Merge branch 'beta' of https://code-repo.d4science.org/antonis.lempesis/dnet-hadoop into convert_hive_to_spark_actions
This commit is contained in:
commit
69a9ac7393
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@ -145,105 +145,6 @@ public class AuthorMerger {
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return null;
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}
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||||
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||||
/**
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||||
* This method tries to figure out when two author are the same in the contest
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* of ORCID enrichment
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||||
*
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||||
* @param left Author in the OAF entity
|
||||
* @param right Author ORCID
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||||
* @return based on a heuristic on the names of the authors if they are the same.
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||||
*/
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||||
public static boolean checkORCIDSimilarity(final Author left, final Author right) {
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final Person pl = parse(left);
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final Person pr = parse(right);
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||||
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||||
// If one of them didn't have a surname we verify if they have the fullName not empty
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||||
// 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))) {
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||||
|
||||
if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
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&& !pr.getFullname().isEmpty()) {
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return pl
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.getFullname()
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.stream()
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.anyMatch(
|
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fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
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} else {
|
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return false;
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||||
}
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}
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// The Authors have one surname in common
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if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
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|
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// If one of them has only a surname and is the same we can say that they are the same author
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if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
|
||||
(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
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return true;
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||||
// The authors have the same initials of Name in common
|
||||
if (pl
|
||||
.getName()
|
||||
.stream()
|
||||
.anyMatch(
|
||||
nl -> pr
|
||||
.getName()
|
||||
.stream()
|
||||
.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
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||||
return true;
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||||
}
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||||
|
||||
// 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
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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))))
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||||
return true;
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else
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return false;
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||||
}
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//
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|
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/**
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* Method to enrich ORCID information in one list of authors based on another list
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||||
*
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* @param baseAuthor the Author List in the OAF Entity
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* @param orcidAuthor The list of ORCID Author intersected
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* @return The Author List of the OAF Entity enriched with the orcid Author
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*/
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public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
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|
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if (baseAuthor == null || baseAuthor.isEmpty())
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return orcidAuthor;
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|
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if (orcidAuthor == null || orcidAuthor.isEmpty())
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return baseAuthor;
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|
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if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
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return baseAuthor;
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|
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final List<Author> oAuthor = new ArrayList<>();
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oAuthor.addAll(orcidAuthor);
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|
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baseAuthor.forEach(ba -> {
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Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
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if (aMatch.isPresent()) {
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final Author sameAuthor = aMatch.get();
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addPid(ba, sameAuthor.getPid());
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oAuthor.remove(sameAuthor);
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}
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});
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return baseAuthor;
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}
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|
||||
private static void addPid(final Author a, final List<StructuredProperty> pids) {
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|
||||
if (a.getPid() == null) {
|
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a.setPid(new ArrayList<>());
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}
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|
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a.getPid().addAll(pids);
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|
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}
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|
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public static String pidToComparableString(StructuredProperty pid) {
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final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
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: "";
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|
|
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|
|
@ -14,7 +14,7 @@ import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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|
|
@ -26,7 +26,7 @@ import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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|
@ -135,10 +135,10 @@ public class GroupEntitiesSparkJob {
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.applyCoarVocabularies(entity, vocs),
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OAFENTITY_KRYO_ENC)
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.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
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.reduceGroups((ReduceFunction<OafEntity>) OafMapperUtils::mergeEntities)
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.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeGroup, OAFENTITY_KRYO_ENC)
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.map(
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(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
|
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t._2().getClass().getName(), t._2()),
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(MapFunction<OafEntity, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
|
||||
t.getClass().getName(), t),
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Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
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|
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// pivot on "_1" (classname of the entity)
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|
|
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|
|
@ -0,0 +1,76 @@
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|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
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|
||||
import java.util.HashSet;
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||||
import java.util.Objects;
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||||
import java.util.Optional;
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||||
import java.util.Set;
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||||
|
||||
import org.apache.commons.lang3.StringUtils;
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||||
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||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class CleaningFunctions {
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||||
|
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public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
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||||
public static final String DOI_PREFIX = "10.";
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||||
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||||
public static final Set<String> PID_BLACKLIST = new HashSet<>();
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||||
|
||||
static {
|
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PID_BLACKLIST.add("none");
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PID_BLACKLIST.add("na");
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||||
}
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||||
|
||||
public CleaningFunctions() {
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||||
}
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||||
|
||||
/**
|
||||
* Utility method that filter PID values on a per-type basis.
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||||
* @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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,6 +1,8 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
public class DoiCleaningRule {
|
||||
|
||||
public static String clean(final String doi) {
|
||||
|
|
@ -11,4 +13,26 @@ public class DoiCleaningRule {
|
|||
.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
|
||||
}
|
||||
|
||||
public static String normalizeDoi(final String input) {
|
||||
if (input == null)
|
||||
return null;
|
||||
final String replaced = input
|
||||
.replaceAll("\\n|\\r|\\t|\\s", "")
|
||||
.toLowerCase()
|
||||
.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
|
||||
if (StringUtils.isEmpty(replaced))
|
||||
return null;
|
||||
|
||||
if (!replaced.contains("10."))
|
||||
return null;
|
||||
|
||||
final String ret = replaced.substring(replaced.indexOf("10."));
|
||||
|
||||
if (!ret.startsWith(CleaningFunctions.DOI_PREFIX))
|
||||
return null;
|
||||
|
||||
return ret;
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -92,6 +92,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
INVALID_AUTHOR_NAMES.add("null anonymous");
|
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INVALID_AUTHOR_NAMES.add("unbekannt");
|
||||
INVALID_AUTHOR_NAMES.add("unknown");
|
||||
INVALID_AUTHOR_NAMES.add("autor, Sin");
|
||||
INVALID_AUTHOR_NAMES.add("Desconocido / Inconnu,");
|
||||
|
||||
INVALID_URL_HOSTS.add("creativecommons.org");
|
||||
INVALID_URL_HOSTS.add("www.academia.edu");
|
||||
|
|
@ -312,7 +314,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
}
|
||||
|
||||
if (value instanceof Datasource) {
|
||||
// nothing to evaluate here
|
||||
final Datasource d = (Datasource) value;
|
||||
return Objects.nonNull(d.getOfficialname()) && StringUtils.isNotBlank(d.getOfficialname().getValue());
|
||||
} else if (value instanceof Project) {
|
||||
final Project p = (Project) value;
|
||||
return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue());
|
||||
|
|
@ -505,6 +508,8 @@ 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())) {
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
|
|
|
|||
|
|
@ -0,0 +1,46 @@
|
|||
|
||||
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) {
|
||||
if (left == null) {
|
||||
return right == null ? 0 : -1;
|
||||
} else if (right == null) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
|
||||
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
|
||||
|
||||
if (lClass.equals(rClass))
|
||||
return 0;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -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>> {
|
||||
}
|
||||
|
|
@ -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() {
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||
|
||||
/**
|
||||
* 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) {
|
||||
if (left == null || left.getClassid() == null) {
|
||||
return (right == null || right.getClassid() == null) ? 0 : -1;
|
||||
} else if (right == null || right.getClassid() == null) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
String lClass = left.getClassid();
|
||||
String rClass = right.getClassid();
|
||||
|
||||
if (lClass.equals(rClass))
|
||||
return 0;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
|
||||
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(rClass))
|
||||
return 0;
|
||||
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
|
||||
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> {
|
||||
|
||||
public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
|
||||
|
||||
@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)) {
|
||||
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<>());
|
||||
}
|
||||
}
|
||||
|
|
@ -1,5 +1,8 @@
|
|||
package eu.dnetlib.dhp.application
|
||||
|
||||
import eu.dnetlib.dhp.common.Constants
|
||||
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
|
||||
|
||||
import scala.io.Source
|
||||
|
||||
/** This is the main Interface SparkApplication
|
||||
|
|
@ -70,4 +73,13 @@ abstract class AbstractScalaApplication(
|
|||
.getOrCreate()
|
||||
}
|
||||
|
||||
def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {
|
||||
val total_items = spark.read.text(targetPath).count()
|
||||
writeHdfsFile(
|
||||
spark.sparkContext.hadoopConfiguration,
|
||||
s"$total_items",
|
||||
outputBasePath + Constants.MDSTORE_SIZE_PATH
|
||||
)
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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());
|
||||
}
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
|
||||
|
|
|
|||
|
|
@ -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"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/462::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":"6.33235333753e-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":"0.36"}]},{"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":"5.00285265116e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/462"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/731::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":"10.0001/731"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/ijllis.v9i4.2066.g2482::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":"8.48190886761e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/ijllis.v9i4.2066.g2482"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0118/alfahim.v3i1.140::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":"9.88840807598e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0118/alfahim.v3i1.140"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0166/fk2.stagefigshare.6442896.v3::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":"7.28336930301e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0166/fk2.stagefigshare.6442896.v3"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0301/jttb.v2i1.64::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":"7.28336930301e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0301/jttb.v2i1.64"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0809/seruni.v1i1.567::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":"2.62959564033e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0809/seruni.v1i1.567"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0809/seruni.v2i1.765::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":"9.40178571921e-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":"0.0559872"}]},{"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":"3.67659957614e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0809/seruni.v2i1.765"}]}]}
|
||||
