forked from D-Net/dnet-hadoop
refactoring
This commit is contained in:
parent
08227cfcbd
commit
fd5d792e35
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@ -121,9 +121,9 @@ public class SparkCountryPropagationJob2 {
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.map(r -> new Tuple2<>(r.getId(), r),
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.map(r -> new Tuple2<>(r.getId(), r),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(resultClazz)));
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Encoders.tuple(Encoders.STRING(), Encoders.bean(resultClazz)));
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Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
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// Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
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pu),
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// pu),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
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// Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
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Dataset<R> new_table = result_pair
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Dataset<R> new_table = result_pair
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.joinWith(potentialUpdates, result_pair.col("_1").equalTo(potentialUpdates.col("resultId")), "left_outer")
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.joinWith(potentialUpdates, result_pair.col("_1").equalTo(potentialUpdates.col("resultId")), "left_outer")
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@ -0,0 +1,88 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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 org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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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.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareResultOrcidAssociation {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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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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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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prepareInfo(spark, inputPath, outputPath, resultClazz, resultType);
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});
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}
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private static <R extends Result> void prepareInfo(SparkSession spark, String inputPath,
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String outputPath, Class<R> resultClazz,
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String resultType) {
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//read the relation table and the table related to the result it is using
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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relation.createOrReplaceTempView("relation");
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log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
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Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
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}
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}
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@ -0,0 +1,119 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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 org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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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 java.util.Arrays;
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import java.util.List;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareResultOrcidAssociationStep1 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep1.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(SparkOrcidToResultFromSemRelJob3.class
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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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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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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrel").split(";"));
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log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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prepareInfo(spark, inputPath, outputPath, resultClazz, resultType, allowedsemrel);
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});
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}
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private static <R extends Result> void prepareInfo(SparkSession spark, String inputPath,
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String outputPath, Class<R> resultClazz,
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String resultType,
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List<String> allowedsemrel) {
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//read the relation table and the table related to the result it is using
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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relation.createOrReplaceTempView("relation");
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log.info("Reading Graph table from: {}", inputPath + "/" + resultType);
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Dataset<R> result = readPathEntity(spark, inputPath + "/" + resultType, resultClazz);
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result.createOrReplaceTempView("result");
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getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath);
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}
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private static void getPossibleResultOrcidAssociation(SparkSession spark, List<String> allowedsemrel, String outputPath){
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String query = " select target resultId, author authorList" +
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" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
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" from ( " +
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" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
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" from result " +
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" lateral view explode (author) a as MyT " +
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" lateral view explode (MyT.pid) p as MyP " +
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" where MyP.qualifier.classid = 'ORCID') tmp " +
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" group by id) r_t " +
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" join (" +
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" select source, target " +
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" from relation " +
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" where datainfo.deletedbyinference = false " +
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getConstraintList(" relclass = '" ,allowedsemrel) + ") rel_rel " +
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" on source = id";
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spark.sql(query)
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.as(Encoders.bean(ResultOrcidList.class))
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.toJSON()
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.write()
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.mode(SaveMode.Append)
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.option("compression","gzip")
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.text(outputPath)
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;
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}
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}
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@ -0,0 +1,26 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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public class ResultWithOrcid implements Serializable {
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String id;
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List<AutoritativeAuthor> authorList = new ArrayList<>();
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public String getId() {
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return id;
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}
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public void setId(String id) {
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this.id = id;
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}
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public List<AutoritativeAuthor> getAuthorList() {
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return authorList;
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}
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public void setAuthorList(List<AutoritativeAuthor> authorList) {
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this.authorList = authorList;
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}
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}
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@ -1,4 +0,0 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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public class ResultWithOrcid {
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}
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@ -0,0 +1,398 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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.schema.oaf.*;
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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.hadoop.fs.FileSystem;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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public class SparkOrcidToResultFromSemRelJob2 {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkOrcidToResultFromSemRelJob2.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/orcidtoresult";
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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boolean writeUpdate = TRUE.equals(parser.get("writeUpdate"));
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boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
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org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
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org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
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org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
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relation.createOrReplaceTempView("relation");
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String query = "Select source, target " +
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"from relation " +
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"where datainfo.deletedbyinference = false " + getConstraintList(" relclass = '" , allowedsemrel);
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org.apache.spark.sql.Dataset<Row> result_result = spark.sql(query);
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publication.createOrReplaceTempView("publication");
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org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid = getResultWithOrcid("publication", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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dataset.createOrReplaceTempView("dataset");
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org.apache.spark.sql.Dataset<ResultWithOrcid> dats_with_orcid = getResultWithOrcid("dataset", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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other.createOrReplaceTempView("orp");
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org.apache.spark.sql.Dataset<ResultWithOrcid> orp_with_orcid = getResultWithOrcid("orp", spark)
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||||||
|
.as(Encoders.bean(ResultWithOrcid.class));
|
||||||
|
|
||||||
|
dataset.createOrReplaceTempView("software");
|
||||||
|
org.apache.spark.sql.Dataset<ResultWithOrcid> software_with_orcid = getResultWithOrcid("software", spark)
|
||||||
|
.as(Encoders.bean(ResultWithOrcid.class));
|
||||||
|
//get the results having at least one author pid we are interested in
|
||||||
|
|
||||||
|
//target of the relation from at least one source with orcid.
|
||||||
|
//the set of authors contains all those that have orcid and are related to target
|
||||||
|
//from any source with allowed semantic relationship
|
||||||
|
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_pubs = getTargetAutoritativeAuthorList(pubs_with_orcid);
|
||||||
|
|
||||||
|
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_dats = getTargetAutoritativeAuthorList(dats_with_orcid);
|
||||||
|
|
||||||
|
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_orp = getTargetAutoritativeAuthorList(orp_with_orcid);
|
||||||
|
|
||||||
|
JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_sw = getTargetAutoritativeAuthorList(software_with_orcid);
|
||||||
|
|
||||||
|
if(writeUpdate){
|
||||||
|
target_authorlist_from_dats.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||||
|
.saveAsTextFile(outputPath + "/" + "update_dats");
|
||||||
|
target_authorlist_from_pubs.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||||
|
.saveAsTextFile(outputPath + "/" + "update_pubs");
|
||||||
|
target_authorlist_from_orp.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||||
|
.saveAsTextFile(outputPath + "/" + "update_orp");
|
||||||
|
target_authorlist_from_sw.map(r -> new ObjectMapper().writeValueAsString(r))
|
||||||
|
.saveAsTextFile(outputPath + "/" + "update_sw");
|
||||||
|
}
|
||||||
|
|
||||||
|
if(saveGraph){
|
||||||
|
sc.textFile(inputPath + "/publication")
|
||||||
|
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class))
|
||||||
|
.mapToPair(p -> new Tuple2<>(p.getId(),p))
|
||||||
|
.leftOuterJoin(target_authorlist_from_pubs)
|
||||||
|
.map(c -> {
|
||||||
|
Result r = c._2()._1();
|
||||||
|
if(!c._2()._2().isPresent()){
|
||||||
|
return r;
|
||||||
|
}
|
||||||
|
List<eu.dnetlib.dhp.schema.oaf.Author> toenrich_author = r.getAuthor();
|
||||||
|
List<AutoritativeAuthor> autoritativeAuthors = c._2()._2().get();
|
||||||
|
for(eu.dnetlib.dhp.schema.oaf.Author author: toenrich_author){
|
||||||
|
if (!containsAllowedPid(author)){
|
||||||
|
enrichAuthor(author, autoritativeAuthors);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return r;
|
||||||
|
});
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
|
||||||
|
for (AutoritativeAuthor aa: au){
|
||||||
|
if(enrichAuthor(aa, a)){
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
// private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
|
||||||
|
// return pubs_with_orcid
|
||||||
|
// .toJavaRDD()
|
||||||
|
// .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
|
||||||
|
// .join(result_result.toJavaRDD().mapToPair(rel -> new Tuple2<>(rel.getString(0), rel.getString(1))))
|
||||||
|
// .mapToPair(c -> new Tuple2<>(c._2._2(), c._2()._1()))
|
||||||
|
// .reduceByKey((a, b) -> {
|
||||||
|
// if(a == null){
|
||||||
|
// return b;
|
||||||
|
// }
|
||||||
|
// if(b==null){
|
||||||
|
// return a;
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// Set<String> authSet = new HashSet<>();
|
||||||
|
// a.stream().forEach(au -> authSet.add(au.getOrcid()));
|
||||||
|
//
|
||||||
|
// b.stream().forEach(au -> {
|
||||||
|
// if (!authSet.contains(au.getOrcid())) {
|
||||||
|
// a.add(au);
|
||||||
|
// }
|
||||||
|
