mergin with branch beta
commit
c6a9f0a1a8
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import java.util.Optional;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class Constants {
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public static final String DOI = "doi";
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public static final String UPDATE_DATA_INFO_TYPE = "update";
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public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
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public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
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public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
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public static final String FOS_CLASS_ID = "FOS";
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public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
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public static final String NULL = "NULL";
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private Constants() {
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}
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public static Boolean isSparkSessionManaged(ArgumentApplicationParser parser) {
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return Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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}
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public static <R> Dataset<R> readPath(
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SparkSession spark, String inputPath, Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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}
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@ -0,0 +1,77 @@
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.Serializable;
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import java.util.Objects;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.collection.GetCSV;
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public class GetFOSData implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
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public static final char DEFAULT_DELIMITER = '\t';
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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GetFOSData.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json"))));
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parser.parseArgument(args);
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// the path where the original fos csv file is stored
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final String sourcePath = parser.get("sourcePath");
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log.info("sourcePath {}", sourcePath);
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// the path where to put the file as json
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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final String hdfsNameNode = parser.get("hdfsNameNode");
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log.info("hdfsNameNode {}", hdfsNameNode);
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final String classForName = parser.get("classForName");
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log.info("classForName {}", classForName);
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final char delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.map(s -> s.charAt(0))
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.orElse(DEFAULT_DELIMITER);
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log.info("delimiter {}", delimiter);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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new GetFOSData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
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}
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public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
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throws IOException, ClassNotFoundException {
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// reads the csv and writes it as its json equivalent
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try (InputStreamReader reader = new InputStreamReader(fs.open(new Path(inputPath)))) {
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GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
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}
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}
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}
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
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import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UPDATE_CLASS_NAME;
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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.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.hdfs.client.HdfsUtils;
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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.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipDeserialize;
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import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipScore;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Measure;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class PrepareBipFinder implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.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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PrepareBipFinder.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String sourcePath = parser.get("sourcePath");
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log.info("sourcePath {}: ", sourcePath);
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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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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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prepareResults(spark, sourcePath, outputPath);
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});
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}
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private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
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spark
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.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
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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(), Encoders.bean(BipScore.class))
