250 lines
8.6 KiB
Java
250 lines
8.6 KiB
Java
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package eu.dnetlib.dhp.oa.provision;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
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import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
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import scala.Tuple2;
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/**
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* CreateRelatedEntitiesJob: (phase 1): prepare tuples [relation - target entity] (R - T): for each entity type E_i map E_i as RelatedEntity
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* T_i to simplify the model and extracting only the necessary information join (R.target = T_i.id) save the tuples (R_i, T_i)
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*/
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public class CreateRelatedEntitiesJob_phase1 {
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private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase1.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final String jsonConfiguration = IOUtils
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.toString(
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Objects
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.requireNonNull(
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CreateRelatedEntitiesJob_phase1.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json")));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputRelationsPath = parser.get("inputRelationsPath");
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log.info("inputRelationsPath: {}", inputRelationsPath);
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final String inputEntityPath = parser.get("inputEntityPath");
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log.info("inputEntityPath: {}", inputEntityPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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@SuppressWarnings("unchecked")
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final Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
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final SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, outputPath);
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joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
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});
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}
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private static <E extends OafEntity> void joinRelationEntity(
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final SparkSession spark,
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final String inputRelationsPath,
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final String inputEntityPath,
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final Class<E> clazz,
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final String outputPath) {
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final Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
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.map(
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(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
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r),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)))
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.cache();
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final Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
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.filter("dataInfo.invisible == false")
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.map(
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(MapFunction<E, Tuple2<String, RelatedEntity>>) e -> new Tuple2<>(e.getId(), asRelatedEntity(e, clazz)),
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Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class)))
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.cache();
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relsByTarget
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.joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner")
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.map(
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(MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, RelatedEntity>>, RelatedEntityWrapper>) t -> new RelatedEntityWrapper(
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t._1()._2(), t._2()._2()),
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Encoders.kryo(RelatedEntityWrapper.class))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(outputPath);
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}
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private static <E extends OafEntity> Dataset<E> readPathEntity(
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final SparkSession spark,
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final String inputEntityPath,
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final Class<E> entityClazz) {
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log.info("Reading Graph table from: {}", inputEntityPath);
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return spark
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.read()
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.textFile(inputEntityPath)
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.map(
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(MapFunction<String, E>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz));
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}
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public static <E extends OafEntity> RelatedEntity asRelatedEntity(final E entity, final Class<E> clazz) {
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final RelatedEntity re = new RelatedEntity();
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re.setId(entity.getId());
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re.setType(EntityType.fromClass(clazz).name());
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// TODO move the max number of PIDs to eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits
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if (Objects.nonNull(entity.getPid())) {
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re.setPid(entity.getPid().stream().limit(400).collect(Collectors.toList()));
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}
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re.setCollectedfrom(entity.getCollectedfrom());
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switch (EntityType.fromClass(clazz)) {
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case publication:
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case dataset:
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case otherresearchproduct:
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case software:
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final Result result = (Result) entity;
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if (result.getTitle() != null && !result.getTitle().isEmpty()) {
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final StructuredProperty title = result.getTitle().stream().findFirst().get();
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title.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH));
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re.setTitle(title);
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}
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re.setDateofacceptance(getValue(result.getDateofacceptance()));
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re.setPublisher(getValue(result.getPublisher()));
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re.setResulttype(result.getResulttype());
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if (Objects.nonNull(result.getInstance())) {
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re
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.setInstances(
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result
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.getInstance()
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.stream()
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.filter(Objects::nonNull)
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.limit(ModelHardLimits.MAX_INSTANCES)
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.collect(Collectors.toList()));
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}
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// TODO still to be mapped
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// re.setCodeRepositoryUrl(j.read("$.coderepositoryurl"));
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break;
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case datasource:
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final Datasource d = (Datasource) entity;
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re.setOfficialname(getValue(d.getOfficialname()));
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re.setWebsiteurl(getValue(d.getWebsiteurl()));
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re.setDatasourcetype(d.getDatasourcetype());
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re.setDatasourcetypeui(d.getDatasourcetypeui());
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re.setOpenairecompatibility(d.getOpenairecompatibility());
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break;
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case organization:
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final Organization o = (Organization) entity;
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re.setLegalname(getValue(o.getLegalname()));
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re.setLegalshortname(getValue(o.getLegalshortname()));
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re.setCountry(o.getCountry());
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re.setWebsiteurl(getValue(o.getWebsiteurl()));
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break;
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case project:
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final Project p = (Project) entity;
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re.setProjectTitle(getValue(p.getTitle()));
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re.setCode(getValue(p.getCode()));
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re.setAcronym(getValue(p.getAcronym()));
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re.setContracttype(p.getContracttype());
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final List<Field<String>> f = p.getFundingtree();
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if (!f.isEmpty()) {
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re.setFundingtree(f.stream().map(Field::getValue).collect(Collectors.toList()));
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}
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break;
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}
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return re;
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}
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private static String getValue(final Field<String> field) {
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return getFieldValueWithDefault(field, "");
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}
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private static <T> T getFieldValueWithDefault(final Field<T> f, final T defaultValue) {
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return Optional
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.ofNullable(f)
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.filter(Objects::nonNull)
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.map(Field::getValue)
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.orElse(defaultValue);
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}
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/**
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* Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
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* file
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*
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* @param spark the SparkSession
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* @param relationPath the path storing the relation objects
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* @return the Dataset<SortableRelation> containing all the relationships
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*/
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private static Dataset<Relation> readPathRelation(
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final SparkSession spark,
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final String relationPath) {
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log.info("Reading relations from: {}", relationPath);
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return spark.read().load(relationPath).as(Encoders.bean(Relation.class));
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}
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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