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0901/jkip.v7i3.485::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":"6.26204125721e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0901/jkip.v7i3.485"}]}]}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1 @@
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||||
"fulltext": [],
|
||||
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|
||||
"instance": [
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||||
{
|
||||
"accessright": {
|
||||
"classid": "OPEN",
|
||||
"classname": "Open Access",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": {
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||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "Digital Object Identifier",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.46298/cst.12132"
|
||||
}
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||||
],
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||||
"collectedfrom": {
|
||||
"key": "10|openaire____::6824b298c96ba906a3e6a70593affbf5",
|
||||
"value": "Episciences"
|
||||
},
|
||||
"dateofacceptance": {
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "2013-11-30"
|
||||
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|
||||
"hostedby": {
|
||||
"key": "10|openaire____::6824b298c96ba906a3e6a70593affbf5",
|
||||
"value": "Episciences"
|
||||
},
|
||||
"instanceTypeMapping": [
|
||||
{
|
||||
"originalType": "http://purl.org/coar/resource_type/c_6501",
|
||||
"typeCode": "http://purl.org/coar/resource_type/c_6501",
|
||||
"typeLabel": "journal article",
|
||||
"vocabularyName": "openaire::coar_resource_types_3_1"
|
||||
},
|
||||
{
|
||||
"originalType": "http://purl.org/coar/resource_type/c_6501",
|
||||
"typeCode": "Article",
|
||||
"typeLabel": "Article",
|
||||
"vocabularyName": "openaire::user_resource_types"
|
||||
}
|
||||
],
|
||||
"instancetype": {
|
||||
"classid": "0001",
|
||||
"classname": "Article",
|
||||
"schemeid": "dnet:publication_resource",
|
||||
"schemename": "dnet:publication_resource"
|
||||
},
|
||||
"license": {
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "CC BY NC SA"
|
||||
},
|
||||
"pid": [],
|
||||
"refereed": {
|
||||
"classid": "0002",
|
||||
"classname": "nonPeerReviewed",
|
||||
"schemeid": "dnet:review_levels",
|
||||
"schemename": "dnet:review_levels"
|
||||
},
|
||||
"url": [
|
||||
"https://doi.org/10.46298/cst.12132",
|
||||
"https://cst.episciences.org/12132"
|
||||
]
|
||||
}
|
||||
],
|
||||
"language": {
|
||||
"classid": "fra/fre",
|
||||
"classname": "French",
|
||||
"schemeid": "dnet:languages",
|
||||
"schemename": "dnet:languages"
|
||||
},
|
||||
"lastupdatetimestamp": 1710636106633,
|
||||
"metaResourceType": {
|
||||
"classid": "Research Literature",
|
||||
"classname": "Research Literature",
|
||||
"schemeid": "openaire::meta_resource_types",
|
||||
"schemename": "openaire::meta_resource_types"
|
||||
},
|
||||
"originalId": [
|
||||
"oai:episciences.org:cst:12132",
|
||||
"50|06cdd3ff4700::4826ac62a11a957fe332e2c291dcfcca"
|
||||
],
|
||||
"pid": [],
|
||||
"publisher": {
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "episciences.org"
|
||||
},
|
||||
"relevantdate": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "Accepted",
|
||||
"classname": "Accepted",
|
||||
"schemeid": "dnet:dataCite_date",
|
||||
"schemename": "dnet:dataCite_date"
|
||||
},
|
||||
"value": "2024-02-11"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "issued",
|
||||
"classname": "issued",
|
||||
"schemeid": "dnet:dataCite_date",
|
||||
"schemename": "dnet:dataCite_date"
|
||||
},
|
||||
"value": "2013-11-30"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "available",
|
||||
"classname": "available",
|
||||
"schemeid": "dnet:dataCite_date",
|
||||
"schemename": "dnet:dataCite_date"
|
||||
},
|
||||
"value": "2013-11-30"
|
||||
}
|
||||
],
|
||||
"resourcetype": {
|
||||
"classid": "journal article",
|
||||
"classname": "journal article",
|
||||
"schemeid": "dnet:dataCite_resource",
|
||||
"schemename": "dnet:dataCite_resource"
|
||||
},
|
||||
"resulttype": {
|
||||
"classid": "publication",
|
||||
"classname": "publication",
|
||||
"schemeid": "dnet:result_typologies",
|
||||
"schemename": "dnet:result_typologies"
|
||||
},
|
||||
"source": [],
|
||||
"subject": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "keyword",
|
||||
"classname": "keyword",
|
||||
"schemeid": "dnet:subject_classification_typologies",
|
||||
"schemename": "dnet:subject_classification_typologies"
|
||||
},
|
||||
"value": "JEL: H - Public Economics/H.H7 - State and Local Government • Intergovernmental Relations/H.H7.H72 - State and Local Budget and Expenditures"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "keyword",
|
||||
"classname": "keyword",
|
||||
"schemeid": "dnet:subject_classification_typologies",
|
||||
"schemename": "dnet:subject_classification_typologies"
|
||||
},
|
||||
"value": "Local public finance"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "keyword",
|
||||
"classname": "keyword",
|
||||
"schemeid": "dnet:subject_classification_typologies",
|
||||
"schemename": "dnet:subject_classification_typologies"
|
||||
},
|
||||
"value": "JEL: R - Urban, Rural, Regional, Real Estate, and Transportation Economics/R.R5 - Regional Government Analysis/R.R5.R51 - Finance in Urban and Rural Economies"
|
||||
}
|
||||
],
|
||||
"title": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"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"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -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"
|
||||
}
|
||||
]
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -20,7 +20,7 @@ public class WordsStatsSuffixPrefixChain extends AbstractClusteringFunction {
|
|||
return suffixPrefixChain(s, param("mod"));
|
||||
}
|
||||
|
||||
private Collection<String> suffixPrefixChain(String s, int mod) {
|
||||
static Collection<String> suffixPrefixChain(String s, int mod) {
|
||||
|
||||
// create the list of words from the string (remove short words)
|
||||
List<String> wordsList = Arrays
|
||||
|
|
@ -38,7 +38,7 @@ public class WordsStatsSuffixPrefixChain extends AbstractClusteringFunction {
|
|||
|
||||
}
|
||||
|
||||
private Collection<String> doSuffixPrefixChain(List<String> wordsList, String prefix) {
|
||||
static private Collection<String> doSuffixPrefixChain(List<String> wordsList, String prefix) {
|
||||
|
||||
Set<String> set = Sets.newLinkedHashSet();
|
||||
switch (wordsList.size()) {
|
||||
|
|
@ -80,12 +80,16 @@ public class WordsStatsSuffixPrefixChain extends AbstractClusteringFunction {
|
|||
|
||||
}
|
||||
|
||||
private String suffix(String s, int len) {
|
||||
private static String suffix(String s, int len) {
|
||||
return s.substring(s.length() - len);
|
||||
}
|
||||
|
||||
private String prefix(String s, int len) {
|
||||
private static String prefix(String s, int len) {
|
||||
return s.substring(0, len);
|
||||
}
|
||||
|
||||
static public void main(String[] args) {
|
||||
String title = "MY LIFE AS A BOSON: THE STORY OF \"THE HIGGS\"".toLowerCase();
|
||||
System.out.println(suffixPrefixChain(title, 10));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,16 +1,18 @@
|
|||
|
||||
package eu.dnetlib.pace.tree;
|
||||
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import com.wcohen.ss.AbstractStringDistance;
|
||||
|
||||
import eu.dnetlib.pace.config.Config;
|
||||
import eu.dnetlib.pace.model.Person;
|
||||
import eu.dnetlib.pace.tree.support.AbstractListComparator;
|
||||
import eu.dnetlib.pace.tree.support.ComparatorClass;
|
||||
import eu.dnetlib.pace.util.AuthorMatchers;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.function.BiFunction;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
@ComparatorClass("authorsMatch")
|
||||
public class AuthorsMatch extends AbstractListComparator {
|
||||
|
|
@ -41,24 +43,36 @@ public class AuthorsMatch extends AbstractListComparator {
|
|||
}
|
||||
|
||||
@Override
|
||||
public double compare(final List<String> a, final List<String> b, final Config conf) {
|
||||
if (a.isEmpty() || b.isEmpty())
|
||||
public double compare(final List<String> left, final List<String> right, final Config conf) {
|
||||
if (left.isEmpty() || right.isEmpty())
|
||||
return -1;
|
||||
|
||||
if (a.size() > SIZE_THRESHOLD || b.size() > SIZE_THRESHOLD)
|
||||
if (left.size() > SIZE_THRESHOLD || right.size() > SIZE_THRESHOLD)
|
||||
return 1.0;
|
||||
|
||||
int maxMiss = Integer.MAX_VALUE;
|
||||
List<Person> bList = b.stream().map(author -> new Person(author, false)).collect(Collectors.toList());
|
||||
|
||||
Double threshold = getDoubleParam("threshold");
|
||||
int maxMiss = Integer.MAX_VALUE;
|
||||
|
||||
if (threshold != null && threshold >= 0.0 && threshold <= 1.0 && a.size() == b.size()) {
|
||||
maxMiss = (int) Math.floor((1 - threshold) * Math.max(a.size(), b.size()));
|
||||
if (threshold != null && threshold >= 0.0 && threshold <= 1.0 && left.size() == right.size()) {
|
||||
maxMiss = (int) Math.floor((1 - threshold) * Math.max(left.size(), right.size()));
|
||||
}
|
||||
|
||||
int common = 0;
|
||||
|
||||
List<String> a = new ArrayList<>(left);
|
||||
List<String> b = new ArrayList<>(right);
|
||||
|
||||
common += AuthorMatchers
|
||||
.removeMatches(a, b, (BiFunction<String, String, Object>) AuthorMatchers::matchEqualsIgnoreCase)
|
||||
.size() / 2;
|
||||
common += AuthorMatchers
|
||||
.removeMatches(a, b, (BiFunction<String, String, Object>) AuthorMatchers::matchOrderedTokenAndAbbreviations)
|
||||
.size() / 2;
|
||||
|
||||
List<Person> bList = b.stream().map(author -> new Person(author, false)).collect(Collectors.toList());
|
||||
|
||||
// compare each element of List1 with each element of List2
|
||||
int alreadyMatched = common;
|
||||
for (int i = 0; i < a.size(); i++) {
|
||||
Person p1 = new Person(a.get(i), false);
|
||||
|
||||
|
|
@ -123,13 +137,13 @@ public class AuthorsMatch extends AbstractListComparator {
|
|||
}
|
||||
}
|
||||
|
||||
if (i - common > maxMiss) {
|
||||
if (i - common - alreadyMatched > maxMiss) {
|
||||
return 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
// normalization factor to compute the score
|
||||
int normFactor = a.size() == b.size() ? a.size() : (a.size() + b.size() - common);
|
||||
int normFactor = left.size() == right.size() ? left.size() : (left.size() + right.size() - common);
|
||||
|
||||
if (TYPE.equals("percentage")) {
|
||||
return (double) common / normFactor;
|
||||
|
|
@ -160,5 +174,4 @@ public class AuthorsMatch extends AbstractListComparator {
|
|||
public String normalization(String s) {
|
||||
return normalize(utf8(cleanup(s)));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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");
|
||||
|
|
|
|||
|
|
@ -0,0 +1,112 @@
|
|||
package eu.dnetlib.pace.util
|
||||
|
||||
import java.util.Locale
|
||||
import java.util.regex.Pattern
|
||||
import scala.util.control.Breaks.{break, breakable}
|
||||
|
||||
object AuthorMatchers {
|
||||
val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+")
|
||||
|
||||
val WORD_DIFF = 2
|
||||
|
||||
def matchEqualsIgnoreCase(a1: String, a2: String): Boolean = {
|
||||
if (a1 == null || a2 == null)
|
||||
false
|
||||
else
|
||||
a1 == a2 || a1.toLowerCase(Locale.ROOT).equals(a2.toLowerCase(Locale.ROOT))
|
||||
}
|
||||
|
||||
def matchOtherNames(fullName: String, otherNames: Seq[String]): Boolean = {
|
||||
if (otherNames != null) {
|
||||
otherNames.exists(matchEqualsIgnoreCase(fullName, _))
|
||||
} else {
|
||||
false
|
||||
}
|
||||
}
|
||||
|
||||
def matchOrderedTokenAndAbbreviations(a1: String, a2: String): Boolean = {
|
||||
val p1: Array[String] = SPLIT_REGEX.split(a1.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted
|
||||
val p2: Array[String] = SPLIT_REGEX.split(a2.trim.toLowerCase(Locale.ROOT)).filter(_.nonEmpty).sorted
|
||||
|
||||