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.map((MapFunction<BipScore, Result>) v -> {
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Result r = new Result();
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r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
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r.setMeasures(getMeasure(v));
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return r;
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}, Encoders.bean(Result.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/bip");
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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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}
|
@ -0,0 +1,133 @@
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.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.*;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.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 eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
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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.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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public class PrepareFOSSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareFOSSparkJob.class
|
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
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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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String sourcePath = parser.get("sourcePath");
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log.info("sourcePath: {}", sourcePath);
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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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distributeFOSdois(
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spark,
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sourcePath,
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|
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outputPath);
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});
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}
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private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
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Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
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fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
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List<FOSDataModel> fosList = new ArrayList<>();
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final String level1 = v.getLevel1();
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final String level2 = v.getLevel2();
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final String level3 = v.getLevel3();
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Arrays
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.stream(v.getDoi().split("\u0002"))
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.forEach(d -> fosList.add(FOSDataModel.newInstance(d, level1, level2, level3)));
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return fosList.iterator();
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}, Encoders.bean(FOSDataModel.class))
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.map((MapFunction<FOSDataModel, Result>) value -> {
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Result r = new Result();
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r.setId(DHPUtils.generateUnresolvedIdentifier(value.getDoi(), DOI));
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r.setSubject(getSubjects(value));
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return r;
|
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}, Encoders.bean(Result.class))
|
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.write()
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.mode(SaveMode.Overwrite)
|
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.option("compression", "gzip")
|
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.json(outputPath + "/fos");
|
||||
}
|
||||
|
||||
private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
|
||||
return Arrays
|
||||
.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
private static StructuredProperty getSubject(String sbj) {
|
||||
if (sbj.equals(NULL))
|
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return null;
|
||||
StructuredProperty sp = new StructuredProperty();
|
||||
sp.setValue(sbj);
|
||||
sp
|
||||
.setQualifier(
|
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OafMapperUtils
|
||||
.qualifier(
|
||||
FOS_CLASS_ID,
|
||||
FOS_CLASS_NAME,
|
||||
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
|
||||
ModelConstants.DNET_SUBJECT_TYPOLOGIES));
|
||||
sp
|
||||
.setDataInfo(
|
||||
OafMapperUtils
|
||||
.dataInfo(
|
||||
false,
|
||||
UPDATE_DATA_INFO_TYPE,
|
||||
true,
|
||||
false,
|
||||
OafMapperUtils
|
||||
.qualifier(
|
||||
UPDATE_SUBJECT_FOS_CLASS_ID,
|
||||
UPDATE_CLASS_NAME,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS),
|
||||
""));
|
||||
|
||||
return sp;
|
||||
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,79 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
|
||||
|
||||
import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.MapGroupsFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class SparkSaveUnresolved implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
|
||||
String jsonConfiguration = IOUtils
|
||||
.toString(
|
||||
PrepareFOSSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json"));
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
String sourcePath = parser.get("sourcePath");
|
||||
log.info("sourcePath: {}", sourcePath);
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath: {}", outputPath);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
saveUnresolved(
|
||||
spark,
|
||||
sourcePath,
|
||||
|
||||
outputPath);
|
||||
});
|
||||
}
|
||||
|
||||
private static void saveUnresolved(SparkSession spark, String sourcePath, String outputPath) {
|
||||
|
||||
spark
|
||||
.read()
|
||||
.textFile(sourcePath + "/*")
|
||||
.map(
|
||||
(MapFunction<String, Result>) l -> OBJECT_MAPPER.readValue(l, Result.class),
|
||||
Encoders.bean(Result.class))
|
||||
.groupByKey((MapFunction<Result, String>) r -> r.getId(), Encoders.STRING())
|
||||
.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
|
||||
Result ret = it.next();
|
||||
it.forEachRemaining(r -> ret.mergeFrom(r));
|
||||
return ret;
|
||||
}, Encoders.bean(Result.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,28 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Class that maps the model of the bipFinder! input data.
