forked from D-Net/dnet-hadoop
refactoring
This commit is contained in:
parent
8c5dac5cc3
commit
d8dc31d4af
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@ -1,38 +1,38 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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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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 java.util.Arrays;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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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 Logger log =
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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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String jsonConfiguration =
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IOUtils.toString(
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SparkOrcidToResultFromSemRelJob3.class.getResourceAsStream(
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"/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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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -51,33 +51,44 @@ public class PrepareResultOrcidAssociationStep1 {
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").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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final String resultType =
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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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Class<? extends Result> resultClazz =
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(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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runWithSparkHiveSession(
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conf,
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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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prepareInfo(
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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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private static <R extends Result> void prepareInfo(
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SparkSession spark,
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String inputPath,
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String outputPath,
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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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// 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 -> OBJECT_MAPPER.readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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org.apache.spark.sql.Dataset<Relation> relation =
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spark.createDataset(
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sc.textFile(inputPath + "/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
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.rdd(),
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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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@ -86,38 +97,38 @@ public class PrepareResultOrcidAssociationStep1 {
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result.createOrReplaceTempView("result");
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getPossibleResultOrcidAssociation(spark, allowedsemrel, outputPath + "/" + resultType);
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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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private static void getPossibleResultOrcidAssociation(
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SparkSession spark, List<String> allowedsemrel, String outputPath) {
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String query =
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" 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)
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+ ") 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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.toJavaRDD()
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.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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// .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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@ -1,7 +1,12 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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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 java.util.HashSet;
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import java.util.Set;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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@ -9,22 +14,20 @@ import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.util.HashSet;
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import java.util.Set;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class PrepareResultOrcidAssociationStep2 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.class);
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private static final Logger log =
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LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.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(PrepareResultOrcidAssociationStep2.class
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.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json"));
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String jsonConfiguration =
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IOUtils.toString(
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PrepareResultOrcidAssociationStep2.class.getResourceAsStream(
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"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -39,56 +42,60 @@ public class PrepareResultOrcidAssociationStep2 {
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SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged,
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runWithSparkSession(
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conf,
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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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mergeInfo(spark, inputPath, outputPath);
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mergeInfo(spark, inputPath, outputPath);
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});
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}
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private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
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Dataset<ResultOrcidList> resultOrcidAssoc = readAssocResultOrcidList(spark, inputPath + "/publication")
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.union(readAssocResultOrcidList(spark, inputPath + "/dataset"))
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.union(readAssocResultOrcidList(spark, inputPath + "/otherresearchproduct"))
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.union(readAssocResultOrcidList(spark, inputPath + "/software"));
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Dataset<ResultOrcidList> resultOrcidAssoc =
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readAssocResultOrcidList(spark, inputPath + "/publication")
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.union(readAssocResultOrcidList(spark, inputPath + "/dataset"))
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.union(readAssocResultOrcidList(spark, inputPath + "/otherresearchproduct"))
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.union(readAssocResultOrcidList(spark, inputPath + "/software"));
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resultOrcidAssoc
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.toJavaRDD()
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.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
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.reduceByKey((a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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Set<String> orcid_set = new HashSet<>();
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a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
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.reduceByKey(
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(a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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Set<String> orcid_set = new HashSet<>();
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a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
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b.getAuthorList().stream().forEach(aa -> {
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if (!orcid_set.contains(aa.getOrcid())) {
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a.getAuthorList().add(aa);
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orcid_set.add(aa.getOrcid());
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}
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});
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return a;
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})
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b.getAuthorList().stream()
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.forEach(
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aa -> {
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if (!orcid_set.contains(aa.getOrcid())) {
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a.getAuthorList().add(aa);
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orcid_set.add(aa.getOrcid());
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}
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});