if (p1.length < 2 || p2.length < 2) return false
|
||||
if (Math.abs(p1.length - p2.length) > WORD_DIFF) return false // use alternative comparison algo
|
||||
|
||||
var p1Idx: Int = 0
|
||||
var p2Idx: Int = 0
|
||||
var shortMatches: Int = 0
|
||||
var longMatches: Int = 0
|
||||
while (p1Idx < p1.length && p2Idx < p2.length) {
|
||||
val e1: String = p1(p1Idx)
|
||||
val c1: Char = e1.charAt(0)
|
||||
val e2: String = p2(p2Idx)
|
||||
val c2: Char = e2.charAt(0)
|
||||
if (c1 < c2) p1Idx += 1
|
||||
else if (c1 > c2) p2Idx += 1
|
||||
else {
|
||||
var res: Boolean = false
|
||||
if (e1.length != 1 && e2.length != 1) {
|
||||
res = e1 == e2
|
||||
if (res)
|
||||
longMatches += 1
|
||||
} else {
|
||||
res = true
|
||||
shortMatches += 1
|
||||
}
|
||||
if (res) {
|
||||
p1Idx += 1
|
||||
p2Idx += 1
|
||||
} else {
|
||||
val diff: Int = e1.compareTo(e2)
|
||||
if (diff < 0) p1Idx += 1
|
||||
else if (diff > 0) p2Idx += 1
|
||||
}
|
||||
}
|
||||
}
|
||||
longMatches > 0 && (shortMatches + longMatches) == Math.min(p1.length, p2.length)
|
||||
}
|
||||
|
||||
def removeMatches(
|
||||
graph_authors: java.util.List[String],
|
||||
orcid_authors: java.util.List[String],
|
||||
matchingFunc: java.util.function.BiFunction[String,String,Boolean]
|
||||
) : java.util.List[String] = {
|
||||
removeMatches(graph_authors, orcid_authors, (a, b) => matchingFunc(a,b))
|
||||
}
|
||||
|
||||
|
||||
def removeMatches(
|
||||
graph_authors: java.util.List[String],
|
||||
orcid_authors: java.util.List[String],
|
||||
matchingFunc: (String, String) => Boolean
|
||||
) : java.util.List[String] = {
|
||||
val matched = new java.util.ArrayList[String]()
|
||||
|
||||
if (graph_authors != null && !graph_authors.isEmpty) {
|
||||
val ait = graph_authors.iterator
|
||||
|
||||
while (ait.hasNext) {
|
||||
val author = ait.next()
|
||||
val oit = orcid_authors.iterator
|
||||
|
||||
breakable {
|
||||
while (oit.hasNext) {
|
||||
val orcid = oit.next()
|
||||
|
||||
if (matchingFunc(author, orcid)) {
|
||||
ait.remove()
|
||||
oit.remove()
|
||||
|
||||
matched.add(author)
|
||||
matched.add(orcid)
|
||||
|
||||
break()
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
matched
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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")
|
||||
|
|
|
|||
|
|
@ -0,0 +1,39 @@
|
|||
/*
|
||||
* Copyright (c) 2024.
|
||||
* SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
|
||||
* SPDX-License-Identifier: AGPL-3.0-or-later
|
||||
*/
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.promote;
|
||||
|
||||
/** Encodes the Actionset promotion strategies */
|
||||
public class PromoteAction {
|
||||
|
||||
/** The supported actionset promotion strategies
|
||||
*
|
||||
* ENRICH: promotes only records in the actionset matching another record in the
|
||||
* graph and enriches them applying the given MergeAndGet strategy
|
||||
* UPSERT: promotes all the records in an actionset, matching records are updated
|
||||
* using the given MergeAndGet strategy, the non-matching record as inserted as they are.
|
||||
*/
|
||||
public enum Strategy {
|
||||
ENRICH, UPSERT
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns the string representation of the join type implementing the given PromoteAction.
|
||||
*
|
||||
* @param strategy the strategy to be used to promote the Actionset contents
|
||||
* @return the join type used to implement the promotion strategy
|
||||
*/
|
||||
public static String joinTypeForStrategy(PromoteAction.Strategy strategy) {
|
||||
switch (strategy) {
|
||||
case ENRICH:
|
||||
return "left_outer";
|
||||
case UPSERT:
|
||||
return "full_outer";
|
||||
default:
|
||||
throw new IllegalStateException("unsupported PromoteAction: " + strategy.toString());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -67,8 +67,9 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
String outputGraphTablePath = parser.get("outputGraphTablePath");
|
||||
logger.info("outputGraphTablePath: {}", outputGraphTablePath);
|
||||
|
||||
MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
|
||||
logger.info("strategy: {}", strategy);
|
||||
MergeAndGet.Strategy mergeAndGetStrategy = MergeAndGet.Strategy
|
||||
.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
|
||||
logger.info("mergeAndGetStrategy: {}", mergeAndGetStrategy);
|
||||
|
||||
Boolean shouldGroupById = Optional
|
||||
.ofNullable(parser.get("shouldGroupById"))
|
||||
|
|
@ -76,6 +77,12 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
.orElse(true);
|
||||
logger.info("shouldGroupById: {}", shouldGroupById);
|
||||
|
||||
PromoteAction.Strategy promoteActionStrategy = Optional
|
||||
.ofNullable(parser.get("promoteActionStrategy"))
|
||||
.map(PromoteAction.Strategy::valueOf)
|
||||
.orElse(PromoteAction.Strategy.UPSERT);
|
||||
logger.info("promoteActionStrategy: {}", promoteActionStrategy);
|
||||
|
||||
@SuppressWarnings("unchecked")
|
||||
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
|
||||
@SuppressWarnings("unchecked")
|
||||
|
|
@ -97,7 +104,8 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
inputGraphTablePath,
|
||||
inputActionPayloadPath,
|
||||
outputGraphTablePath,
|
||||
strategy,
|
||||
mergeAndGetStrategy,
|
||||
promoteActionStrategy,
|
||||
rowClazz,
|
||||
actionPayloadClazz,
|
||||
shouldGroupById);
|
||||
|
|
@ -124,14 +132,16 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
String inputGraphTablePath,
|
||||
String inputActionPayloadPath,
|
||||
String outputGraphTablePath,
|
||||
MergeAndGet.Strategy strategy,
|
||||
MergeAndGet.Strategy mergeAndGetStrategy,
|
||||
PromoteAction.Strategy promoteActionStrategy,
|
||||
Class<G> rowClazz,
|
||||
Class<A> actionPayloadClazz, Boolean shouldGroupById) {
|
||||
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
|
||||
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
|
||||
|
||||
Dataset<G> result = promoteActionPayloadForGraphTable(
|
||||
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz, shouldGroupById)
|
||||
rowDS, actionPayloadDS, mergeAndGetStrategy, promoteActionStrategy, rowClazz, actionPayloadClazz,
|
||||
shouldGroupById)
|
||||
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
|
||||
|
||||
saveGraphTable(result, outputGraphTablePath);
|
||||
|
|
@ -183,7 +193,8 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(
|
||||
Dataset<G> rowDS,
|
||||
Dataset<A> actionPayloadDS,
|
||||
MergeAndGet.Strategy strategy,
|
||||
MergeAndGet.Strategy mergeAndGetStrategy,
|
||||
PromoteAction.Strategy promoteActionStrategy,
|
||||
Class<G> rowClazz,
|
||||
Class<A> actionPayloadClazz,
|
||||
Boolean shouldGroupById) {
|
||||
|
|
@ -195,8 +206,9 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
|
||||
SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
|
||||
SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
|
||||
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
|
||||
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
|
||||
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet
|
||||
.functionFor(mergeAndGetStrategy);
|
||||
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(mergeAndGetStrategy);
|
||||
SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
|
||||
SerializableSupplier<Function<G, Boolean>> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSourceAndTarget;
|
||||
|
||||
|
|
@ -207,6 +219,7 @@ public class PromoteActionPayloadForGraphTableJob {
|
|||
rowIdFn,
|
||||
actionPayloadIdFn,
|
||||
mergeRowWithActionPayloadAndGetFn,
|
||||
promoteActionStrategy,
|
||||
rowClazz,
|
||||
actionPayloadClazz);
|
||||
|
||||
|
|
|
|||
|
|
@ -34,6 +34,7 @@ public class PromoteActionPayloadFunctions {
|
|||
* @param rowIdFn Function used to get the id of graph table row
|
||||
* @param actionPayloadIdFn Function used to get id of action payload instance
|
||||
* @param mergeAndGetFn Function used to merge graph table row and action payload instance
|
||||
* @param promoteActionStrategy the Actionset promotion strategy
|
||||
* @param rowClazz Class of graph table
|
||||
* @param actionPayloadClazz Class of action payload
|
||||
* @param <G> Type of graph table row
|
||||
|
|
@ -46,6 +47,7 @@ public class PromoteActionPayloadFunctions {
|
|||
SerializableSupplier<Function<G, String>> rowIdFn,
|
||||
SerializableSupplier<Function<A, String>> actionPayloadIdFn,
|
||||
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
|
||||
PromoteAction.Strategy promoteActionStrategy,
|
||||
Class<G> rowClazz,
|
||||
Class<A> actionPayloadClazz) {
|
||||
if (!isSubClass(rowClazz, actionPayloadClazz)) {
|
||||
|
|
@ -61,7 +63,7 @@ public class PromoteActionPayloadFunctions {
|
|||
.joinWith(
|
||||
actionPayloadWithIdDS,
|
||||
rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")),
|
||||
"full_outer")
|
||||
PromoteAction.joinTypeForStrategy(promoteActionStrategy))
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>) value -> {
|
||||
Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);
|
||||
|
|
|
|||
|
|
@ -41,6 +41,12 @@
|
|||
"paramDescription": "strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "pas",
|
||||
"paramLongName": "promoteActionStrategy",
|
||||
"paramDescription": "strategy for promoting the actionset contents into the graph tables, ENRICH or UPSERT (default)",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "sgid",
|
||||
"paramLongName": "shouldGroupById",
|
||||
|
|
|
|||
|
|
@ -115,6 +115,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${workingDir}/dataset</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="DecisionPromoteResultActionPayloadForDatasetTable"/>
|
||||
|
|
@ -167,6 +168,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/dataset</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -106,6 +106,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/datasource</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -106,6 +106,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/organization</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -114,6 +114,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="DecisionPromoteResultActionPayloadForOtherResearchProductTable"/>
|
||||
|
|
@ -166,6 +167,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/otherresearchproduct</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -106,6 +106,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/project</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -115,6 +115,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${workingDir}/publication</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="DecisionPromoteResultActionPayloadForPublicationTable"/>
|
||||
|
|
@ -167,6 +168,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/publication</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -107,6 +107,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/relation</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -114,6 +114,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${workingDir}/software</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="DecisionPromoteResultActionPayloadForSoftwareTable"/>
|
||||
|
|
@ -166,6 +167,7 @@
|
|||
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
|
||||
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/software</arg>
|
||||
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
|
||||
<arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
|
||||
<arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -54,7 +54,7 @@ public class PromoteActionPayloadFunctionsTest {
|
|||
RuntimeException.class,
|
||||
() -> PromoteActionPayloadFunctions
|
||||
.joinGraphTableWithActionPayloadAndMerge(
|
||||
null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
|
||||
null, null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -104,6 +104,7 @@ public class PromoteActionPayloadFunctionsTest {
