197 lines
6.2 KiB
Java
197 lines
6.2 KiB
Java
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package eu.dnetlib.dhp.actionmanager.transformativeagreement;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.*;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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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.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Country;
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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.utils.*;
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import scala.Tuple2;
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public class CreateActionSetSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63";
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private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement";
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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CreateActionSetSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json"))));
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parser.parseArgument(args);
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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 inputPath = parser.get("inputPath");
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log.info("inputPath {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> createActionSet(spark, inputPath, outputPath));
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}
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private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
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JavaRDD<AtomicAction> relations = spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
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.readValue(value, TransformativeAgreementModel.class),
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Encoders.bean(TransformativeAgreementModel.class))
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.flatMap(
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(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
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value)
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.iterator(),
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Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) Objects::nonNull)
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p));
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spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
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.readValue(value, TransformativeAgreementModel.class),
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Encoders.bean(TransformativeAgreementModel.class))
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.map(
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(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
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value),
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Encoders.bean(Result.class))
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.filter((FilterFunction<Result>) r -> r != null)
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.union(relations)
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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}
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private static Result createResult(TransformativeAgreementModel value) {
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Result r = new Result();
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r
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.setId(
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"50|doi_________::"
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())));
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r.setTransformativeAgreement(value.getAgreement());
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Country country = new Country();
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country.setClassid(value.getCountry());
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country.setClassname(value.getCountry());
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country
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false, ModelConstants.SYSIMPORT_ACTIONSET, false, false,
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OafMapperUtils
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.qualifier(
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"openapc::transformativeagreement",
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"Harvested from Trnasformative Agreement file from OpenAPC",
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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"0.9"));
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country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
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country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
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r.setCountry(Arrays.asList(country));
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return r;
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}
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private static List<Relation> createRelation(TransformativeAgreementModel value) {
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List<Relation> relationList = new ArrayList<>();
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if (value.getAgreement().startsWith("IReL")) {
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String paper;
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paper = "50|doi_________::"
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+ IdentifierFactory
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.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()));
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relationList
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.add(
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getRelation(
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paper,
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IREL_PROJECT, ModelConstants.IS_PRODUCED_BY));
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relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES));
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}
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return relationList;
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}
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public static Relation getRelation(
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String source,
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String target,
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String relClass) {
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return OafMapperUtils
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.getRelation(
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source,
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target,
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ModelConstants.RESULT_PROJECT,
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ModelConstants.OUTCOME,
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relClass,
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Arrays
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.asList(
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OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)),
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OafMapperUtils
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.dataInfo(
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false, null, false, false,
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OafMapperUtils
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.qualifier(
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TRANSFORMATIVE_AGREEMENT, "Transformative Agreement",
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ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
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"0.9"),
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null);
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}
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}
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