forked from D-Net/dnet-hadoop
130 lines
5.3 KiB
Java
130 lines
5.3 KiB
Java
package eu.dnetlib.dhp.countrypropagation;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.apache.spark.sql.SaveMode;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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/**
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* For the association of the country to the datasource
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* The association is computed only for datasource of specific type or having whitelisted ids
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* The country is registered in the Organization associated to the Datasource, so the
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* relation provides between Datasource and Organization is exploited to get the country for the datasource
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*/
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public class PrepareDatasourceCountryAssociation {
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private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(PrepareDatasourceCountryAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareDatasourceCountryAssociation(spark,
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Arrays.asList(parser.get("whitelist").split(";")),
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Arrays.asList(parser.get("allowedtypes").split(";")),
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inputPath,
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outputPath);
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});
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}
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private static void prepareDatasourceCountryAssociation(SparkSession spark,
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List<String> whitelist,
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List<String> allowedtypes,
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String inputPath,
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String outputPath) {
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String whitelisted = "";
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for (String i : whitelist){
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whitelisted += " OR id = '" + i + "'";
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}
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
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.map(item -> OBJECT_MAPPER.readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
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Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
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.map(item -> OBJECT_MAPPER.readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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datasource.createOrReplaceTempView("datasource");
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relation.createOrReplaceTempView("relation");
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organization.createOrReplaceTempView("organization");
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String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " +
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"FROM ( SELECT id " +
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" FROM datasource " +
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" WHERE (datainfo.deletedbyinference = false " + whitelisted + ") " +
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getConstraintList("datasourcetype.classid = '", allowedtypes) + ") d " +
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"JOIN ( SELECT source, target " +
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" FROM relation " +
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" WHERE relclass = 'provides' " +
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" AND datainfo.deletedbyinference = false ) rel " +
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"ON d.id = rel.source " +
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"JOIN (SELECT id, country " +
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" FROM organization " +
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" WHERE datainfo.deletedbyinference = false " +
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" AND length(country.classid)>0) o " +
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"ON o.id = rel.target";
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spark.sql(query)
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.as(Encoders.bean(DatasourceCountry.class))
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.toJavaRDD()
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.map(c -> OBJECT_MAPPER.writeValueAsString(c))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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}
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