|
|||
rowIdFn,
|
||||
actionPayloadIdFn,
|
||||
mergeAndGetFn,
|
||||
PromoteAction.Strategy.UPSERT,
|
||||
OafImplSubSub.class,
|
||||
OafImplSubSub.class)
|
||||
.collectAsList();
|
||||
|
|
@ -183,6 +184,7 @@ public class PromoteActionPayloadFunctionsTest {
|
|||
rowIdFn,
|
||||
actionPayloadIdFn,
|
||||
mergeAndGetFn,
|
||||
PromoteAction.Strategy.UPSERT,
|
||||
OafImplSubSub.class,
|
||||
OafImplSub.class)
|
||||
.collectAsList();
|
||||
|
|
|
|||
|
|
@ -64,6 +64,12 @@ 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 dataciteInputPath = parser.get("dataciteInputPath");
|
||||
log.info("dataciteInputPath: {}", dataciteInputPath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
|
|
@ -85,8 +91,20 @@ 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);
|
||||
|
||||
List<KeyValue> collectedFromDatacite = OafMapperUtils
|
||||
.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
|
||||
JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
|
||||
spark, dataciteInputPath, collectedFromDatacite);
|
||||
|
||||
crossrefRelations
|
||||
.union(pubmedRelations)
|
||||
.union(openAPCRelations)
|
||||
.union(dataciteRelations)
|
||||
.saveAsHadoopFile(
|
||||
outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
|
||||
|
||||
|
|
|
|||
|
|
@ -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) {
|
||||
|
||||
|
|
|
|||
|
|
@ -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));
|
||||
|
|
|
|||
|
|
@ -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")
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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))
|
||||
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;
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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"));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.actionmanager.Constants.*;
|
|||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
|
@ -13,7 +14,9 @@ import org.apache.commons.io.IOUtils;
|
|||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
|
|
@ -68,18 +71,59 @@ public class SparkAtomicActionUsageJob implements Serializable {
|
|||
|
||||
final String workingPath = parser.get("workingPath");
|
||||
|
||||
final String datasourcePath = parser.get("datasourcePath");
|
||||
|
||||
runWithSparkHiveSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
removeOutputDir(spark, outputPath);
|
||||
prepareData(dbname, spark, workingPath + "/usageDb", "usage_stats", "result_id");
|
||||
prepareResultData(
|
||||
dbname, spark, workingPath + "/usageDb",
|
||||
"usage_stats",
|
||||
"result_id",
|
||||
"repository_id",
|
||||
datasourcePath);
|
||||
prepareData(dbname, spark, workingPath + "/projectDb", "project_stats", "id");
|
||||
prepareData(dbname, spark, workingPath + "/datasourceDb", "datasource_stats", "repository_id");
|
||||
writeActionSet(spark, workingPath, outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void prepareResultData(String dbname, SparkSession spark, String workingPath, String tableName,
|
||||
String resultAttributeName, String datasourceAttributeName,
|
||||
String datasourcePath) {
|
||||
Dataset<UsageStatsResultModel> resultModel = spark
|
||||
.sql(
|
||||
String
|
||||
.format(
|
||||
"select %s as id, %s as datasourceId, sum(downloads) as downloads, sum(views) as views " +
|
||||
"from %s.%s group by %s, %s",
|
||||
resultAttributeName, datasourceAttributeName, dbname, tableName, resultAttributeName,
|
||||
datasourceAttributeName))
|
||||
.as(Encoders.bean(UsageStatsResultModel.class));
|
||||
Dataset<Datasource> datasource = readPath(spark, datasourcePath, Datasource.class)
|
||||
.filter((FilterFunction<Datasource>) d -> !d.getDataInfo().getDeletedbyinference())
|
||||
.map((MapFunction<Datasource, Datasource>) d -> {
|
||||
d.setId(d.getId().substring(3));
|
||||
return d;
|
||||
}, Encoders.bean(Datasource.class));
|
||||
resultModel
|
||||
.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
|
||||
.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
|
||||
UsageStatsResultModel usrm = t2._1();
|
||||
if (Optional.ofNullable(t2._2()).isPresent())
|
||||
usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
|
||||
else
|
||||
usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
|
||||
return usrm;
|
||||
}, Encoders.bean(UsageStatsResultModel.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(workingPath);
|
||||
}
|
||||
|
||||
private static void prepareData(String dbname, SparkSession spark, String workingPath, String tableName,
|
||||
String attribute_name) {
|
||||
spark
|
||||
|
|
@ -115,15 +159,62 @@ public class SparkAtomicActionUsageJob implements Serializable {
|
|||
|
||||
}
|
||||
|
||||
public static Measure newMeasureInstance(String id) {
|
||||
Measure m = new Measure();
|
||||
m.setId(id);
|
||||
m.setUnit(new ArrayList<>());
|
||||
return m;
|
||||
}
|
||||
|
||||
private static Dataset<Result> getFinalIndicatorsResult(SparkSession spark, String inputPath) {
|
||||
|
||||
return readPath(spark, inputPath, UsageStatsModel.class)
|
||||
.map((MapFunction<UsageStatsModel, Result>) usm -> {
|
||||
return readPath(spark, inputPath, UsageStatsResultModel.class)
|
||||
.groupByKey((MapFunction<UsageStatsResultModel, String>) usm -> usm.getId(), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, UsageStatsResultModel, Result>) (k, it) -> {
|
||||
Result r = new Result();
|
||||
r.setId("50|" + usm.getId());
|
||||
r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
|
||||
r.setId("50|" + k);
|
||||
// id = download or view and unit = list of key value pairs
|
||||
Measure download = newMeasureInstance("downloads");
|
||||
Measure view = newMeasureInstance("views");
|
||||
UsageStatsResultModel first = it.next();
|
||||
addCountForDatasource(download, first, view);
|
||||
it.forEachRemaining(usm -> {
|
||||
addCountForDatasource(download, usm, view);
|
||||
});
|
||||
