WIP: refactoring the internal graph data model and its utilities
This commit is contained in:
parent
d05ca53a14
commit
1845dcfedf
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@ -73,11 +73,11 @@ public class Vocabulary implements Serializable {
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public Qualifier getTermAsQualifier(final String termId, boolean strict) {
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final VocabularyTerm term = getTerm(termId);
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if (Objects.nonNull(term)) {
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return OafMapperUtils.qualifier(term.getId(), term.getName(), getId(), getName());
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return OafMapperUtils.qualifier(term.getId(), term.getName(), getId());
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} else if (Objects.isNull(term) && strict) {
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return OafMapperUtils.unknown(getId(), getName());
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return OafMapperUtils.unknown(getId());
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} else {
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return OafMapperUtils.qualifier(termId, termId, getId(), getName());
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return OafMapperUtils.qualifier(termId, termId, getId());
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}
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}
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@ -125,12 +125,12 @@ public class VocabularyGroup implements Serializable {
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if (vocabularyExists(vocId)) {
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return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
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}
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return OafMapperUtils.qualifier(id, id, "", "");
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return OafMapperUtils.qualifier(id, id, "");
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}
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public Qualifier getSynonymAsQualifier(final String vocId, final String syn) {
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if (StringUtils.isBlank(vocId)) {
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return OafMapperUtils.unknown("", "");
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return OafMapperUtils.unknown("");
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}
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return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn);
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}
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@ -142,7 +142,7 @@ public class VocabularyGroup implements Serializable {
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*/
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public Qualifier getSynonymAsQualifierCaseSensitive(final String vocId, final String syn) {
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if (StringUtils.isBlank(vocId)) {
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return OafMapperUtils.unknown("", "");
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return OafMapperUtils.unknown("");
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}
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return vocs.get(vocId).getSynonymAsQualifier(syn);
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}
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@ -10,6 +10,7 @@ import org.apache.commons.lang3.StringUtils;
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import com.wcohen.ss.JaroWinkler;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.AuthorPid;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.pace.model.Person;
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import scala.Tuple2;
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@ -75,7 +76,7 @@ public class AuthorMerger {
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.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
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// <pid, Author> (list of pid that are missing in the other list)
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final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
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final List<Tuple2<AuthorPid, Author>> pidToEnrich = enrich
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.flatMap(
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@ -111,7 +112,7 @@ public class AuthorMerger {
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// TERRIBLE HACK but for some reason when we create and Array with Arrays.asList,
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// it creates of fixed size, and the add method raise UnsupportedOperationException at
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// java.util.AbstractList.add
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final List<StructuredProperty> tmp = new ArrayList<>(r.getPid());
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final List<AuthorPid> tmp = new ArrayList<>(r.getPid());
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tmp.add(a._1());
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r.setPid(tmp);
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}
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@ -21,8 +21,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.Entity;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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public class DispatchEntitiesSparkJob {
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@ -58,7 +58,7 @@ public class DispatchEntitiesSparkJob {
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log.info("graphTableClassName: {}", graphTableClassName);
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@SuppressWarnings("unchecked")
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Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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Class<? extends Entity> entityClazz = (Class<? extends Entity>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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@ -87,17 +87,17 @@ public class GroupEntitiesSparkJob {
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String inputPath,
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String outputPath) {
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final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
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final TypedColumn<Entity, Entity> aggregator = new GroupingAggregator().toColumn();
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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spark
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.read()
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.textFile(toSeq(listEntityPaths(inputPath, sc)))
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.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
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.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
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.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
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.map((MapFunction<String, Entity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(Entity.class))
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.filter((FilterFunction<Entity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
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.groupByKey((MapFunction<Entity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
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.agg(aggregator)
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.map(
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(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
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(MapFunction<Tuple2<String, Entity>, String>) t -> t._2().getClass().getName() +
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"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
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Encoders.STRING())
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.write()
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@ -106,19 +106,19 @@ public class GroupEntitiesSparkJob {
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.text(outputPath);
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}
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public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
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public static class GroupingAggregator extends Aggregator<Entity, Entity, Entity> {
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@Override
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public OafEntity zero() {
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public Entity zero() {
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return null;
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}
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@Override
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public OafEntity reduce(OafEntity b, OafEntity a) {
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public Entity reduce(Entity b, Entity a) {
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return mergeAndGet(b, a);
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}
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private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
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private Entity mergeAndGet(Entity b, Entity a) {
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if (Objects.nonNull(a) && Objects.nonNull(b)) {
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return OafMapperUtils.mergeEntities(b, a);
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}
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@ -126,28 +126,28 @@ public class GroupEntitiesSparkJob {
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}
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@Override
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public OafEntity merge(OafEntity b, OafEntity a) {
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public Entity merge(Entity b, Entity a) {
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return mergeAndGet(b, a);
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}
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@Override
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public OafEntity finish(OafEntity j) {
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public Entity finish(Entity j) {
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return j;
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}
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@Override
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public Encoder<OafEntity> bufferEncoder() {
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return Encoders.kryo(OafEntity.class);
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public Encoder<Entity> bufferEncoder() {
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return Encoders.kryo(Entity.class);
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}
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@Override
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public Encoder<OafEntity> outputEncoder() {
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return Encoders.kryo(OafEntity.class);
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public Encoder<Entity> outputEncoder() {
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return Encoders.kryo(Entity.class);
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}
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}
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private static OafEntity parseOaf(String s) {
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private static Entity parseOaf(String s) {
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DocumentContext dc = JsonPath
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.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
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@ -184,7 +184,7 @@ public class GroupEntitiesSparkJob {
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}
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}
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private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
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private static <T extends Entity> Entity parse(String s, Class<T> clazz) {
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try {
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return OBJECT_MAPPER.readValue(s, clazz);
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} catch (IOException e) {
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@ -0,0 +1,69 @@
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package eu.dnetlib.dhp.schema.oaf.common;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import java.util.Comparator;
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public class AccessRightComparator<T extends Qualifier> implements Comparator<T> {
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@Override
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public int compare(T left, T right) {
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if (left == null && right == null)
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return 0;
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if (left == null)
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return 1;
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if (right == null)
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return -1;
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String lClass = left.getClassid();
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String rClass = right.getClassid();
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if (lClass.equals(rClass))
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return 0;
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if (lClass.equals("OPEN SOURCE"))
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return -1;
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if (rClass.equals("OPEN SOURCE"))
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return 1;
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if (lClass.equals("OPEN"))
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return -1;
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if (rClass.equals("OPEN"))
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return 1;
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if (lClass.equals("6MONTHS"))
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return -1;
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if (rClass.equals("6MONTHS"))
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return 1;
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if (lClass.equals("12MONTHS"))
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return -1;
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if (rClass.equals("12MONTHS"))
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return 1;
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if (lClass.equals("EMBARGO"))
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return -1;
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if (rClass.equals("EMBARGO"))
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return 1;
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if (lClass.equals("RESTRICTED"))
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return -1;
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if (rClass.equals("RESTRICTED"))
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return 1;
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if (lClass.equals("CLOSED"))
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return -1;
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if (rClass.equals("CLOSED"))
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return 1;
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if (lClass.equals("UNKNOWN"))
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return -1;
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if (rClass.equals("UNKNOWN"))
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return 1;
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// Else (but unlikely), lexicographical ordering will do.
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return lClass.compareTo(rClass);
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}
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}
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@ -0,0 +1,21 @@
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package eu.dnetlib.dhp.schema.oaf.common;
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import eu.dnetlib.dhp.schema.oaf.Entity;
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/** Actual entity types in the Graph */
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public enum EntityType {
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publication, dataset, otherresearchproduct, software, datasource, organization, project;
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/**
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* Resolves the EntityType, given the relative class name
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*
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* @param clazz the given class name
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* @param <T> actual OafEntity subclass
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* @return the EntityType associated to the given class
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*/
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public static <T extends Entity> EntityType fromClass(Class<T> clazz) {
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return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
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}
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}
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@ -0,0 +1,7 @@
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package eu.dnetlib.dhp.schema.oaf.common;
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/** Main entity types in the Graph */
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public enum MainEntityType {
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result, datasource, organization, project
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}
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@ -0,0 +1,417 @@
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package eu.dnetlib.dhp.schema.oaf.common;
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import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.codec.binary.Hex;
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import org.apache.commons.lang3.StringUtils;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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import java.security.NoSuchAlgorithmException;
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import java.text.ParseException;
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import java.util.Date;
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import java.util.Map;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.function.Function;
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import static com.google.common.base.Preconditions.checkArgument;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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/** Oaf model utility methods. */
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public class ModelSupport {
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/** Defines the mapping between the actual entity type and the main entity type */
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private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
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static {
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entityMapping.put(EntityType.publication, MainEntityType.result);
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entityMapping.put(EntityType.dataset, MainEntityType.result);
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entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result);
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entityMapping.put(EntityType.software, MainEntityType.result);
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entityMapping.put(EntityType.datasource, MainEntityType.datasource);
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entityMapping.put(EntityType.organization, MainEntityType.organization);
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entityMapping.put(EntityType.project, MainEntityType.project);
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}
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/**
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* Defines the mapping between the actual entity types and the relative classes implementing them
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*/
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public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
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static {
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entityTypes.put(EntityType.datasource, Datasource.class);
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entityTypes.put(EntityType.organization, Organization.class);
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entityTypes.put(EntityType.project, Project.class);
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entityTypes.put(EntityType.dataset, Dataset.class);
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entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
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entityTypes.put(EntityType.software, Software.class);
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entityTypes.put(EntityType.publication, Publication.class);
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}
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public static final Map<String, Class> oafTypes = Maps.newHashMap();
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static {
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oafTypes.put("datasource", Datasource.class);
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oafTypes.put("organization", Organization.class);
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oafTypes.put("project", Project.class);
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oafTypes.put("dataset", Dataset.class);
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oafTypes.put("otherresearchproduct", OtherResearchProduct.class);
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oafTypes.put("software", Software.class);
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oafTypes.put("publication", Publication.class);
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oafTypes.put("relation", Relation.class);
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}
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public static final Map<Class, String> idPrefixMap = Maps.newHashMap();
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static {
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idPrefixMap.put(Datasource.class, "10");
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idPrefixMap.put(Organization.class, "20");
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idPrefixMap.put(Project.class, "40");
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idPrefixMap.put(Dataset.class, "50");
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idPrefixMap.put(OtherResearchProduct.class, "50");
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idPrefixMap.put(Software.class, "50");
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idPrefixMap.put(Publication.class, "50");
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}
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public static final Map<String, String> entityIdPrefix = Maps.newHashMap();
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static {
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entityIdPrefix.put("datasource", "10");
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entityIdPrefix.put("organization", "20");
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entityIdPrefix.put("project", "40");
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entityIdPrefix.put("result", "50");
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}
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public static final Map<String, String> idPrefixEntity = Maps.newHashMap();
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static {
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idPrefixEntity.put("10", "datasource");
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idPrefixEntity.put("20", "organization");
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idPrefixEntity.put("40", "project");
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idPrefixEntity.put("50", "result");
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}
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public static final Map<String, RelationInverse> relationInverseMap = Maps.newHashMap();
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static {
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set(relationInverseMap, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, HAS_PARTICIPANT);
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set(relationInverseMap, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF, HAS_AUTHOR_INSTITUTION);
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set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, MERGES);
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set(relationInverseMap, ORG_ORG_RELTYPE, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
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set(relationInverseMap, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, PRODUCES);
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set(relationInverseMap, DATASOURCE_ORGANIZATION, PROVISION, IS_PROVIDED_BY, PROVIDES);
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set(relationInverseMap, RESULT_RESULT, SIMILARITY, IS_AMONG_TOP_N_SIMILAR_DOCS, HAS_AMONG_TOP_N_SIMILAR_DOCS);
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set(relationInverseMap, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, IS_SUPPLEMENTED_BY);
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set(relationInverseMap, RESULT_RESULT, PART, IS_PART_OF, HAS_PART);
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set(relationInverseMap, RESULT_RESULT, DEDUP, IS_MERGED_IN, MERGES);
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set(relationInverseMap, RESULT_RESULT, DEDUP, IS_SIMILAR_TO, IS_SIMILAR_TO);
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set(relationInverseMap, RESULT_RESULT, CITATION, IS_CITED_BY, CITES);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_IDENTICAL_TO, IS_IDENTICAL_TO);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REFERENCED_BY, REFERENCES);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_CONTINUED_BY, CONTINUES);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DOCUMENTED_BY, DOCUMENTS);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DERIVED_FROM, IS_SOURCE_OF);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, IS_RELATED_TO);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_COMPILED_BY, COMPILES);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_DESCRIBED_BY, DESCRIBES);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_METADATA_FOR, IS_METADATA_OF);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, HAS_ASSOCIATION_WITH, HAS_ASSOCIATION_WITH);
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set(relationInverseMap, RESULT_RESULT, RELATIONSHIP, IS_REQUIRED_BY, REQUIRES);
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set(relationInverseMap, RESULT_RESULT, VERSION, IS_PREVIOUS_VERSION_OF, IS_NEW_VERSION_OF);
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set(relationInverseMap, RESULT_RESULT, VERSION, IS_VARIANT_FORM_OF, IS_ORIGINAL_FORM_OF);
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set(relationInverseMap, RESULT_RESULT, VERSION, IS_OBSOLETED_BY, OBSOLETES);
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set(relationInverseMap, RESULT_RESULT, VERSION, IS_VERSION_OF, HAS_VERSION);
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|
||||
set(relationInverseMap, RESULT_RESULT, REVIEW, IS_REVIEWED_BY, REVIEWS);
|
||||
}
|
||||
|
||||
private static void set(Map<String, RelationInverse> relationInverseMap, String relType, String subRelType, String relClass, String inverseRelClass) {
|
||||
relationInverseMap
|
||||
.put(
|
||||
rel(relType, subRelType, relClass), new RelationInverse()
|
||||
.setInverseRelClass(inverseRelClass)
|
||||
.setRelClass(relClass)
|
||||
.setRelType(relType)
|
||||
.setSubReltype(subRelType));
|
||||
if (!relClass.equals(inverseRelClass)) {
|
||||
relationInverseMap
|
||||
.put(
|
||||
rel(relType, subRelType, inverseRelClass), new RelationInverse()
|
||||
.setInverseRelClass(relClass)
|
||||
.setRelClass(inverseRelClass)
|
||||
.setRelType(relType)
|
||||
.setSubReltype(subRelType));
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Helper method: lookup relation inverse, given the direct relation encoding (case insensitive)
|
||||
* @param encoding
|
||||
* @return the relation inverse descriptor, throws @IllegalArgumentException when not found.
|
||||
*/
|
||||
public static RelationInverse findInverse(String encoding) {
|
||||
return ModelSupport.relationInverseMap
|
||||
.entrySet()
|
||||
.stream()
|
||||
.filter(r -> encoding.equalsIgnoreCase(r.getKey()))
|
||||
.findFirst()
|
||||
.map(r -> r.getValue())
|
||||
.orElseThrow(() -> new IllegalArgumentException("invalid relationship: " + encoding));
|
||||
}
|
||||
|
||||
/**
|
||||
* Helper method: fina a relation filtering by a relation name
|
||||
* @param relationName
|
||||
* @return
|
||||
*/
|
||||
public static RelationInverse findRelation(final String relationName) {
|
||||
return relationInverseMap.values()
|
||||
.stream()
|
||||
.filter(r -> relationName.equalsIgnoreCase(r.getRelClass()))
|
||||
.findFirst()
|
||||
.orElse(null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Helper method: combines the relation attributes
|
||||
* @param relType
|
||||
* @param subRelType
|
||||
* @param relClass
|
||||
* @return
|
||||
*/
|
||||
public static String rel(String relType, String subRelType, String relClass) {
|
||||
return String.format("%s_%s_%s", relType, subRelType, relClass);
|
||||
}
|
||||
|
||||
private static final String schemeTemplate = "dnet:%s_%s_relations";
|
||||
|
||||
public static final String DATE_FORMAT = "yyyy-MM-dd";
|
||||
|
||||
private ModelSupport() {
|
||||
}
|
||||
|
||||
public static <E extends Entity> String getIdPrefix(Class<E> clazz) {
|
||||
return idPrefixMap.get(clazz);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks subclass-superclass relationship.
|
||||
*
|
||||
* @param subClazzObject Subclass object instance
|
||||
* @param superClazzObject Superclass object instance
|
||||
* @param <X> Subclass type
|
||||
* @param <Y> Superclass type
|
||||
* @return True if X is a subclass of Y
|
||||
*/
|
||||
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
|
||||
X subClazzObject, Y superClazzObject) {
|
||||
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks subclass-superclass relationship.
|
||||
*
|
||||
* @param subClazzObject Subclass object instance
|
||||
* @param superClazz Superclass class
|
||||
* @param <X> Subclass type
|
||||
* @param <Y> Superclass type
|
||||
* @return True if X is a subclass of Y
|
||||
*/
|
||||
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
|
||||
X subClazzObject, Class<Y> superClazz) {
|
||||
return isSubClass(subClazzObject.getClass(), superClazz);
|
||||
}
|
||||
|
||||
/**
|
||||
* Checks subclass-superclass relationship.
|
||||
*
|
||||
* @param subClazz Subclass class
|
||||
* @param superClazz Superclass class
|
||||
* @param <X> Subclass type
|
||||
* @param <Y> Superclass type
|
||||
* @return True if X is a subclass of Y
|
||||
*/
|
||||
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
|
||||
Class<X> subClazz, Class<Y> superClazz) {
|
||||
return superClazz.isAssignableFrom(subClazz);
|
||||
}
|
||||
|
||||
/**
|
||||
* Lists all the OAF model classes
|
||||
*
|
||||
* @param <T>
|
||||
* @return
|
||||
*/
|
||||
public static <T extends Entity> Class<T>[] getOafModelClasses() {
|
||||
return new Class[] {
|
||||
AccessRight.class,
|
||||
Author.class,
|
||||
AuthorPid.class,
|
||||
Context.class,
|
||||
Country.class,
|
||||
DataInfo.class,
|
||||
Dataset.class,
|
||||
Datasource.class,
|
||||
Entity.class,
|
||||
EntityDataInfo.class,
|
||||
EoscIfGuidelines.class,
|
||||
ExternalReference.class,
|
||||
ExtraInfo.class,
|
||||
GeoLocation.class,
|
||||
H2020Classification.class,
|
||||
H2020Programme.class,
|
||||
Instance.class,
|
||||
Journal.class,
|
||||
KeyValue.class,
|
||||
License.class,
|
||||
Measure.class,
|
||||
OAIProvenance.class,
|
||||
OpenAccessRoute.class,
|
||||
Organization.class,
|
||||
OriginDescription.class,
|
||||
OtherResearchProduct.class,
|
||||
Project.class,
|
||||
Provenance.class,
|
||||
Publication.class,
|
||||
Publisher.class,
|
||||
Qualifier.class,
|
||||
Relation.class,
|
||||
Result.class,
|
||||
Software.class,
|
||||
StructuredProperty.class,
|
||||
Subject.class
|
||||
};
|
||||
}
|
||||
|
||||
public static String getMainType(final EntityType type) {
|
||||
return entityMapping.get(type).name();
|
||||
}
|
||||
|
||||
public static boolean isResult(EntityType type) {
|
||||
return MainEntityType.result.name().equals(getMainType(type));
|
||||
}
|
||||
|
||||
public static String getScheme(final String sourceType, final String targetType) {
|
||||
return String
|
||||
.format(
|
||||
schemeTemplate,
|
||||
entityMapping.get(EntityType.valueOf(sourceType)).name(),
|
||||
entityMapping.get(EntityType.valueOf(targetType)).name());
|
||||
}
|
||||
|
||||
public static String tableIdentifier(String dbName, String tableName) {
|
||||
|
||||
checkArgument(StringUtils.isNotBlank(dbName), "DB name cannot be empty");
|
||||
checkArgument(StringUtils.isNotBlank(tableName), "table name cannot be empty");
|
||||
|
||||
return String.format("%s.%s", dbName, tableName);
|
||||
}
|
||||
|
||||
public static <T extends Entity> String tableIdentifier(String dbName, Class<T> clazz) {
|
||||
|
||||
checkArgument(Objects.nonNull(clazz), "clazz is needed to derive the table name, thus cannot be null");
|
||||
|
||||
return tableIdentifier(dbName, clazz.getSimpleName().toLowerCase());
|
||||
}
|
||||
|
||||
public static <T extends Oaf> Function<T, String> idFn() {
|
||||
return x -> {
|
||||
if (isSubClass(x, Relation.class)) {
|
||||
return idFnForRelation(x);
|
||||
}
|
||||
return idFnForOafEntity(x);
|
||||
};
|
||||
}
|
||||
|
||||
private static <T extends Oaf> String idFnForRelation(T t) {
|
||||
Relation r = (Relation) t;
|
||||
return Optional
|
||||
.ofNullable(r.getSource())
|
||||
.map(
|
||||
source -> Optional
|
||||
.ofNullable(r.getTarget())
|
||||
.map(
|
||||
target -> Optional
|
||||
.ofNullable(r.getRelType())
|
||||
.map(
|
||||
relType -> Optional
|
||||
.ofNullable(r.getSubRelType())
|
||||
.map(
|
||||
subRelType -> Optional
|
||||
.ofNullable(r.getRelClass())
|
||||
.map(
|
||||
relClass -> String
|
||||
.join(
|
||||
source,
|
||||
target,
|
||||
relType,
|
||||
subRelType,
|
||||
relClass))
|
||||
.orElse(
|
||||
String
|
||||
.join(
|
||||
source,
|
||||
target,
|
||||
relType,
|
||||
subRelType)))
|
||||
.orElse(String.join(source, target, relType)))
|
||||
.orElse(String.join(source, target)))
|
||||
.orElse(source))
|
||||
.orElse(null);
|
||||
}
|
||||
|
||||
private static <T extends Oaf> String idFnForOafEntity(T t) {
|
||||
return ((Entity) t).getId();
|
||||
}
|
||||
|
||||
public static String md5(final String s) {
|
||||
try {
|
||||
final MessageDigest md = MessageDigest.getInstance("MD5");
|
||||
md.update(s.getBytes(StandardCharsets.UTF_8));
|
||||
return new String(Hex.encodeHex(md.digest()));
|
||||
} catch (final NoSuchAlgorithmException e) {
|
||||
throw new IllegalStateException(e);
|
||||
}
|
||||
}
|
||||
|
||||
public static String generateIdentifier(final String originalId, final String nsPrefix) {
|
||||
return String.format("%s::%s", nsPrefix, md5(originalId));
|
||||
}
|
||||
|
||||
public static String oldest(String dateA, String dateB) throws ParseException {
|
||||
|
||||
if (StringUtils.isBlank(dateA)) {
|
||||
return dateB;
|
||||
}
|
||||
if (StringUtils.isBlank(dateB)) {
|
||||
return dateA;
|
||||
}
|
||||
if (StringUtils.isNotBlank(dateA) && StringUtils.isNotBlank(dateB)) {
|
||||
|
||||
final Date a = DateParserUtils.parseDate(dateA);
|
||||
final Date b = DateParserUtils.parseDate(dateB);
|
||||
|
||||
if (Objects.nonNull(a) && Objects.nonNull(b)) {
|
||||
return a.before(b) ? dateA : dateB;
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.common;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Qualifier;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
public class RefereedComparator implements Comparator<Qualifier> {
|
||||
|
||||
@Override
|
||||
public int compare(Qualifier left, Qualifier right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
String lClass = left.getClassid();
|
||||
String rClass = right.getClassid();
|
||||
|
||||
if (lClass.equals(rClass))
|
||||
return 0;
|
||||
|
||||
if (lClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.PEER_REVIEWED_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.NON_PEER_REVIEWED_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.UNKNOWN))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.UNKNOWN))
|
||||
return 1;
|
||||
|
||||
// Else (but unlikely), lexicographical ordering will do.
|
||||
return lClass.compareTo(rClass);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.common;
|
||||
|
||||
public class RelationInverse {
|
||||
private String relClass;
|
||||
private String inverseRelClass;
|
||||
private String relType;
|
||||
private String subReltype;
|
||||
|
||||
public String getRelType() {
|
||||
return relType;
|
||||
}
|
||||
|
||||
public RelationInverse setRelType(String relType) {
|
||||
this.relType = relType;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getSubReltype() {
|
||||
return subReltype;
|
||||
}
|
||||
|
||||
public RelationInverse setSubReltype(String subReltype) {
|
||||
this.subReltype = subReltype;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getRelClass() {
|
||||
return relClass;
|
||||
}
|
||||
|
||||
public RelationInverse setRelClass(String relClass) {
|
||||
this.relClass = relClass;
|
||||
return this;
|
||||
}
|
||||
|
||||
public String getInverseRelClass() {
|
||||
return inverseRelClass;
|
||||
}
|
||||
|
||||
public RelationInverse setInverseRelClass(String inverseRelClass) {
|
||||
this.inverseRelClass = inverseRelClass;
|
||||
return this;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.HashSet;
|
||||
import java.util.Objects;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class CleaningFunctions {
|
||||
|
||||
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
|
||||
public static final String DOI_PREFIX = "10.";
|
||||
|
||||
public static final Set<String> PID_BLACKLIST = new HashSet<>();
|
||||
|
||||
static {
|
||||
PID_BLACKLIST.add("none");
|
||||
PID_BLACKLIST.add("na");
|
||||
}
|
||||
|
||||
public CleaningFunctions() {
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method that filter PID values on a per-type basis.
|
||||
* @param s the PID whose value will be checked.
|
||||
* @return false if the pid matches the filter criteria, true otherwise.
|
||||
*/
|
||||
public static boolean pidFilter(StructuredProperty s) {
|
||||
final String pidValue = s.getValue();
|
||||
if (Objects.isNull(s.getQualifier()) ||
|
||||
StringUtils.isBlank(pidValue) ||
|
||||
StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
|
||||
return false;
|
||||
}
|
||||
if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
|
||||
return false;
|
||||
}
|
||||
return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
|
||||
}
|
||||
|
||||
/**
|
||||
* Utility method that normalises PID values on a per-type basis.
|
||||
* @param pid the PID whose value will be normalised.
|
||||
* @return the PID containing the normalised value.
|
||||
*/
|
||||
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
|
||||
pid
|
||||
.setValue(
|
||||
normalizePidValue(
|
||||
pid.getQualifier().getClassid(),
|
||||
pid.getValue()));
|
||||
|
||||
return pid;
|
||||
}
|
||||
|
||||
public static String normalizePidValue(String pidType, String pidValue) {
|
||||
String value = Optional
|
||||
.ofNullable(pidValue)
|
||||
.map(String::trim)
|
||||
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
|
||||
|
||||
switch (pidType) {
|
||||
|
||||
// TODO add cleaning for more PID types as needed
|
||||
case "doi":
|
||||
return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
|
||||
}
|
||||
return value;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -13,6 +13,8 @@ import java.util.stream.Collectors;
|
|||
import java.util.stream.Stream;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
||||
import com.github.sisyphsu.dateparser.DateParserUtils;
|
||||
import com.google.common.collect.Lists;
|
||||
|
|
@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import me.xuender.unidecode.Unidecode;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
|
||||
public class GraphCleaningFunctions extends CleaningFunctions {
|
||||
|
||||
|
|
@ -91,48 +91,31 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
}
|
||||
|
||||
public static <T extends Oaf> boolean filter(T value) {
|
||||
if (Boolean.TRUE
|
||||
.equals(
|
||||
Optional
|
||||
.ofNullable(value)
|
||||
.map(
|
||||
o -> Optional
|
||||
.ofNullable(o.getDataInfo())
|
||||
.map(
|
||||
d -> Optional
|
||||
.ofNullable(d.getInvisible())
|
||||
.orElse(true))
|
||||
.orElse(true))
|
||||
.orElse(true))) {
|
||||
return true;
|
||||
}
|
||||
|
||||
if (value instanceof Datasource) {
|
||||
// nothing to evaluate here
|
||||
} else if (value instanceof Project) {
|
||||
// nothing to evaluate here
|
||||
} else if (value instanceof Organization) {
|
||||
// nothing to evaluate here
|
||||
} else if (value instanceof Relation) {
|
||||
// nothing to clean here
|
||||
} else if (value instanceof Result) {
|
||||
|
||||
Result r = (Result) value;
|
||||
|
||||
if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) {
|
||||
return false;
|
||||
}
|
||||
|
||||
if (value instanceof Publication) {
|
||||
|
||||
} else if (value instanceof Dataset) {
|
||||
|
||||
} else if (value instanceof OtherResearchProduct) {
|
||||
|
||||
} else if (value instanceof Software) {
|
||||
if (value instanceof Entity) {
|
||||
Entity entity = (Entity) value;
|
||||
if (Boolean.TRUE
|
||||
.equals(
|
||||
Optional
|
||||
.ofNullable(entity)
|
||||
.map(
|
||||
o -> Optional
|
||||
.ofNullable(o.getDataInfo())
|
||||
.map(
|
||||
d -> Optional
|
||||
.ofNullable(d.getInvisible())
|
||||
.orElse(true))
|
||||
.orElse(true))
|
||||
.orElse(true))) {
|
||||
return true;
|
||||
} else if (value instanceof Result) {
|
||||
Result r = (Result) value;
|
||||
|
||||
if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
|
|
@ -164,7 +147,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
if (Objects.nonNull(r.getDateofacceptance())) {
|
||||
Optional<String> date = cleanDateField(r.getDateofacceptance());
|
||||
if (date.isPresent()) {
|
||||
r.getDateofacceptance().setValue(date.get());
|
||||
r.setDateofacceptance(date.get());
|
||||
} else {
|
||||
r.setDateofacceptance(null);
|
||||
}
|
||||
|
|
@ -185,7 +168,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
|
||||
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getName())) {
|
||||
r.setPublisher(null);
|
||||
}
|
||||
if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
|
||||
|
|
@ -267,7 +250,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
.getDescription()
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
|
||||
.filter(s -> StringUtils.isNotBlank(s))
|
||||
.map(GraphCleaningFunctions::cleanValue)
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
|
|
@ -288,29 +271,25 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
.setInstancetype(
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
} else if (r instanceof Dataset) {
|
||||
i
|
||||
.setInstancetype(
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
} else if (r instanceof Software) {
|
||||
i
|
||||
.setInstancetype(
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
} else if (r instanceof OtherResearchProduct) {
|
||||
i
|
||||
.setInstancetype(
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
||||
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -348,7 +327,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
if (Objects.nonNull(i.getDateofacceptance())) {
|
||||
Optional<String> date = cleanDateField(i.getDateofacceptance());
|
||||
if (date.isPresent()) {
|
||||
i.getDateofacceptance().setValue(date.get());
|
||||
i.setDateofacceptance(date.get());
|
||||
} else {
|
||||
i.setDateofacceptance(null);
|
||||
}
|
||||
|
|
@ -456,10 +435,9 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
return value;
|
||||
}
|
||||
|
||||
private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
|
||||
private static Optional<String> cleanDateField(String dateofacceptance) {
|
||||
return Optional
|
||||
.ofNullable(dateofacceptance)
|
||||
.map(Field::getValue)
|
||||
.map(GraphCleaningFunctions::cleanDate)
|
||||
.filter(Objects::nonNull);
|
||||
}
|
||||
|
|
@ -513,7 +491,6 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
private static void fixVocabName(Qualifier q, String vocabularyName) {
|
||||
if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
|
||||
q.setSchemeid(vocabularyName);
|
||||
q.setSchemename(vocabularyName);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -524,9 +501,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
}
|
||||
|
||||
private static Qualifier qualifier(String classid, String classname, String scheme) {
|
||||
return OafMapperUtils
|
||||
.qualifier(
|
||||
classid, classname, scheme, scheme);
|
||||
return OafMapperUtils.qualifier(classid, classname, scheme);
|
||||
}
|
||||
|
||||
protected static StructuredProperty cleanValue(StructuredProperty s) {
|
||||
|
|
@ -539,9 +514,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
|
|||
return s;
|
||||
}
|
||||
|
||||
protected static Field<String> cleanValue(Field<String> s) {
|
||||
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
|
||||
return s;
|
||||
protected static String cleanValue(String s) {
|
||||
return s.replaceAll(CLEANING_REGEX, " ");
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -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 eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
|
||||
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.oaf.*;
|
||||
|
||||
/**
|
||||
* Factory class for OpenAIRE identifiers in the Graph
|
||||
*/
|
||||
public class IdentifierFactory implements Serializable {
|
||||
|
||||
public static final String ID_SEPARATOR = "::";
|
||||
public static final String ID_PREFIX_SEPARATOR = "|";
|
||||
|
||||
public static final int ID_PREFIX_LEN = 12;
|
||||
|
||||
/**
|
||||
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
|
||||
* The id of the record (source_::id) will be rewritten as pidType_::id)
|
||||
*/
|
||||
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
|
||||
|
||||
static {
|
||||
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
|
||||
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
|
||||
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
|
||||
PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
|
||||
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
|
||||
|
||||
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
|
||||
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
|
||||
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
|
||||
|
||||
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
|
||||
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
|
||||
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
|
||||
|
||||
PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
|
||||
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
|
||||
|
||||
PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
|
||||
PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
|
||||
}
|
||||
|
||||
/**
|
||||
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
|
||||
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
|
||||
*
|
||||
* If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
|
||||
* See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
|
||||
*/
|
||||
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
|
||||
|
||||
static {
|
||||
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
|
||||
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
|
||||
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
|
||||
DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
|
||||
DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
|
||||
}
|
||||
|
||||
/**
|
||||
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
|
||||
* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
|
||||
* the same OpenAIRE id.
|
||||
*/
|
||||
public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
|
||||
|
||||
static {
|
||||
ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
|
||||
ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
|
||||
}
|
||||
|
||||
public static Set<String> delegatedAuthorityDatasourceIds() {
|
||||
return DELEGATED_PID_AUTHORITY
|
||||
.values()
|
||||
.stream()
|
||||
.flatMap(m -> m.keySet().stream())
|
||||
.collect(Collectors.toCollection(HashSet::new));
|
||||
}
|
||||
|
||||
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
|
||||
return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
|
||||
if (entity == null)
|
||||
return null;
|
||||
|
||||
StructuredProperty pid = null;
|
||||
if (entity.getPid() != null) {
|
||||
pid = entity
|
||||
.getPid()
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.findAny()
|
||||
.orElse(null);
|
||||
} else {
|
||||
if (entity.getInstance() != null) {
|
||||
pid = entity
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getPid() != null)
|
||||
.flatMap(i -> i.getPid().stream())
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.findAny()
|
||||
.orElse(null);
|
||||
}
|
||||
}
|
||||
if (pid != null)
|
||||
return idFromPid(entity, pid, true);
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
|
||||
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
|
||||
*
|
||||
* @param entity the entity providing PIDs and a default ID.
|
||||
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
|
||||
* @param md5 indicates whether should hash the PID value or not.
|
||||
* @return an identifier from the most relevant PID, entity.id otherwise
|
||||
*/
|
||||
public static <T extends Entity> String createIdentifier(T entity, boolean md5) {
|
||||
|
||||
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
|
||||
|
||||
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
|
||||
|
||||
return pids
|
||||
.values()
|
||||
.stream()
|
||||
.flatMap(Set::stream)
|
||||
.min(new PidComparator<>(entity))
|
||||
.map(
|
||||
min -> Optional
|
||||
.ofNullable(pids.get(min.getQualifier().getClassid()))
|
||||
.map(
|
||||
p -> p
|
||||
.stream()
|
||||
.sorted(new PidValueComparator())
|
||||
.findFirst()
|
||||
.map(s -> idFromPid(entity, s, md5))
|
||||
.orElseGet(entity::getId))
|
||||
.orElseGet(entity::getId))
|
||||
.orElseGet(entity::getId);
|
||||
}
|
||||
|
||||
private static <T extends Entity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
|
||||
if (entity instanceof Result) {
|
||||
return Optional
|
||||
.ofNullable(((Result) entity).getInstance())
|
||||
.map(IdentifierFactory::mapPids)
|
||||
.orElse(new HashMap<>());
|
||||
} else {
|
||||
return entity
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(CleaningFunctions::normalizePidValue)
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.collect(
|
||||
Collectors
|
||||
.groupingBy(
|
||||
p -> p.getQualifier().getClassid(),
|
||||
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
|
||||
}
|
||||
}
|
||||
|
||||
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
|
||||
return instance
|
||||
.stream()
|
||||
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
|
||||
.flatMap(Function.identity())
|
||||
.collect(
|
||||
Collectors
|
||||
.groupingBy(
|
||||
p -> p.getQualifier().getClassid(),
|
||||
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
|
||||
}
|
||||
|
||||
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
|
||||
boolean mapHandles) {
|
||||
return Optional
|
||||
.ofNullable(pid)
|
||||
.map(
|
||||
pp -> pp
|
||||
.stream()
|
||||
// filter away PIDs provided by a DS that is not considered an authority for the
|
||||
// given PID Type
|
||||
.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
|
||||
.map(CleaningFunctions::normalizePidValue)
|
||||
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
|
||||
.filter(CleaningFunctions::pidFilter))
|
||||
.orElse(Stream.empty());
|
||||
}
|
||||
|
||||
private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
|
||||
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
|
||||
|
||||
if (Objects.isNull(collectedFrom)) {
|
||||
return false;
|
||||
}
|
||||
|
||||
boolean isEnrich = Optional
|
||||
.ofNullable(ENRICHMENT_PROVIDER.get(pType))
|
||||
.map(
|
||||
enrich -> enrich.containsKey(collectedFrom.getKey())
|
||||
|| enrich.containsValue(collectedFrom.getValue()))
|
||||
.orElse(false);
|
||||
|
||||
boolean isAuthority = Optional
|
||||
.ofNullable(PID_AUTHORITY.get(pType))
|
||||
.map(
|
||||
authorities -> authorities.containsKey(collectedFrom.getKey())
|
||||
|| authorities.containsValue(collectedFrom.getValue()))
|
||||
.orElse(false);
|
||||
|
||||
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
|
||||
}
|
||||
|
||||
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
|
||||
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
|
||||
|
||||
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
|
||||
if (Objects.isNull(da)) {
|
||||
return true;
|
||||
}
|
||||
if (!da.containsKey(collectedFrom.getKey())) {
|
||||
return true;
|
||||
}
|
||||
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
|
||||
}
|
||||
|
||||
/**
|
||||
* @see {@link IdentifierFactory#createIdentifier(Entity, boolean)}
|
||||
*/
|
||||
public static <T extends Entity> String createIdentifier(T entity) {
|
||||
|
||||
return createIdentifier(entity, true);
|
||||
}
|
||||
|
||||
private static <T extends Entity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
|
||||
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
|
||||
}
|
||||
|
||||
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
|
||||
return new StringBuilder()
|
||||
.append(numericPrefix)
|
||||
.append(ID_PREFIX_SEPARATOR)
|
||||
.append(createPrefix(pidType))
|
||||
.append(ID_SEPARATOR)
|
||||
.append(md5 ? md5(pidValue) : pidValue)
|
||||
.toString();
|
||||
}
|
||||
|
||||
// create the prefix (length = 12)
|
||||
private static String createPrefix(String pidType) {
|
||||
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
|
||||
while (prefix.length() < ID_PREFIX_LEN) {
|
||||
prefix.append("_");
|
||||
}
|
||||
return prefix.substring(0, ID_PREFIX_LEN);
|
||||
}
|
||||
|
||||
public static String md5(final String s) {
|
||||
try {
|
||||
final MessageDigest md = MessageDigest.getInstance("MD5");
|
||||
md.update(s.getBytes(StandardCharsets.UTF_8));
|
||||
return new String(Hex.encodeHex(md.digest()));
|
||||
} catch (final Exception e) {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.lang.reflect.InvocationTargetException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import org.apache.commons.beanutils.BeanUtilsBean;
|
||||
|
||||
public class MergeBeanUtils {
|
||||
|
||||
/**
|
||||
* Copies all properties from sources to destination, does not copy null values and any nested objects will attempted to be
|
||||
* either cloned or copied into the existing object. This is recursive. Should not cause any infinite recursion.
|
||||
* @param dest object to copy props into (will mutate)
|
||||
* @param sources
|
||||
* @param <T> dest
|
||||
* @return
|
||||
* @throws IllegalAccessException
|
||||
* @throws InvocationTargetException
|
||||
*/
|
||||
public static <T> T mergeIn(T dest, T... sources) {
|
||||
// to keep from any chance infinite recursion lets limit each object to 1 instance at a time in the stack
|
||||
final List<Object> lookingAt = new ArrayList<>();
|
||||
|
||||
BeanUtilsBean recursiveBeanUtils = new BeanUtilsBean() {
|
||||
|
||||
/**
|
||||
* Check if the class name is an internal one
|
||||
* @param name
|
||||
* @return
|
||||
*/
|
||||
private boolean isInternal(String name) {
|
||||
return name.startsWith("java.") || name.startsWith("javax.")
|
||||
|| name.startsWith("com.sun.") || name.startsWith("javax.")
|
||||
|| name.startsWith("oracle.");
|
||||
}
|
||||
|
||||
/**
|
||||
* Override to ensure that we dont end up in infinite recursion
|
||||
* @param dest
|
||||
* @param orig
|
||||
* @throws IllegalAccessException
|
||||
* @throws InvocationTargetException
|
||||
*/
|
||||
@Override
|
||||
public void copyProperties(Object dest, Object orig)
|
||||
throws IllegalAccessException, InvocationTargetException {
|
||||
try {
|
||||
// if we have an object in our list, that means we hit some sort of recursion, stop here.
|
||||
if (lookingAt.stream().anyMatch(o -> o == dest)) {
|
||||
return; // recursion detected
|
||||
}
|
||||
lookingAt.add(dest);
|
||||
super.copyProperties(dest, orig);
|
||||
} finally {
|
||||
lookingAt.remove(dest);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void copyProperty(Object dest, String name, Object value)
|
||||
throws IllegalAccessException, InvocationTargetException {
|
||||
|
||||
if ("resulttype".equals(name)) {
|
||||
return;
|
||||
} else if (value != null) {
|
||||
// dont copy over null values
|
||||
// attempt to check if the value is a pojo we can clone using nested calls
|
||||
if (!value.getClass().isPrimitive() && !value.getClass().isSynthetic()
|
||||
&& !isInternal(value.getClass().getName())) {
|
||||
try {
|
||||
Object prop = super.getPropertyUtils().getProperty(dest, name);
|
||||
// get current value, if its null then clone the value and set that to the value
|
||||
if (prop == null) {
|
||||
super.setProperty(dest, name, super.cloneBean(value));
|
||||
} else {
|
||||
// get the destination value and then recursively call
|
||||
copyProperties(prop, value);
|
||||
}
|
||||
} catch (NoSuchMethodException e) {
|
||||
return;
|
||||
} catch (InstantiationException e) {
|
||||
throw new RuntimeException("Nested property could not be cloned.", e);
|
||||
}
|
||||
} else {
|
||||
super.copyProperty(dest, name, value);
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
|
||||
for (Object source : sources) {
|
||||
try {
|
||||
recursiveBeanUtils.copyProperties(dest, source);
|
||||
} catch (IllegalAccessException | InvocationTargetException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
return dest;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,661 @@
|
|||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.common.AccessRightComparator;
|
||||
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.lang3.tuple.ImmutablePair;
|
||||
import org.apache.commons.lang3.tuple.Pair;
|
||||
|
||||
import java.text.ParseException;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static com.google.common.base.Preconditions.checkArgument;
|
||||
|
||||
public class MergeUtils {
|
||||
|
||||
public static Result mergeResult(Result original, Result enrich) {
|
||||
|
||||
final Result mergedResult = (Result) mergeEntity(original, enrich);
|
||||
|
||||
if(StringUtils.isBlank(mergedResult.getProcessingchargeamount())){
|
||||
mergedResult.setProcessingchargeamount(enrich.getProcessingchargeamount());
|
||||
mergedResult.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
|
||||
}
|
||||
|
||||
mergedResult.setMeasures(mergeLists(mergedResult.getMeasures(), enrich.getMeasures()));
|
||||
|
||||
if( !isAnEnrichment(mergedResult) && !isAnEnrichment(enrich))
|
||||
mergedResult.setInstance(mergeLists(mergedResult.getInstance(), enrich.getInstance()));
|
||||
else {
|
||||
final List<Instance> enrichmentInstances = isAnEnrichment(mergedResult) ? mergedResult.getInstance() : enrich.getInstance();
|
||||
final List<Instance> enrichedInstances= isAnEnrichment(mergedResult) ? enrich.getInstance(): mergedResult.getInstance();
|
||||
if (isAnEnrichment(mergedResult))
|
||||
mergedResult.setDataInfo(enrich.getDataInfo());
|
||||
mergedResult.setInstance(enrichInstances(enrichedInstances,enrichmentInstances));
|
||||
}
|
||||
|
||||
if (enrich.getBestaccessright() != null
|
||||
&& new AccessRightComparator<>().compare(enrich.getBestaccessright(), mergedResult.getBestaccessright()) < 0)
|
||||
mergedResult.setBestaccessright(enrich.getBestaccessright());
|
||||
|
||||
final int trustCompareResult = compareTrust(mergedResult, enrich);
|
||||
|
||||
if (enrich.getResulttype() != null && trustCompareResult < 0)
|
||||
mergedResult.setResulttype(enrich.getResulttype());
|
||||
|
||||
if (enrich.getLanguage() != null && trustCompareResult < 0)
|
||||
mergedResult.setLanguage(enrich.getLanguage());
|
||||
|
||||
if (Objects.nonNull(enrich.getDateofacceptance())) {
|
||||
if (Objects.isNull(mergedResult.getDateofacceptance())) {
|
||||
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
|
||||
} else if (trustCompareResult < 0) {
|
||||
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
|
||||
}
|
||||
}
|
||||
|
||||
mergedResult.setCountry(mergeLists(mergedResult.getCountry(), enrich.getCountry()));
|
||||
|
||||
mergedResult.setSubject(mergeLists(mergedResult.getSubject(), enrich.getSubject()));
|
||||
|
||||
if (enrich.getJournal() != null && trustCompareResult < 0)
|
||||
mergedResult.setJournal(enrich.getJournal());
|
||||
|
||||
// merge title lists: main title with higher trust and distinct between the others
|
||||
StructuredProperty baseMainTitle = null;
|
||||
if (mergedResult.getTitle() != null) {
|
||||
baseMainTitle = getMainTitle(mergedResult.getTitle());
|
||||
if (baseMainTitle != null) {
|
||||
final StructuredProperty p = baseMainTitle;
|
||||
mergedResult.setTitle(mergedResult.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
StructuredProperty newMainTitle = null;
|
||||
if (enrich.getTitle() != null) {
|
||||
newMainTitle = getMainTitle(enrich.getTitle());
|
||||
if (newMainTitle != null) {
|
||||
final StructuredProperty p = newMainTitle;
|
||||
enrich.setTitle(enrich.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
if (newMainTitle != null && trustCompareResult < 0) {
|
||||
baseMainTitle = newMainTitle;
|
||||
}
|
||||
|
||||
mergedResult.setTitle(mergeLists(mergedResult.getTitle(), enrich.getTitle()));
|
||||
if (mergedResult.getTitle() != null && baseMainTitle != null) {
|
||||
mergedResult.getTitle().add(baseMainTitle);
|
||||
}
|
||||
|
||||
mergedResult.setRelevantdate(mergeLists(mergedResult.getRelevantdate(), enrich.getRelevantdate()));
|
||||
|
||||
mergedResult.setDescription(longestLists(mergedResult.getDescription(), enrich.getDescription()));
|
||||
|
||||
if (enrich.getPublisher() != null && trustCompareResult < 0)
|
||||
mergedResult.setPublisher(enrich.getPublisher());
|
||||
|
||||
if (enrich.getEmbargoenddate() != null && trustCompareResult < 0)
|
||||
mergedResult.setEmbargoenddate(enrich.getEmbargoenddate());
|
||||
|
||||
mergedResult.setSource(mergeLists(mergedResult.getSource(), enrich.getSource()));
|
||||
|
||||
mergedResult.setFulltext(mergeLists(mergedResult.getFulltext(), enrich.getFulltext()));
|
||||
|
||||
mergedResult.setFormat(mergeLists(mergedResult.getFormat(), enrich.getFormat()));
|
||||
|
||||
