diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java index eadca231ef..2a31b264c4 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java @@ -1,6 +1,24 @@ package eu.dnetlib.dhp.oa.merge; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.col; +import static org.apache.spark.sql.functions.when; + +import java.util.Map; +import java.util.Optional; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.ForkJoinPool; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.ReduceFunction; +import org.apache.spark.sql.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -12,182 +30,165 @@ import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.api.java.function.ReduceFunction; -import org.apache.spark.sql.*; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; import scala.Tuple2; -import java.util.Map; -import java.util.Optional; -import java.util.concurrent.ExecutionException; -import java.util.concurrent.ForkJoinPool; -import java.util.stream.Collectors; - -import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import static org.apache.spark.sql.functions.col; -import static org.apache.spark.sql.functions.when; - /** * Groups the graph content by entity identifier to ensure ID uniqueness */ public class GroupEntitiesSparkJob { - private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); + private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); - private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); + private static final Encoder OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class); - private ArgumentApplicationParser parser; + private ArgumentApplicationParser parser; - public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { - this.parser = parser; - } + public GroupEntitiesSparkJob(ArgumentApplicationParser parser) { + this.parser = parser; + } - public static void main(String[] args) throws Exception { + public static void main(String[] args) throws Exception { - String jsonConfiguration = IOUtils - .toString( - GroupEntitiesSparkJob.class - .getResourceAsStream( - "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); - final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); - parser.parseArgument(args); + String jsonConfiguration = IOUtils + .toString( + GroupEntitiesSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); - Boolean isSparkSessionManaged = Optional - .ofNullable(parser.get("isSparkSessionManaged")) - .map(Boolean::valueOf) - .orElse(Boolean.TRUE); - log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); - final String isLookupUrl = parser.get("isLookupUrl"); - log.info("isLookupUrl: {}", isLookupUrl); + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); - final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); - new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); - } + new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService); + } - public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) - throws ISLookUpException { + public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService) + throws ISLookUpException { - String graphInputPath = parser.get("graphInputPath"); - log.info("graphInputPath: {}", graphInputPath); + String graphInputPath = parser.get("graphInputPath"); + log.info("graphInputPath: {}", graphInputPath); - String checkpointPath = parser.get("checkpointPath"); - log.info("checkpointPath: {}", checkpointPath); + String checkpointPath = parser.get("checkpointPath"); + log.info("checkpointPath: {}", checkpointPath); - String outputPath = parser.get("outputPath"); - log.info("outputPath: {}", outputPath); + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); - boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); - log.info("filterInvisible: {}", filterInvisible); + boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible")); + log.info("filterInvisible: {}", filterInvisible); - SparkConf conf = new SparkConf(); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); - final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); - runWithSparkSession( - conf, - isSparkSessionManaged, - spark -> { - HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); - groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); - }); - } + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration()); + groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs); + }); + } - private static void groupEntities( - SparkSession spark, - String inputPath, - String checkpointPath, - String outputPath, - boolean filterInvisible, VocabularyGroup vocs) { + private static void groupEntities( + SparkSession spark, + String inputPath, + String checkpointPath, + String outputPath, + boolean filterInvisible, VocabularyGroup vocs) { - Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); + Dataset allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC); - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); - String entityInputPath = inputPath + "/" + entity; + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); + String entityInputPath = inputPath + "/" + entity; - if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { - continue; - } + if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) { + continue; + } - allEntities = allEntities - .union( - ((Dataset) spark - .read() - .schema(Encoders.bean(entityClass).schema()) - .json(entityInputPath) - .filter("length(id) > 0") - .as(Encoders.bean(entityClass))) - .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); - } + allEntities = allEntities + .union( + ((Dataset) spark + .read() + .schema(Encoders.bean(entityClass).schema()) + .json(entityInputPath) + .filter("length(id) > 0") + .as(Encoders.bean(entityClass))) + .map((MapFunction) r -> r, OAFENTITY_KRYO_ENC)); + } - Dataset groupedEntities = allEntities - .map( - (MapFunction) entity -> GraphCleaningFunctions - .applyCoarVocabularies(entity, vocs), - OAFENTITY_KRYO_ENC) - .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) - .reduceGroups((ReduceFunction) MergeUtils::checkedMerge) - .map( - (MapFunction, Tuple2>) t -> new Tuple2<>( - t._2().getClass().getName(), t._2()), - Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); + Dataset groupedEntities = allEntities + .map( + (MapFunction) entity -> GraphCleaningFunctions + .applyCoarVocabularies(entity, vocs), + OAFENTITY_KRYO_ENC) + .groupByKey((MapFunction) OafEntity::getId, Encoders.STRING()) + .reduceGroups((ReduceFunction) MergeUtils::checkedMerge) + .map( + (MapFunction, Tuple2>) t -> new Tuple2<>( + t._2().getClass().getName(), t._2()), + Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC)); - // pivot on "_1" (classname of the entity) - // created columns containing only entities of the same class - for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + // pivot on "_1" (classname of the entity) + // created columns containing only entities of the same class + for (Map.Entry e : ModelSupport.entityTypes.entrySet()) { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - groupedEntities = groupedEntities - .withColumn( - entity, - when(col("_1").equalTo(entityClass.getName()), col("_2"))); - } + groupedEntities = groupedEntities + .withColumn( + entity, + when(col("_1").equalTo(entityClass.getName()), col("_2"))); + } - groupedEntities - .drop("_1", "_2") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .save(checkpointPath); + groupedEntities + .drop("_1", "_2") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .save(checkpointPath); - ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); + ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size()); - ModelSupport.entityTypes - .entrySet() - .stream() - .map(e -> parPool.submit(() -> { - String entity = e.getKey().name(); - Class entityClass = e.getValue(); + ModelSupport.entityTypes + .entrySet() + .stream() + .map(e -> parPool.submit(() -> { + String entity = e.getKey().name(); + Class entityClass = e.getValue(); - spark - .read() - .load(checkpointPath) - .select(col(entity).as("value")) - .filter("value IS NOT NULL") - .as(OAFENTITY_KRYO_ENC) - .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) - .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") - .write() - .mode(SaveMode.Overwrite) - .option("compression", "gzip") - .json(outputPath + "/" + entity); - })) - .collect(Collectors.toList()) - .forEach(t -> { - try { - t.get(); - } catch (InterruptedException | ExecutionException e) { - throw new RuntimeException(e); - } - }); - } + spark + .read() + .load(checkpointPath) + .select(col(entity).as("value")) + .filter("value IS NOT NULL") + .as(OAFENTITY_KRYO_ENC) + .map((MapFunction) r -> r, (Encoder) Encoders.bean(entityClass)) + .filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE") + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/" + entity); + })) + .collect(Collectors.toList()) + .forEach(t -> { + try { + t.get(); + } catch (InterruptedException | ExecutionException e) { + throw new RuntimeException(e); + } + }); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java new file mode 100644 index 0000000000..17635c3399 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java @@ -0,0 +1,73 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import org.apache.commons.lang3.StringUtils; + +import java.util.HashSet; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; + +public class CleaningFunctions { + + public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)"; + public static final String DOI_PREFIX = "10."; + + public static final Set 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; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java new file mode 100644 