r.setMeasures(Arrays.asList(download, view));
|
||||
return r;
|
||||
}, Encoders.bean(Result.class));
|
||||
}, Encoders.bean(Result.class))
|
||||
// .map((MapFunction<UsageStatsResultModel, Result>) usm -> {
|
||||
// Result r = new Result();
|
||||
// r.setId("50|" + usm.getId());
|
||||
// r.setMeasures(getMeasure(usm.getDownloads(), usm.getViews()));
|
||||
// return r;
|
||||
// }, Encoders.bean(Result.class));
|
||||
;
|
||||
}
|
||||
|
||||
private static void addCountForDatasource(Measure download, UsageStatsResultModel usm, Measure view) {
|
||||
DataInfo dataInfo = OafMapperUtils
|
||||
.dataInfo(
|
||||
false,
|
||||
UPDATE_DATA_INFO_TYPE,
|
||||
true,
|
||||
false,
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID,
|
||||
UPDATE_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS),
|
||||
"");
|
||||
download
|
||||
.getUnit()
|
||||
.add(
|
||||
OafMapperUtils
|
||||
.newKeyValueInstance(usm.getDatasourceId(), String.valueOf(usm.getDownloads()), dataInfo));
|
||||
view
|
||||
.getUnit()
|
||||
.add(OafMapperUtils.newKeyValueInstance(usm.getDatasourceId(), String.valueOf(usm.getViews()), dataInfo));
|
||||
}
|
||||
|
||||
private static Dataset<Project> getFinalIndicatorsProject(SparkSession spark, String inputPath) {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,18 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.usagestats;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 30/06/23
|
||||
*/
|
||||
public class UsageStatsResultModel extends UsageStatsModel {
|
||||
private String datasourceId;
|
||||
|
||||
public String getDatasourceId() {
|
||||
return datasourceId;
|
||||
}
|
||||
|
||||
public void setDatasourceId(String datasourceId) {
|
||||
this.datasourceId = datasourceId;
|
||||
}
|
||||
}
|
||||
|
|
@ -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"))
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -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();
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -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;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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();
|
||||
|
|
|
|||
|
|
@ -17,6 +17,18 @@
|
|||
"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": "dip",
|
||||
"paramLongName": "dataciteInputPath",
|
||||
"paramDescription": "the path to get the input data from Datacite",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
|
|
|
|||
|
|
@ -31,6 +31,9 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
|
|||
# The following is needed as a property of a workflow
|
||||
oozie.wf.application.path=${oozieTopWfApplicationPath}
|
||||
|
||||
crossrefInputPath=/data/bip-affiliations/data.json
|
||||
crossrefInputPath=/data/bip-affiliations/crossref-data.json
|
||||
pubmedInputPath=/data/bip-affiliations/pubmed-data.json
|
||||
openapcInputPath=/data/bip-affiliations/openapc-data.json
|
||||
dataciteInputPath=/data/bip-affiliations/datacite-data.json
|
||||
|
||||
outputPath=/tmp/crossref-affiliations-output-v5
|
||||
|
|
|
|||
|
|
@ -9,6 +9,14 @@
|
|||
<name>pubmedInputPath</name>
|
||||
<description>the path where to find the inferred affiliation relations from Pubmed</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>openapcInputPath</name>
|
||||
<description>the path where to find the inferred affiliation relations from OpenAPC</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dataciteInputPath</name>
|
||||
<description>the path where to find the inferred affiliation relations from Datacite</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the path where to store the actionset</description>
|
||||
|
|
@ -102,6 +110,9 @@
|
|||
</spark-opts>
|
||||
<arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
|
||||
<arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
|
||||
<arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
|
||||
<arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
|
||||
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
}
|
||||
]
|
||||
|
|
@ -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
|
||||
}
|
||||
]
|
||||
|
|
@ -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>
|
||||
|
|
@ -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>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,13 +1,13 @@
|
|||
[
|
||||
{
|
||||
"paramName": "if",
|
||||
"paramLongName": "inputFile",
|
||||
"paramName": "ip",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the zipped opencitations file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "wp",
|
||||
"paramLongName": "workingPath",
|
||||
"paramName": "op",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the working path",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
|
@ -16,11 +16,5 @@
|
|||
"paramLongName": "hdfsNameNode",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "p",
|
||||
"paramLongName": "prefix",
|
||||
"paramDescription": "COCI or POCI",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
[
|
||||
{
|
||||
"paramName": "wp",
|
||||
"paramLongName": "workingPath",
|
||||
"paramName": "ip",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the zipped opencitations file",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
|
@ -24,15 +24,9 @@
|
|||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "if",
|
||||
"paramLongName": "inputFile",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": true
|
||||
}, {
|
||||
"paramName": "f",
|
||||
"paramLongName": "format",
|
||||
}, {
|
||||
"paramName": "nn",
|
||||
"paramLongName": "hdfsNameNode",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": true
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,9 @@
|
|||
<case to="download">${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"/>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
}
|
||||
]
|
||||
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Reference in New Issue