|
||||
* Only needed for deserialization purposes
|
||||
*/
|
||||
|
||||
public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
|
||||
|
||||
public BipDeserialize() {
|
||||
super();
|
||||
}
|
||||
|
||||
public List<Score> get(String key) {
|
||||
|
||||
if (super.get(key) == null) {
|
||||
return new ArrayList<>();
|
||||
}
|
||||
return super.get(key);
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,30 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
|
||||
*/
|
||||
|
||||
public class BipScore implements Serializable {
|
||||
private String id; // doi
|
||||
private List<Score> scoreList; // unit as given in the inputfile
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public List<Score> getScoreList() {
|
||||
return scoreList;
|
||||
}
|
||||
|
||||
public void setScoreList(List<Score> scoreList) {
|
||||
this.scoreList = scoreList;
|
||||
}
|
||||
}
|
@ -0,0 +1,71 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import com.opencsv.bean.CsvBindByPosition;
|
||||
|
||||
public class FOSDataModel implements Serializable {
|
||||
@CsvBindByPosition(position = 1)
|
||||
// @CsvBindByName(column = "doi")
|
||||
private String doi;
|
||||
|
||||
@CsvBindByPosition(position = 2)
|
||||
// @CsvBindByName(column = "level1")
|
||||
private String level1;
|
||||
|
||||
@CsvBindByPosition(position = 3)
|
||||
// @CsvBindByName(column = "level2")
|
||||
private String level2;
|
||||
|
||||
@CsvBindByPosition(position = 4)
|
||||
// @CsvBindByName(column = "level3")
|
||||
private String level3;
|
||||
|
||||
public FOSDataModel() {
|
||||
|
||||
}
|
||||
|
||||
public FOSDataModel(String doi, String level1, String level2, String level3) {
|
||||
this.doi = doi;
|
||||
this.level1 = level1;
|
||||
this.level2 = level2;
|
||||
this.level3 = level3;
|
||||
}
|
||||
|
||||
public static FOSDataModel newInstance(String d, String level1, String level2, String level3) {
|
||||
return new FOSDataModel(d, level1, level2, level3);
|
||||
}
|
||||
|
||||
public String getDoi() {
|
||||
return doi;
|
||||
}
|
||||
|
||||
public void setDoi(String doi) {
|
||||
this.doi = doi;
|
||||
}
|
||||
|
||||
public String getLevel1() {
|
||||
return level1;
|
||||
}
|
||||
|
||||
public void setLevel1(String level1) {
|
||||
this.level1 = level1;
|
||||
}
|
||||
|
||||
public String getLevel2() {
|
||||
return level2;
|
||||
}
|
||||
|
||||
public void setLevel2(String level2) {
|
||||
this.level2 = level2;
|
||||
}
|
||||
|
||||
public String getLevel3() {
|
||||
return level3;
|
||||
}
|
||||
|
||||
public void setLevel3(String level3) {
|
||||
this.level3 = level3;
|
||||
}
|
||||
}
|
@ -0,0 +1,26 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class KeyValue implements Serializable {
|
||||
|
||||
private String key;
|
||||
private String value;
|
||||
|
||||
public String getKey() {
|
||||
return key;
|
||||
}
|
||||
|
||||
public void setKey(String key) {
|
||||
this.key = key;
|
||||
}
|
||||
|
||||
public String getValue() {
|
||||
return value;
|
||||
}
|
||||
|
||||
public void setValue(String value) {
|
||||
this.value = value;
|
||||
}
|
||||
}
|
@ -0,0 +1,30 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* represents the score in the input file
|
||||
*/
|
||||
public class Score implements Serializable {
|
||||
|
||||
private String id;
|
||||
private List<KeyValue> unit;
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public List<KeyValue> getUnit() {
|
||||
return unit;
|
||||
}
|
||||
|
||||
public void setUnit(List<KeyValue> unit) {
|
||||
this.unit = unit;
|
||||
}
|
||||
}
|
@ -0,0 +1,181 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.opencitations;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.util.*;
|
||||
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class CreateActionSetSparkJob implements Serializable {
|
||||
public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
|
||||
public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
|
||||
private static final String ID_PREFIX = "50|doi_________::";
|
||||
private static final String TRUST = "0.91";
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
public static void main(final String[] args) throws IOException, ParseException {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
CreateActionSetSparkJob.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
Boolean isSparkSessionManaged = Optional
|
||||
.ofNullable(parser.get("isSparkSessionManaged"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.TRUE);
|
||||
|
||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
||||
|
||||
final String inputPath = parser.get("inputPath");
|
||||
log.info("inputPath {}", inputPath.toString());
|
||||
|
||||
final String outputPath = parser.get("outputPath");
|
||||
log.info("outputPath {}", outputPath);
|
||||
|
||||
final boolean shouldDuplicateRels = Optional
|
||||
.ofNullable(parser.get("shouldDuplicateRels"))
|
||||
.map(Boolean::valueOf)
|
||||
.orElse(Boolean.FALSE);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
runWithSparkSession(
|
||||
conf,
|
||||
isSparkSessionManaged,
|
||||
spark -> {
|
||||
extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
private static void extractContent(SparkSession spark, String inputPath, String outputPath,
|
||||
boolean shouldDuplicateRels) {
|
||||
spark
|
||||
.sqlContext()
|
||||
.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
|
||||
.flatMap(
|
||||
(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
|
||||
Encoders.bean(Relation.class))
|
||||
.filter((FilterFunction<Relation>) value -> value != null)
|
||||
.toJavaRDD()
|
||||
.map(p -> new AtomicAction(p.getClass(), p))
|
||||
.mapToPair(
|
||||
aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
|
||||
new Text(OBJECT_MAPPER.writeValueAsString(aa))))
|
||||
.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
|
||||
|
||||
}
|
||||
|
||||
private static List<Relation> createRelation(String value, boolean duplicate) {
|
||||
String[] line = value.split(",");
|
||||
if (!line[1].startsWith("10.")) {
|
||||
return new ArrayList<>();
|
||||
}
|
||||
List<Relation> relationList = new ArrayList<>();
|
||||
|
||||
String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
|
||||
final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
|
||||
|
||||
relationList
|
||||
.addAll(
|
||||
getRelations(
|
||||
citing,
|
||||
cited));
|
||||
|
||||
if (duplicate && line[1].endsWith(".refs")) {
|
||||
citing = ID_PREFIX + IdentifierFactory
|
||||
.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
|
||||
relationList.addAll(getRelations(citing, cited));
|
||||
}
|
||||
|
||||
return relationList;
|
||||
}
|
||||