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return a;
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})
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.map(c -> c._2())
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
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return spark
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.read()
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private static Dataset<ResultOrcidList> readAssocResultOrcidList(
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SparkSession spark, String relationPath) {
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return spark.read()
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.textFile(relationPath)
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.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
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.map(
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value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class),
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Encoders.bean(ResultOrcidList.class));
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}
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}
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@ -1,10 +1,15 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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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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.Author;
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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 java.util.List;
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import java.util.Optional;
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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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@ -15,30 +20,25 @@ 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.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 SparkOrcidToResultFromSemRelJob3 {
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private static final Logger log = LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob3.class);
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private static final Logger log =
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LoggerFactory.getLogger(SparkOrcidToResultFromSemRelJob3.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_orcidtoresult_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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SparkOrcidToResultFromSemRelJob3.class.getResourceAsStream(
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"/eu/dnetlib/dhp/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(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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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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@ -51,96 +51,116 @@ public class SparkOrcidToResultFromSemRelJob3 {
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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final Boolean saveGraph =
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Optional.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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Class<? extends Result> resultClazz =
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(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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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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if(isTest(parser)) {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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if(saveGraph)
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if (saveGraph)
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execPropagation(spark, possibleUpdates, inputPath, outputPath, resultClazz);
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});
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}
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private static <R extends Result> void execPropagation(SparkSession spark, String possibleUpdatesPath, String inputPath,
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String outputPath, Class<R> resultClazz ) {
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private static <R extends Result> void execPropagation(
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SparkSession spark,
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String possibleUpdatesPath,
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String inputPath,
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String outputPath,
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Class<R> resultClazz) {
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//read possible updates (resultId and list of possible orcid to add
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Dataset<ResultOrcidList> possible_updates = readAssocResultOrcidList(spark, possibleUpdatesPath);
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//read the result we have been considering
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// read possible updates (resultId and list of possible orcid to add
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Dataset<ResultOrcidList> possible_updates =
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readAssocResultOrcidList(spark, possibleUpdatesPath);
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// read the result we have been considering
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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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//make join result left_outer with possible updates
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// make join result left_outer with possible updates
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result.joinWith(possible_updates, result.col("id").equalTo(possible_updates.col("resultId")),
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"left_outer")
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.map(value -> {
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R ret = value._1();
|
||||
Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
|
||||
if(rol.isPresent()) {
|
||||
List<Author> toenrich_author = ret.getAuthor();
|
||||
List<AutoritativeAuthor> autoritativeAuthors = rol.get().getAuthorList();
|
||||
for(Author author: toenrich_author){
|
||||
if (!containsAllowedPid(author)){
|
||||
enrichAuthor(author, autoritativeAuthors);
|
||||
result.joinWith(
|
||||
possible_updates,
|
||||
result.col("id").equalTo(possible_updates.col("resultId")),
|
||||
"left_outer")
|
||||
.map(
|
||||
value -> {
|
||||
R ret = value._1();
|
||||
Optional<ResultOrcidList> rol = Optional.ofNullable(value._2());
|
||||
if (rol.isPresent()) {
|
||||
List<Author> toenrich_author = ret.getAuthor();
|
||||
List<AutoritativeAuthor> autoritativeAuthors =
|
||||
rol.get().getAuthorList();
|
||||
for (Author author : toenrich_author) {
|
||||
if (!containsAllowedPid(author)) {
|
||||
enrichAuthor(author, autoritativeAuthors);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return ret;
|
||||
}, Encoders.bean(resultClazz))
|
||||
.toJSON()
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.text(outputPath);
|
||||
|
||||
|
||||
return ret;
|
||||
},
|
||||
Encoders.bean(resultClazz))
|
||||
.toJSON()
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.text(outputPath);
|
||||
}
|
||||
|
||||
private static Dataset<ResultOrcidList> readAssocResultOrcidList(SparkSession spark, String relationPath) {
|
||||
return spark
|
||||
.read()
|
||||
private static Dataset<ResultOrcidList> readAssocResultOrcidList(
|
||||
SparkSession spark, String relationPath) {
|
||||
return spark.read()
|
||||
.textFile(relationPath)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class), Encoders.bean(ResultOrcidList.class));
|
||||
.map(
|
||||
value -> OBJECT_MAPPER.readValue(value, ResultOrcidList.class),
|
||||
Encoders.bean(ResultOrcidList.class));
|
||||
}
|
||||
|
||||
private static void enrichAuthor(Author a, List<AutoritativeAuthor> au){
|
||||
for (AutoritativeAuthor aa: au){
|
||||
if(enrichAuthor(aa, a)){
|
||||
private static void enrichAuthor(Author a, List<AutoritativeAuthor> au) {
|
||||
for (AutoritativeAuthor aa : au) {
|
||||
if (enrichAuthor(aa, a)) {
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, 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())) {
|
||||
if (autoritative_author
|
||||
.getSurname()
|
||||
.trim()
|
||||
.equalsIgnoreCase(author.getSurname().trim())) {
|
||||
|
||||
//have the same surname. Check the name
|
||||
// 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())) {
|
||||
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))) {
|
||||
// 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;
|
||||
}
|
||||
}
|
||||
|
|
@ -148,21 +168,20 @@ public class SparkOrcidToResultFromSemRelJob3 {
|
|||
}
|
||||
}
|
||||
}
|
||||
if (toaddpid){
|
||||
if (toaddpid) {
|
||||
StructuredProperty p = new StructuredProperty();
|
||||
p.setValue(autoritative_author.getOrcid());
|
||||
p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID ));
|
||||
p.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
|
||||
p.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID));
|
||||
p.setDataInfo(
|
||||
getDataInfo(
|
||||
PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID,
|
||||
PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
|
||||
author.addPid(p);
|
||||
|
||||
}
|
||||
return toaddpid;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
private static boolean containsAllowedPid(Author a) {
|
||||
for (StructuredProperty pid : a.getPid()) {
|
||||
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
||||
|
|
@ -171,5 +190,4 @@ public class SparkOrcidToResultFromSemRelJob3 {
|
|||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue