114 lines
3.7 KiB
Java
114 lines
3.7 KiB
Java
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package eu.dnetlib.dhp.actionmanager.dblp;
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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.Arrays;
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import java.util.List;
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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.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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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.Constants;
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import eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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/**
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* Creates action sets for DBLP data
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*/
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public class PrepareDblpActionSets implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(PrepareDblpActionSets.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ID_PREFIX = "50|doi_________::";
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public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
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public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
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public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
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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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PrepareDblpActionSets.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/dblp/input_actionset_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String dblpInputPath = parser.get("dblpInputPath");
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log.info("dblpInputPath: {}", dblpInputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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// TODO: add DBLP ID in ModelConstants
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List<KeyValue> collectedFromDBLP = OafMapperUtils
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.listKeyValues(ModelConstants.CROSSREF_ID, "DBLP");
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JavaPairRDD<Text, Text> dblpData = prepareDblpData(
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spark, dblpInputPath, collectedFromDBLP);
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dblpData
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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});
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}
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private static <I extends Result> JavaPairRDD<Text, Text> prepareDblpData(SparkSession spark,
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String inputPath,
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List<KeyValue> collectedFrom) {
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log.info("Reading DBLP XML data");
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//
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// TODO: load DBLP data into a Dataset
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Dataset<Row> df = spark
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.read()
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.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
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.json(inputPath);
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return df.map((MapFunction<Row, Result>) bs -> {
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Result result = new Result();
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// TODO: map DBLP data to Result objects
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return result;
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}, Encoders.bean(Result.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Result.class, p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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}
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