mergedResult.setContributor(mergeLists(mergedResult.getContributor(), enrich.getContributor()));
|
||||
|
||||
if (enrich.getResourcetype() != null)
|
||||
mergedResult.setResourcetype(enrich.getResourcetype());
|
||||
|
||||
mergedResult.setCoverage(mergeLists(mergedResult.getCoverage(), enrich.getCoverage()));
|
||||
|
||||
mergedResult.setContext(mergeLists(mergedResult.getContext(), enrich.getContext()));
|
||||
|
||||
mergedResult.setExternalReference(mergeLists(mergedResult.getExternalReference(), enrich.getExternalReference()));
|
||||
|
||||
if (enrich.getOaiprovenance() != null && trustCompareResult < 0)
|
||||
mergedResult.setOaiprovenance(enrich.getOaiprovenance());
|
||||
|
||||
return mergedResult;
|
||||
}
|
||||
|
||||
public static OtherResearchProduct mergeORP(OtherResearchProduct original, OtherResearchProduct enrich) {
|
||||
final OtherResearchProduct mergedORP = (OtherResearchProduct) mergeResult(original, enrich);
|
||||
|
||||
mergedORP.setContactperson(mergeLists(mergedORP.getContactperson(), enrich.getContactperson()));
|
||||
mergedORP.setContactgroup(mergeLists(mergedORP.getContactgroup(), enrich.getContactgroup()));
|
||||
mergedORP.setTool(mergeLists(mergedORP.getTool(), enrich.getTool()));
|
||||
mergeEntityDataInfo(mergedORP, enrich);
|
||||
|
||||
return mergedORP;
|
||||
}
|
||||
|
||||
public static Software mergeSoftware(Software original, Software enrich) {
|
||||
final Software mergedSoftware = (Software) mergeResult(original, enrich);
|
||||
|
||||
mergedSoftware.setDocumentationUrl(mergeLists(mergedSoftware.getDocumentationUrl(), enrich.getDocumentationUrl()));
|
||||
|
||||
mergedSoftware.setCodeRepositoryUrl(enrich.getCodeRepositoryUrl() != null && compareTrust(mergedSoftware,enrich) < 0
|
||||
? enrich.getCodeRepositoryUrl()
|
||||
: mergedSoftware.getCodeRepositoryUrl());
|
||||
|
||||
mergedSoftware.setProgrammingLanguage(enrich.getProgrammingLanguage() != null && compareTrust(mergedSoftware, enrich) < 0
|
||||
? enrich.getProgrammingLanguage()
|
||||
: mergedSoftware.getProgrammingLanguage());
|
||||
|
||||
mergeEntityDataInfo(mergedSoftware, enrich);
|
||||
return mergedSoftware;
|
||||
}
|
||||
|
||||
public static Dataset mergeDataset(Dataset original, Dataset enrich) {
|
||||
|
||||
final Dataset mergedDataset = (Dataset) mergeResult(original, enrich);
|
||||
|
||||
mergedDataset.setStoragedate(enrich.getStoragedate() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getStoragedate() : mergedDataset.getStoragedate());
|
||||
|
||||
mergedDataset.setDevice(enrich.getDevice() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getDevice() : mergedDataset.getDevice());
|
||||
|
||||
mergedDataset.setSize(enrich.getSize() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getSize() : mergedDataset.getSize());
|
||||
|
||||
mergedDataset.setVersion(enrich.getVersion() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getVersion() : mergedDataset.getVersion());
|
||||
|
||||
mergedDataset.setLastmetadataupdate(
|
||||
enrich.getLastmetadataupdate() != null && compareTrust(mergedDataset,enrich) < 0
|
||||
? enrich.getLastmetadataupdate()
|
||||
: mergedDataset.getLastmetadataupdate());
|
||||
|
||||
mergedDataset.setMetadataversionnumber(
|
||||
enrich.getMetadataversionnumber() != null && compareTrust(mergedDataset, enrich) < 0
|
||||
? enrich.getMetadataversionnumber()
|
||||
: mergedDataset.getMetadataversionnumber());
|
||||
|
||||
mergedDataset.setGeolocation(mergeLists(mergedDataset.getGeolocation(), enrich.getGeolocation()));
|
||||
|
||||
mergeEntityDataInfo(mergedDataset, enrich);
|
||||
|
||||
return mergedDataset;
|
||||
}
|
||||
|
||||
public static Publication mergePublication(Publication original, Publication enrich) {
|
||||
|
||||
final Publication mergedPublication = (Publication) mergeResult(original, enrich);
|
||||
|
||||
mergeEntityDataInfo(mergedPublication, enrich);
|
||||
return mergedPublication;
|
||||
}
|
||||
|
||||
public static Oaf mergeOrganization(Organization original, Organization enrich) {
|
||||
|
||||
final Organization mergedOrganization = (Organization) mergeEntity(original, enrich);
|
||||
|
||||
int ct = compareTrust(mergedOrganization, enrich);
|
||||
mergedOrganization.setLegalshortname(enrich.getLegalshortname() != null && ct < 0
|
||||
? enrich.getLegalshortname()
|
||||
: mergedOrganization.getLegalname());
|
||||
|
||||
|
||||
mergedOrganization.setLegalname(enrich.getLegalname() != null && ct < 0 ?
|
||||
enrich.getLegalname()
|
||||
: mergedOrganization.getLegalname());
|
||||
|
||||
mergedOrganization.setAlternativeNames(mergeLists(enrich.getAlternativeNames(), mergedOrganization.getAlternativeNames()));
|
||||
|
||||
|
||||
mergedOrganization.setWebsiteurl(enrich.getWebsiteurl() != null && ct < 0
|
||||
? enrich.getWebsiteurl()
|
||||
: mergedOrganization.getWebsiteurl());
|
||||
|
||||
mergedOrganization.setLogourl(enrich.getLogourl() != null && ct < 0
|
||||
? enrich.getLogourl()
|
||||
: mergedOrganization.getLogourl());
|
||||
|
||||
mergedOrganization.setEclegalbody(enrich.getEclegalbody() != null && ct < 0
|
||||
? enrich.getEclegalbody()
|
||||
: mergedOrganization.getEclegalbody());
|
||||
|
||||
mergedOrganization.setEclegalperson(enrich.getEclegalperson() != null && ct < 0
|
||||
? enrich.getEclegalperson()
|
||||
: mergedOrganization.getEclegalperson());
|
||||
|
||||
mergedOrganization.setEcnonprofit (enrich.getEcnonprofit() != null && ct< 0
|
||||
? enrich.getEcnonprofit()
|
||||
: mergedOrganization.getEcnonprofit());
|
||||
|
||||
mergedOrganization.setEcresearchorganization (enrich.getEcresearchorganization() != null && ct < 0
|
||||
? enrich.getEcresearchorganization()
|
||||
: mergedOrganization.getEcresearchorganization());
|
||||
|
||||
mergedOrganization.setEchighereducation (enrich.getEchighereducation() != null && ct < 0
|
||||
? enrich.getEchighereducation()
|
||||
: mergedOrganization.getEchighereducation());
|
||||
|
||||
mergedOrganization.setEcinternationalorganizationeurinterests (enrich.getEcinternationalorganizationeurinterests() != null && ct< 0
|
||||
? enrich.getEcinternationalorganizationeurinterests()
|
||||
: mergedOrganization.getEcinternationalorganizationeurinterests());
|
||||
|
||||
mergedOrganization.setEcinternationalorganization (enrich.getEcinternationalorganization() != null && ct < 0
|
||||
? enrich.getEcinternationalorganization()
|
||||
: mergedOrganization.getEcinternationalorganization());
|
||||
|
||||
mergedOrganization.setEcenterprise (enrich.getEcenterprise() != null && ct < 0
|
||||
? enrich.getEcenterprise()
|
||||
: mergedOrganization.getEcenterprise());
|
||||
|
||||
mergedOrganization.setEcsmevalidated (enrich.getEcsmevalidated() != null && ct < 0
|
||||
? enrich.getEcsmevalidated()
|
||||
: mergedOrganization.getEcsmevalidated());
|
||||
mergedOrganization.setEcnutscode( enrich.getEcnutscode() != null && ct < 0
|
||||
? enrich.getEcnutscode()
|
||||
: mergedOrganization.getEcnutscode());
|
||||
|
||||
mergedOrganization.setCountry (enrich.getCountry() != null && ct < 0 ?
|
||||
enrich.getCountry()
|
||||
:mergedOrganization.getCountry());
|
||||
|
||||
mergeEntityDataInfo(mergedOrganization, enrich);
|
||||
|
||||
return mergedOrganization;
|
||||
}
|
||||
|
||||
public static Oaf mergeOAFProject(Project original, Project enrich) {
|
||||
|
||||
final Project mergedProject = (Project) mergeEntity(original, enrich);
|
||||
|
||||
int ct = compareTrust(mergedProject, enrich);
|
||||
|
||||
|
||||
mergedProject.setWebsiteurl (enrich.getWebsiteurl() != null && ct < 0
|
||||
? enrich.getWebsiteurl()
|
||||
: mergedProject.getWebsiteurl());
|
||||
|
||||
mergedProject.setCode(enrich.getCode() != null && ct < 0 ?
|
||||
enrich.getCode() :
|
||||
mergedProject.getCode());
|
||||
|
||||
mergedProject.setAcronym(enrich.getAcronym() != null && ct < 0
|
||||
? enrich.getAcronym()
|
||||
: mergedProject.getAcronym());
|
||||
|
||||
mergedProject.setTitle (enrich.getTitle() != null && ct < 0
|
||||
? enrich.getTitle()
|
||||
: mergedProject.getTitle());
|
||||
mergedProject.setStartdate (enrich.getStartdate() != null && ct < 0
|
||||
? enrich.getStartdate()
|
||||
: mergedProject.getStartdate());
|
||||
mergedProject.setEnddate (enrich.getEnddate() != null && ct < 0
|
||||
? enrich.getEnddate()
|
||||
: mergedProject.getEnddate());
|
||||
mergedProject.setCallidentifier ( enrich.getCallidentifier() != null && ct < 0
|
||||
? enrich.getCallidentifier()
|
||||
: mergedProject.getCallidentifier());
|
||||
mergedProject.setKeywords ( enrich.getKeywords() != null && ct < 0
|
||||
? enrich.getKeywords()
|
||||
: mergedProject.getKeywords());
|
||||
|
||||
mergedProject.setDuration ( enrich.getDuration() != null && ct < 0
|
||||
? enrich.getDuration()
|
||||
: mergedProject.getDuration());
|
||||
mergedProject.setEcsc39 ( enrich.getEcsc39() != null && ct < 0
|
||||
? enrich.getEcsc39() :
|
||||
mergedProject.getEcsc39());
|
||||
mergedProject.setOamandatepublications ( enrich.getOamandatepublications() != null && ct < 0
|
||||
? enrich.getOamandatepublications()
|
||||
: mergedProject.getOamandatepublications());
|
||||
mergedProject.setEcarticle29_3 (enrich.getEcarticle29_3() != null && ct < 0
|
||||
? enrich.getEcarticle29_3()
|
||||
: mergedProject.getEcarticle29_3());
|
||||
|
||||
mergedProject.setSubjects (mergeLists(mergedProject.getSubjects(), enrich.getSubjects()));
|
||||
mergedProject.setFundingtree (mergeLists(mergedProject.getFundingtree(), enrich.getFundingtree()));
|
||||
mergedProject.setContracttype (enrich.getContracttype() != null && ct < 0
|
||||
? enrich.getContracttype()
|
||||
: mergedProject.getContracttype());
|
||||
mergedProject.setOptional1 ( enrich.getOptional1() != null && ct < 0
|
||||
? enrich.getOptional1()
|
||||
: mergedProject.getOptional1());
|
||||
mergedProject.setOptional2 (enrich.getOptional2() != null && ct < 0
|
||||
? enrich.getOptional2()
|
||||
: mergedProject.getOptional2());
|
||||
|
||||
mergedProject.setJsonextrainfo ( enrich.getJsonextrainfo() != null && ct < 0
|
||||
? enrich.getJsonextrainfo()
|
||||
: mergedProject.getJsonextrainfo());
|
||||
|
||||
mergedProject.setContactfullname ( enrich.getContactfullname() != null && ct < 0
|
||||
? enrich.getContactfullname()
|
||||
: mergedProject.getContactfullname());
|
||||
|
||||
mergedProject.setContactfax ( enrich.getContactfax() != null && ct < 0
|
||||
? enrich.getContactfax()
|
||||
: mergedProject.getContactfax());
|
||||
|
||||
mergedProject.setContactphone (enrich.getContactphone() != null && ct < 0
|
||||
? enrich.getContactphone()
|
||||
: mergedProject.getContactphone());
|
||||
|
||||
mergedProject.setContactemail ( enrich.getContactemail() != null && ct < 0
|
||||
? enrich.getContactemail()
|
||||
: mergedProject.getContactemail());
|
||||
|
||||
mergedProject.setSummary ( enrich.getSummary() != null && ct < 0
|
||||
? enrich.getSummary()
|
||||
: mergedProject.getSummary());
|
||||
|
||||
mergedProject.setCurrency( enrich.getCurrency() != null && ct < 0
|
||||
? enrich.getCurrency()
|
||||
: mergedProject.getCurrency());
|
||||
|
||||
if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(mergedProject.getH2020topiccode())){
|
||||
mergedProject.setH2020topiccode(enrich.getH2020topiccode());
|
||||
mergedProject.setH2020topicdescription(enrich.getH2020topicdescription());
|
||||
}
|
||||
|
||||
mergedProject.setH2020classification(mergeLists(mergedProject.getH2020classification(), enrich.getH2020classification()));
|
||||
|
||||
mergeEntityDataInfo(mergedProject, enrich);
|
||||
|
||||
return mergedProject;
|
||||
}
|
||||
|
||||
private static Entity mergeEntity(Entity original, Entity enrich) {
|
||||
|
||||
final Entity mergedEntity = original;
|
||||
|
||||
mergedEntity.setOriginalId(mergeLists(mergedEntity.getOriginalId(), enrich.getOriginalId()));
|
||||
mergedEntity.setCollectedfrom(mergeLists(mergedEntity.getCollectedfrom(), enrich.getCollectedfrom()));
|
||||
|
||||
if (mergedEntity.getLastupdatetimestamp() == null && enrich.getLastupdatetimestamp() != null) {
|
||||
mergedEntity.setLastupdatetimestamp(enrich.getLastupdatetimestamp());
|
||||
} else if (mergedEntity.getLastupdatetimestamp() != null && enrich.getLastupdatetimestamp() != null) {
|
||||
mergedEntity.setLastupdatetimestamp(Long.max(mergedEntity.getLastupdatetimestamp(), enrich.getLastupdatetimestamp()));
|
||||
}
|
||||
|
||||
mergedEntity.setPid(mergeLists(mergedEntity.getPid(), enrich.getPid()));
|
||||
|
||||
final int trustCompareResult = compareTrust(mergedEntity, enrich);
|
||||
if (enrich.getDateofcollection() != null && trustCompareResult < 0)
|
||||
mergedEntity.setDateofcollection(enrich.getDateofcollection());
|
||||
|
||||
if (enrich.getDateoftransformation() != null && trustCompareResult < 0)
|
||||
mergedEntity.setDateoftransformation(enrich.getDateoftransformation());
|
||||
|
||||
mergedEntity.setMeasures(mergeLists(mergedEntity.getMeasures(), enrich.getMeasures()));
|
||||
mergedEntity.setExtraInfo(mergeLists(mergedEntity.getExtraInfo(), enrich.getExtraInfo()));
|
||||
|
||||
return mergedEntity;
|
||||
}
|
||||
|
||||
public static Relation mergeRelation(Relation original, Relation enrich) {
|
||||
|
||||
checkArgument(Objects.equals(original.getSource(), enrich.getSource()), "source ids must be equal");
|
||||
checkArgument(Objects.equals(original.getTarget(), enrich.getTarget()), "target ids must be equal");
|
||||
checkArgument(Objects.equals(original.getRelType(), enrich.getRelType()), "relType(s) must be equal");
|
||||
checkArgument(
|
||||
Objects.equals(original.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
|
||||
checkArgument(Objects.equals(original.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
|
||||
|
||||
original.setProvenance(mergeLists(original.getProvenance(), enrich.getProvenance()));
|
||||
|
||||
original.setValidated(original.getValidated() || enrich.getValidated());
|
||||
try {
|
||||
original.setValidationDate(ModelSupport.oldest(original.getValidationDate(), enrich.getValidationDate()));
|
||||
} catch (ParseException e) {
|
||||
throw new IllegalArgumentException(String
|
||||
.format(
|
||||
"invalid validation date format in relation [s:%s, t:%s]: %s", original.getSource(), original.getTarget(),
|
||||
original.getValidationDate()));
|
||||
}
|
||||
|
||||
return original;
|
||||
}
|
||||
|
||||
private static void mergeEntityDataInfo(Entity from, Entity to) {
|
||||
Optional.ofNullable(to)
|
||||
.ifPresent(other -> Optional.ofNullable(other.getDataInfo())
|
||||
.ifPresent(otherDataInfo -> Optional.ofNullable(from.getDataInfo())
|
||||
.ifPresent(thisDataInfo -> {
|
||||
if (compareTrust(from, other) < 0 || thisDataInfo.getInvisible()) {
|
||||
from.setDataInfo(otherDataInfo);
|
||||
}
|
||||
})));
|
||||
}
|
||||
|
||||
/**
|
||||
* Gets main title.