// }
|
||||||
|
// );
|
||||||
|
// return a;
|
||||||
|
// });
|
||||||
|
// }
|
||||||
|
private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList( org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
|
||||||
|
return pubs_with_orcid
|
||||||
|
.toJavaRDD()
|
||||||
|
.mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
|
||||||
|
.reduceByKey((a, b) -> {
|
||||||
|
if(a == null){
|
||||||
|
return b;
|
||||||
|
}
|
||||||
|
if(b==null){
|
||||||
|
return a;
|
||||||
|
}
|
||||||
|
Set<String> authSet = new HashSet<>();
|
||||||
|
a.stream().forEach(au -> authSet.add(au.getOrcid()));
|
||||||
|
|
||||||
|
b.stream().forEach(au -> {
|
||||||
|
if (!authSet.contains(au.getOrcid())) {
|
||||||
|
a.add(au);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
);
|
||||||
|
return a;
|
||||||
|
});
|
||||||
|
}
|
||||||
|
|
||||||
|
private static org.apache.spark.sql.Dataset<Row> getResultWithOrcid(String table, SparkSession spark){
|
||||||
|
String query = " select target, author " +
|
||||||
|
" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
|
||||||
|
" from ( " +
|
||||||
|
" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
|
||||||
|
" from " + table +
|
||||||
|
" lateral view explode (author) a as MyT " +
|
||||||
|
" lateral view explode (MyT.pid) p as MyP " +
|
||||||
|
" where MyP.qualifier.classid = 'ORCID') tmp " +
|
||||||
|
" group by id) r_t " +
|
||||||
|
" join (" +
|
||||||
|
" select source, target " +
|
||||||
|
" from relation " +
|
||||||
|
" where datainfo.deletedbyinference = false and (relclass = 'isSupplementedBy' or relclass = 'isSupplementTo') rel_rel " +
|
||||||
|
" on source = id";
|
||||||
|
|
||||||
|
return spark.sql(query);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
|
||||||
|
boolean toaddpid = false;
|
||||||
|
|
||||||
|
if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
|
||||||
|
if (StringUtils.isNoneEmpty(author.getSurname())) {
|
||||||
|
if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
|
||||||
|
|
||||||
|
//have the same surname. Check the name
|
||||||
|
if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
|
||||||
|
if (StringUtils.isNoneEmpty(author.getName())) {
|
||||||
|
if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
|
||||||
|
toaddpid = true;
|
||||||
|
}
|
||||||
|
//they could be differently written (i.e. only the initials of the name in one of the two
|
||||||
|
if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
|
||||||
|
toaddpid = true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (toaddpid){
|
||||||
|
StructuredProperty pid = new StructuredProperty();
|
||||||
|
String aa_pid = autoritative_author.getOrcid();
|
||||||
|
pid.setValue(aa_pid);
|
||||||
|
pid.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID ));
|
||||||
|
pid.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
|
||||||
|
if(author.getPid() == null){
|
||||||
|
author.setPid(Arrays.asList(pid));
|
||||||
|
}else{
|
||||||
|
author.getPid().add(pid);
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
return toaddpid;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
// private static List<Author> enrichAuthors(List<Author> autoritative_authors, List<Author> to_enrich_authors, boolean filter){
|
||||||
|
//// List<Author> autoritative_authors = p._2()._2().get().getAuthors();
|
||||||
|
//// List<Author> to_enrich_authors = r.getAuthor();
|
||||||
|
//
|
||||||
|
// return to_enrich_authors
|
||||||
|
// .stream()
|
||||||
|
// .map(a -> {
|
||||||
|
// if (filter) {
|
||||||
|
// if (containsAllowedPid(a)) {
|
||||||
|
// return a;
|
||||||
|
// }
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// List<Author> lst = autoritative_authors.stream()
|
||||||
|
// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||||
|
// if (lst.size() == 0) {
|
||||||
|
// return a;
|
||||||
|
// }
|
||||||
|
// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||||
|
//
|
||||||
|
// }).collect(Collectors.toList());
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// private static void writeResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
|
||||||
|
// String outputPath, String type) {
|
||||||
|
//
|
||||||
|
// results.join(toupdateresult)
|
||||||
|
// .map(p -> {
|
||||||
|
// Result r = p._2()._1();
|
||||||
|
//
|
||||||
|
// List<Author> autoritative_authors = p._2()._2().getAuthors();
|
||||||
|
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
||||||
|
//
|
||||||
|
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, false));
|
||||||
|
//// .stream()
|
||||||
|
//// .map(a -> {
|
||||||
|
//// if(filter) {
|
||||||
|
//// if (containsAllowedPid(a)) {
|
||||||
|
//// return a;
|
||||||
|
//// }
|
||||||
|
//// }
|
||||||
|
////
|
||||||
|
//// List<Author> lst = autoritative_authors.stream()
|
||||||
|
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||||
|
//// if(lst.size() == 0){
|
||||||
|
//// return a;
|
||||||
|
//// }
|
||||||
|
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||||
|
////
|
||||||
|
//// }).collect(Collectors.toList()));
|
||||||
|
//
|
||||||
|
// return r;
|
||||||
|
// })
|
||||||
|
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
||||||
|
// .saveAsTextFile(outputPath + "/" + type + "_update");
|
||||||
|
// }
|
||||||
|
|
||||||
|
|
||||||
|
// private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
|
||||||
|
// String outputPath, String type) {
|
||||||
|
// results.leftOuterJoin(toupdateresult)
|
||||||
|
// .map(p -> {
|
||||||
|
// Result r = p._2()._1();
|
||||||
|
// if (p._2()._2().isPresent()){
|
||||||
|
// List<AutoritativeAuthor> autoritative_authors = p._2()._2().get().getAuthors();
|
||||||
|
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
||||||
|
//
|
||||||
|
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, true));
|
||||||
|
//// .stream()
|
||||||
|
//// .map(a -> {
|
||||||
|
//// if(filter) {
|
||||||
|
//// if (containsAllowedPid(a)) {
|
||||||
|
//// return a;
|
||||||
|
//// }
|
||||||
|
//// }
|
||||||
|
////
|
||||||
|
//// List<Author> lst = autoritative_authors.stream()
|
||||||
|
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||||||
|
//// if(lst.size() == 0){
|
||||||
|
//// return a;
|
||||||
|
//// }
|
||||||
|
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||||||
|
////
|
||||||
|
//// }).collect(Collectors.toList()));
|
||||||
|
// }
|
||||||
|
// return r;
|
||||||
|
// })
|
||||||
|
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
||||||
|
// .saveAsTextFile(outputPath+"/"+type);
|
||||||
|
// }
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a) {
|
||||||
|
for (StructuredProperty pid : a.getPid()) {
|
||||||
|
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
|
||||||
|
ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
|
||||||
|
boolean updated = false;
|
||||||
|
|
||||||
|
for (FieldTypeProtos.Author a: author_list){
|
||||||
|
FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
|
||||||
|
if(author != null){
|
||||||
|
updated = true;
|
||||||
|
metadataBuilder.addAuthor(author);
|
||||||
|
}else{
|
||||||
|
metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if(updated)
|
||||||
|
return metadataBuilder;
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
|
||||||
|
if(containsOrcid(a.getPidList()))
|
||||||
|
return null;
|
||||||
|
for(FieldTypeProtos.Author autoritative_author : author_list) {
|
||||||
|
if (equals(autoritative_author, a)) {
|
||||||
|
if(!containsOrcid(a.getPidList()))
|
||||||
|
return update(a, autoritative_author);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return null;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
|
||||||
|
if(pidList == null)
|
||||||
|
return false;
|
||||||
|
return pidList
|
||||||
|
.stream()
|
||||||
|
.filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
|
||||||
|
.collect(Collectors.toList()).size() > 0;
|
||||||
|
}
|
||||||
|
*/
|
||||||
|
|
@ -1,18 +0,0 @@
|
||||||
<configuration>
|
|
||||||
<property>
|
|
||||||
<name>jobTracker</name>
|
|
||||||
<value>yarnRM</value>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>nameNode</name>
|
|
||||||
<value>hdfs://nameservice1</value>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>oozie.use.system.libpath</name>
|
|
||||||
<value>true</value>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>oozie.action.sharelib.for.spark</name>
|
|
||||||
<value>spark2</value>
|
|
||||||
</property>
|
|
||||||
</configuration>
|
|
||||||
|
|
@ -1,55 +0,0 @@
|
||||||
<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
|
|
||||||
<parameters>
|
|
||||||
<property>
|
|
||||||
<name>sourcePath</name>
|
|
||||||
<description>the source path</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>allowedsemrels</name>
|
|
||||||
<description>the semantic relationships allowed for propagation</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>sparkDriverMemory</name>
|
|
||||||
<description>memory for driver process</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>sparkExecutorMemory</name>
|
|
||||||
<description>memory for individual executor</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>sparkExecutorCores</name>
|
|
||||||
<description>number of cores used by single executor</description>
|
|
||||||
</property>
|
|
||||||
</parameters>
|
|
||||||
|
|
||||||
<start to="OrcidToResultFromSemRelPropagation"/>
|
|
||||||
|
|
||||||
<kill name="Kill">
|
|
||||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
|
||||||
</kill>
|
|
||||||
|
|
||||||
<action name="OrcidToResultFromSemRelPropagation">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<master>yarn-cluster</master>
|
|
||||||
<mode>cluster</mode>
|
|
||||||
<name>AffiliatioPropagation</name>
|
|
||||||
<class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>
|
|
||||||
<jar>dhp-propagation-${projectVersion}.jar</jar>
|
|
||||||
<spark-opts>--executor-memory ${sparkExecutorMemory}
|
|
||||||
--executor-cores ${sparkExecutorCores}
|
|
||||||
--driver-memory=${sparkDriverMemory}
|
|
||||||
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
|
|
||||||
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
|
|
||||||
</spark-opts>
|
|
||||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
|
||||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
|
||||||
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
|
|
||||||
</spark>
|
|
||||||
<ok to="End"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<end name="End"/>
|
|
||||||
</workflow-app>
|
|
||||||
|
|
@ -16,5 +16,17 @@
|
||||||
"paramLongName":"allowedsemrels",
|
"paramLongName":"allowedsemrels",
|
||||||
"paramDescription": "the allowed sematinc relations for propagation",
|
"paramDescription": "the allowed sematinc relations for propagation",
|
||||||
"paramRequired": true
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"wu",
|
||||||
|
"paramLongName":"writeUpdate",
|
||||||
|
"paramDescription": "true if the update must be writte. No double check if information is already present",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"sg",
|
||||||
|
"paramLongName":"saveGraph",
|
||||||
|
"paramDescription": "true if the new version of the graph must be saved",
|
||||||
|
"paramRequired": true
|
||||||
}
|
}
|
||||||
]
|
]
|
||||||
|
|
@ -0,0 +1,32 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName":"mt",
|
||||||
|
"paramLongName":"master",
|
||||||
|
"paramDescription": "should be local or yarn",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"s",
|
||||||
|
"paramLongName":"sourcePath",
|
||||||
|
"paramDescription": "the path of the sequencial file to read",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"as",
|
||||||
|
"paramLongName":"allowedsemrels",
|
||||||
|
"paramDescription": "the allowed sematinc relations for propagation",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"wu",
|
||||||
|
"paramLongName":"writeUpdate",
|
||||||
|
"paramDescription": "true if the update must be writte. No double check if information is already present",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"sg",
|
||||||
|
"paramLongName":"saveGraph",
|
||||||
|
"paramDescription": "true if the new version of the graph must be saved",
|
||||||
|
"paramRequired": true
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,38 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName":"s",
|
||||||
|
"paramLongName":"sourcePath",
|
||||||
|
"paramDescription": "the path of the sequencial file to read",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"as",
|
||||||
|
"paramLongName":"allowedsemrels",
|
||||||
|
"paramDescription": "the allowed sematinc relations for propagation",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"h",
|
||||||
|
"paramLongName":"hive_metastore_uris",
|
||||||
|
"paramDescription": "the hive metastore uris",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "out",
|
||||||
|
"paramLongName": "outputPath",
|
||||||
|
"paramDescription": "the path used to store temporary output files",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "ssm",
|
||||||
|
"paramLongName": "isSparkSessionManaged",
|
||||||
|
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName":"tn",
|
||||||
|
"paramLongName":"resultTableName",
|
||||||
|
"paramDescription": "the name of the result table we are currently working on",
|
||||||
|
"paramRequired": true
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,54 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>spark2</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<value>/user/spark/spark2ApplicationHistory</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorNumber</name>
|
||||||
|
<value>4</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<value>15G</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<value>6G</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<value>1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2MaxExecutors</name>
|
||||||
|
<value>50</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,71 @@
|
||||||
|
<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>the source path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>allowedsemrels</name>
|
||||||
|
<description>the semantic relationships allowed for propagation</description>
|
||||||
|
</property>
|
||||||
|
<!-- <property>-->
|
||||||
|
<!-- <name>sparkDriverMemory</name>-->
|
||||||
|
<!-- <description>memory for driver process</description>-->
|
||||||
|
<!-- </property>-->
|
||||||
|
<!-- <property>-->
|
||||||
|
<!-- <name>sparkExecutorMemory</name>-->
|
||||||
|
<!-- <description>memory for individual executor</description>-->
|
||||||
|
<!-- </property>-->
|
||||||
|
<!-- <property>-->
|
||||||
|
<!-- <name>sparkExecutorCores</name>-->
|
||||||
|
<!-- <description>number of cores used by single executor</description>-->
|
||||||
|
<!-- </property>-->
|
||||||
|
<property>
|
||||||
|
<name>writeUpdate</name>
|
||||||
|
<description>writes the information found for the update. No double check done if the information is already present</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>saveGraph</name>
|
||||||
|
<description>writes new version of the graph after the propagation step</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<start to="OrcidToResultFromSemRelPropagation"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="OrcidToResultFromSemRelPropagation">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<master>yarn-cluster</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>OrcidToResultFromSemRelPropagation</name>
|
||||||
|
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
|
||||||
|
<jar>dhp-propagation-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--num-executors=${sparkExecutorNumber}
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.dynamicAllocation.enabled=true
|
||||||
|
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
|
||||||
|
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
|
||||||
|
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
</workflow-app>
|
||||||
Loading…
Reference in New Issue