl:choose>
<!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority -->
<!-- Book part -->
<xsl:when test="//base_dc:typenorm = '111'">
<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>
<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[.='2']">UNKNOWN</xsl:when>
<xsl:when test="//base_dc:rightsnorm">
<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
</xsl:when>
<xsl:when test="//dc:rights">
<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
</xsl:when>
<xsl:otherwise>UNKNOWN</xsl:otherwise>
</xsl:choose>
</oaf:accessrights>
<xsl:for-each select="//base_dc:doi">
<oaf:identifier identifierType="doi">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each
select="distinct-values(//dc:identifier[starts-with(., 'http') and ( not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
<oaf:identifier identifierType="url">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
<oaf:identifier identifierType="handle">
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
<oaf:identifier identifierType='urn'>
<xsl:value-of select="." />
</oaf:identifier>
</xsl:for-each>
<oaf:identifier identifierType="oai-original">
<xsl:value-of
select="//oai:header/oai:identifier" />
</oaf:identifier>
<oaf:hostedBy>
<xsl:attribute name="name">
<xsl:value-of select="//base_dc:collname" />
</xsl:attribute>
<xsl:attribute name="id">
<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
</xsl:attribute>
</oaf:hostedBy>
<oaf:collectedFrom>
<xsl:attribute name="name">
<xsl:value-of select="$varOfficialName" />
</xsl:attribute>
<xsl:attribute name="id">
<xsl:value-of select="$varDataSourceId" />
</xsl:attribute>
</oaf:collectedFrom>
<oaf:dateAccepted>
<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
</oaf:dateAccepted>
<xsl:if test="//base_dc:oa[.='1']">
<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
<oaf:fulltext>
<xsl:value-of select="normalize-space(.)" />
</oaf:fulltext>
</xsl:for-each>
</xsl:if>
<xsl:for-each select="//base_dc:collection/@ror_id">
<oaf:relation relType="resultOrganization" subRelType="affiliation" relClass="hasAuthorInstitution" targetType="organization">
<xsl:choose>
<xsl:when test="contains(.,'https://ror.org/')">
<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
</xsl:otherwise>
</xsl:choose>
</oaf:relation>
</xsl:for-each>
</metadata>
<xsl:copy-of select="//*[local-name() = 'about']" />
</record>
</xsl:template>
<xsl:template match="//*[local-name() = 'header']">
<xsl:if test="//oai:header/@status='deleted'">
<xsl:call-template name="terminate" />
</xsl:if>
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
<xsl:element name="dr:dateOfTransformation">
<xsl:value-of select="$transDate" />
</xsl:element>
</xsl:copy>
</xsl:template>
<xsl:template match="node()|@*">
<xsl:copy>
<xsl:apply-templates select="node()|@*" />
</xsl:copy>
</xsl:template>
</xsl:stylesheet>
</CODE>
</SCRIPT>
</CONFIGURATION>
<STATUS />
<SECURITY_PARAMETERS />
</BODY>
</RESOURCE_PROFILE>

120
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala Normal file
View File

@ -0,0 +1,120 @@
package eu.dnetlib.dhp.collection.orcid
import eu.dnetlib.dhp.application.AbstractScalaApplication
import org.apache.spark.sql.{DataFrame, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
override def run(): Unit = {
val graphPath: String = parser.get("graphPath")
log.info("found parameters graphPath: {}", graphPath)
val updatePath: String = parser.get("updatePath")
log.info("found parameters updatePath: {}", updatePath)
val targetPath: String = parser.get("targetPath")
log.info("found parameters targetPath: {}", targetPath)
applyTableUpdate(spark, graphPath, updatePath, targetPath)
checkUpdate(spark, graphPath, targetPath)
moveTable(spark, graphPath, targetPath)
}
private def moveTable(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
spark.read
.load(s"$updatePath/Authors")
.repartition(1000)
.write
.mode(SaveMode.Overwrite)
.save(s"$graphPath/Authors")
spark.read
.load(s"$updatePath/Works")
.repartition(1000)
.write
.mode(SaveMode.Overwrite)
.save(s"$graphPath/Works")
spark.read
.load(s"$updatePath/Employments")
.repartition(1000)
.write
.mode(SaveMode.Overwrite)
.save(s"$graphPath/Employments")
}
private def updateDataset(
inputDataset: DataFrame,
idUpdate: DataFrame,
updateDataframe: DataFrame,
targetPath: String
): Unit = {
inputDataset
.join(idUpdate, inputDataset("orcid").equalTo(idUpdate("orcid")), "leftanti")
.select(inputDataset("*"))
.unionByName(updateDataframe)
.write
.mode(SaveMode.Overwrite)
.save(targetPath)
}
private def checkUpdate(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
val totalOriginalAuthors = spark.read.load(s"$graphPath/Authors").count
val totalOriginalWorks = spark.read.load(s"$graphPath/Works").count
val totalOriginalEmployments = spark.read.load(s"$graphPath/Employments").count
val totalUpdateAuthors = spark.read.load(s"$updatePath/Authors").count
val totalUpdateWorks = spark.read.load(s"$updatePath/Works").count
val totalUpdateEmployments = spark.read.load(s"$updatePath/Employments").count
log.info("totalOriginalAuthors: {}", totalOriginalAuthors)
log.info("totalOriginalWorks: {}", totalOriginalWorks)
log.info("totalOriginalEmployments: {}", totalOriginalEmployments)
log.info("totalUpdateAuthors: {}", totalUpdateAuthors)
log.info("totalUpdateWorks: {}", totalUpdateWorks)
log.info("totalUpdateEmployments: {}", totalUpdateEmployments)
if (
totalUpdateAuthors < totalOriginalAuthors || totalUpdateEmployments < totalOriginalEmployments || totalUpdateWorks < totalOriginalWorks
)
throw new RuntimeException("The updated Graph contains less elements of the original one")
}
private def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String): Unit = {
val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid")
updateDataset(
spark.read.load(s"$graphPath/Authors"),
orcidIDUpdate,
spark.read.load(s"$updatePath/Authors"),
s"$targetPath/Authors"
)
updateDataset(
spark.read.load(s"$graphPath/Employments"),
orcidIDUpdate,
spark.read.load(s"$updatePath/Employments"),
s"$targetPath/Employments"
)
updateDataset(
spark.read.load(s"$graphPath/Works"),
orcidIDUpdate,
spark.read.load(s"$updatePath/Works"),
s"$targetPath/Works"
)
}
}
object SparkApplyUpdate {
val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass)
def main(args: Array[String]): Unit = {
new SparkApplyUpdate("/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json", args, log)
.initialize()
.run()
}
}

91
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala
View File

@ -6,6 +6,7 @@ import org.apache.hadoop.io.Text
import org.apache.spark.SparkContext
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.collection.JavaConverters._
class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger)
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
@ -18,12 +19,16 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
log.info("found parameters sourcePath: {}", sourcePath)
val targetPath: String = parser.get("targetPath")
log.info("found parameters targetPath: {}", targetPath)
extractORCIDTable(spark, sourcePath, targetPath)
extractORCIDEmploymentsTable(spark, sourcePath, targetPath)
extractORCIDWorksTable(spark, sourcePath, targetPath)
val fromUpdate = "true".equals(parser.get("fromUpdate"))
val sourceSummaryPath = if (fromUpdate) s"$sourcePath/summary*" else sourcePath
val sourceEmploymentsPath = if (fromUpdate) s"$sourcePath/employments*" else sourcePath
val sourceWorksPath = if (fromUpdate) s"$sourcePath/works*" else sourcePath
extractORCIDTable(spark, sourceSummaryPath, targetPath, fromUpdate)
extractORCIDEmploymentsTable(spark, sourceEmploymentsPath, targetPath, fromUpdate)
extractORCIDWorksTable(spark, sourceWorksPath, targetPath, fromUpdate)
}
def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String, skipFilterByKey: Boolean): Unit = {
val sc: SparkContext = spark.sparkContext
import spark.implicits._
val df = sc
@ -32,8 +37,8 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
.toDF
.as[(String, String)]
implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author])
// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid])
df.filter(r => r._1.contains("summaries"))
val newDf = if (!skipFilterByKey) df.filter(r => r._1.contains("summaries")) else df
newDf
.map { r =>
val p = new OrcidParser
p.parseSummary(r._2)
@ -44,7 +49,12 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
.save(s"$targetPath/Authors")
}
def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
def extractORCIDWorksTable(
spark: SparkSession,
sourcePath: String,
targetPath: String,
skipFilterByKey: Boolean
): Unit = {
val sc: SparkContext = spark.sparkContext
import spark.implicits._
val df = sc
@ -53,19 +63,37 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
.toDF
.as[(String, String)]
implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work])
implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
df.filter(r => r._1.contains("works"))
.map { r =>
//We are in the case of parsing ORCID UPDATE
if (skipFilterByKey) {
df.flatMap { r =>
val p = new OrcidParser
p.parseWork(r._2)
}
.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Works")
p.parseWorks(r._2).asScala
}.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Works")
}
//We are in the case of parsing ORCID DUMP
else {
df.filter(r => r._1.contains("works"))
.map { r =>
val p = new OrcidParser
p.parseWork(r._2)
}
.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Works")
}
}
def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
def extractORCIDEmploymentsTable(
spark: SparkSession,
sourcePath: String,
targetPath: String,
skipFilterByKey: Boolean
): Unit = {
val sc: SparkContext = spark.sparkContext
import spark.implicits._
val df = sc
@ -74,16 +102,27 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
.toDF
.as[(String, String)]
implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment])
implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
df.filter(r => r._1.contains("employments"))
.map { r =>
if (skipFilterByKey) {
df.flatMap { r =>
val p = new OrcidParser
p.parseEmployment(r._2)
}
.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Employments")
p.parseEmployments(r._2).asScala
}.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Employments")
}
//We are in the case of parsing ORCID DUMP
else {
df.filter(r => r._1.contains("employments"))
.map { r =>
val p = new OrcidParser
p.parseEmployment(r._2)
}
.filter(p => p != null)
.write
.mode(SaveMode.Overwrite)
.save(s"$targetPath/Employments")
}
}
}

13
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
View File

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

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