index 0000000000..32a784eb80 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java @@ -0,0 +1,290 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import com.google.common.collect.HashBiMap; +import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.codec.binary.Hex; +import org.apache.commons.lang3.StringUtils; + +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 static com.google.common.base.Preconditions.checkArgument; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; + +/** + * 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> 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> 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> 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 delegatedAuthorityDatasourceIds() { + return DELEGATED_PID_AUTHORITY.values() + .stream() + .flatMap(m -> m.keySet().stream()) + .collect(Collectors.toCollection(HashSet::new)); + } + + public static List getPids(List pid, KeyValue collectedFrom) { + return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList()); + } + + public static 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 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 String createIdentifier(T entity, boolean md5) { + + checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier"); + + final Map> 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 Map> 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> mapPids(List 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 pidFromInstance(List 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 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 String createIdentifier(T entity) { + + return createIdentifier(entity, true); + } + + private static 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; + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java index ffb0e600ab..244b9b4aa1 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java @@ -1,79 +1,78 @@ + package eu.dnetlib.dhp.schema.oaf.utils; -// -// Source code recreated from a .class file by IntelliJ IDEA -// (powered by FernFlower decompiler) -// - - -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; - import java.util.Comparator; import java.util.HashSet; import java.util.Optional; import java.util.stream.Collectors; +// +// 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 { - public MergeComparator() { - } + public MergeComparator() { + } - public int compare(Oaf left, Oaf right) { - // nulls at the end - if (left == null && right == null) { - return 0; - } else if (left == null) { - return -1; - } else if (right == null) { - return 1; - } + public int compare(Oaf left, Oaf right) { + // nulls at the end + if (left == null && right == null) { + return 0; + } else if (left == null) { + return -1; + } else if (right == null) { + return 1; + } - // invisible - if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) { - if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) { - return -1; - } - } + // invisible + if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) { + if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) { + return -1; + } + } - // collectedfrom - HashSet lCf = getCollectedFromIds(left); - HashSet rCf = getCollectedFromIds(right); - if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { - return -1; - } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { - return 1; - } + // collectedfrom + HashSet lCf = getCollectedFromIds(left); + HashSet rCf = getCollectedFromIds(right); + if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") + && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return -1; + } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") + && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) { + return 1; + } + SubEntityType lClass = SubEntityType.fromClass(left.getClass()); + SubEntityType rClass = SubEntityType.fromClass(right.getClass()); + return lClass.ordinal() - rClass.ordinal(); + } - SubEntityType lClass = SubEntityType.fromClass(left.getClass()); - SubEntityType rClass = SubEntityType.fromClass(right.getClass()); - return lClass.ordinal() - rClass.ordinal(); + protected HashSet getCollectedFromIds(Oaf left) { + return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> { + return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); + }).orElse(new HashSet()); + } - } + enum SubEntityType { + publication, dataset, software, otherresearchproduct, datasource, organization, project; - protected HashSet getCollectedFromIds(Oaf left) { - return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> { - return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new)); - }).orElse(new HashSet()); - } - - enum SubEntityType { - publication, dataset, software, otherresearchproduct, datasource, organization, project; - - /** - * Resolves the EntityType, given the relative class name - * - * @param clazz the given class name - * @param actual OafEntity subclass - * @return the EntityType associated to the given class - */ - public static SubEntityType fromClass(Class clazz) { - return valueOf(clazz.getSimpleName().toLowerCase()); - } - } + /** + * Resolves the EntityType, given the relative class name + * + * @param clazz the given class name + * @param actual OafEntity subclass + * @return the EntityType associated to the given class + */ + public static SubEntityType fromClass(Class clazz) { + return valueOf(clazz.getSimpleName().toLowerCase()); + } + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java index 072a86bf1b..3ce62b43b0 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java @@ -1,707 +1,801 @@ 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.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.lang3.tuple.ImmutablePair; -import org.apache.commons.lang3.tuple.Pair; - -import java.text.ParseException; -import java.util.*; -import java.util.stream.Collectors; -import java.util.stream.Stream; - -import static com.google.common.base.Objects.firstNonNull; -import static com.google.common.base.Preconditions.checkArgument; public class MergeUtils { - public static T checkedMerge(final T left, final T right) { - return (T) merge(left, right, false); - } + public static T checkedMerge(final T left, final T right) { + return (T) merge(left, right, false); + } - public static Oaf merge(final Oaf left, final Oaf right) { - return merge(left, right, false); - } + public static Oaf merge(final Oaf left, final Oaf right) { + return merge(left, right, false); + } - public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) { - if (sameClass(left, right, OafEntity.class)) { - return mergeEntities(left, right, checkDelegatedAuthority); - } else if (sameClass(left, right, Relation.class)) { - return mergeRelation((Relation) left, (Relation) right); - } else { - throw new RuntimeException( - String - .format( - "MERGE_FROM_AND_GET incompatible types: %s, %s", - left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); - } - } + public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) { + if (sameClass(left, right, OafEntity.class)) { + return mergeEntities(left, right, checkDelegatedAuthority); + } else if (sameClass(left, right, Relation.class)) { + return mergeRelation((Relation) left, (Relation) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } - private static boolean sameClass(Object left, Object right, Class cls) { - return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass()); - } + private static boolean sameClass(Object left, Object right, Class cls) { + return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass()); + } - private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) { + private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) { - if (sameClass(left, right, Result.class)) { - if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) { - return mergeResultsOfDifferentTypes((Result)left, (Result) right); - } + if (sameClass(left, right, Result.class)) { + if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) { + return mergeResultsOfDifferentTypes((Result) left, (Result) right); + } - if (sameClass(left, right, Publication.class)) { - return mergePublication((Publication) left, (Publication) right); - } - if (sameClass(left, right, Dataset.class)) { - return mergeDataset((Dataset) left, (Dataset) right); - } - if (sameClass(left, right, OtherResearchProduct.class)) { - return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right); - } - if (sameClass(left, right, Software.class)) { - return mergeSoftware((Software) left, (Software) right); - } + if (sameClass(left, right, Publication.class)) { + return mergePublication((Publication) left, (Publication) right); + } + if (sameClass(left, right, Dataset.class)) { + return mergeDataset((Dataset) left, (Dataset) right); + } + if (sameClass(left, right, OtherResearchProduct.class)) { + return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right); + } + if (sameClass(left, right, Software.class)) { + return mergeSoftware((Software) left, (Software) right); + } - return mergeResult((Result) left, (Result) right); - } else if (sameClass(left, right, Datasource.class)) { - // TODO - final int trust = compareTrust(left, right); - return mergeOafEntityFields((Datasource) left, (Datasource) right, trust); - } else if (sameClass(left, right, Organization.class)) { - return mergeOrganization((Organization) left, (Organization) right); - } else if (sameClass(left, right, Project.class)) { - return mergeProject((Project) left, (Project) right); - } else { - throw new RuntimeException( - String - .format( - "MERGE_FROM_AND_GET incompatible types: %s, %s", - left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); - } - } + return mergeResult((Result) left, (Result) right); + } else if (sameClass(left, right, Datasource.class)) { + // TODO + final int trust = compareTrust(left, right); + return mergeOafEntityFields((Datasource) left, (Datasource) right, trust); + } else if (sameClass(left, right, Organization.class)) { + return mergeOrganization((Organization) left, (Organization) right); + } else if (sameClass(left, right, Project.class)) { + return mergeProject((Project) left, (Project) right); + } else { + throw new RuntimeException( + String + .format( + "MERGE_FROM_AND_GET incompatible types: %s, %s", + left.getClass().getCanonicalName(), right.getClass().getCanonicalName())); + } + } - /** - * This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority - * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers - * such version. - *

- * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator} - * and proceeds with the canonical property merging. - * - * @param left - * @param right - * @return - */ - private static T mergeResultsOfDifferentTypes(T left, T right) { + /** + * This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority + * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers + * such version. + *

+ * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator} + * and proceeds with the canonical property merging. + * + * @param left + * @param right + * @return + */ + private static T mergeResultsOfDifferentTypes(T left, T right) { - final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); - final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); + final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left); + final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right); - if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { - return left; - } - if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { - return right; - } - //TODO: raise trust to have preferred fields from one or the other?? - if (new ResultTypeComparator().compare(left, right) < 0) { - return mergeResult(left, right); - } else { - return mergeResult(right, left); - } - } + if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) { + return left; + } + if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) { + return right; + } + // TODO: raise trust to have preferred fields from one or the other?? + if (new ResultTypeComparator().compare(left, right) < 0) { + return mergeResult(left, right); + } else { + return mergeResult(right, left); + } + } - private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) { - if (trust > 0) { - return left; - } else if (trust == 0) { - if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) { - return right; - } else { - return left; - } - } else { - return right; - } - } + private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) { + return right; + } else { + return left; + } + } else { + return right; + } + } - private static String chooseString(String left, String right, int trust) { - if (trust > 0) { - return left; - } else if (trust == 0) { - return StringUtils.isNotBlank(left) ? left : right; - } else { - return right; - } - } + private static String chooseString(String left, String right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return StringUtils.isNotBlank(left) ? left : right; + } else { + return right; + } + } - private static T chooseReference(T left, T right, int trust) { - if (trust > 0) { - return left; - } else if (trust == 0) { - return left != null ? left : right; - } else { - return right; - } - } + private static T chooseReference(T left, T right, int trust) { + if (trust > 0) { + return left; + } else if (trust == 0) { + return left != null ? left : right; + } else { + return right; + } + } - private static Long max(Long left, Long right) { - if (left == null) - return right; - if (right == null) - return left; + private static Long max(Long left, Long right) { + if (left == null) + return right; + if (right == null) + return left; - return Math.max(left, right); - } + return Math.max(left, right); + } - // trust ?? - private static Boolean booleanOR(Boolean a, Boolean b) { - if (a == null) { - return b; - } else if (b == null) { - return a; - } + // trust ?? + private static Boolean booleanOR(Boolean a, Boolean b) { + if (a == null) { + return b; + } else if (b == null) { + return a; + } - return a || b; - } + return a || b; + } + private static List mergeLists(final List left, final List right, int trust, Function keyExtractor, BinaryOperator merger) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } - private static List unionDistinctLists(final List left, final List right, int trust) { - if (left == null) { - return right; - } else if (right == null) { - return left; - } + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; - List h = trust >= 0 ? left : right; - List 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.toList()); - } - - private static List unionDistinctListOfString(final List l, final List r) { - if (l == null) { - return r; - } else if (r == null) { - return l; - } - - return Stream.concat(l.stream(), r.stream()) - .filter(StringUtils::isNotBlank) - .distinct() - .collect(Collectors.toList()); - } - - //TODO review - private static List mergeKeyValue(List left, List right, int trust) { - if (trust < 0) { - List s = left; - left = right; - right = s; - } - - HashMap values = new HashMap<>(); - left.forEach(kv -> values.put(kv.getKey(), kv)); - right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv)); - - return new ArrayList<>(values.values()); - } - - private static List unionTitle(List left, List right, int trust) { - if (left == null) { - return right; - } else if (right == null) { - return left; - } - - List h = trust >= 0 ? left : right; - List l = trust >= 0 ? right : left; - - return Stream.concat(h.stream(), l.stream()) - .filter(Objects::isNull) - .distinct() - .collect(Collectors.toList()); - } - - /** - * Internal utility that merges the common OafEntity fields - * - * @param merged - * @param enrich - * @param - * @return - */ - private static T mergeOafFields(T merged, T enrich, int trust) { - - //TODO: union of all values, but what does it mean with KeyValue pairs??? - merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust)); - merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust)); - merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp())); - - return merged; - } - - /** - * Internal utility that merges the common OafEntity fields - * - * @param original - * @param enrich - * @param - * @return - */ - private static T mergeOafEntityFields(T original, T enrich, int trust) { - final T merged = mergeOafFields(original, enrich, trust); - - merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId())); - merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust)); - // dateofcollection mettere today quando si fa merge - merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust)); - // setDateoftransformation mettere vuota in dedup, nota per Claudio - merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust)); - // TODO: was missing in OafEntity.merge - merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust)); - //oaiprovenanze da mettere a null quando si genera merge - merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust)); - merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust)); - - return merged; - } - - - public static T mergeRelation(T original, T enrich) { - int trust = compareTrust(original, enrich); - T merge = mergeOafFields(original, enrich, trust); - - checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal"); - checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal"); - checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal"); - checkArgument( - Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal"); - checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal"); - - //merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance())); - - //TODO: trust ?? - merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated())); - try { - merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate())); - } catch (ParseException e) { - throw new IllegalArgumentException(String - .format( - "invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(), - merge.getTarget(), - merge.getValidationDate())); - } - - // TODO keyvalue merge - merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust)); - - return merge; - } - - public static T mergeResult(T original, T enrich) { - final int trust = compareTrust(original, enrich); - T merge = mergeOafEntityFields(original, enrich, trust); - - if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) { - merge.setProcessingchargeamount(enrich.getProcessingchargeamount()); - merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency()); - } - - // author = usare la stessa logica che in dedup - merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust)); - // il primo che mi arriva secondo l'ordinamento per priorita' - merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust)); - // gestito come il resulttype perche' e' un subtype - merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust)); - // spostiamo nell'instance e qui prendo il primo che arriva - merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust)); - // country lasicamo,o cosi' -> parentesi sul datainfo - merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust)); - //ok - merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust)); - // union per priority quindi vanno in append - merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust)); - //ok - merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust)); - // prima trust e poi longest list - merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription())); - // trust piu' alto e poi piu' vecchia - merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust)); - // ok, ma publisher va messo ripetibile - merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust)); - // ok - merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust)); - // ok - merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust)); - // ok - merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust)); - // ok - merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust)); - // ok - merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust)); - - // prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO - // trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario) - // vedi note - merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype())); - - // ok - merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust)); - - // most open ok - if (enrich.getBestaccessright() != null - && new AccessRightComparator<>() - .compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) { - merge.setBestaccessright(enrich.getBestaccessright()); - } - - // TODO merge of datainfo given same id - merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust)); - - //ok - merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust)); - - //instance enrichment or union - // review instance equals => add pid to comparision - if (!isAnEnrichment(merge) && !isAnEnrichment(enrich)) - merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust)); - else { - final List enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance() - : enrich.getInstance(); - final List enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance() - : merge.getInstance(); - if (isAnEnrichment(merge)) - merge.setDataInfo(enrich.getDataInfo()); - merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances)); - } - - merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust)); - merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen())); - // OK but should be list of values - merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust)); - merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal())); - merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded())); - - return merge; - } - - private static T mergeORP(T original, T enrich) { - int trust = compareTrust(original, enrich); - final T merge = mergeResult(original, enrich); - - merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust)); - merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust)); - merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust)); - - return merge; - } - - private static T mergeSoftware(T original, T enrich) { - int trust = compareTrust(original, enrich); - final T merge = mergeResult(original, enrich); - - merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust)); - merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust)); - merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust)); - merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust)); - - return merge; - } - - private static T mergeDataset(T original, T enrich) { - int trust = compareTrust(original, enrich); - T merge = mergeResult(original, enrich); - - merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust)); - merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust)); - merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust)); - merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust)); - merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust)); - merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust)); - merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust)); - - return merge; - } - - public static T mergePublication(T original, T enrich) { - final int trust = compareTrust(original, enrich); - T merged = mergeResult(original, enrich); - - merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust)); - - return merged; - } - - private static T mergeOrganization(T left, T enrich) { - int trust = compareTrust(left, enrich); - T merged = mergeOafEntityFields(left, enrich, trust); - - merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust)); - merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust)); - merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust)); - merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); - merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust)); - merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust)); - merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust)); - merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust)); - merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust)); - merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust)); - merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust)); - merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust)); - merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust)); - merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust)); - merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust)); - merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust)); - - return merged; - } - - public static T mergeProject(T original, T enrich) { - int trust = compareTrust(original, enrich); - T merged = mergeOafEntityFields(original, enrich, trust); - - merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); - merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust)); - merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust)); - merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust)); - merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust)); - merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust)); - merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust)); - merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust)); - merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust)); - merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust)); - merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust)); - merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust)); - merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust)); - merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust)); - merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust)); - merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust)); - merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust)); - merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust)); - merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust)); - merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust)); - merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust)); - merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust)); - merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust)); - merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust)); - - //missin in Project.merge - merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust)); - merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust)); - - // trust ?? - if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) { - merged.setH2020topiccode(enrich.getH2020topiccode()); - merged.setH2020topicdescription(enrich.getH2020topicdescription()); - } - - merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust)); - - return merged; - } - - - /** - * Longest lists list. - * - * @param a the a - * @param b the b - * @return the list - */ - public static List> longestLists(List> a, List> b) { - if (a == null || b == null) - return a == null ? b : a; - - return a.size() >= b.size() ? a : b; - } - - /** - * This main method apply the enrichment of the instances - * - * @param toEnrichInstances the instances that could be enriched - * @param enrichmentInstances the enrichment instances - * @return list of instances possibly enriched - */ - private static List enrichInstances(final List toEnrichInstances, - final List enrichmentInstances) { - final List enrichmentResult = new ArrayList<>(); - - if (toEnrichInstances == null) { - return enrichmentResult; - } - if (enrichmentInstances == null) { - return enrichmentResult; - } - Map ri = toInstanceMap(enrichmentInstances); - - toEnrichInstances.forEach(i -> { - final List e = findEnrichmentsByPID(i.getPid(), ri); - if (e != null && e.size() > 0) { - e.forEach(enr -> applyEnrichment(i, enr)); - } else { - final List 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 toInstanceMap(final List ri) { - return ri - .stream() - .filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null) - .flatMap(i -> { - final List> result = new ArrayList<>(); - if (i.getPid() != null) - i - .getPid() - .stream() - .filter(MergeUtils::validPid) - .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); - if (i.getAlternateIdentifier() != null) - i - .getAlternateIdentifier() - .stream() - .filter(MergeUtils::validPid) - .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); - return result.stream(); - }) - .collect( - Collectors - .toMap( - Pair::getLeft, - Pair::getRight, - (a, b) -> a)); - } - - private static boolean isFromDelegatedAuthority(Result r) { - return Optional - .ofNullable(r.getInstance()) - .map( - instance -> instance - .stream() - .filter(i -> Objects.nonNull(i.getCollectedfrom())) - .map(i -> i.getCollectedfrom().getKey()) - .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) - .orElse(false); - } - - /** - * Valid pid boolean. - * - * @param p the p - * @return the boolean - */ - private static boolean validPid(final StructuredProperty p) { - return p.getValue() != null && p.getQualifier() != null && p.getQualifier().getClassid() != null; - } - - /** - * Normalize pid string. - * - * @param pid the pid - * @return the string - */ - private static String extractKeyFromPid(final StructuredProperty pid) { - if (pid == null) - return null; - final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid); - - return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue()); - } - - /** - * This utility method finds the list of enrichment instances - * that match one or more PIDs in the input list - * - * @param pids the list of PIDs - * @param enrichments the List of enrichment instances having the same pid - * @return the list - */ - private static List findEnrichmentsByPID(final List pids, - final Map enrichments) { - if (pids == null || enrichments == null) - return null; - return pids - .stream() - .map(MergeUtils::extractKeyFromPid) - .map(enrichments::get) - .filter(Objects::nonNull) - .collect(Collectors.toList()); - } - - /** - * Is an enrichment boolean. - * - * @param e the e - * @return the boolean - */ - private static boolean isAnEnrichment(OafEntity e) { - return e.getDataInfo() != null && - e.getDataInfo().getProvenanceaction() != null - && ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid()); - } - - /** - * This method apply enrichment on a single instance - * The enrichment consists of replacing values on - * single attribute only if in the current instance is missing - * The only repeatable field enriched is measures - * - * @param merge the current instance - * @param enrichment the enrichment instance - */ - private static void applyEnrichment(final Instance merge, final Instance enrichment) { - if (merge == null || enrichment == null) - return; - - merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense())); - merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright())); - merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype())); - merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping())); - merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby())); - merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0)); - merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation())); - merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom())); - // pid and alternateId are used for matching - merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance())); - merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount())); - merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency())); - merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed())); - merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0)); - merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext())); - } - - private static int compareTrust(Oaf a, Oaf b) { - String left = Optional - .ofNullable(a.getDataInfo()) - .map(DataInfo::getTrust) - .orElse("0.0"); - - String right = Optional - .ofNullable(b.getDataInfo()) - .map(DataInfo::getTrust) - .orElse("0.0"); - - return left.compareTo(right); - } + .collect(Collectors.toMap(keyExtractor, v -> v, merger)) + .values()); + } + + private static List unionDistinctLists(final List left, final List right, int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream + .concat(h.stream(), l.stream()) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + + private static List unionDistinctListOfString(final List l, final List r) { + if (l == null) { + return r; + } else if (r == null) { + return l; + } + + return Stream + .concat(l.stream(), r.stream()) + .filter(StringUtils::isNotBlank) + .distinct() + .collect(Collectors.toList()); + } + + // TODO review + private static List mergeKeyValue(List left, List right, int trust) { + if (trust < 0) { + List s = left; + left = right; + right = s; + } + + HashMap values = new HashMap<>(); + left.forEach(kv -> values.put(kv.getKey(), kv)); + right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv)); + + return new ArrayList<>(values.values()); + } + + private static List unionTitle(List left, List right, + int trust) { + if (left == null) { + return right; + } else if (right == null) { + return left; + } + + List h = trust >= 0 ? left : right; + List l = trust >= 0 ? right : left; + + return Stream + .concat(h.stream(), l.stream()) + .filter(Objects::isNull) + .distinct() + .collect(Collectors.toList()); + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param merged + * @param enrich + * @param + * @return + */ + private static T mergeOafFields(T merged, T enrich, int trust) { + + // TODO: union of all values, but what does it mean with KeyValue pairs??? + merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust)); + merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust)); + merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp())); + + return merged; + } + + /** + * Internal utility that merges the common OafEntity fields + * + * @param original + * @param enrich + * @param + * @return + */ + private static T mergeOafEntityFields(T original, T enrich, int trust) { + final T merged = mergeOafFields(original, enrich, trust); + + merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId())); + merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust)); + // dateofcollection mettere today quando si fa merge + merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust)); + // setDateoftransformation mettere vuota in dedup, nota per Claudio + merged + .setDateoftransformation( + chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust)); + // TODO: was missing in OafEntity.merge + merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust)); + // oaiprovenanze da mettere a null quando si genera merge + merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust)); + merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust)); + + return merged; + } + + public static T mergeRelation(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeOafFields(original, enrich, trust); + + checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal"); + checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal"); + checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal"); + checkArgument( + Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal"); + checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal"); + + // merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance())); + + // TODO: trust ?? + merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated())); + try { + merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate())); + } catch (ParseException e) { + throw new IllegalArgumentException(String + .format( + "invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(), + merge.getTarget(), + merge.getValidationDate())); + } + + // TODO keyvalue merge + merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust)); + + return merge; + } + + public static T mergeResult(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merge = mergeOafEntityFields(original, enrich, trust); + + if (merge.getProcessingchargeamount() == null + || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) { + merge.setProcessingchargeamount(enrich.getProcessingchargeamount()); + merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency()); + } + + // author = usare la stessa logica che in dedup + merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust)); + // il primo che mi arriva secondo l'ordinamento per priorita' + merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust)); + // gestito come il resulttype perche' e' un subtype + merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust)); + // spostiamo nell'instance e qui prendo il primo che arriva + merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust)); + // country lasicamo,o cosi' -> parentesi sul datainfo + merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust)); + // ok + merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust)); + // union per priority quindi vanno in append + merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust)); + // ok + merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust)); + // prima trust e poi longest list + merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription())); + // trust piu' alto e poi piu' vecchia + merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust)); + // ok, ma publisher va messo ripetibile + merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust)); + // ok + merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust)); + // ok + merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust)); + // ok + merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust)); + // ok + merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust)); + // ok + merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust)); + + // prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO + // trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario) + // vedi note + // cannot use com.google.common.base.Objects.firstNonNull as it throws NPE when both terms are null + merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype())); + + // ok + merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust)); + + // most open ok + if (enrich.getBestaccessright() != null + && new AccessRightComparator<>() + .compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) { + merge.setBestaccessright(enrich.getBestaccessright()); + } + + // TODO merge of datainfo given same id + merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust)); + + // ok + merge + .setExternalReference( + unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust)); + + // instance enrichment or union + // review instance equals => add pid to comparision + if (!isAnEnrichment(merge) && !isAnEnrichment(enrich)) + merge.setInstance( + mergeLists(merge.getInstance(), enrich.getInstance(), trust, + MergeUtils::instanceKeyExtractor, + MergeUtils::instanceMerger + )); + else { + final List enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance() + : enrich.getInstance(); + final List enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance() + : merge.getInstance(); + if (isAnEnrichment(merge)) + merge.setDataInfo(enrich.getDataInfo()); + merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances)); + } + + merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust)); + merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen())); + // OK but should be list of values + merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust)); + merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal())); + merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded())); + + return merge; + } + + private static String instanceKeyExtractor(Instance i) { + return String.join("::", + kvKeyExtractor(i.getHostedby()), + 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 FieldKeyExtractor(Field 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 mergeORP(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust)); + merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust)); + merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust)); + + return merge; + } + + private static T mergeSoftware(T original, T enrich) { + int trust = compareTrust(original, enrich); + final T merge = mergeResult(original, enrich); + + merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust)); + merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust)); + merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust)); + merge + .setProgrammingLanguage( + chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust)); + + return merge; + } + + private static T mergeDataset(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merge = mergeResult(original, enrich); + + merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust)); + merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust)); + merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust)); + merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust)); + merge + .setLastmetadataupdate( + chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust)); + merge + .setMetadataversionnumber( + chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust)); + merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust)); + + return merge; + } + + public static T mergePublication(T original, T enrich) { + final int trust = compareTrust(original, enrich); + T merged = mergeResult(original, enrich); + + merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust)); + + return merged; + } + + private static T mergeOrganization(T left, T enrich) { + int trust = compareTrust(left, enrich); + T merged = mergeOafEntityFields(left, enrich, trust); + + merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust)); + merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust)); + merged + .setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust)); + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust)); + merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust)); + merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust)); + merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust)); + merged + .setEcresearchorganization( + chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust)); + merged + .setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust)); + merged + .setEcinternationalorganizationeurinterests( + chooseReference( + merged.getEcinternationalorganizationeurinterests(), + enrich.getEcinternationalorganizationeurinterests(), trust)); + merged + .setEcinternationalorganization( + chooseReference( + merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust)); + merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust)); + merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust)); + merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust)); + merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust)); + + return merged; + } + + public static T mergeProject(T original, T enrich) { + int trust = compareTrust(original, enrich); + T merged = mergeOafEntityFields(original, enrich, trust); + + merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust)); + merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust)); + merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust)); + merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust)); + merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust)); + merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust)); + merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust)); + merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust)); + merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust)); + merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust)); + merged + .setOamandatepublications( + chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust)); + merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust)); + merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust)); + merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust)); + merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust)); + merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust)); + merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust)); + merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust)); + merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust)); + merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust)); + merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust)); + merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust)); + merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust)); + merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust)); + + // missin in Project.merge + merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust)); + merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust)); + + // trust ?? + if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) { + merged.setH2020topiccode(enrich.getH2020topiccode()); + merged.setH2020topicdescription(enrich.getH2020topicdescription()); + } + + merged + .setH2020classification( + unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust)); + + return merged; + } + + /** + * Longest lists list. + * + * @param a the a + * @param b the b + * @return the list + */ + public static List> longestLists(List> a, List> b) { + if (a == null || b == null) + return a == null ? b : a; + + return a.size() >= b.size() ? a : b; + } + + /** + * This main method apply the enrichment of the instances + * + * @param toEnrichInstances the instances that could be enriched + * @param enrichmentInstances the enrichment instances + * @return list of instances possibly enriched + */ + private static List enrichInstances(final List toEnrichInstances, + final List enrichmentInstances) { + final List enrichmentResult = new ArrayList<>(); + + if (toEnrichInstances == null) { + return enrichmentResult; + } + if (enrichmentInstances == null) { + return enrichmentResult; + } + Map ri = toInstanceMap(enrichmentInstances); + + toEnrichInstances.forEach(i -> { + final List e = findEnrichmentsByPID(i.getPid(), ri); + if (e != null && e.size() > 0) { + e.forEach(enr -> applyEnrichment(i, enr)); + } else { + final List 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 toInstanceMap(final List ri) { + return ri + .stream() + .filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null) + .flatMap(i -> { + final List> result = new ArrayList<>(); + if (i.getPid() != null) + i + .getPid() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + if (i.getAlternateIdentifier() != null) + i + .getAlternateIdentifier() + .stream() + .filter(MergeUtils::validPid) + .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i))); + return result.stream(); + }) + .collect( + Collectors + .toMap( + Pair::getLeft, + Pair::getRight, + (a, b) -> a)); + } + + private static boolean isFromDelegatedAuthority(Result r) { + return Optional + .ofNullable(r.getInstance()) + .map( + instance -> instance + .stream() + .filter(i -> Objects.nonNull(i.getCollectedfrom())) + .map(i -> i.getCollectedfrom().getKey()) + .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId))) + .orElse(false); + } + + /** + * Valid pid boolean. + * + * @param p the p + * @return the boolean + */ + private static boolean validPid(final StructuredProperty p) { + return p.getValue() != null && p.getQualifier() != null && p.getQualifier().getClassid() != null; + } + + /** + * Normalize pid string. + * + * @param pid the pid + * @return the string + */ + private static String extractKeyFromPid(final StructuredProperty pid) { + if (pid == null) + return null; + final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid); + + return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue()); + } + + /** + * This utility method finds the list of enrichment instances + * that match one or more PIDs in the input list + * + * @param pids the list of PIDs + * @param enrichments the List of enrichment instances having the same pid + * @return the list + */ + private static List findEnrichmentsByPID(final List pids, + final Map enrichments) { + if (pids == null || enrichments == null) + return null; + return pids + .stream() + .map(MergeUtils::extractKeyFromPid) + .map(enrichments::get) + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } + + /** + * Is an enrichment boolean. + * + * @param e the e + * @return the boolean + */ + private static boolean isAnEnrichment(OafEntity e) { + return e.getDataInfo() != null && + e.getDataInfo().getProvenanceaction() != null + && ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid()); + } + + /** + * This method apply enrichment on a single instance + * The enrichment consists of replacing values on + * single attribute only if in the current instance is missing + * The only repeatable field enriched is measures + * + * @param merge the current instance + * @param enrichment the enrichment instance + */ + private static void applyEnrichment(final Instance merge, final Instance enrichment) { + if (merge == null || enrichment == null) + return; + + merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense())); + merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright())); + merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype())); + merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping())); + merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby())); + merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0)); + merge + .setDistributionlocation( + firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation())); + merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom())); + // pid and alternateId are used for matching + merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance())); + merge + .setProcessingchargeamount( + firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount())); + merge + .setProcessingchargecurrency( + firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency())); + merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed())); + merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0)); + merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext())); + } + + private static int compareTrust(Oaf a, Oaf b) { + String left = Optional + .ofNullable(a.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + String right = Optional + .ofNullable(b.getDataInfo()) + .map(DataInfo::getTrust) + .orElse("0.0"); + + return left.compareTo(right); + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java new file mode 100644 index 0000000000..443a496042 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java @@ -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; + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java new file mode 100644 index 0000000000..b215de4ff1 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java @@ -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 { + + @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; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java new file mode 100644 index 0000000000..0b8e5e3f15 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java @@ -0,0 +1,8 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import java.util.HashMap; +import java.util.HashSet; + +public class PidBlacklist extends HashMap> { +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java new file mode 100644 index 0000000000..ec108eb27c --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java @@ -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 getBlacklist(String pidType) { + return Optional + .ofNullable(getBlacklist().get(pidType)) + .orElse(new HashSet<>()); + } + + private PidBlacklistProvider() {} + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java new file mode 100644 index 0000000000..cc3aa3ef86 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java @@ -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 implements Comparator { + + 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); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java new file mode 100644 index 0000000000..6f3cfe30a1 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java @@ -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; + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java new file mode 100644 index 0000000000..d349b4b54c --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java @@ -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 { + + @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); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java new file mode 100644 index 0000000000..565ef89048 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java @@ -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 { + + @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; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java new file mode 100644 index 0000000000..822a588f4c --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java @@ -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 { + + @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 lCf = getCollectedFromIds(left); + HashSet 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 getCollectedFromIds(Result left) { + return Optional + .ofNullable(left.getCollectedfrom()) + .map( + cf -> cf + .stream() + .map(KeyValue::getKey) + .collect(Collectors.toCollection(HashSet::new))) + .orElse(new HashSet<>()); + } +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java new file mode 100644 index 0000000000..5c2f9f03ab --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java @@ -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 xxx = PidBlacklistProvider.getBlacklist("xxx"); + Assertions.assertNotNull(xxx); + Assertions.assertEquals(0, xxx.size()); + } +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java new file mode 100644 index 0000000000..2628a30fce --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java @@ -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); + } + +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java index ef35b50fb2..e79bef4245 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java @@ -5,11 +5,14 @@ import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.assertEquals; import java.io.IOException; +import java.lang.reflect.InvocationTargetException; import java.util.HashSet; import java.util.List; import java.util.stream.Collectors; -import 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.junit.jupiter.api.Test; @@ -17,16 +20,33 @@ import com.fasterxml.jackson.databind.DeserializationFeature; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.common.ModelSupport; public class MergeUtilsTest { private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Test + void testMergePubs_new() throws IOException { + Publication pt = read("publication_test.json", Publication.class); + Publication p1 = read("publication_test.json", Publication.class); + + assertEquals(1, pt.getCollectedfrom().size()); + assertEquals(ModelConstants.CROSSREF_ID, pt.getCollectedfrom().get(0).getKey()); + + Instance i = new Instance(); + i.setUrl(Lists.newArrayList("https://...")); + p1.getInstance().add(i); + + Publication ptp1 = MergeUtils.mergePublication(pt, p1); + + assertNotNull(ptp1.getInstance()); + assertEquals(2, ptp1.getInstance().size()); + + } + @Test void testMergePubs() throws IOException { Publication p1 = read("publication_1.json", Publication.class); @@ -45,7 +65,7 @@ public class MergeUtilsTest { assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID)); final Result p1d2 = MergeUtils.checkedMerge(p1, d2); - assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid()); + assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid()); assertTrue(p1d2 instanceof Publication); assertEquals(p1.getId(), p1d2.getId()); } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index 2bbc3bc3ea..50683dc816 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -178,8 +178,8 @@ class OafMapperUtilsTest { assertEquals( ModelConstants.DATASET_RESULTTYPE_CLASSID, - MergeUtils - .mergeResult(p2, d1) + ((Result) MergeUtils + .merge(p2, d1)) .getResulttype() .getClassid()); } diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json new file mode 100644 index 0000000000..a26b106ce9 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json @@ -0,0 +1,12 @@ 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By looking for a reduction in energy consumption, cities have favoured a compact planning development. Then reflection has broadened from the simple density to the wider, multi-dimensional concept of urban form. This controversy has led to a renewal of analysis in term of the costs of urban growth, notably by comparing the costs of \"compact\" and \"sprawled\" development. The idea is to compare the mobility costs of different urban forms. However, most often because of a lack of data, such studies are scarce. This paper suggests an innovative method to compute mobility costs at an infra-urban scale : The Spatialized Travel Account (STA). It is based on the CERTU's travel account methodology at a metropolitan scale. It puts forward an accurate estimate of the mobility costs for each transport mode (individual and public) and for each type of payer (households, firms, local authorities...). In order to test the relationships between mobility costs and urban form, we link the computed costs to morphological characteristics of infra-urban zones, taking in account sociodemographic characteristics of households." + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "Harvested", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "value": "L'interaction réciproque entre étalement urbain et usage de l'automobile a conduit la recherche à se focaliser sur le lien entre les densités urbaines et la mobilité. En cherchant à réduire leur consommation d'énergie pour les transports, et donc leurs émissions de Gaz à Effet de Serre, les villes ont alors cherché à planifier la \" ville compacte \", privilégiant notamment la reconstruction de la ville sur elle-même et la densification. Par la suite, la réflexion s'est élargie de la simple densité à la notion de forme urbaine et à toutes ses dimensions. Cette controverse devait conduire à un renouveau des analyses en termes de coûts de la croissance urbaine : le débat reste vif, encore aujourd'hui, sur les coûts comparés de la ville étalée et de la ville compacte. Plus largement, il s'agit d'explorer les coûts des différentes formes urbaines en termes de mobilité. Malgré cela, généralement pour des raisons de disponibilité de données, les études sur le sujet restent extrêmement rares. Cet article propose un outil novateur pour mesurer les coûts de la mobilité à l'échelle intraurbaine : le Compte Déplacements Territorialisé (CDT). Il s'inspire de la méthode développée par le CERTU pour l'établissement des Comptes Déplacements Voyageurs à l'échelle métropolitaine. Le CDT propose, pour chacune des zones de l'agglomération, une estimation précise de l'ensemble des coûts liés aux déplacements de personnes, ventilés par mode de transport (individuels et collectifs) et par type de financeurs (ménages, entreprises, collectivités territoriales, etc.). Nous proposons une application de cette méthode à la controverse sur le lien entre forme urbaine et coûts de la mobilité. Les coûts sont reliés aux caractéristiques morphologiques des zones (en termes de densité et de diversité, notamment), en prenant soin de contrôler les facteurs socio-économiques qui influent traditionnellement sur les comportements de mobilité (taille du ménage, revenu, etc.)." + } + ], + "eoscifguidelines": [], + "externalReference": [], + "extraInfo": [], + "format": [ + { + "dataInfo": { + "deletedbyinference": false, + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:repository", + "classname": "Harvested", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "value": "application/pdf" + } + ], + "fulltext": [], + "id": "50|06cdd3ff4700::4826ac62a11a957fe332e2c291dcfcca", + "instance": [ + { + "accessright": { + "classid": "OPEN", + "classname": "Open Access", + "schemeid": "dnet:access_modes", + "schemename": "dnet:access_modes" + }, + "alternateIdentifier": [ + { + 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The spatialized travel account tool and its application to the Bordeaux metropolitan area" + } + ] +} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json new file mode 100644 index 0000000000..5323ac8bd6 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn1.json @@ -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" + } + ] +} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publications.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publications.json new file mode 100644 index 0000000000..ef0cc58198 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publications.json @@ -0,0 +1,12 @@ +{"author":[{"fullname":"Levande, Paul","name":"Paul","pid":[],"rank":1,"surname":"Levande"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::6824b298c96ba906a3e6a70593affbf5","value":"Episciences"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Coordination Episciences iam"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2011-01-01"},"dateofcollection":"2021-11-09T19:00:42.081Z","dateoftransformation":"2021-11-09T19:36:08.397Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"We examine the $q=1$ and $t=0$ special cases of the parking functions conjecture. The parking functions conjecture states that the Hilbert series for the space of diagonal harmonics is equal to the bivariate generating function of $area$ and $dinv$ over the set of parking functions. Haglund recently proved that the Hilbert series for the space of diagonal harmonics is equal to a bivariate generating function over the set of Tesler matrices–upper-triangular matrices with every hook sum equal to one. We give a combinatorial interpretation of the Haglund generating function at $q=1$ and prove the corresponding case of the parking functions conjecture (first proven by Garsia and Haiman). We also discuss a possible proof of the $t = 0$ case consistent with this combinatorial interpretation. We conclude by briefly discussing possible refinements of the parking functions conjecture arising from this research and point of view. $\\textbf{Note added in proof}$: We have since found such a proof of the $t = 0$ case and conjectured more detailed refinements. This research will most likely be presented in full in a forthcoming article."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"On examine les cas spéciaux $q=1$ et $t=0$ de la conjecture des fonctions de stationnement. Cette conjecture déclare que la série de Hilbert pour l'espace des harmoniques diagonaux est égale à la fonction génératrice bivariée (paramètres $area$ et $dinv$) sur l'ensemble des fonctions de stationnement. Haglund a prouvé récemment que la série de Hilbert pour l'espace des harmoniques diagonaux est égale à une fonction génératrice bivariée sur l'ensemble des matrices de Tesler triangulaires supérieures dont la somme de chaque équerre vaut un. On donne une interprétation combinatoire de la fonction génératrice de Haglund pour $q=1$ et on prouve le cas correspondant de la conjecture dans le cas des fonctions de stationnement (prouvé d'abord par Garsia et Haiman). On discute aussi d'une preuve possible du cas $t=0$, cohérente avec cette interprétation combinatoire. On conclut en discutant brièvement les raffinements possibles de la conjecture des fonctions de stationnement de ce point de vue. $\\textbf{Note ajoutée sur épreuve}$: j'ai trouvé depuis cet article une preuve du cas $t=0$ et conjecturé des raffinements possibles. 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Another objective was to find new means to remove nitrogenous compounds from hot gasification gas. In fluidised-bed and fixed-bed types of gasifier NH3 is the predominant nitrogenous compound in addition to N2. In thermodynamic equilibrium the NH3 content of gasification gas is low. The equilibrium content ranges from 1 to 350 ppms depending on the temperature, pressure and stoichiometric ratio. The highest equilibrium content is usually encountered at high pressure. The real NH3 content of gasifier product gas is usually at least an order of magnitude higher. The fraction of fuel nitrogen that is converted to NH3 in gasification is affected by several factors. During pyrolysis young biomass fuels tend to release part of the fuel nitrogen directly as NH3, whereas coals seem to release fuel nitrogen primarily from structures that favour HCN formation. A low heating rate and factors that increase the extent of secondary reactions of gases and char during pyrolysis also increase the conversion of HCN to NH3. In fluidised-bed (and fixed-bed) gasifiers the conditions seem to favour NH3 formation but in entrained-bed gasifiers a high heating rate may promote HCN formation. Factors affecting the release of char nitrogen in gasifiers are poorly known. In this work, a statistical model was developed, which can predict the conversion of fuel nitrogen to NH3 in a laboratory-scale fluidised-bed gasifier and a larger entrained-bed gasifier. It was found that the formation of NH3 was mostly dependent on the freeboard temperature of the gasifier, and on the iron, calcium, ash and volatile matter content of fuel. Increasing the iron content of the fuel resulted in a strong decreasing effect in the NH3 formation in the fluidised-bed gasifier, but it had a smaller effect in the entrained-bed gasifier. The decomposition rate of NH3 may be increased by adding or creating suitable reactive gas species into the hot gas. In selective catalytic oxidation oxidisers like O2, NO or a mixture of these are added to the gasification gas before flowing the gas through the catalyst bed. Aluminium oxide and aluminium silicate catalysts proved to be the most effective of the materials tested in promoting NH3 decomposition in the presence of oxidisers. The temperature of optimum NH3 reduction was tightly dependent on the composition of the oxidiser used. If NO was allowed to convert to NO2 in the oxidiser mixture before feeding the oxidiser to the reactor, the best conversion was achieved at temperatures below 500 °C. If pure NO and O2 were used, the best conversion was achieved at 500 - 600 °C. An important finding in this work was the ability of aluminium oxide to catalyse the reaction between added O2 and NH3. No nitrogen oxides were formed during this type of NH3 oxidation on the aluminium oxide catalyst. The reaction product was probably N2. When O2/NH3 ratio was 4 in the experiments with synthetic gasification gas, 75% of the NH3 was decomposed in the aluminium oxide bed at the temperature range of 550 - 700 °C. The development of a gas cleaning process based on these results of selective catalytic oxidation still leaves several questions unanswered. The most important questions are connected with optimising the process, with the effect of gas impurities on the reactions and with the alternatives of oxidising HCN to N2 simultaneously with NH3."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::ad8d151a2ef39d827b1b591ec856d886","instance":[{"accessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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