|
||||
private static Collection<Relation> getRelations(String citing, String cited) {
|
||||
|
||||
return Arrays
|
||||
.asList(
|
||||
getRelation(citing, cited, ModelConstants.CITES),
|
||||
getRelation(cited, citing, ModelConstants.IS_CITED_BY));
|
||||
}
|
||||
|
||||
public static Relation getRelation(
|
||||
String source,
|
||||
String target,
|
||||
String relclass) {
|
||||
Relation r = new Relation();
|
||||
r.setCollectedfrom(getCollectedFrom());
|
||||
r.setSource(source);
|
||||
r.setTarget(target);
|
||||
r.setRelClass(relclass);
|
||||
r.setRelType(ModelConstants.RESULT_RESULT);
|
||||
r.setSubRelType(ModelConstants.CITATION);
|
||||
r
|
||||
.setDataInfo(
|
||||
getDataInfo());
|
||||
return r;
|
||||
}
|
||||
|
||||
public static List<KeyValue> getCollectedFrom() {
|
||||
KeyValue kv = new KeyValue();
|
||||
kv.setKey(ModelConstants.OPENOCITATIONS_ID);
|
||||
kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
|
||||
|
||||
return Arrays.asList(kv);
|
||||
}
|
||||
|
||||
public static DataInfo getDataInfo() {
|
||||
DataInfo di = new DataInfo();
|
||||
di.setInferred(false);
|
||||
di.setDeletedbyinference(false);
|
||||
di.setTrust(TRUST);
|
||||
|
||||
di
|
||||
.setProvenanceaction(
|
||||
getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
return di;
|
||||
}
|
||||
|
||||
public static Qualifier getQualifier(String class_id, String class_name,
|
||||
String qualifierSchema) {
|
||||
Qualifier pa = new Qualifier();
|
||||
pa.setClassid(class_id);
|
||||
pa.setClassname(class_name);
|
||||
pa.setSchemeid(qualifierSchema);
|
||||
pa.setSchemename(qualifierSchema);
|
||||
return pa;
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,93 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.opencitations;
|
||||
|
||||
import java.io.*;
|
||||
import java.io.Serializable;
|
||||
import java.util.Objects;
|
||||
import java.util.zip.GZIPOutputStream;
|
||||
import java.util.zip.ZipEntry;
|
||||
import java.util.zip.ZipInputStream;
|
||||
|
||||
import org.apache.commons.cli.ParseException;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FSDataInputStream;
|
||||
import org.apache.hadoop.fs.FSDataOutputStream;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class GetOpenCitationsRefs implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
|
||||
|
||||
public static void main(final String[] args) throws IOException, ParseException {
|
||||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
Objects
|
||||
.requireNonNull(
|
||||
GetOpenCitationsRefs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json"))));
|
||||
|
||||
parser.parseArgument(args);
|
||||
|
||||
final String[] inputFile = parser.get("inputFile").split(";");
|
||||
log.info("inputFile {}", inputFile.toString());
|
||||
|
||||
final String workingPath = parser.get("workingPath");
|
||||
log.info("workingPath {}", workingPath);
|
||||
|
||||
final String hdfsNameNode = parser.get("hdfsNameNode");
|
||||
log.info("hdfsNameNode {}", hdfsNameNode);
|
||||
|
||||
Configuration conf = new Configuration();
|
||||
conf.set("fs.defaultFS", hdfsNameNode);
|
||||
|
||||
FileSystem fileSystem = FileSystem.get(conf);
|
||||
|
||||
GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
|
||||
|
||||
for (String file : inputFile) {
|
||||
ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
|
||||
throws IOException {
|
||||
|
||||
final Path path = new Path(inputFile);
|
||||
|
||||
FSDataInputStream oc_zip = fileSystem.open(path);
|
||||
|
||||
int count = 1;
|
||||
try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
|
||||
ZipEntry entry = null;
|
||||
while ((entry = zis.getNextEntry()) != null) {
|
||||
|
||||
if (!entry.isDirectory()) {
|
||||
String fileName = entry.getName();
|
||||
fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
|
||||
count++;
|
||||
try (
|
||||
FSDataOutputStream out = fileSystem
|
||||
.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
|
||||
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
|
||||
|
||||
IOUtils.copy(zis, gzipOs);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,33 @@
|
||||
[
|
||||
{
|
||||
"paramName":"s",
|
||||
"paramLongName":"sourcePath",
|
||||
"paramDescription": "the path of the sequencial file to read",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName":"out",
|
||||
"paramLongName":"outputPath",
|
||||
"paramDescription": "the output path",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
||||
{
|
||||
"paramName": "ssm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "true if the spark session is managed, false otherwise",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "hnn",
|
||||
"paramLongName": "hdfsNameNode",
|
||||
"paramDescription": "the path used to store the HostedByMap",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "cfn",
|
||||
"paramLongName": "classForName",
|
||||
"paramDescription": "the path used to store the HostedByMap",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
@ -0,0 +1,30 @@
|
||||
<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>hiveMetastoreUris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveJdbcUrl</name>
|
||||
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hiveDbName</name>
|
||||
<value>openaire</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
@ -0,0 +1,174 @@
|
||||
|
||||
<workflow-app name="UnresolvedEntities" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>fosPath</name>
|
||||
<description>the input path of the resources to be extended</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>bipScorePath</name>
|
||||
<description>the path where to find the bipFinder scores</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>the path where to store the actionset</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>oozieActionShareLibForSpark2</name>
|
||||
<description>oozie action sharelib for spark 2.*</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||
<description>spark 2.* extra listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||
<description>spark 2.* sql query execution listeners classname</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<description>spark 2.* yarn history server address</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<description>spark 2.* event log dir location</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapreduce.job.queuename</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||
<value>${oozieLauncherQueueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
|
||||
</configuration>
|
||||
</global>
|
||||
<start to="prepareInfo"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<fork name="prepareInfo">
|
||||
<path start="prepareBip"/>
|
||||
<path start="getFOS"/>
|
||||