|
||||
*
|
||||
* @param titles the titles
|
||||
* @return the main title
|
||||
*/
|
||||
private static StructuredProperty getMainTitle(List<StructuredProperty> titles) {
|
||||
// need to check if the list of titles contains more than 1 main title? (in that case, we should chose which
|
||||
// main title select in the list)
|
||||
for (StructuredProperty t : titles) {
|
||||
if (t.getQualifier() != null && t.getQualifier().getClassid() != null)
|
||||
if (t.getQualifier().getClassid().equals("main title"))
|
||||
return t;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Longest lists list.
|
||||
*
|
||||
* @param a the a
|
||||
* @param b the b
|
||||
* @return the list
|
||||
*/
|
||||
public static List<String> longestLists(List<String> a, List<String> b) {
|
||||
if (a == null || b == null)
|
||||
return a == null ? b : a;
|
||||
if (a.size() == b.size()) {
|
||||
int msa = a
|
||||
.stream()
|
||||
.filter(i -> i != null)
|
||||
.map(i -> i.length())
|
||||
.max(Comparator.naturalOrder())
|
||||
.orElse(0);
|
||||
int msb = b
|
||||
.stream()
|
||||
.filter(i -> i != null )
|
||||
.map(i -> i.length())
|
||||
.max(Comparator.naturalOrder())
|
||||
.orElse(0);
|
||||
return msa > msb ? a : b;
|
||||
}
|
||||
return a.size() > b.size() ? a : b;
|
||||
}
|
||||
|
||||
/**
|
||||
* This main method apply the enrichment of the instances
|
||||
*
|
||||
* @param toEnrichInstances the instances that could be enriched
|
||||
* @param enrichmentInstances the enrichment instances
|
||||
* @return list of instances possibly enriched
|
||||
*/
|
||||
private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,final List<Instance> enrichmentInstances) {
|
||||
final List<Instance> enrichmentResult = new ArrayList<>();
|
||||
|
||||
if (toEnrichInstances == null) {
|
||||
return enrichmentResult;
|
||||
}
|
||||
if (enrichmentInstances == null) {
|
||||
return enrichmentResult;
|
||||
}
|
||||
Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
|
||||
|
||||
toEnrichInstances.forEach(i -> {
|
||||
final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
|
||||
if (e!= null && e.size()> 0) {
|
||||
e.forEach(enr -> applyEnrichment(i, enr));
|
||||
} else {
|
||||
final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
|
||||
if (a!= null && a.size()> 0) {
|
||||
a.forEach(enr -> applyEnrichment(i, enr));
|
||||
}
|
||||
}
|
||||
enrichmentResult.add(i);
|
||||
});
|
||||
return enrichmentResult;
|
||||
}
|
||||
|
||||
/**
|
||||
* This method converts the list of instance enrichments
|
||||
* into a Map where the key is the normalized identifier
|
||||
* and the value is the instance itself
|
||||
*
|
||||
* @param ri the list of enrichment instances
|
||||
* @return the result map
|
||||
*/
|
||||
private static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
|
||||
return ri
|
||||
.stream()
|
||||
.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
|
||||
.flatMap(i -> {
|
||||
final List<Pair<String, Instance>> result = new ArrayList<>();
|
||||
if (i.getPid() != null)
|
||||
i.getPid().stream().filter(MergeUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
|
||||
if (i.getAlternateIdentifier() != null)
|
||||
i.getAlternateIdentifier().stream().filter(MergeUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
|
||||
return result.stream();
|
||||
}).collect(Collectors.toMap(
|
||||
Pair::getLeft,
|
||||
Pair::getRight,
|
||||
(a, b) -> a
|
||||
));
|
||||
}
|
||||
|
||||
/**
|
||||
* Valid pid boolean.
|
||||
*
|
||||
* @param p the p
|
||||
* @return the boolean
|
||||
*/
|
||||
private static boolean validPid(final StructuredProperty p) {
|
||||
return p.getValue()!= null && p.getQualifier()!= null && p.getQualifier().getClassid()!=null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Normalize pid string.
|
||||
*
|
||||
* @param pid the pid
|
||||
* @return the string
|
||||
*/
|
||||
private static String extractKeyFromPid(final StructuredProperty pid) {
|
||||
if (pid == null)
|
||||
return null;
|
||||
final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
|
||||
|
||||
return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* This utility method finds the list of enrichment instances
|
||||
* that match one or more PIDs in the input list
|
||||
*
|
||||
* @param pids the list of PIDs
|
||||
* @param enrichments the List of enrichment instances having the same pid
|
||||
* @return the list
|
||||
*/
|
||||
private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
|
||||
if (pids == null || enrichments == null)
|
||||
return null;
|
||||
return pids
|
||||
.stream()
|
||||
.map(MergeUtils::extractKeyFromPid)
|
||||
.map(enrichments::get)
|
||||
.filter(Objects::nonNull)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
/**
|
||||
* Is an enrichment boolean.
|
||||
*
|
||||
* @param e the e
|
||||
* @return the boolean
|
||||
*/
|
||||
public static boolean isAnEnrichment(Entity e) {
|
||||
return e.getDataInfo() != null &&
|
||||
e.getDataInfo().getProvenanceaction()!= null
|
||||
&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
|
||||
}
|
||||
|
||||
/**
|
||||
* This method apply enrichment on a single instance
|
||||
* The enrichment consists of replacing values on
|
||||
* single attribute only if in the current instance is missing
|
||||
* The only repeatable field enriched is measures
|
||||
*
|
||||
* @param currentInstance the current instance
|
||||
* @param enrichment the enrichment instance
|
||||
*/
|
||||
private static void applyEnrichment(final Instance currentInstance, final Instance enrichment) {
|
||||
if (currentInstance == null || enrichment == null)
|
||||
return;
|
||||
|
||||
//ENRICH accessright
|
||||
if (enrichment.getAccessright()!=null && currentInstance.getAccessright() == null)
|
||||
currentInstance.setAccessright(enrichment.getAccessright());
|
||||
|
||||
//ENRICH license
|
||||
if (enrichment.getLicense()!=null && currentInstance.getLicense() == null)
|
||||
currentInstance.setLicense(enrichment.getLicense());
|
||||
|
||||
//ENRICH instanceType
|
||||
if (enrichment.getInstancetype()!=null && currentInstance.getInstancetype() == null)
|
||||
currentInstance.setInstancetype(enrichment.getInstancetype());
|
||||
|
||||
//ENRICH hostedby
|
||||
if (enrichment.getHostedby()!=null && currentInstance.getHostedby() == null)
|
||||
currentInstance.setHostedby(enrichment.getHostedby());
|
||||
|
||||
//ENRICH distributionlocation
|
||||
if (enrichment.getDistributionlocation()!=null && currentInstance.getDistributionlocation() == null)
|
||||
currentInstance.setDistributionlocation(enrichment.getDistributionlocation());
|
||||
|
||||
//ENRICH collectedfrom
|
||||
if (enrichment.getCollectedfrom()!=null && currentInstance.getCollectedfrom() == null)
|
||||
currentInstance.setCollectedfrom(enrichment.getCollectedfrom());
|
||||
|
||||
//ENRICH dateofacceptance
|
||||
if (enrichment.getDateofacceptance()!=null && currentInstance.getDateofacceptance() == null)
|
||||
currentInstance.setDateofacceptance(enrichment.getDateofacceptance());
|
||||
|
||||
//ENRICH processingchargeamount
|
||||
if (enrichment.getProcessingchargeamount()!=null && currentInstance.getProcessingchargeamount() == null)
|
||||
currentInstance.setProcessingchargeamount(enrichment.getProcessingchargeamount());
|
||||
|
||||
//ENRICH refereed
|
||||
if (enrichment.getRefereed()!=null && currentInstance.getRefereed() == null)
|
||||
currentInstance.setRefereed(enrichment.getRefereed());
|
||||
|
||||
//TODO check the other Instance fields
|
||||
}
|
||||
|
||||
private static <T> List<T> mergeLists(final List<T>... lists) {
|
||||
return Arrays
|
||||
.stream(lists)
|
||||
.filter(Objects::nonNull)
|
||||
.flatMap(List::stream)
|
||||
.filter(Objects::nonNull)
|
||||
.distinct()
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
private static int compareTrust(Entity a, Entity b) {
|
||||
return Float.compare(
|
||||
Optional.ofNullable(a.getDataInfo())
|
||||
.map(DataInfo::getTrust)
|
||||
.orElse(0f),
|
||||
Optional.ofNullable(b.getDataInfo())
|
||||
.map(DataInfo::getTrust)
|
||||
.orElse(0f));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,156 @@
|
|||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.lang.reflect.Field;
|
||||
import java.util.Collection;
|
||||
import java.util.Iterator;
|
||||
|
||||
public class MergeUtils2 {
|
||||
|
||||
/**
|
||||
* Recursively merges the fields of the provider into the receiver.
|
||||
*
|
||||
* @param receiver the receiver instance.
|
||||
* @param provider the provider instance.
|
||||
*/
|
||||
public static <T> void merge(final T receiver, final T provider) {
|
||||
Field[] fields = receiver.getClass().getDeclaredFields();
|
||||
for (Field field : fields) {
|
||||
|
||||
try {
|
||||
field.setAccessible(true);
|
||||
Object receiverObject = field.get(receiver);
|
||||
Object providerObject = field.get(provider);
|
||||
|
||||
if (receiverObject == null || providerObject == null) {
|
||||
/* One is null */
|
||||
|
||||
field.set(receiver, providerObject);
|
||||
} else if (field.getType().isAssignableFrom(Collection.class)) {
|
||||
/* Collection field */
|
||||
// noinspection rawtypes
|
||||
mergeCollections((Collection) receiverObject, (Collection) providerObject);
|
||||
} else if (field.getType().isPrimitive() || field.getType().isEnum()
|
||||
|| field.getType().equals(String.class)) {
|
||||
/* Primitive, Enum or String field */
|
||||
field.set(receiver, providerObject);
|
||||
} else {
|
||||
/* Mergeable field */
|
||||
merge(receiverObject, providerObject);
|
||||
}
|
||||
} catch (IllegalAccessException e) {
|
||||
/* Should not happen */
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively merges the items in the providers collection into the receivers collection.
|
||||
* Receivers not present in providers will be removed, providers not present in receivers will be added.
|
||||
* If the item has a field called 'id', this field will be compared to match the items.
|
||||
*
|
||||
* @param receivers the collection containing the receiver instances.
|
||||
* @param providers the collection containing the provider instances.
|
||||
*/
|
||||
public static <T> void mergeCollections(final Collection<T> receivers, final Collection<T> providers) {
|
||||
if (receivers.isEmpty() && providers.isEmpty()) {
|
||||
return;
|
||||
}
|
||||
|
||||
if (providers.isEmpty()) {
|
||||
receivers.clear();
|
||||
return;
|
||||
}
|
||||
|
||||
if (receivers.isEmpty()) {
|
||||
receivers.addAll(providers);
|
||||
return;
|
||||
}
|
||||
|
||||
Field idField;
|
||||
try {
|
||||
T t = providers.iterator().next();
|
||||
idField = t.getClass().getDeclaredField("id");
|
||||
idField.setAccessible(true);
|
||||
} catch (NoSuchFieldException ignored) {
|
||||
idField = null;
|
||||
}
|
||||
|
||||
try {
|
||||
if (idField != null) {
|
||||
mergeCollectionsWithId(receivers, providers, idField);
|
||||
} else {
|
||||
mergeCollectionsSimple(receivers, providers);
|
||||
}
|
||||
} catch (IllegalAccessException e) {
|
||||
/* Should not happen */
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively merges the items in the collections for which the id's are equal.
|
||||
*
|
||||
* @param receivers the collection containing the receiver items.
|
||||
* @param providers the collection containing the provider items.
|
||||
* @param idField the id field.
|
||||
*
|
||||
* @throws IllegalAccessException if the id field is not accessible.
|
||||
*/
|
||||
private static <T> void mergeCollectionsWithId(final Collection<T> receivers, final Iterable<T> providers,
|
||||
final Field idField) throws IllegalAccessException {
|
||||
/* Find a receiver for each provider */
|
||||
for (T provider : providers) {
|
||||
boolean found = false;
|
||||
for (T receiver : receivers) {
|
||||
if (idField.get(receiver).equals(idField.get(provider))) {
|
||||
merge(receiver, provider);
|
||||
found = true;
|
||||
}
|
||||
}
|
||||
if (!found) {
|
||||
receivers.add(provider);
|
||||
}
|
||||
}
|
||||
|
||||
/* Remove receivers not in providers */
|
||||
for (Iterator<T> iterator = receivers.iterator(); iterator.hasNext();) {
|
||||
T receiver = iterator.next();
|
||||
boolean found = false;
|
||||
for (T provider : providers) {
|
||||
if (idField.get(receiver).equals(idField.get(provider))) {
|
||||
found = true;
|
||||
}
|
||||
}
|
||||
if (!found) {
|
||||
iterator.remove();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively merges the items in the collections one by one. Disregards equality.
|
||||
*
|
||||
* @param receivers the collection containing the receiver items.
|
||||
* @param providers the collection containing the provider items.
|
||||
*/
|
||||
private static <T> void mergeCollectionsSimple(final Collection<T> receivers, final Iterable<T> providers) {
|
||||
Iterator<T> receiversIterator = receivers.iterator();
|
||||
Iterator<T> providersIterator = providers.iterator();
|
||||
while (receiversIterator.hasNext() && providersIterator.hasNext()) {
|
||||
merge(receiversIterator.next(), providersIterator.next());
|
||||
}
|
||||
|
||||
/* Remove excessive receivers if present */
|
||||
while (receiversIterator.hasNext()) {
|
||||
receiversIterator.next();
|
||||
receiversIterator.remove();
|
||||
}
|
||||
|
||||
/* Add residual providers to receivers if present */
|
||||
while (providersIterator.hasNext()) {
|
||||
receivers.add(providersIterator.next());
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.lang.reflect.Field;
|
||||
import java.math.BigDecimal;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Collection;
|
||||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
|
||||
|
||||
import static org.apache.commons.lang3.ClassUtils.isPrimitiveOrWrapper;
|
||||
|
||||
public class MergeUtils3 {
|
||||
|
||||
private final List<Object> selfObjects;
|
||||
private final Object source;
|
||||
private final Object target;
|
||||
|
||||
private MergeUtils3(Object source, Object target) {
|
||||
this.source = source;
|
||||
this.target = target;
|
||||
this.selfObjects = new ArrayList<>();
|
||||
}
|
||||
|
||||
public static MergeUtils3 mergerOf(Object source, Object target) {
|
||||
return new MergeUtils3(source, target);
|
||||
}
|
||||
|
||||
public final void merge() {
|
||||
try {
|
||||
merge(source, target);
|
||||
} catch (IllegalAccessException | NoSuchFieldException e) {
|
||||
throw new RuntimeException("Merge error: ", e);
|
||||
}
|
||||
}
|
||||
|
||||
private void merge(Object source, Object target) throws IllegalAccessException, NoSuchFieldException {
|
||||
selfObjects.add(source);
|
||||
|
||||
Field[] declaredFields = source.getClass().getDeclaredFields();
|
||||
for (Field declaredField : declaredFields) {
|
||||
declaredField.setAccessible(true);
|
||||
|
||||
Object fieldValue = declaredField.get(source);
|
||||
if (fieldValue == null || selfObjects.contains(fieldValue)) {
|
||||
continue;
|
||||
}
|
||||
|
||||
Class<?> declaredFieldType = declaredField.getType();
|
||||
if (isJdkType(declaredField)) {
|
||||
Field targetField = target.getClass().getDeclaredField(declaredField.getName());
|
||||
targetField.setAccessible(true);
|
||||
|
||||
targetField.set(target, fieldValue);
|
||||
continue;
|
||||
}
|
||||
|
||||
if (Collection.class.isAssignableFrom(declaredFieldType)) {
|
||||
Iterable sourceCollection = (Iterable) declaredField.get(source);
|
||||
Iterable targetCollection = (Iterable) declaredField.get(target);
|
||||
|
||||
merge(sourceCollection, targetCollection);
|
||||
continue;
|
||||
}
|
||||
|
||||
merge(declaredField.get(source), declaredField.get(target));
|
||||
}
|
||||
}
|
||||
|
||||
private boolean isJdkType(Field field) {
|
||||
Class<?> declaredFieldType = field.getType();
|
||||
String fieldTypeName = declaredFieldType.getName();
|
||||
|
||||
return isPrimitiveOrWrapper(declaredFieldType)
|
||||
|| fieldTypeName.equals(String.class.getName())
|
||||
|| fieldTypeName.equals(BigDecimal.class.getName());
|
||||
}
|
||||
|
||||
private void merge(Iterable source, Iterable target) throws NoSuchFieldException, IllegalAccessException {
|
||||
Iterator sourceIterator = source.iterator();
|
||||
Iterator targetIterator = target.iterator();
|
||||
|
||||
while (sourceIterator.hasNext()) {
|
||||
merge(sourceIterator.next(), targetIterator.next());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
public class ModelHardLimits {
|
||||
|
||||
private ModelHardLimits() {
|
||||
}
|
||||
|
||||
public static final String LAYOUT = "index";
|
||||
public static final String INTERPRETATION = "openaire";
|
||||
public static final String SEPARATOR = "-";
|
||||
|
||||
public static final int MAX_EXTERNAL_ENTITIES = 50;
|
||||
public static final int MAX_AUTHORS = 200;
|
||||
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
|
||||
public static final int MAX_TITLE_LENGTH = 5000;
|
||||
public static final int MAX_TITLES = 10;
|
||||
public static final int MAX_ABSTRACT_LENGTH = 150000;
|
||||
public static final int MAX_INSTANCES = 10;
|
||||
|
||||
public static String getCollectionName(String format) {
|
||||
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -11,11 +11,10 @@ import java.util.function.Function;
|
|||
import java.util.function.Predicate;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.common.AccessRightComparator;
|
||||
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
public class OafMapperUtils {
|
||||
|
|
@ -24,29 +23,25 @@ public class OafMapperUtils {
|
|||
}
|
||||
|
||||
public static Oaf merge(final Oaf left, final Oaf right) {
|
||||
if (ModelSupport.isSubClass(left, OafEntity.class)) {
|
||||
return mergeEntities((OafEntity) left, (OafEntity) right);
|
||||
if (ModelSupport.isSubClass(left, Entity.class)) {
|
||||
return mergeEntities((Entity) left, (Entity) right);
|
||||
} else if (ModelSupport.isSubClass(left, Relation.class)) {
|
||||
((Relation) left).mergeFrom((Relation) right);
|
||||
return MergeUtils.mergeRelation((Relation) left, (Relation) right);
|
||||
} else {
|
||||
throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
|
||||
}
|
||||
return left;
|
||||
}
|
||||
|
||||
public static OafEntity mergeEntities(OafEntity left, OafEntity right) {
|
||||
public static Entity mergeEntities(Entity left, Entity right) {
|
||||
if (ModelSupport.isSubClass(left, Result.class)) {
|
||||
return mergeResults((Result) left, (Result) right);
|
||||
} else if (ModelSupport.isSubClass(left, Datasource.class)) {
|
||||
left.mergeFrom(right);
|
||||
} else if (ModelSupport.isSubClass(left, Organization.class)) {
|
||||
left.mergeFrom(right);
|
||||
} else if (ModelSupport.isSubClass(left, Project.class)) {
|
||||
left.mergeFrom(right);
|
||||
} else if (ModelSupport.isSubClass(left, Datasource.class) ||
|
||||
ModelSupport.isSubClass(left, Organization.class) ||
|
||||
ModelSupport.isSubClass(left, Project.class)) {
|
||||
return (Entity) merge(left, right);
|
||||
} else {
|
||||
throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
|
||||
throw new IllegalArgumentException("invalid Entity subtype:" + left.getClass().getCanonicalName());
|
||||
}
|
||||
return left;
|
||||
}
|
||||
|
||||
public static Result mergeResults(Result left, Result right) {
|
||||
|
|
@ -60,13 +55,10 @@ public class OafMapperUtils {
|
|||
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
|
||||
return right;
|
||||
}
|
||||
|
||||
if (new ResultTypeComparator().compare(left, right) < 0) {
|
||||
left.mergeFrom(right);
|
||||
return left;
|
||||
return MergeUtils.mergeResult(left, right);
|
||||
} else {
|
||||
right.mergeFrom(left);
|
||||
return right;
|
||||
return MergeUtils.mergeResult(right, left);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -101,26 +93,6 @@ public class OafMapperUtils {
|
|||
return list;
|
||||
}
|
||||
|
||||
public static <T> Field<T> field(final T value, final DataInfo info) {
|
||||
if (value == null || StringUtils.isBlank(value.toString())) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final Field<T> field = new Field<>();
|
||||
field.setValue(value);
|
||||
field.setDataInfo(info);
|
||||
return field;
|
||||
}
|
||||
|
||||
public static List<Field<String>> listFields(final DataInfo info, final String... values) {
|
||||
return Arrays
|
||||
.stream(values)
|
||||
.map(v -> field(v, info))
|
||||
.filter(Objects::nonNull)
|
||||
.filter(distinctByKey(Field::getValue))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static <T> List<T> listValues(Array values) throws SQLException {
|
||||
if (Objects.isNull(values)) {
|
||||
return null;
|
||||
|
|
@ -132,17 +104,8 @@ public class OafMapperUtils {
|
|||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
|
||||
return values
|
||||
.stream()
|
||||
.map(v -> field(v, info))
|
||||
.filter(Objects::nonNull)
|
||||
.filter(distinctByKey(Field::getValue))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static Qualifier unknown(final String schemeid, final String schemename) {
|
||||
return qualifier(UNKNOWN, "Unknown", schemeid, schemename);
|
||||
public static Qualifier unknown(final String schemeid) {
|
||||
return qualifier(UNKNOWN, "Unknown", schemeid);
|
||||
}
|
||||
|
||||
public static AccessRight accessRight(
|
||||
|
|
@ -163,7 +126,6 @@ public class OafMapperUtils {
|
|||
accessRight.setClassid(classid);
|
||||
accessRight.setClassname(classname);
|
||||
accessRight.setSchemeid(schemeid);
|
||||
accessRight.setSchemename(schemename);
|
||||
accessRight.setOpenAccessRoute(openAccessRoute);
|
||||
return accessRight;
|
||||
}
|
||||
|
|
@ -171,13 +133,11 @@ public class OafMapperUtils {
|
|||
public static Qualifier qualifier(
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename) {
|
||||
final String schemeid) {
|
||||
final Qualifier q = new Qualifier();
|
||||
q.setClassid(classid);
|
||||
q.setClassname(classname);
|
||||
q.setSchemeid(schemeid);
|
||||
q.setSchemename(schemename);
|
||||
return q;
|
||||
}
|
||||
|
||||
|
|
@ -186,7 +146,6 @@ public class OafMapperUtils {
|
|||
q.setClassid(qualifier.getClassid());
|
||||
q.setClassname(qualifier.getClassname());
|
||||
q.setSchemeid(qualifier.getSchemeid());
|
||||
q.setSchemename(qualifier.getSchemename());
|
||||
return q;
|
||||
}
|
||||
|
||||
|
|
@ -195,21 +154,18 @@ public class OafMapperUtils {
|
|||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename,
|
||||
final DataInfo dataInfo) {
|
||||
|
||||
return subject(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
|
||||
return subject(value, qualifier(classid, classname, schemeid), dataInfo);
|
||||
}
|
||||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename,
|
||||
final DataInfo dataInfo) {
|
||||
final String schemeid) {
|
||||
|
||||
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
|
||||
return structuredProperty(value, qualifier(classid, classname, schemeid));
|
||||
}
|
||||
|
||||
public static Subject subject(
|
||||
|
|
@ -228,18 +184,42 @@ public class OafMapperUtils {
|
|||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo dataInfo) {
|
||||
final Qualifier qualifier) {
|
||||
if (value == null) {
|
||||
return null;
|
||||
}
|
||||
final StructuredProperty sp = new StructuredProperty();
|
||||
sp.setValue(value);
|
||||
sp.setQualifier(qualifier);
|
||||
sp.setDataInfo(dataInfo);
|
||||
return sp;
|
||||
}
|
||||
|
||||
public static Publisher publisher(final String name) {
|
||||
final Publisher p = new Publisher();
|
||||
p.setName(name);
|
||||
return p;
|
||||
}
|
||||
|
||||
public static License license(final String url) {
|
||||
final License l = new License();
|
||||
l.setUrl(url);
|
||||
return l;
|
||||
}
|
||||
|
||||
public static AuthorPid authorPid(
|
||||
final String value,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo dataInfo) {
|
||||
if (value == null) {
|
||||
return null;
|
||||
}
|
||||
final AuthorPid ap = new AuthorPid();
|
||||
ap.setValue(value);
|
||||
ap.setQualifier(qualifier);
|
||||
ap.setDataInfo(dataInfo);
|
||||
return ap;
|
||||
}
|
||||
|
||||
public static ExtraInfo extraInfo(
|
||||
final String name,
|
||||
final String value,
|
||||
|
|
@ -340,19 +320,32 @@ public class OafMapperUtils {
|
|||
}
|
||||
|
||||
public static DataInfo dataInfo(
|
||||
final Boolean deletedbyinference,
|
||||
final float trust,
|
||||
final String inferenceprovenance,
|
||||
final Boolean inferred,
|
||||
final Boolean invisible,
|
||||
final Qualifier provenanceaction,
|
||||
final String trust) {
|
||||
final boolean inferred,
|
||||
final Qualifier provenanceaction) {
|
||||
final DataInfo d = new DataInfo();
|
||||
d.setTrust(trust);
|
||||
d.setInferenceprovenance(inferenceprovenance);
|
||||
d.setInferred(inferred);
|
||||
d.setProvenanceaction(provenanceaction);
|
||||
return d;
|
||||
}
|
||||
|
||||
public static EntityDataInfo dataInfo(
|
||||
final boolean invisible,
|
||||
final boolean deletedbyinference,
|
||||
final float trust,
|
||||
final String inferenceprovenance,
|
||||
final boolean inferred,
|
||||
final Qualifier provenanceaction) {
|
||||
final EntityDataInfo d = new EntityDataInfo();
|
||||
d.setTrust(trust);
|
||||
d.setInvisible(invisible);
|
||||
d.setDeletedbyinference(deletedbyinference);
|
||||
d.setInferenceprovenance(inferenceprovenance);
|
||||
d.setInferred(inferred);
|
||||
d.setInvisible(invisible);
|
||||
d.setProvenanceaction(provenanceaction);
|
||||
d.setTrust(trust);
|
||||
return d;
|
||||
}
|
||||
|
||||
|
|
@ -422,9 +415,6 @@ public class OafMapperUtils {
|
|||
if (StringUtils.isBlank(rights.getSchemeid())) {
|
||||
rights.setSchemeid(DNET_ACCESS_MODES);
|
||||
}
|
||||
if (StringUtils.isBlank(rights.getSchemename())) {
|
||||
rights.setSchemename(DNET_ACCESS_MODES);
|
||||
}
|
||||
|
||||
return rights;
|
||||
}
|
||||
|
|
@ -433,7 +423,6 @@ public class OafMapperUtils {
|
|||
|
||||
public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) {
|
||||
KeyValue kv = new KeyValue();
|
||||
kv.setDataInfo(dataInfo);
|
||||
kv.setKey(key);
|
||||
kv.setValue(value);
|
||||
return kv;
|
||||
|
|
@ -451,7 +440,7 @@ public class OafMapperUtils {
|
|||
final String relType,
|
||||
final String subRelType,
|
||||
final String relClass,
|
||||
final OafEntity entity) {
|
||||
final Entity entity) {
|
||||
return getRelation(source, target, relType, subRelType, relClass, entity, null);
|
||||
}
|
||||
|
||||
|
|
@ -460,11 +449,12 @@ public class OafMapperUtils {
|
|||
final String relType,
|
||||
final String subRelType,
|
||||
final String relClass,
|
||||
final OafEntity entity,
|
||||
final Entity entity,
|
||||
final String validationDate) {
|
||||
|
||||
final List<Provenance> provenance = getProvenance(entity.getCollectedfrom(), entity.getDataInfo());
|
||||
return getRelation(
|
||||
source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(),
|
||||
entity.getLastupdatetimestamp(), validationDate, null);
|
||||
source, target, relType, subRelType, relClass, provenance, validationDate, null);
|
||||
}
|
||||
|
||||
public static Relation getRelation(final String source,
|
||||
|
|
@ -472,11 +462,9 @@ public class OafMapperUtils {
|
|||
final String relType,
|
||||
final String subRelType,
|
||||
final String relClass,
|
||||
final List<KeyValue> collectedfrom,
|
||||
final DataInfo dataInfo,
|
||||
final Long lastupdatetimestamp) {
|
||||
final List<Provenance> provenance) {
|
||||
return getRelation(
|
||||
source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null);
|
||||
source, target, relType, subRelType, relClass, provenance, null, null);
|
||||
}
|
||||
|
||||
public static Relation getRelation(final String source,
|
||||
|
|
@ -484,9 +472,7 @@ public class OafMapperUtils {
|
|||
final String relType,
|
||||
final String subRelType,
|
||||
final String relClass,
|
||||
final List<KeyValue> collectedfrom,
|
||||
final DataInfo dataInfo,
|
||||
final Long lastupdatetimestamp,
|
||||
final List<Provenance> provenance,
|
||||
final String validationDate,
|
||||
final List<KeyValue> properties) {
|
||||
final Relation rel = new Relation();
|
||||
|
|
@ -495,15 +481,27 @@ public class OafMapperUtils {
|
|||
rel.setRelClass(relClass);
|
||||
rel.setSource(source);
|
||||
rel.setTarget(target);
|
||||
rel.setCollectedfrom(collectedfrom);
|
||||
rel.setDataInfo(dataInfo);
|
||||
rel.setLastupdatetimestamp(lastupdatetimestamp);
|
||||
rel.setProvenance(provenance);
|
||||
rel.setValidated(StringUtils.isNotBlank(validationDate));
|
||||
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
|
||||
rel.setProperties(properties);
|
||||
return rel;
|
||||
}
|
||||
|
||||
public static List<Provenance> getProvenance(final List<KeyValue> collectedfrom, final DataInfo dataInfo) {
|
||||
return collectedfrom
|
||||
.stream()
|
||||
.map(cf -> getProvenance(cf, dataInfo))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static Provenance getProvenance(final KeyValue collectedfrom, final DataInfo dataInfo) {
|
||||
final Provenance prov = new Provenance();
|
||||
prov.setCollectedfrom(collectedfrom);
|
||||
prov.setDataInfo(dataInfo);
|
||||
return prov;
|
||||
}
|
||||
|
||||
public static String getProvenance(DataInfo dataInfo) {
|
||||
return Optional
|
||||
.ofNullable(dataInfo)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,38 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
|
||||
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
|
||||
|
||||
if (lClass.equals(PidType.openorgs))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.openorgs))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.GRID))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.GRID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.mag_id))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.mag_id))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.urn))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.urn))
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
|
@ -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.oaf.Entity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
|
||||
|
||||
public class PidComparator<T extends Entity> implements Comparator<StructuredProperty> {
|
||||
|
||||
private final T entity;
|
||||
|
||||
public PidComparator(T entity) {
|
||||
this.entity = entity;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
if (ModelSupport.isSubClass(entity, Result.class)) {
|
||||
return compareResultPids(left, right);
|
||||
}
|
||||
if (ModelSupport.isSubClass(entity, Organization.class)) {
|
||||
return compareOrganizationtPids(left, right);
|
||||
}
|
||||
|
||||
// Else (but unlikely), lexicographical ordering will do.
|
||||
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
|
||||
}
|
||||
|
||||
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
|
||||
return new ResultPidComparator().compare(left, right);
|
||||
}
|
||||
|
||||
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
|
||||
return new OrganizationPidComparator().compare(left, right);
|
||||
}
|
||||
}
|
||||
|
|
@ -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, corda, corda_h2020, GRID, mag_id, urn,
|
||||
|
||||
// Used by dedup
|
||||
undefined, original;
|
||||
|
||||
public static boolean isValid(String type) {
|
||||
return EnumUtils.isValidEnum(PidType.class, type);
|
||||
}
|
||||
|
||||
public static PidType tryValueOf(String s) {
|
||||
try {
|
||||
return PidType.valueOf(s);
|
||||
} catch (Exception e) {
|
||||
return PidType.original;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -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 +1,53 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class ResultPidComparator implements Comparator<StructuredProperty> {
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
|
||||
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
|
||||
|
||||
if (lClass.equals(PidType.doi))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.doi))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pmid))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pmid))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pmc))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pmc))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.handle))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.handle))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.arXiv))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.arXiv))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.nct))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.nct))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pdb))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pdb))
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,77 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
|
||||
|
||||
import java.util.Comparator;
|
||||
import java.util.HashSet;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class ResultTypeComparator implements Comparator<Result> {
|
||||
|
||||
@Override
|
||||
public int compare(Result left, Result right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
HashSet<String> lCf = getCollectedFromIds(left);
|
||||
HashSet<String> rCf = getCollectedFromIds(right);
|
||||
|
||||
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
|
||||
return -1;
|
||||
}
|
||||
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
String lClass = left.getResulttype();
|
||||
String rClass = right.getResulttype();
|
||||
|
||||
if (lClass.equals(rClass))
|
||||
return 0;
|
||||
|
||||
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
// Else (but unlikely), lexicographical ordering will do.
|
||||
return lClass.compareTo(rClass);
|
||||
}
|
||||
|
||||
protected HashSet<String> getCollectedFromIds(Result left) {
|
||||
return Optional
|
||||
.ofNullable(left.getCollectedfrom())
|
||||
.map(
|
||||
cf -> cf
|
||||
.stream()
|
||||
.map(KeyValue::getKey)
|
||||
.collect(Collectors.toCollection(HashSet::new)))
|
||||
.orElse(new HashSet<>());
|
||||
}
|
||||
}
|
||||
|
|
@ -175,12 +175,11 @@ object ScholixUtils extends Serializable {
|
|||
}
|
||||
|
||||
def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
|
||||
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
|
||||
|
||||
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map { c =>
|
||||
if (relation.getProvenance != null && !relation.getProvenance.isEmpty) {
|
||||
val l: List[ScholixEntityId] = relation.getProvenance.asScala.map { p =>
|
||||
new ScholixEntityId(
|
||||
c.getValue,
|
||||
List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava
|
||||
p.getCollectedfrom.getValue,
|
||||
List(new ScholixIdentifier(p.getCollectedfrom.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava
|
||||
)
|
||||
}.toList
|
||||
l
|
||||
|
|
@ -402,15 +401,15 @@ object ScholixUtils extends Serializable {
|
|||
.getInstance()
|
||||
.asScala
|
||||
.filter(i => i.getDateofacceptance != null)
|
||||
.map(i => i.getDateofacceptance.getValue)
|
||||
.map(i => i.getDateofacceptance)
|
||||
.toList
|
||||
if (dt.nonEmpty)
|
||||
s.setDate(dt.distinct.asJava)
|
||||
}
|
||||
if (r.getDescription != null && !r.getDescription.isEmpty) {
|
||||
val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
|
||||
val d = r.getDescription.asScala.find(f => f != null)
|
||||
if (d.isDefined)
|
||||
s.setDescription(d.get.getValue)
|
||||
s.setDescription(d.get)
|
||||
}
|
||||
|
||||
if (r.getSubject != null && !r.getSubject.isEmpty) {
|
||||
|
|
@ -422,7 +421,7 @@ object ScholixUtils extends Serializable {
|
|||
}
|
||||
|
||||
if (r.getPublisher != null)
|
||||
s.setPublisher(List(r.getPublisher.getValue).asJava)
|
||||
s.setPublisher(List(r.getPublisher.getName).asJava)
|
||||
|
||||
if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
|
||||
val cf: List[CollectedFromType] = r.getCollectedfrom.asScala
|
||||
|
|
|
|||
|
|
@ -0,0 +1,52 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.common;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Entity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import org.junit.jupiter.api.Nested;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import java.io.IOException;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
public class ModelSupportTest {
|
||||
|
||||
@Nested
|
||||
class IsSubClass {
|
||||
|
||||
@Test
|
||||
void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
|
||||
// when
|
||||
Boolean result = ModelSupport.isSubClass(Relation.class, Entity.class);
|
||||
|
||||
// then
|
||||
assertFalse(result);
|
||||
}
|
||||
|
||||
@Test
|
||||
void shouldReturnTrueWhenSubClassExtendsSuperClass() {
|
||||
// when
|
||||
Boolean result = ModelSupport.isSubClass(Result.class, Entity.class);
|
||||
|
||||
// then
|
||||
assertTrue(result);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
class InverseRelation {
|
||||
|
||||
@Test
|
||||
void findRelations() throws IOException {
|
||||
assertNotNull(ModelSupport.findRelation("isMetadataFor"));
|
||||
assertNotNull(ModelSupport.findRelation("ismetadatafor"));
|
||||
assertNotNull(ModelSupport.findRelation("ISMETADATAFOR"));
|
||||
assertNotNull(ModelSupport.findRelation("isRelatedTo"));
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -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);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -164,24 +164,38 @@ class OafMapperUtilsTest {
|
|||
assertEquals(1, d2.getCollectedfrom().size());
|
||||
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
|
||||
|
||||
assertEquals(
|
||||
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
|
||||
OafMapperUtils
|
||||
.mergeResults(p1, d2)
|
||||
.getResulttype()
|
||||
.getClassid());
|
||||
|
||||
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));
|
||||
|
||||
assertEquals(
|
||||
ModelConstants.DATASET_RESULTTYPE_CLASSID,
|
||||
OafMapperUtils
|
||||
.mergeResults(p2, d1)
|
||||
.getResulttype()
|
||||
.getClassid());
|
||||
final Result p1d2 = OafMapperUtils.mergeResults(p1, d2);
|
||||
assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype());
|
||||
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 = OafMapperUtils.mergeResults(p2, d1);
|
||||
assertEquals(ModelConstants.DATASET_RESULTTYPE_CLASSID, p2d1.getResulttype());
|
||||
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 = OafMapperUtils.mergeResults(p1, p2);
|
||||
assertTrue(p1p2 instanceof Publication);
|
||||
assertEquals(p1.getId(), p1p2.getId());
|
||||
assertEquals(2, p1p2.getCollectedfrom().size());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -1 +1,28 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}
|
||||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
|
||||
"resuttype": "dataset",
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2011.03.013"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "urn"},
|
||||
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "scp-number"},
|
||||
"value": "79953761260"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
}
|
||||
],
|
||||
"collectedfrom": [
|
||||
{
|
||||
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
|
||||
"value": "Crossref"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -1,6 +1,6 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
|
||||
"resuttype": {"classid": "dataset"},
|
||||
"resuttype": "dataset",
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
|
|
@ -30,8 +30,7 @@
|
|||
"refereed": {
|
||||
"classid": "0000",
|
||||
"classname": "UNKNOWN",
|
||||
"schemeid": "dnet:review_levels",
|
||||
"schemename": "dnet:review_levels"
|
||||
"schemeid": "dnet:review_levels"
|
||||
},
|
||||
"hostedby": {
|
||||
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
|
|
@ -40,45 +39,15 @@
|
|||
"accessright": {
|
||||
"classid": "OPEN",
|
||||
"classname": "Open Access",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"processingchargecurrency": {
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "EUR"
|
||||
"schemeid": "dnet:access_modes"
|
||||
},
|
||||
"processingchargecurrency": "EUR",
|
||||
"pid": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "Digital Object Identifier",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
"schemeid": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1371/journal.pone.0085605"
|
||||
}
|
||||
|
|
@ -87,24 +56,10 @@
|
|||
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "pmid",
|
||||
"classname": "PubMed ID",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
"schemeid": "dnet:pid_types"
|
||||
},
|
||||
"value": "24454899.0"
|
||||
}
|
||||
|
|
@ -113,27 +68,11 @@
|
|||
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3",
|
||||
"value": "Repository B"
|
||||
},
|
||||
"processingchargeamount": {
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "1022.02"
|
||||
},
|
||||
"processingchargeamount": "1022.02",
|
||||
"instancetype": {
|
||||
"classid": "0004",
|
||||
"classname": "Conference object",
|
||||
"schemeid": "dnet:publication_resource",
|
||||
"schemename": "dnet:publication_resource"
|
||||
"schemeid": "dnet:publication_resource"
|
||||
}
|
||||
}
|
||||
]
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
|
||||
"resuttype": {"classid": "dataset"},
|
||||
"resuttype": "dataset",
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
|
|
@ -30,8 +30,7 @@
|
|||
"refereed": {
|
||||
"classid": "0000",
|
||||
"classname": "UNKNOWN",
|
||||
"schemeid": "dnet:review_levels",
|
||||
"schemename": "dnet:review_levels"
|
||||
"schemeid": "dnet:review_levels"
|
||||
},
|
||||
"hostedby": {
|
||||
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
|
|
@ -40,45 +39,15 @@
|
|||
"accessright": {
|
||||
"classid": "OPEN",
|
||||
"classname": "Open Access",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"processingchargecurrency": {
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "EUR"
|
||||
"schemeid": "dnet:access_modes"
|
||||
},
|
||||
"processingchargecurrency": "EUR",
|
||||
"pid": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "Digital Object Identifier",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
"schemeid": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1371/journal.pone.0085605"
|
||||
}
|
||||
|
|
@ -87,24 +56,10 @@
|
|||
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "pmid",
|
||||
"classname": "PubMed ID",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
"schemeid": "dnet:pid_types"
|
||||
},
|
||||
"value": "24454899.0"
|
||||
}
|
||||
|
|
@ -113,27 +68,11 @@
|
|||
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
"value": "Zenodo"
|
||||
},
|
||||
"processingchargeamount": {
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "1022.02"
|
||||
},
|
||||
"processingchargeamount": "1022.02",
|
||||
"instancetype": {
|
||||
"classid": "0004",
|
||||
"classname": "Conference object",
|
||||
"schemeid": "dnet:publication_resource",
|
||||
"schemename": "dnet:publication_resource"
|
||||
"schemeid": "dnet:publication_resource"
|
||||
}
|
||||
}
|
||||
]
|
||||
|
|
|
|||
|
|
@ -0,0 +1,197 @@
|
|||
{
|
||||
"collectedfrom": [
|
||||
{
|
||||
"key": "10|fairsharing_::1b69ebedb522700034547abc5652ffac",
|
||||
"value": "ROHub",
|
||||
"dataInfo": null
|
||||
}
|
||||
],
|
||||
"dataInfo": {
|
||||
"invisible": false,
|
||||
"inferred": false,
|
||||
"deletedbyinference": false,
|
||||
"trust": "0.9",
|
||||
"inferenceprovenance": null,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:repository",
|
||||
"classname": "sysimport:crosswalk:repository",
|
||||
"schemeid": "dnet:provenanceActions"
|
||||
}
|
||||
},
|
||||
"lastupdatetimestamp": 1663926081966,
|
||||
"id": "50|w3id________::afc7592914ae190a50570db90f55f9c2",
|
||||
"originalId": [
|
||||
"50|fsh_____4119::afc7592914ae190a50570db90f55f9c2",
|
||||
"https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca"
|
||||
],
|
||||
"pid": [
|
||||
{
|
||||
"value": "https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca",
|
||||
"qualifier": {
|
||||
"classid": "w3id",
|
||||
"classname": "w3id.org",
|
||||
"schemeid": "dnet:pid_types"
|
||||
}
|
||||
}
|
||||
],
|
||||
"dateofcollection": "2019-03-27T15:15:22.22Z",
|
||||
"dateoftransformation": "2019-04-17T16:04:20.586Z",
|
||||
"extraInfo": [],
|
||||
"oaiprovenance": null,
|
||||
"processingchargeamount": null,
|
||||
"processingchargecurrency": null,
|
||||
"measures": null,
|
||||
"author": [
|
||||
{
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"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
|
||||
"value": "Europe PubMed Central"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
},
|
||||
{
|
||||
"qualifier":{"classid":"pmc"},
|
||||
"value":"21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -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"
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -2,7 +2,7 @@ package eu.dnetlib.dhp.collection
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Entity, Oaf, Entity, Relation}
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode}
|
||||
|
||||
object CollectionUtils {
|
||||
|
|
@ -17,7 +17,7 @@ object CollectionUtils {
|
|||
*/
|
||||
|
||||
def fixRelations(i: Oaf): List[Oaf] = {
|
||||
if (i.isInstanceOf[OafEntity])
|
||||
if (i.isInstanceOf[Entity])
|
||||
return List(i)
|
||||
else {
|
||||
val r: Relation = i.asInstanceOf[Relation]
|
||||
|
|
@ -34,10 +34,9 @@ object CollectionUtils {
|
|||
inverse.setRelType(currentRel.getRelType)
|
||||
inverse.setSubRelType(currentRel.getSubReltype)
|
||||
inverse.setRelClass(currentRel.getInverseRelClass)
|
||||
inverse.setCollectedfrom(r.getCollectedfrom)
|
||||
inverse.setProvenance(r.getProvenance)
|
||||
inverse.setDataInfo(r.getDataInfo)
|
||||
inverse.setProperties(r.getProperties)
|
||||
inverse.setLastupdatetimestamp(r.getLastupdatetimestamp)
|
||||
inverse.setValidated(r.getValidated)
|
||||
inverse.setValidationDate(r.getValidationDate)
|
||||
return List(r, inverse)
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ package eu.dnetlib.dhp.datacite
|
|||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue}
|
||||
import eu.dnetlib.dhp.schema.oaf.{DataInfo, EntityDataInfo, KeyValue}
|
||||
|
||||
import java.io.InputStream
|
||||
import java.time.format.DateTimeFormatter
|
||||
|
|
@ -72,7 +72,7 @@ object DataciteModelConstants {
|
|||
val DOI_CLASS = "doi"
|
||||
val SUBJ_CLASS = "keywords"
|
||||
val DATACITE_NAME = "Datacite"
|
||||
val dataInfo: DataInfo = dataciteDataInfo("0.9")
|
||||
val dataInfo: EntityDataInfo = dataciteDataInfo(0.9f)
|
||||
|
||||
val DATACITE_COLLECTED_FROM: KeyValue =
|
||||
OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME)
|
||||
|
|
@ -221,13 +221,13 @@ object DataciteModelConstants {
|
|||
Source.fromInputStream(stream).getLines().toList
|
||||
}
|
||||
|
||||
def dataciteDataInfo(trust: String): DataInfo = OafMapperUtils.dataInfo(
|
||||
def dataciteDataInfo(trust: Float): EntityDataInfo = OafMapperUtils.dataInfo(
|
||||
false,
|
||||
false,
|
||||
trust,
|
||||
null,
|
||||
false,
|
||||
false,
|
||||
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
|
||||
trust
|
||||
ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER
|
||||
)
|
||||
|
||||
val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern(
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
package eu.dnetlib.dhp.datacite
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.google.common.collect.Lists
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.datacite.DataciteModelConstants._
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction
|
||||
|
|
@ -284,27 +285,24 @@ object DataciteToOAFTransformation {
|
|||
}
|
||||
|
||||
def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
|
||||
OafMapperUtils.structuredProperty(dt, q, null)
|
||||
OafMapperUtils.structuredProperty(dt, q)
|
||||
}
|
||||
|
||||
def generateRelation(
|
||||
sourceId: String,
|
||||
targetId: String,
|
||||
relClass: String,
|
||||
cf: KeyValue,
|
||||
di: DataInfo
|
||||
sourceId: String,
|
||||
targetId: String,
|
||||
relClass: String,
|
||||
collectedFrom: KeyValue,
|
||||
di: DataInfo
|
||||
): Relation = {
|
||||
|
||||
val r = new Relation
|
||||
r.setSource(sourceId)
|
||||
r.setTarget(targetId)
|
||||
r.setRelType(ModelConstants.RESULT_PROJECT)
|
||||
r.setRelClass(relClass)
|
||||
r.setSubRelType(ModelConstants.OUTCOME)
|
||||
r.setCollectedfrom(List(cf).asJava)
|
||||
r.setDataInfo(di)
|
||||
r.setProvenance(Lists.newArrayList(OafMapperUtils.getProvenance(collectedFrom, di)))
|
||||
r
|
||||
|
||||
}
|
||||
|
||||
def get_projectRelation(awardUri: String, sourceId: String): List[Relation] = {
|
||||
|
|
@ -353,10 +351,9 @@ object DataciteToOAFTransformation {
|
|||
val doi_q = OafMapperUtils.qualifier(
|
||||
"doi",
|
||||
"doi",
|
||||
ModelConstants.DNET_PID_TYPES,
|
||||
ModelConstants.DNET_PID_TYPES
|
||||
)
|
||||
val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo)
|
||||
val pid = OafMapperUtils.structuredProperty(doi, doi_q)
|
||||
result.setPid(List(pid).asJava)
|
||||
|
||||
// This identifiere will be replaced in a second moment using the PID logic generation
|
||||
|
|
@ -389,7 +386,7 @@ object DataciteToOAFTransformation {
|
|||
)
|
||||
else null
|
||||
if (ni.nameIdentifier != null && ni.nameIdentifier.isDefined) {
|
||||
OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo)
|
||||
OafMapperUtils.authorPid(ni.nameIdentifier.get, q, dataInfo)
|
||||
} else
|
||||
null
|
||||
|
||||
|
|
@ -397,13 +394,6 @@ object DataciteToOAFTransformation {
|
|||
.asJava
|
||||
)
|
||||
}
|
||||
if (c.affiliation.isDefined)
|
||||
a.setAffiliation(
|
||||
c.affiliation.get
|
||||
.filter(af => af.nonEmpty)
|
||||
.map(af => OafMapperUtils.field(af, dataInfo))
|
||||
.asJava
|
||||
)
|
||||
a.setRank(idx + 1)
|
||||
a
|
||||
}
|
||||
|
|
@ -420,15 +410,13 @@ object DataciteToOAFTransformation {
|
|||
.map(t => {
|
||||
if (t.titleType.isEmpty) {
|
||||
OafMapperUtils
|
||||
.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
|
||||
.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER)
|
||||
} else {
|
||||
OafMapperUtils.structuredProperty(
|
||||
t.title.get,
|
||||
t.titleType.get,
|
||||
t.titleType.get,
|
||||
ModelConstants.DNET_DATACITE_TITLE,
|
||||
ModelConstants.DNET_DATACITE_TITLE,
|
||||
null
|
||||
ModelConstants.DNET_DATACITE_TITLE
|
||||
)
|
||||
}
|
||||
})
|
||||
|
|
@ -449,46 +437,40 @@ object DataciteToOAFTransformation {
|
|||
.map(d => d.get)
|
||||
|
||||
if (a_date.isDefined) {
|
||||
if (doi.startsWith("10.14457"))
|
||||
result.setEmbargoenddate(
|
||||
OafMapperUtils.field(fix_thai_date(a_date.get, "[yyyy-MM-dd]"), null)
|
||||
)
|
||||
else
|
||||
result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
|
||||
if (doi.startsWith("10.14457")) {
|
||||
val date = fix_thai_date(a_date.get, "[yyyy-MM-dd]")
|
||||
result.setEmbargoenddate(date)
|
||||
} else {
|
||||
result.setEmbargoenddate(a_date.get)
|
||||
}
|
||||
}
|
||||
if (i_date.isDefined && i_date.get.isDefined) {
|
||||
if (doi.startsWith("10.14457")) {
|
||||
result.setDateofacceptance(
|
||||
OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null)
|
||||
)
|
||||
val date = fix_thai_date(i_date.get.get, "[yyyy-MM-dd]")
|
||||
result.setDateofacceptance(date)
|
||||
result
|
||||
.getInstance()
|
||||
.get(0)
|
||||
.setDateofacceptance(
|
||||
OafMapperUtils.field(fix_thai_date(i_date.get.get, "[yyyy-MM-dd]"), null)
|
||||
)
|
||||
.setDateofacceptance(date)
|
||||
} else {
|
||||
result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
|
||||
result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
|
||||
result.setDateofacceptance(i_date.get.get)
|
||||
result.getInstance().get(0).setDateofacceptance(i_date.get.get)
|
||||
}
|
||||
} else if (publication_year != null) {
|
||||
val date = s"01-01-$publication_year"
|
||||
if (doi.startsWith("10.14457")) {
|
||||
result.setDateofacceptance(
|
||||
OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null)
|
||||
)
|
||||
val date = fix_thai_date(date, "[dd-MM-yyyy]")
|
||||
result.setDateofacceptance(date)
|
||||
result
|
||||
.getInstance()
|
||||
.get(0)
|
||||
.setDateofacceptance(
|
||||
OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year", "[dd-MM-yyyy]"), null)
|
||||
)
|
||||
|
||||
.setDateofacceptance(date)
|
||||
} else {
|
||||
result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
|
||||
result.setDateofacceptance(date)
|
||||
result
|
||||
.getInstance()
|
||||
.get(0)
|
||||
.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
|
||||
.setDateofacceptance(date)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -519,8 +501,7 @@ object DataciteToOAFTransformation {
|
|||
SUBJ_CLASS,
|
||||
SUBJ_CLASS,
|
||||
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
|
||||
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
|
||||
null
|
||||
dataInfo
|
||||
)
|
||||
)
|
||||
.asJava
|
||||
|
|
@ -533,14 +514,14 @@ object DataciteToOAFTransformation {
|
|||
result.setDescription(
|
||||
descriptions
|
||||
.filter(d => d.description.isDefined)
|
||||
.map(d => OafMapperUtils.field(d.description.get, null))
|
||||
.map(d => d.description.get)
|
||||
.filter(s => s != null)
|
||||
.asJava
|
||||
)
|
||||
|
||||
val publisher = (json \\ "publisher").extractOrElse[String](null)
|
||||
if (publisher != null)
|
||||
result.setPublisher(OafMapperUtils.field(publisher, null))
|
||||
result.setPublisher(OafMapperUtils.publisher(publisher))
|
||||
|
||||
val language: String = (json \\ "language").extractOrElse[String](null)
|
||||
|
||||
|
|
@ -568,7 +549,6 @@ object DataciteToOAFTransformation {
|
|||
a.setClassid(q.getClassid)
|
||||
a.setClassname(q.getClassname)
|
||||
a.setSchemeid(q.getSchemeid)
|
||||
a.setSchemename(q.getSchemename)
|
||||
a
|
||||
})
|
||||
|
||||
|
|
@ -598,7 +578,7 @@ object DataciteToOAFTransformation {
|
|||
)
|
||||
)
|
||||
if (license.isDefined)
|
||||
instance.setLicense(OafMapperUtils.field(license.get, null))
|
||||
instance.setLicense(OafMapperUtils.license(license.get))
|
||||
}
|
||||
|
||||
val awardUris: List[String] = for {
|
||||
|
|
@ -654,7 +634,8 @@ object DataciteToOAFTransformation {
|
|||
)
|
||||
.map(r => {
|
||||
val rel = new Relation
|
||||
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
||||
|
||||
rel.setProvenance(Lists.newArrayList(OafMapperUtils.getProvenance(DATACITE_COLLECTED_FROM, dataInfo)))
|
||||
rel.setDataInfo(dataInfo)
|
||||
|
||||
val subRelType = subRelTypeMapping(r.relationType).relType
|
||||
|
|
@ -670,8 +651,7 @@ object DataciteToOAFTransformation {
|
|||
rel.setTarget(
|
||||
DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
|
||||
)
|
||||
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
|
||||
rel.getCollectedfrom.asScala.map(c => c.getValue).toList
|
||||
|
||||
rel
|
||||
})
|
||||
}
|
||||
|
|
|
|||
|
|
@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
|
|||
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
|
||||
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
|
||||
|
||||
val result = data.linesWithSeparators.map(l =>l.stripLineEnd)
|
||||
val result = data.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.filter(l => l.startsWith("<a href="))
|
||||
.map { l =>
|
||||
val end = l.lastIndexOf("\">")
|
||||
|
|
|
|||
|
|
@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
val records: String = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
|
||||
.mkString
|
||||
val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList
|
||||
val r: List[Oaf] = records.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.toList
|
||||
.map(s => mapper.readValue(s, classOf[PMArticle]))
|
||||
.map(a => PubMedToOaf.convert(a, vocabularies))
|
||||
assertEquals(10, r.size)
|
||||
|
|
@ -173,9 +175,10 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
val records: String = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump"))
|
||||
.mkString
|
||||
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
|
||||
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
|
||||
val result: List[Oaf] =
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
|
||||
|
||||
assertTrue(result.nonEmpty)
|
||||
result.foreach(r => assertNotNull(r))
|
||||
|
|
@ -194,9 +197,10 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
val records: String = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump"))
|
||||
.mkString
|
||||
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
|
||||
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
|
||||
val result: List[Oaf] =
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
|
||||
|
||||
assertTrue(result.nonEmpty)
|
||||
result.foreach(r => assertNotNull(r))
|
||||
|
|
@ -239,9 +243,10 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
val records: String = Source
|
||||
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links"))
|
||||
.mkString
|
||||
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
|
||||
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
|
||||
val result: List[Oaf] =
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
|
||||
|
||||
assertNotNull(result)
|
||||
assertTrue(result.nonEmpty)
|
||||
|
|
@ -276,14 +281,17 @@ class BioScholixTest extends AbstractVocabularyTest {
|
|||
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")
|
||||
)
|
||||
.mkString
|
||||
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
|
||||
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
|
||||
val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input =>
|
||||
lazy val json = parse(input)
|
||||
json.extract[ScholixResolved]
|
||||
}.toList
|
||||
val l: List[ScholixResolved] = records.linesWithSeparators
|
||||
.map(l => l.stripLineEnd)
|
||||
.map { input =>
|
||||
lazy val json = parse(input)
|
||||
json.extract[ScholixResolved]
|
||||
}
|
||||
.toList
|
||||
|
||||
val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))
|
||||
|
||||
|
|
|
|||
|
|
@ -6,6 +6,9 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVENANCE_DEDUP;
|
|||
|
||||
import java.io.IOException;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Entity;
|
||||
import eu.dnetlib.dhp.schema.oaf.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
|
|
@ -77,7 +80,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
|
|||
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
|
||||
final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
|
||||
|
||||
final Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
|
||||
final Class<Entity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
|
||||
final DataInfo dataInfo = getDataInfo(dedupConf);
|
||||
DedupRecordFactory
|
||||
.createDedupRecord(spark, dataInfo, mergeRelPath, entityPath, clazz)
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -807,7 +807,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[3.15.0]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[4.0.0-SNAPSHOT]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue