forked from D-Net/dnet-hadoop
refactoring the Oaf records merge utilities into dhp-common
This commit is contained in:
parent
7ae7e8aa06
commit
aaa73f89d1
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@ -1,6 +1,24 @@
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package eu.dnetlib.dhp.oa.merge;
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package eu.dnetlib.dhp.oa.merge;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.when;
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import java.util.Map;
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import java.util.Optional;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.ForkJoinPool;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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.common.HdfsSupport;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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@ -12,25 +30,8 @@ import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.ReduceFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import scala.Tuple2;
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import java.util.Map;
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import java.util.Optional;
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import java.util.concurrent.ExecutionException;
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import java.util.concurrent.ForkJoinPool;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.when;
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/**
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/**
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* Groups the graph content by entity identifier to ensure ID uniqueness
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* Groups the graph content by entity identifier to ensure ID uniqueness
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*/
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*/
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@ -0,0 +1,73 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import org.apache.commons.lang3.StringUtils;
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import java.util.HashSet;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.Set;
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public class CleaningFunctions {
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public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
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public static final String DOI_PREFIX = "10.";
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public static final Set<String> PID_BLACKLIST = new HashSet<>();
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static {
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PID_BLACKLIST.add("none");
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PID_BLACKLIST.add("na");
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}
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public CleaningFunctions() {}
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/**
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* Utility method that filter PID values on a per-type basis.
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* @param s the PID whose value will be checked.
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* @return false if the pid matches the filter criteria, true otherwise.
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*/
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public static boolean pidFilter(StructuredProperty s) {
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final String pidValue = s.getValue();
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if (Objects.isNull(s.getQualifier()) ||
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StringUtils.isBlank(pidValue) ||
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StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
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return false;
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}
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if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
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return false;
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}
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return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
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}
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/**
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* Utility method that normalises PID values on a per-type basis.
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* @param pid the PID whose value will be normalised.
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* @return the PID containing the normalised value.
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*/
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public static StructuredProperty normalizePidValue(StructuredProperty pid) {
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pid.setValue(
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normalizePidValue(
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pid.getQualifier().getClassid(),
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pid.getValue()));
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return pid;
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}
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public static String normalizePidValue(String pidType, String pidValue) {
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String value = Optional
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.ofNullable(pidValue)
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.map(String::trim)
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.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
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switch (pidType) {
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// TODO add cleaning for more PID types as needed
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case "doi":
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return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
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}
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return value;
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}
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}
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@ -0,0 +1,290 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import com.google.common.collect.HashBiMap;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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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.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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import java.util.*;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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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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/**
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* Factory class for OpenAIRE identifiers in the Graph
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*/
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public class IdentifierFactory implements Serializable {
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public static final String ID_SEPARATOR = "::";
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public static final String ID_PREFIX_SEPARATOR = "|";
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public static final int ID_PREFIX_LEN = 12;
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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
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* The id of the record (source_::id) will be rewritten as pidType_::id)
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*/
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public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
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static {
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PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
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PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
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PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
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PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
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PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
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PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
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PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
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PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
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PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
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PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
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PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
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PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
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PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
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PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
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PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
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}
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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
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* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
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*
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* 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.
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* 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
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*/
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public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
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static {
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DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
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DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
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DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
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DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
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DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
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}
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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
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* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
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* the same OpenAIRE id.
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*/
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public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
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static {
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ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
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ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
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}
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public static Set<String> delegatedAuthorityDatasourceIds() {
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return DELEGATED_PID_AUTHORITY.values()
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.stream()
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.flatMap(m -> m.keySet().stream())
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.collect(Collectors.toCollection(HashSet::new));
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}
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public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
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return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
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}
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public static <T extends Result> String createDOIBoostIdentifier(T entity) {
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if (entity == null)
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return null;
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StructuredProperty pid = null;
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if (entity.getPid() != null) {
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pid = entity
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
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.filter(CleaningFunctions::pidFilter)
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.findAny()
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.orElse(null);
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} else {
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if (entity.getInstance() != null) {
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pid = entity
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.getInstance()
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.stream()
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.filter(i -> i.getPid() != null)
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.flatMap(i -> i.getPid().stream())
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.filter(CleaningFunctions::pidFilter)
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.findAny()
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.orElse(null);
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}
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}
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if (pid != null)
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return idFromPid(entity, pid, true);
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return null;
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}
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/**
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* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
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* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
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*
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* @param entity the entity providing PIDs and a default ID.
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* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
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* @param md5 indicates whether should hash the PID value or not.
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* @return an identifier from the most relevant PID, entity.id otherwise
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*/
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public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
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checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
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final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
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return pids
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.values()
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.stream()
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.flatMap(Set::stream)
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.min(new PidComparator<>(entity))
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.map(
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min -> Optional
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.ofNullable(pids.get(min.getQualifier().getClassid()))
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.map(
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p -> p
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.stream()
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.sorted(new PidValueComparator())
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.findFirst()
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.map(s -> idFromPid(entity, s, md5))
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.orElseGet(entity::getId))
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.orElseGet(entity::getId))
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.orElseGet(entity::getId);
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}
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private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
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if (entity instanceof Result) {
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return Optional
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.ofNullable(((Result) entity).getInstance())
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.map(IdentifierFactory::mapPids)
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.orElse(new HashMap<>());
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} else {
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return entity
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.getPid()
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.stream()
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.map(CleaningFunctions::normalizePidValue)
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.filter(CleaningFunctions::pidFilter)
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.collect(
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Collectors
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.groupingBy(
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p -> p.getQualifier().getClassid(),
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Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
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}
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}
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private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
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return instance
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.stream()
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.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
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.flatMap(Function.identity())
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.collect(
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Collectors
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.groupingBy(
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p -> p.getQualifier().getClassid(),
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Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
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}
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private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
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boolean mapHandles) {
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return Optional
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.ofNullable(pid)
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.map(
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pp -> pp
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.stream()
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// filter away PIDs provided by a DS that is not considered an authority for the
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// given PID Type
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.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
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.map(CleaningFunctions::normalizePidValue)
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.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
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.filter(CleaningFunctions::pidFilter))
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.orElse(Stream.empty());
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}
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private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
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final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
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if (Objects.isNull(collectedFrom)) {
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return false;
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}
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boolean isEnrich = Optional
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.ofNullable(ENRICHMENT_PROVIDER.get(pType))
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.map(enrich -> enrich.containsKey(collectedFrom.getKey())
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||||||
|
|| enrich.containsValue(collectedFrom.getValue()))
|
||||||
|
.orElse(false);
|
||||||
|
|
||||||
|
boolean isAuthority = Optional
|
||||||
|
.ofNullable(PID_AUTHORITY.get(pType))
|
||||||
|
.map(authorities -> authorities.containsKey(collectedFrom.getKey())
|
||||||
|
|| authorities.containsValue(collectedFrom.getValue()))
|
||||||
|
.orElse(false);
|
||||||
|
|
||||||
|
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
|
||||||
|
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
|
||||||
|
|
||||||
|
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
|
||||||
|
if (Objects.isNull(da)) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
if (!da.containsKey(collectedFrom.getKey())) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
|
||||||
|
*/
|
||||||
|
public static <T extends OafEntity> String createIdentifier(T entity) {
|
||||||
|
|
||||||
|
return createIdentifier(entity, true);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
|
||||||
|
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
|
||||||
|
return new StringBuilder()
|
||||||
|
.append(numericPrefix)
|
||||||
|
.append(ID_PREFIX_SEPARATOR)
|
||||||
|
.append(createPrefix(pidType))
|
||||||
|
.append(ID_SEPARATOR)
|
||||||
|
.append(md5 ? md5(pidValue) : pidValue)
|
||||||
|
.toString();
|
||||||
|
}
|
||||||
|
|
||||||
|
// create the prefix (length = 12)
|
||||||
|
private static String createPrefix(String pidType) {
|
||||||
|
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
|
||||||
|
while (prefix.length() < ID_PREFIX_LEN) {
|
||||||
|
prefix.append("_");
|
||||||
|
}
|
||||||
|
return prefix.substring(0, ID_PREFIX_LEN);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static String md5(final String s) {
|
||||||
|
try {
|
||||||
|
final MessageDigest md = MessageDigest.getInstance("MD5");
|
||||||
|
md.update(s.getBytes(StandardCharsets.UTF_8));
|
||||||
|
return new String(Hex.encodeHex(md.digest()));
|
||||||
|
} catch (final Exception e) {
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,22 +1,21 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
//
|
|
||||||
// Source code recreated from a .class file by IntelliJ IDEA
|
|
||||||
// (powered by FernFlower decompiler)
|
|
||||||
//
|
|
||||||
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
||||||
|
|
||||||
import java.util.Comparator;
|
import java.util.Comparator;
|
||||||
import java.util.HashSet;
|
import java.util.HashSet;
|
||||||
import java.util.Optional;
|
import java.util.Optional;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
//
|
||||||
|
// Source code recreated from a .class file by IntelliJ IDEA
|
||||||
|
// (powered by FernFlower decompiler)
|
||||||
|
//
|
||||||
|
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
public class MergeComparator implements Comparator<Oaf> {
|
public class MergeComparator implements Comparator<Oaf> {
|
||||||
public MergeComparator() {
|
public MergeComparator() {
|
||||||
}
|
}
|
||||||
|
|
@ -41,14 +40,14 @@ public class MergeComparator implements Comparator<Oaf> {
|
||||||
// collectedfrom
|
// collectedfrom
|
||||||
HashSet<String> lCf = getCollectedFromIds(left);
|
HashSet<String> lCf = getCollectedFromIds(left);
|
||||||
HashSet<String> rCf = getCollectedFromIds(right);
|
HashSet<String> rCf = getCollectedFromIds(right);
|
||||||
if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
|
if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
|
||||||
|
&& !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
|
||||||
return -1;
|
return -1;
|
||||||
} else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
|
} else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
|
||||||
|
&& rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
|
||||||
return 1;
|
return 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
SubEntityType lClass = SubEntityType.fromClass(left.getClass());
|
SubEntityType lClass = SubEntityType.fromClass(left.getClass());
|
||||||
SubEntityType rClass = SubEntityType.fromClass(right.getClass());
|
SubEntityType rClass = SubEntityType.fromClass(right.getClass());
|
||||||
return lClass.ordinal() - rClass.ordinal();
|
return lClass.ordinal() - rClass.ordinal();
|
||||||
|
|
|
||||||
|
|
@ -1,21 +1,26 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import static org.apache.commons.lang3.ObjectUtils.firstNonNull;
|
||||||
|
import static com.google.common.base.Preconditions.checkArgument;
|
||||||
|
|
||||||
|
import java.text.ParseException;
|
||||||
|
import java.util.*;
|
||||||
|
import java.util.function.BinaryOperator;
|
||||||
|
import java.util.function.Function;
|
||||||
|
import java.util.function.Supplier;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
import java.util.stream.Stream;
|
||||||
|
|
||||||
|
import com.google.common.base.Joiner;
|
||||||
|
import org.apache.commons.lang3.StringUtils;
|
||||||
|
import org.apache.commons.lang3.tuple.ImmutablePair;
|
||||||
|
import org.apache.commons.lang3.tuple.Pair;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
|
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
import eu.dnetlib.dhp.schema.oaf.*;
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.apache.commons.lang3.tuple.ImmutablePair;
|
|
||||||
import org.apache.commons.lang3.tuple.Pair;
|
|
||||||
|
|
||||||
import java.text.ParseException;
|
|
||||||
import java.util.*;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
import java.util.stream.Stream;
|
|
||||||
|
|
||||||
import static com.google.common.base.Objects.firstNonNull;
|
|
||||||
import static com.google.common.base.Preconditions.checkArgument;
|
|
||||||
|
|
||||||
public class MergeUtils {
|
public class MergeUtils {
|
||||||
|
|
||||||
|
|
@ -168,8 +173,7 @@ public class MergeUtils {
|
||||||
return a || b;
|
return a || b;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust, Function<T, K> keyExtractor, BinaryOperator<T> merger) {
|
||||||
private static <T> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
|
|
||||||
if (left == null) {
|
if (left == null) {
|
||||||
return right;
|
return right;
|
||||||
} else if (right == null) {
|
} else if (right == null) {
|
||||||
|
|
@ -179,7 +183,26 @@ public class MergeUtils {
|
||||||
List<T> h = trust >= 0 ? left : right;
|
List<T> h = trust >= 0 ? left : right;
|
||||||
List<T> l = trust >= 0 ? right : left;
|
List<T> l = trust >= 0 ? right : left;
|
||||||
|
|
||||||
return Stream.concat(h.stream(), l.stream())
|
return new ArrayList<>(Stream
|
||||||
|
.concat(h.stream(), l.stream())
|
||||||
|
.filter(Objects::nonNull)
|
||||||
|
.distinct()
|
||||||
|
.collect(Collectors.toMap(keyExtractor, v -> v, merger))
|
||||||
|
.values());
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T, K> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
|
||||||
|
if (left == null) {
|
||||||
|
return right;
|
||||||
|
} else if (right == null) {
|
||||||
|
return left;
|
||||||
|
}
|
||||||
|
|
||||||
|
List<T> h = trust >= 0 ? left : right;
|
||||||
|
List<T> l = trust >= 0 ? right : left;
|
||||||
|
|
||||||
|
return Stream
|
||||||
|
.concat(h.stream(), l.stream())
|
||||||
.filter(Objects::nonNull)
|
.filter(Objects::nonNull)
|
||||||
.distinct()
|
.distinct()
|
||||||
.collect(Collectors.toList());
|
.collect(Collectors.toList());
|
||||||
|
|
@ -192,7 +215,8 @@ public class MergeUtils {
|
||||||
return l;
|
return l;
|
||||||
}
|
}
|
||||||
|
|
||||||
return Stream.concat(l.stream(), r.stream())
|
return Stream
|
||||||
|
.concat(l.stream(), r.stream())
|
||||||
.filter(StringUtils::isNotBlank)
|
.filter(StringUtils::isNotBlank)
|
||||||
.distinct()
|
.distinct()
|
||||||
.collect(Collectors.toList());
|
.collect(Collectors.toList());
|
||||||
|
|
@ -213,7 +237,8 @@ public class MergeUtils {
|
||||||
return new ArrayList<>(values.values());
|
return new ArrayList<>(values.values());
|
||||||
}
|
}
|
||||||
|
|
||||||
private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right, int trust) {
|
private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right,
|
||||||
|
int trust) {
|
||||||
if (left == null) {
|
if (left == null) {
|
||||||
return right;
|
return right;
|
||||||
} else if (right == null) {
|
} else if (right == null) {
|
||||||
|
|
@ -223,7 +248,8 @@ public class MergeUtils {
|
||||||
List<StructuredProperty> h = trust >= 0 ? left : right;
|
List<StructuredProperty> h = trust >= 0 ? left : right;
|
||||||
List<StructuredProperty> l = trust >= 0 ? right : left;
|
List<StructuredProperty> l = trust >= 0 ? right : left;
|
||||||
|
|
||||||
return Stream.concat(h.stream(), l.stream())
|
return Stream
|
||||||
|
.concat(h.stream(), l.stream())
|
||||||
.filter(Objects::isNull)
|
.filter(Objects::isNull)
|
||||||
.distinct()
|
.distinct()
|
||||||
.collect(Collectors.toList());
|
.collect(Collectors.toList());
|
||||||
|
|
@ -263,7 +289,9 @@ public class MergeUtils {
|
||||||
// dateofcollection mettere today quando si fa merge
|
// dateofcollection mettere today quando si fa merge
|
||||||
merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust));
|
merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust));
|
||||||
// setDateoftransformation mettere vuota in dedup, nota per Claudio
|
// setDateoftransformation mettere vuota in dedup, nota per Claudio
|
||||||
merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
|
merged
|
||||||
|
.setDateoftransformation(
|
||||||
|
chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
|
||||||
// TODO: was missing in OafEntity.merge
|
// TODO: was missing in OafEntity.merge
|
||||||
merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
|
merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
|
||||||
// oaiprovenanze da mettere a null quando si genera merge
|
// oaiprovenanze da mettere a null quando si genera merge
|
||||||
|
|
@ -273,7 +301,6 @@ public class MergeUtils {
|
||||||
return merged;
|
return merged;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
public static <T extends Relation> T mergeRelation(T original, T enrich) {
|
public static <T extends Relation> T mergeRelation(T original, T enrich) {
|
||||||
int trust = compareTrust(original, enrich);
|
int trust = compareTrust(original, enrich);
|
||||||
T merge = mergeOafFields(original, enrich, trust);
|
T merge = mergeOafFields(original, enrich, trust);
|
||||||
|
|
@ -309,7 +336,8 @@ public class MergeUtils {
|
||||||
final int trust = compareTrust(original, enrich);
|
final int trust = compareTrust(original, enrich);
|
||||||
T merge = mergeOafEntityFields(original, enrich, trust);
|
T merge = mergeOafEntityFields(original, enrich, trust);
|
||||||
|
|
||||||
if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
|
if (merge.getProcessingchargeamount() == null
|
||||||
|
|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
|
||||||
merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
|
merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
|
||||||
merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
|
merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
|
||||||
}
|
}
|
||||||
|
|
@ -350,6 +378,7 @@ public class MergeUtils {
|
||||||
// prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO
|
// prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO
|
||||||
// trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario)
|
// trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario)
|
||||||
// vedi note
|
// vedi note
|
||||||
|
// cannot use com.google.common.base.Objects.firstNonNull as it throws NPE when both terms are null
|
||||||
merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype()));
|
merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype()));
|
||||||
|
|
||||||
// ok
|
// ok
|
||||||
|
|
@ -366,12 +395,18 @@ public class MergeUtils {
|
||||||
merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust));
|
merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust));
|
||||||
|
|
||||||
// ok
|
// ok
|
||||||
merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
|
merge
|
||||||
|
.setExternalReference(
|
||||||
|
unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
|
||||||
|
|
||||||
// instance enrichment or union
|
// instance enrichment or union
|
||||||
// review instance equals => add pid to comparision
|
// review instance equals => add pid to comparision
|
||||||
if (!isAnEnrichment(merge) && !isAnEnrichment(enrich))
|
if (!isAnEnrichment(merge) && !isAnEnrichment(enrich))
|
||||||
merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust));
|
merge.setInstance(
|
||||||
|
mergeLists(merge.getInstance(), enrich.getInstance(), trust,
|
||||||
|
MergeUtils::instanceKeyExtractor,
|
||||||
|
MergeUtils::instanceMerger
|
||||||
|
));
|
||||||
else {
|
else {
|
||||||
final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
|
final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
|
||||||
: enrich.getInstance();
|
: enrich.getInstance();
|
||||||
|
|
@ -392,6 +427,39 @@ public class MergeUtils {
|
||||||
return merge;
|
return merge;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
private static String instanceKeyExtractor(Instance i) {
|
||||||
|
return String.join("::",
|
||||||
|
kvKeyExtractor(i.getHostedby()),
|
||||||
|
qualifierKeyExtractor(i.getAccessright()),
|
||||||
|
qualifierKeyExtractor(i.getInstancetype()),
|
||||||
|
Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
|
||||||
|
Optional.ofNullable(i.getPid()).map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::"))).orElse(null));
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String kvKeyExtractor(KeyValue kv) {
|
||||||
|
return Optional.ofNullable(kv).map(KeyValue::getKey).orElse(null);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String qualifierKeyExtractor(Qualifier q) {
|
||||||
|
return Optional.ofNullable(q).map(Qualifier::getClassid).orElse(null);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static <T> T FieldKeyExtractor(Field<T> f) {
|
||||||
|
return Optional.ofNullable(f).map(Field::getValue).orElse(null);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static String spKeyExtractor(StructuredProperty sp) {
|
||||||
|
return Optional.ofNullable(sp).map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier()))).orElse(null);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Instance instanceMerger(Instance i1, Instance i2) {
|
||||||
|
|
||||||
|
// TODO implement me!
|
||||||
|
|
||||||
|
return i1;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
|
private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
|
||||||
int trust = compareTrust(original, enrich);
|
int trust = compareTrust(original, enrich);
|
||||||
final T merge = mergeResult(original, enrich);
|
final T merge = mergeResult(original, enrich);
|
||||||
|
|
@ -410,7 +478,9 @@ public class MergeUtils {
|
||||||
merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
|
merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
|
||||||
merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
|
merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
|
||||||
merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
|
merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
|
||||||
merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
|
merge
|
||||||
|
.setProgrammingLanguage(
|
||||||
|
chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
|
||||||
|
|
||||||
return merge;
|
return merge;
|
||||||
}
|
}
|
||||||
|
|
@ -423,8 +493,12 @@ public class MergeUtils {
|
||||||
merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
|
merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
|
||||||
merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
|
merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
|
||||||
merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
|
merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
|
||||||
merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
|
merge
|
||||||
merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
|
.setLastmetadataupdate(
|
||||||
|
chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
|
||||||
|
merge
|
||||||
|
.setMetadataversionnumber(
|
||||||
|
chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
|
||||||
merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
|
merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
|
||||||
|
|
||||||
return merge;
|
return merge;
|
||||||
|
|
@ -445,16 +519,27 @@ public class MergeUtils {
|
||||||
|
|
||||||
merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
|
merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
|
||||||
merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
|
merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
|
||||||
merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
|
merged
|
||||||
|
.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
|
||||||
merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
|
merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
|
||||||
merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
|
merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
|
||||||
merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
|
merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
|
||||||
merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
|
merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
|
||||||
merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
|
merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
|
||||||
merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
|
merged
|
||||||
merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
|
.setEcresearchorganization(
|
||||||
merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust));
|
chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
|
||||||
merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
|
merged
|
||||||
|
.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
|
||||||
|
merged
|
||||||
|
.setEcinternationalorganizationeurinterests(
|
||||||
|
chooseReference(
|
||||||
|
merged.getEcinternationalorganizationeurinterests(),
|
||||||
|
enrich.getEcinternationalorganizationeurinterests(), trust));
|
||||||
|
merged
|
||||||
|
.setEcinternationalorganization(
|
||||||
|
chooseReference(
|
||||||
|
merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
|
||||||
merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
|
merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
|
||||||
merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
|
merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
|
||||||
merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
|
merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
|
||||||
|
|
@ -477,7 +562,9 @@ public class MergeUtils {
|
||||||
merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust));
|
merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust));
|
||||||
merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
|
merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
|
||||||
merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
|
merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
|
||||||
merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
|
merged
|
||||||
|
.setOamandatepublications(
|
||||||
|
chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
|
||||||
merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
|
merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
|
||||||
merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
|
merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
|
||||||
merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
|
merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
|
||||||
|
|
@ -502,12 +589,13 @@ public class MergeUtils {
|
||||||
merged.setH2020topicdescription(enrich.getH2020topicdescription());
|
merged.setH2020topicdescription(enrich.getH2020topicdescription());
|
||||||
}
|
}
|
||||||
|
|
||||||
merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
|
merged
|
||||||
|
.setH2020classification(
|
||||||
|
unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
|
||||||
|
|
||||||
return merged;
|
return merged;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Longest lists list.
|
* Longest lists list.
|
||||||
*
|
*
|
||||||
|
|
@ -679,12 +767,18 @@ public class MergeUtils {
|
||||||
merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping()));
|
merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping()));
|
||||||
merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
|
merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
|
||||||
merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
|
merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
|
||||||
merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
|
merge
|
||||||
|
.setDistributionlocation(
|
||||||
|
firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
|
||||||
merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
|
merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
|
||||||
// pid and alternateId are used for matching
|
// pid and alternateId are used for matching
|
||||||
merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
|
merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
|
||||||
merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
|
merge
|
||||||
merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
|
.setProcessingchargeamount(
|
||||||
|
firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
|
||||||
|
merge
|
||||||
|
.setProcessingchargecurrency(
|
||||||
|
firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
|
||||||
merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
|
merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
|
||||||
merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
|
merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
|
||||||
merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
|
merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
public class ModelHardLimits {
|
||||||
|
|
||||||
|
private ModelHardLimits() {}
|
||||||
|
|
||||||
|
public static final String LAYOUT = "index";
|
||||||
|
public static final String INTERPRETATION = "openaire";
|
||||||
|
public static final String SEPARATOR = "-";
|
||||||
|
|
||||||
|
public static final int MAX_EXTERNAL_ENTITIES = 50;
|
||||||
|
public static final int MAX_AUTHORS = 200;
|
||||||
|
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
|
||||||
|
public static final int MAX_TITLE_LENGTH = 5000;
|
||||||
|
public static final int MAX_TITLES = 10;
|
||||||
|
public static final int MAX_ABSTRACTS = 10;
|
||||||
|
public static final int MAX_ABSTRACT_LENGTH = 150000;
|
||||||
|
public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
|
||||||
|
public static final int MAX_INSTANCES = 10;
|
||||||
|
|
||||||
|
public static String getCollectionName(String format) {
|
||||||
|
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
import java.util.Comparator;
|
||||||
|
|
||||||
|
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 +1,38 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.Optional;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
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 eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
import java.util.Comparator;
|
||||||
|
|
||||||
|
public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
|
||||||
|
|
||||||
|
private final T entity;
|
||||||
|
|
||||||
|
public PidComparator(T entity) {
|
||||||
|
this.entity = entity;
|
||||||
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||||
|
|
||||||
|
if (left == null && right == null)
|
||||||
|
return 0;
|
||||||
|
if (left == null)
|
||||||
|
return 1;
|
||||||
|
if (right == null)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
if (ModelSupport.isSubClass(entity, Result.class)) {
|
||||||
|
return compareResultPids(left, right);
|
||||||
|
}
|
||||||
|
if (ModelSupport.isSubClass(entity, Organization.class)) {
|
||||||
|
return compareOrganizationtPids(left, right);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Else (but unlikely), lexicographical ordering will do.
|
||||||
|
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
|
||||||
|
}
|
||||||
|
|
||||||
|
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
|
||||||
|
return new ResultPidComparator().compare(left, right);
|
||||||
|
}
|
||||||
|
|
||||||
|
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
|
||||||
|
return new OrganizationPidComparator().compare(left, right);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,79 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import org.apache.commons.lang3.EnumUtils;
|
||||||
|
|
||||||
|
public enum PidType {
|
||||||
|
|
||||||
|
/**
|
||||||
|
* The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
|
||||||
|
*
|
||||||
|
* There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
|
||||||
|
*
|
||||||
|
* The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
|
||||||
|
* of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
|
||||||
|
* defined for an application by the ISO 26324 Registration Authority.
|
||||||
|
*
|
||||||
|
*
|
||||||
|
* DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
|
||||||
|
* These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
|
||||||
|
* distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
|
||||||
|
* resolution system.
|
||||||
|
*
|
||||||
|
* Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
|
||||||
|
* unique string assigned to a registrant.
|
||||||
|
*
|
||||||
|
* DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
|
||||||
|
* Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
|
||||||
|
* or it might incorporate an identifier generated from or based on another system used by the registrant
|
||||||
|
* (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
|
||||||
|
* specified, as in Example 1).
|
||||||
|
*
|
||||||
|
* Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
|
||||||
|
*/
|
||||||
|
doi,
|
||||||
|
|
||||||
|
/**
|
||||||
|
* PubMed Unique Identifier (PMID)
|
||||||
|
*
|
||||||
|
* This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
|
||||||
|
* accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
|
||||||
|
*
|
||||||
|
* Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
|
||||||
|
* (e.g., 21804956.2). All citations are considered version 1 until replaced. The extended PMID is not displayed
|
||||||
|
* on the MEDLINE format.
|
||||||
|
*
|
||||||
|
* View the citation in abstract format in PubMed to access additional versions when available (see the article in
|
||||||
|
* the Jan-Feb 2012 NLM Technical Bulletin).
|
||||||
|
*
|
||||||
|
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
|
||||||
|
*/
|
||||||
|
pmid,
|
||||||
|
|
||||||
|
/**
|
||||||
|
* This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
|
||||||
|
* prefix PMC.
|
||||||
|
*
|
||||||
|
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
|
||||||
|
*/
|
||||||
|
pmc, handle, arXiv, nct, pdb, w3id,
|
||||||
|
|
||||||
|
// Organization
|
||||||
|
openorgs, ROR, GRID, PIC, ISNI, Wikidata, FundRef, corda, corda_h2020, mag_id, urn,
|
||||||
|
|
||||||
|
// Used by dedup
|
||||||
|
undefined, original;
|
||||||
|
|
||||||
|
public static boolean isValid(String type) {
|
||||||
|
return EnumUtils.isValidEnum(PidType.class, type);
|
||||||
|
}
|
||||||
|
|
||||||
|
public static PidType tryValueOf(String s) {
|
||||||
|
try {
|
||||||
|
return PidType.valueOf(s);
|
||||||
|
} catch (Exception e) {
|
||||||
|
return PidType.original;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,33 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
import java.util.Comparator;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
|
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 eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||||
|
|
||||||
|
import java.util.Comparator;
|
||||||
|
|
||||||
|
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 eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||||
|
|
||||||
|
import java.util.Comparator;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.Optional;
|
||||||
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
|
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
|
||||||
|
|
||||||
|
public class ResultTypeComparator implements Comparator<Result> {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public int compare(Result left, Result right) {
|
||||||
|
|
||||||
|
if (left == null && right == null)
|
||||||
|
return 0;
|
||||||
|
if (left == null)
|
||||||
|
return 1;
|
||||||
|
if (right == null)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
HashSet<String> lCf = getCollectedFromIds(left);
|
||||||
|
HashSet<String> rCf = getCollectedFromIds(right);
|
||||||
|
|
||||||
|
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
String lClass = left.getResulttype().getClassid();
|
||||||
|
String rClass = right.getResulttype().getClassid();
|
||||||
|
|
||||||
|
if (lClass.equals(rClass))
|
||||||
|
return 0;
|
||||||
|
|
||||||
|
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||||
|
return -1;
|
||||||
|
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||||
|
return 1;
|
||||||
|
|
||||||
|
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||||
|
return -1;
|
||||||
|
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||||
|
return 1;
|
||||||
|
|
||||||
|
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||||
|
return -1;
|
||||||
|
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||||
|
return 1;
|
||||||
|
|
||||||
|
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||||
|
return -1;
|
||||||
|
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||||
|
return 1;
|
||||||
|
|
||||||
|
// Else (but unlikely), lexicographical ordering will do.
|
||||||
|
return lClass.compareTo(rClass);
|
||||||
|
}
|
||||||
|
|
||||||
|
protected HashSet<String> getCollectedFromIds(Result left) {
|
||||||
|
return Optional
|
||||||
|
.ofNullable(left.getCollectedfrom())
|
||||||
|
.map(
|
||||||
|
cf -> cf
|
||||||
|
.stream()
|
||||||
|
.map(KeyValue::getKey)
|
||||||
|
.collect(Collectors.toCollection(HashSet::new)))
|
||||||
|
.orElse(new HashSet<>());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,21 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
class BlackListProviderTest {
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void blackListTest() {
|
||||||
|
|
||||||
|
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
|
||||||
|
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
|
||||||
|
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
|
||||||
|
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
|
||||||
|
Assertions.assertNotNull(xxx);
|
||||||
|
Assertions.assertEquals(0, xxx.size());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,85 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
|
import org.apache.commons.io.IOUtils;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
|
|
||||||
|
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);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -5,11 +5,14 @@ import static org.junit.jupiter.api.Assertions.*;
|
||||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
|
import java.lang.reflect.InvocationTargetException;
|
||||||
import java.util.HashSet;
|
import java.util.HashSet;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
import java.util.stream.Collectors;
|
import java.util.stream.Collectors;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
import com.google.common.collect.Lists;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.*;
|
||||||
|
import org.apache.commons.beanutils.BeanUtils;
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
|
|
@ -17,16 +20,33 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
|
||||||
|
|
||||||
public class MergeUtilsTest {
|
public class MergeUtilsTest {
|
||||||
|
|
||||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||||
|
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testMergePubs_new() throws IOException {
|
||||||
|
Publication pt = read("publication_test.json", Publication.class);
|
||||||
|
Publication p1 = read("publication_test.json", Publication.class);
|
||||||
|
|
||||||
|
assertEquals(1, pt.getCollectedfrom().size());
|
||||||
|
assertEquals(ModelConstants.CROSSREF_ID, pt.getCollectedfrom().get(0).getKey());
|
||||||
|
|
||||||
|
Instance i = new Instance();
|
||||||
|
i.setUrl(Lists.newArrayList("https://..."));
|
||||||
|
p1.getInstance().add(i);
|
||||||
|
|
||||||
|
Publication ptp1 = MergeUtils.mergePublication(pt, p1);
|
||||||
|
|
||||||
|
assertNotNull(ptp1.getInstance());
|
||||||
|
assertEquals(2, ptp1.getInstance().size());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
void testMergePubs() throws IOException {
|
void testMergePubs() throws IOException {
|
||||||
Publication p1 = read("publication_1.json", Publication.class);
|
Publication p1 = read("publication_1.json", Publication.class);
|
||||||
|
|
|
||||||
|
|
@ -178,8 +178,8 @@ class OafMapperUtilsTest {
|
||||||
|
|
||||||
assertEquals(
|
assertEquals(
|
||||||
ModelConstants.DATASET_RESULTTYPE_CLASSID,
|
ModelConstants.DATASET_RESULTTYPE_CLASSID,
|
||||||
MergeUtils
|
((Result) MergeUtils
|
||||||
.mergeResult(p2, d1)
|
.merge(p2, d1))
|
||||||
.getResulttype()
|
.getResulttype()
|
||||||
.getClassid());
|
.getClassid());
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,12 @@
|
||||||
|
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|
||||||
|
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|
||||||
|
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/1587::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.39172290649e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/1587"}]}]}
|
||||||
|
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/462::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"6.33235333753e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.36"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.00285265116e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/462"}]}]}
|
||||||
|
{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0001/731::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"4.01810569717e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0001/731"}]}]}
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{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0118/alfahim.v3i1.140::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"9.88840807598e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0118/alfahim.v3i1.140"}]}]}
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{"dataInfo":{"deletedbyinference":false,"inferred":true,"invisible":false,"provenanceaction":{"classid":"sysimport:enrich","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"id":"unresolved::10.0301/jttb.v2i1.64::doi","instance":[{"measures":[{"id":"influence","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"5.91019644836e-09"}]},{"id":"popularity_alt","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"0.0"}]},{"id":"popularity","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"7.28336930301e-09"}]}],"pid":[{"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.0301/jttb.v2i1.64"}]}]}
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@ -0,0 +1,23 @@
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File diff suppressed because one or more lines are too long
2
pom.xml
2
pom.xml
|
|
@ -888,7 +888,7 @@
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<mockito-core.version>3.3.3</mockito-core.version>
|
<mockito-core.version>3.3.3</mockito-core.version>
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<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
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<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
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<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
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<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
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|
|
|
||||||
Loading…
Reference in New Issue