</fork>
|
||||
|
||||
<action name="prepareBip">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the unresolved from bip finder!</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${bipScorePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
|
||||
</spark>
|
||||
<ok to="join"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="getFOS">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSData</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--sourcePath</arg><arg>${fosPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
|
||||
<arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel</arg>
|
||||
</java>
|
||||
<ok to="prepareFos"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="prepareFos">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the unresolved from FOS!</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/input/fos</arg>
|
||||
<arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="join"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<join name="join" to="produceUnresolved"/>
|
||||
|
||||
<action name="produceUnresolved">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Saves the result produced for bip and fos by grouping results with the same id</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.SparkSaveUnresolved</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--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.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/prepared</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
@ -0,0 +1,20 @@
|
||||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "sp",
|
||||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the URL from where to get the programme file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path of the new ActionSet",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
@ -0,0 +1,20 @@
|
||||
[
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "when true will stop SparkSession after job execution",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "sp",
|
||||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the URL from where to get the programme file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path of the new ActionSet",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
@ -0,0 +1,25 @@
|
||||
[
|
||||
{
|
||||
"paramName": "ip",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the zipped opencitations file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "op",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the working path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "issm",
|
||||
"paramLongName": "isSparkSessionManaged",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": false
|
||||
}, {
|
||||
"paramName": "sdr",
|
||||
"paramLongName": "shouldDuplicateRels",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": false
|
||||
}
|
||||
]
|
@ -0,0 +1,20 @@
|
||||
[
|
||||
{
|
||||
"paramName": "if",
|
||||
"paramLongName": "inputFile",
|
||||
"paramDescription": "the zipped opencitations file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "wp",
|
||||
"paramLongName": "workingPath",
|
||||
"paramDescription": "the working path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "hnn",
|
||||
"paramLongName": "hdfsNameNode",
|
||||
"paramDescription": "the hdfs name node",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
@ -0,0 +1,58 @@
|
||||
<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>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</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>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorNumber</name>
|
||||
<value>4</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</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>
|
||||
</configuration>
|
@ -0,0 +1,2 @@
|
||||
#!/bin/bash
|
||||
for file in $(echo $1 | tr ";" "\n"); do curl -L $(echo $file | cut -d '@' -f 1 ) | hdfs dfs -put - $2/$(echo $file | cut -d '@' -f 2) ; done;
|
@ -0,0 +1,91 @@
|
||||
<workflow-app name="OpenCitations Integration" xmlns="uri:oozie:workflow:0.5">
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapreduce.job.queuename</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||
<value>${oozieLauncherQueueName}</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
|
||||
<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
|
||||
<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
<action name="download">
|
||||
<shell xmlns="uri:oozie:shell-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>mapred.job.queue.name</name>
|
||||
<value>${queueName}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<exec>download.sh</exec>
|
||||
<argument>${filelist}</argument>
|
||||
<argument>${workingPath}/Original</argument>
|
||||
<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
|
||||
<file>download.sh</file>
|
||||
<capture-output/>
|
||||
</shell>
|
||||
<ok to="extract"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="extract">
|
||||
<java>
|
||||
<main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
|
||||
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
|
||||
<arg>--inputFile</arg><arg>${inputFile}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</java>
|
||||
<ok to="create_actionset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="create_actionset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the AS for OC</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${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}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${workingPath}/COCI</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
@ -0,0 +1,8 @@
|
||||
[
|
||||
{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true},
|
||||
{"paramName":"f", "paramLongName":"opencitationFile", "paramDescription": "the name of the file", "paramRequired": true},
|
||||
{"paramName":"issm", "paramLongName":"isSparkSessionManaged", "paramDescription": "the name of the activities orcid file", "paramRequired": false},
|
||||
{"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the name of the activities orcid file", "paramRequired": true}
|
||||
|
||||
]
|
@ -0,0 +1,9 @@
|
||||
##DHP-Aggregation
|
||||
|
||||
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
|
||||
|
||||
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
|
||||
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
|
||||
of each MDStore.
|
||||
|
||||
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
|
@ -0,0 +1,7 @@
|
||||
##DHP-Aggregation
|
||||
|
||||
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
|
||||
|
||||
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
|
||||
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
|
||||
of each MDStore.
|
@ -0,0 +1,18 @@
|
||||
DHP Aggregation
|
||||
===============
|
||||
|
||||
DHP-Aggregations contains different mappings from original data format into OAF Data Format,
|
||||
which converge in the graph in different ways:
|
||||
|
||||
- Via Action Manager
|
||||
- Direct in the MdStore on Hadoop
|
||||
|
||||
Below the list of the implemented mapping
|
||||
|
||||
|
||||
Mappings
|
||||
=======
|
||||
|
||||
1. [PubMed](pubmed.md)
|
||||
2. [Datacite](datacite.md)
|
||||
|
@ -0,0 +1,62 @@
|
||||
#Pubmed Mapping
|
||||
This section describes the mapping implemented for [MEDLINE/PubMed](https://pubmed.ncbi.nlm.nih.gov/).
|
||||
|
||||
Collection
|
||||
---------
|
||||
The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with
|
||||
the following [shcema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
|
||||
|
||||
|
||||
Parsing
|
||||
-------
|
||||
The resposible class of parsing is [PMParser](./scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
|
||||
an intermediate mapping of PubMed Article defined [here](/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
|
||||
|
||||
|
||||
Mapping
|
||||
-------
|
||||
|
||||
The table below describes the mapping from the XML Native to the OAF mapping
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
| Xpath Source | Oaf Field | Notes |
|
||||
| ----------- | ----------- | ----------- |
|
||||
| //PMID | pid | classid = classname = pmid
|
||||
| | **Instance Mapping** | |
|
||||
|//PublicationType | InstanceType | If the article contains the typology **Journal Article** then we apply this type else We have to find a terms that match the vocabulary otherwise we discard it
|
||||
|//PMID | instance/PID | Map the pmid also in the pid in the instance |
|
||||
| //ArticleId[./@IdType="doi" | instance/alternateIdentifier |classid = classname = doi
|
||||
|//PMID | instance/URL | prepend to the PMId the base url https://pubmed.ncbi.nlm.nih.gov/
|
||||
| //PubmedPubDate | instance/Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it
|
||||
| FOR ALL INSTANCE | CollectedFrom | datasourceName: *Europe PubMed Central* DatasourceId:
|
||||
| | **Journal Mapping** | |
|
||||
|//Journal/PubDate| Journal/Conferencedate | map the date of the Journal
|
||||
|//Journal/Title| Journal/Name | |
|
||||
|//Journal/Volume| Journal/Vol | |
|
||||
|//Journal/ISSN| Journal/issPrinted | |
|
||||
|//Journal/Issue| Journal/Iss | |
|
||||
| | **Publication Mapping** | |
|
||||
| //PubmedPubDate | Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it
|
||||
| //Title | title | with qualifier ModelConstants.MAIN_TITLE_QUALIFIER
|
||||
| //AbstractText | Description ||
|
||||
|//Language| Language| cleaning vocabulary -> dnet:languages
|
||||
|//DescriptorName| Subject | classId, className = keyword
|
||||
| | **Author Mapping** | |
|
||||
|//Author/LastName| author.Surname| |
|
||||
|//Author/ForeName| author.Forename| |
|
||||
|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
|
||||
|FOR ALL AUTHOR | author.rank| sequential number starting from 1|
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
Binary file not shown.
After Width: | Height: | Size: 21 KiB |
@ -0,0 +1,32 @@
|
||||
<?xml version="1.0" encoding="ISO-8859-1"?>
|
||||
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
|
||||
name="DHP-Aggregation">
|
||||
<skin>
|
||||
<groupId>org.apache.maven.skins</groupId>
|
||||
<artifactId>maven-fluido-skin</artifactId>
|
||||
<version>1.8</version>
|
||||
</skin>
|
||||
<poweredBy>
|
||||
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
|
||||
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
|
||||
</poweredBy>
|
||||
<body>
|
||||
<links>
|
||||
<item name="Code" href="https://code-repo.d4science.org/" />
|
||||
</links>
|
||||
<menu name="Documentation">
|
||||
<item name="Mappings" href="mappings.html" collapse="true">
|
||||
<item name="Pubmed" href="pubmed.html"/>
|
||||
<item name="Datacite" href="datacite.html"/>
|
||||
</item>
|
||||
<item name="Release Notes" href="release-notes.html" />
|
||||
<item name="General Information" href="about.html"/>
|
||||
|
||||
<item name="JavaDoc" href="apidocs/" />
|
||||
<item name="ScalaDoc" href="scaladocs/" />
|
||||
|
||||
</menu>
|
||||
<menu ref="reports"/>
|
||||
</body>
|
||||
</project>
|
@ -0,0 +1,250 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
import java.io.BufferedReader;
|
||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
|
||||
import eu.dnetlib.dhp.common.collection.CollectorException;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class PrepareTest {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
|
||||
|
||||
private static Path workingDir;
|
||||
private static SparkSession spark;
|
||||
private static LocalFileSystem fs;
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
|
||||
|
||||
fs = FileSystem.getLocal(new Configuration());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(ProduceTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(PrepareTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void bipPrepareTest() throws Exception {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
|
||||
.getPath();
|
||||
|
||||
PrepareBipFinder
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", sourcePath,
|
||||
"--outputPath", workingDir.toString() + "/work"
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Result> tmp = sc
|
||||
.textFile(workingDir.toString() + "/work/bip")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
|
||||
|
||||
Assertions.assertEquals(86, tmp.count());
|
||||
|
||||
String doi1 = "unresolved::10.0000/096020199389707::doi";
|
||||
|
||||
Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
|
||||
Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"6.34596412687e-09", tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(sl -> sl.getId().equals("influence"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0.641151896994", tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(sl -> sl.getId().equals("popularity_alt"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"2.33375102921e-09", tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.stream()
|
||||
.filter(sl -> sl.getId().equals("popularity"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void getFOSFileTest() throws IOException, ClassNotFoundException {
|
||||
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/h2020_fos_sbs.csv")
|
||||
.getPath();
|
||||
final String outputPath = workingDir.toString() + "/fos.json";
|
||||
|
||||
new GetFOSData()
|
||||
.doRewrite(
|
||||
sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel",
|
||||
'\t', fs);
|
||||
|
||||
BufferedReader in = new BufferedReader(
|
||||
new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
|
||||
|
||||
String line;
|
||||
int count = 0;
|
||||
while ((line = in.readLine()) != null) {
|
||||
FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
|
||||
|
||||
System.out.println(new ObjectMapper().writeValueAsString(fos));
|
||||
count += 1;
|
||||
}
|
||||
|
||||
assertEquals(38, count);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void fosPrepareTest() throws Exception {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
|
||||
.getPath();
|
||||
|
||||
PrepareFOSSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", sourcePath,
|
||||
|
||||
"-outputPath", workingDir.toString() + "/work"
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Result> tmp = sc
|
||||
.textFile(workingDir.toString() + "/work/fos")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
|
||||
|
||||
String doi1 = "unresolved::10.3390/s18072310::doi";
|
||||
|
||||
assertEquals(50, tmp.count());
|
||||
assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
|
||||
assertTrue(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("engineering and technology"));
|
||||
|
||||
assertTrue(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("nano-technology"));
|
||||
assertTrue(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi1))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("nanoscience & nanotechnology"));
|
||||
|
||||
String doi = "unresolved::10.1111/1365-2656.12831::doi";
|
||||
assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
|
||||
assertTrue(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("psychology and cognitive sciences"));
|
||||
|
||||
assertTrue(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("social sciences"));
|
||||
assertFalse(
|
||||
tmp
|
||||
.filter(r -> r.getId().equals(doi))
|
||||
.flatMap(r -> r.getSubject().iterator())
|
||||
.map(sbj -> sbj.getValue())
|
||||
.collect()
|
||||
.contains("NULL"));
|
||||
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,234 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
public class ProduceTest {
|
||||
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
|
||||
|
||||
private static Path workingDir;
|
||||
private static SparkSession spark;
|
||||
private static LocalFileSystem fs;
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
private static final String ID_PREFIX = "50|doi_________";
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(ProduceTest.class.getSimpleName());
|
||||
|
||||
fs = FileSystem.getLocal(new Configuration());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(ProduceTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(ProduceTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void produceTest() throws Exception {
|
||||
|
||||
final String bipPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
|
||||
.getPath();
|
||||
|
||||
PrepareBipFinder
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", bipPath,
|
||||
"--outputPath", workingDir.toString() + "/work"
|
||||
|
||||
});
|
||||
final String fosPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
|
||||
.getPath();
|
||||
|
||||
PrepareFOSSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", fosPath,
|
||||
"-outputPath", workingDir.toString() + "/work"
|
||||
});
|
||||
|
||||
SparkSaveUnresolved.main(new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", workingDir.toString() + "/work",
|
||||
|
||||
"-outputPath", workingDir.toString() + "/unresolved"
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Result> tmp = sc
|
||||
.textFile(workingDir.toString() + "/unresolved")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
|
||||
|
||||
Assertions.assertEquals(135, tmp.count());
|
||||
|
||||
Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")).count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
3, tmp
|
||||
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getSubject()
|
||||
.size());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
3, tmp
|
||||
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.collect()
|
||||
.get(0)
|
||||
.getMeasures()
|
||||
.size());
|
||||
|
||||
List<StructuredProperty> sbjs = tmp
|
||||
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.flatMap(row -> row.getSubject().iterator())
|
||||
.collect();
|
||||
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals("FOS", sbj.getQualifier().getClassid()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals(
|
||||
"Fields of Science and Technology classification", sbj.getQualifier().getClassname()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
|
||||
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
|
||||
sbjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals(
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
|
||||
sbjs
|
||||
.forEach(
|
||||
sbj -> Assertions
|
||||
.assertEquals(
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
sbj.getDataInfo().getProvenanceaction().getSchemename()));
|
||||
|
||||
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("engineering and technology"));
|
||||
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nano-technology"));
|
||||
sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nanoscience & nanotechnology"));
|
||||
|
||||
List<Measure> measures = tmp
|
||||
.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.flatMap(row -> row.getMeasures().iterator())
|
||||
.collect();
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"7.5597134689e-09", measures
|
||||
.stream()
|
||||
.filter(mes -> mes.getId().equals("influence"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"4.903880192", measures
|
||||
.stream()
|
||||
.filter(mes -> mes.getId().equals("popularity_alt"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"1.17977512835e-08", measures
|
||||
.stream()
|
||||
.filter(mes -> mes.getId().equals("popularity"))
|
||||
.collect(Collectors.toList())
|
||||
.get(0)
|
||||
.getUnit()
|
||||
.get(0)
|
||||
.getValue());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
49, tmp
|
||||
.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.filter(row -> row.getSubject() != null)
|
||||
.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
85,
|
||||
tmp
|
||||
.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
|
||||
.filter(r -> r.getMeasures() != null)
|
||||
.count());
|
||||
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,335 @@
|
||||
|
||||
package eu.dnetlib.dhp.actionmanager.opencitations;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
|
||||
public class CreateOpenCitationsASTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(CreateOpenCitationsASTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(CreateOpenCitationsASTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(CreateOpenCitationsASTest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(CreateOpenCitationsASTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testNumberofRelations() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-shouldDuplicateRels",
|
||||
Boolean.TRUE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
assertEquals(60, tmp.count());
|
||||
|
||||
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testNumberofRelations2() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
assertEquals(44, tmp.count());
|
||||
|
||||
// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsCollectedFrom() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> {
|
||||
assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
|
||||
assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsDataInfo() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> {
|
||||
assertEquals(false, r.getDataInfo().getInferred());
|
||||
assertEquals(false, r.getDataInfo().getDeletedbyinference());
|
||||
assertEquals("0.91", r.getDataInfo().getTrust());
|
||||
assertEquals(
|
||||
CreateActionSetSparkJob.OPENCITATIONS_CLASSID, r.getDataInfo().getProvenanceaction().getClassid());
|
||||
assertEquals(
|
||||
CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, r.getDataInfo().getProvenanceaction().getClassname());
|
||||
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
|
||||
assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsSemantics() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> {
|
||||
assertEquals("citation", r.getSubRelType());
|
||||
assertEquals("resultResult", r.getRelType());
|
||||
});
|
||||
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
|
||||
assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsSourceTargetPrefix() throws Exception {
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
tmp.foreach(r -> {
|
||||
assertEquals("50|doi_________::", r.getSource().substring(0, 17));
|
||||
assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
void testRelationsSourceTargetCouple() throws Exception {
|
||||
final String doi1 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
|
||||
final String doi2 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
|
||||
final String doi3 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
|
||||
final String doi4 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
|
||||
final String doi5 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
|
||||
final String doi6 = "50|doi_________::"
|
||||
+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
|
||||
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged",
|
||||
Boolean.FALSE.toString(),
|
||||
"-inputPath",
|
||||
inputPath,
|
||||
"-outputPath",
|
||||
workingDir.toString() + "/actionSet"
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
||||
.map(aa -> ((Relation) aa.getPayload()));
|
||||
|
||||
JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
|
||||
|
||||
assertEquals(10, check.count());
|
||||
|
||||
check.foreach(r -> {
|
||||
if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
|
||||
r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
|
||||
assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
|
||||
assertEquals(doi1, r.getTarget());
|
||||
}
|
||||
});
|
||||
|
||||
assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
|
||||
check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
|
||||
|
||||
}
|
||||
}
|
@ -0,0 +1,86 @@
|
||||
{"10.3390/s18072310": [{"id": "influence", "unit": [{"value": "7.5597134689e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "4.903880192", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.17977512835e-08", "key": "score"}]}]}
|
||||
{"10.0000/096020199389707": [{"id": "influence", "unit": [{"value": "6.34596412687e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.641151896994", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.33375102921e-09", "key": "score"}]}]}
|
||||
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