Read affiliation relations
This commit is contained in:
Serafeim Chatzopoulos
parent
7738372125
commit
347a889b20
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@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager;
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import java.util.Optional;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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@ -93,4 +94,8 @@ public class Constants {
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return s;
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}
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public static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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@ -0,0 +1,168 @@
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package eu.dnetlib.dhp.actionmanager.bipaffiliations;
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import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Iterator;
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import java.util.List;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import eu.dnetlib.dhp.actionmanager.Constants;
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import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
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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.JavaRDD;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.apache.spark.sql.Dataset;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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/**
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* created the Atomic Action for each tipe of results
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*/
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public class PrepareAffiliationRelations implements Serializable {
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private static final String DOI = "doi";
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private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareAffiliationRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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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 -> {
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Constants.removeOutputDir(spark, outputPath);
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prepareAffiliationRelations(spark, inputPath, outputPath);
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});
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}
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private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<AffiliationRelationDeserializer> bipDeserializeJavaRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
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// for(AffiliationRelationDeserializer rel: bipDeserializeJavaRDD.collect()){
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// System.out.println(rel);
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// }
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JavaRDD<AffiliationRelationModel> affiliationRelations =
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bipDeserializeJavaRDD.flatMap(entry ->
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entry.getMatchings().stream().flatMap(matching ->
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matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
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entry.getDoi(),
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rorId,
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matching.getConfidence()
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))).collect(Collectors.toList()).iterator());
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for(AffiliationRelationModel rel: affiliationRelations.collect()){
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System.out.println(rel);
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}
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// Dataset<AffiliationRelationModel> relations = spark
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// .createDataset(bipDeserializeJavaRDD.flatMap(entry -> {
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//// entry.keySet().stream().map(key -> {
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// AffiliationRelationModel rel = new AffiliationRelationModel(entry.getDoi())
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// System.out.println(entry);
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// return entry;
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//// BipScore bs = new BipScore();
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//// bs.setId(key);
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//// bs.setScoreList(entry.get(key));
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//// return bs;
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// }).collect(Collectors.toList()).iterator()).rdd(), Encoßders.bean(AffiliationRelationModel.class));
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// bipScores
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//
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// .map((MapFunction<BipScore, Result>) bs -> {
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// Result ret = new Result();
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//
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// ret.setId(bs.getId());
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//
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// ret.setMeasures(getMeasure(bs));
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//
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// return ret;
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// }, Encoders.bean(Result.class))
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// .toJavaRDD()
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// .map(p -> new AtomicAction(Result.class, p))
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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(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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// }
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//
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// private static List<Measure> getMeasure(BipScore value) {
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// return value
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// .getScoreList()
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// .stream()
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// .map(score -> {
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// Measure m = new Measure();
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// m.setId(score.getId());
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// m
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// .setUnit(
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// score
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// .getUnit()
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// .stream()
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// .map(unit -> {
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// KeyValue kv = new KeyValue();
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// kv.setValue(unit.getValue());
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// kv.setKey(unit.getKey());
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// kv
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// .setDataInfo(
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// OafMapperUtils
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// .dataInfo(
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// false,
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// UPDATE_DATA_INFO_TYPE,
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// true,
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// false,
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// OafMapperUtils
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// .qualifier(
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// UPDATE_MEASURE_BIP_CLASS_ID,
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// UPDATE_CLASS_NAME,
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// ModelConstants.DNET_PROVENANCE_ACTIONS,
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// ModelConstants.DNET_PROVENANCE_ACTIONS),
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// ""));
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// return kv;
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// })
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// .collect(Collectors.toList()));
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// return m;
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// })
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// .collect(Collectors.toList());
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}
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}
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@ -0,0 +1,26 @@
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package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import lombok.Data;
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import java.io.Serializable;
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import java.util.List;
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@Data
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public class AffiliationRelationDeserializer implements Serializable {
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@JsonProperty("DOI")
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private String doi;
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@JsonProperty("Matchings")
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private List<Matching> matchings;
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@Data
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public static class Matching implements Serializable {
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@JsonProperty("RORid")
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private List<String> rorId;
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@JsonProperty("Confidence")
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private double confidence;
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}
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}
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@ -0,0 +1,15 @@
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package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
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import lombok.AllArgsConstructor;
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import lombok.Data;
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import lombok.NoArgsConstructor;
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import java.io.Serializable;
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@Data
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@AllArgsConstructor
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public class AffiliationRelationModel implements Serializable {
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private String doi;
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private String rorId;
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private double confidence;
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}
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@ -0,0 +1,20 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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}
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]
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@ -0,0 +1,139 @@
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package eu.dnetlib.dhp.actionmanager.bipaffiliations;
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import static org.junit.jupiter.api.Assertions.*;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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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.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.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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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.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class PrepareAffiliationRelationsTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory
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.getLogger(PrepareAffiliationRelationsTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(PrepareAffiliationRelationsTest.class.getSimpleName());
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log.info("Using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(PrepareAffiliationRelationsTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(PrepareAffiliationRelationsTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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void testMatch() throws Exception {
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String affiliationRelationsPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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affiliationRelationsPath,
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"-outputPath",
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workingDir.toString() + "/actionSet"
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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// JavaRDD<Result> tmp = sc
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// .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
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// .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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// .map(aa -> ((Result) aa.getPayload()));
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//
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// assertEquals(4, tmp.count());
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//
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// Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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// verificationDataset.createOrReplaceTempView("result");
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//
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// Dataset<Row> execVerification = spark
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// .sql(
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// "Select p.id oaid, mes.id, mUnit.value from result p " +
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// "lateral view explode(measures) m as mes " +
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// "lateral view explode(mes.unit) u as mUnit ");
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//
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// Assertions.assertEquals(12, execVerification.count());
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// Assertions
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// .assertEquals(
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// "6.63451994567e-09", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'influence'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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// Assertions
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// .assertEquals(
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// "0.348694533145", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'popularity_alt'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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// Assertions
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// .assertEquals(
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// "2.16094680115e-09", execVerification
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// .filter(
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// "oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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// "and id = 'popularity'")
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// .select("value")
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// .collectAsList()
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// .get(0)
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// .getString(0));
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//
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}
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}
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@ -0,0 +1,6 @@
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{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":["https:\/\/ror.org\/01teme464"],"Confidence":0.73},{"RORid":["https:\/\/ror.org\/03yxnpp24"],"Confidence":0.7071067812}]}
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{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":["https:\/\/ror.org\/02k40bc56"],"Confidence":0.7071067812}]}
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{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":["https:\/\/ror.org\/00qjgza05"],"Confidence":1}]}
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{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":["https:\/\/ror.org\/05apxxy63"],"Confidence":1},{"RORid":["https:\/\/ror.org\/035xkbk20"],"Confidence":1}]}
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{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":["https:\/\/ror.org\/04j198w64"],"Confidence":0.58}]}
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{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":["https:\/\/ror.org\/057xtrt18"],"Confidence":0.7071067812}]}
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