new parametric implementation of country propagation. Exploits information compute before and broadcasts it to each executor
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@ -4,6 +4,9 @@ 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.CompressionCodec;
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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.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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@ -18,6 +21,9 @@ import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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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.common.SparkSessionSupport.runWithSparkHiveSession;
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public class SparkCountryPropagationJob2 {
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private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob2.class);
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@ -35,30 +41,54 @@ public class SparkCountryPropagationJob2 {
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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 = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
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final String datasourcecountrypath = outputPath + "/prepared_datasource_country";
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final String resultClassName = parser.get("resultTableName");
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".")+1);
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final String datasourcecountrypath = parser.get("preparedInfoPath");
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log.info("preparedInfoPath: {}", datasourcecountrypath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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final Boolean writeUpdates = Optional
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.ofNullable(parser.get("writeUpdate"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("writeUpdate: {}", writeUpdates);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkCountryPropagationJob2.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
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final boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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spark -> {
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//createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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removeOutputDir(spark, outputPath);
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execPropagation(spark, datasourcecountrypath, inputPath, outputPath, resultClazz, resultType,
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writeUpdates, saveGraph);
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});
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}
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private static <R extends Result> void execPropagation(SparkSession spark, String datasourcecountrypath,
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String inputPath, String outputPath, Class<R> resultClazz, String resultType,
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boolean writeUpdates, boolean saveGraph){
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//Load parque file with preprocessed association datasource - country
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@ -74,10 +104,9 @@ public class SparkCountryPropagationJob2 {
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}
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if(saveGraph){
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updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath + "/" + resultType);
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updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath);
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}
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}
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private static <R extends Result> void updateResultTable(SparkSession spark, Dataset<ResultCountrySet> potentialUpdates,
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@ -96,33 +125,32 @@ public class SparkCountryPropagationJob2 {
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Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
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Dataset<R> new_table = result_pair
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.joinWith(potential_update_pair, result_pair.col("_1").equalTo(potential_update_pair.col("_1")), "left")
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.map((MapFunction<Tuple2<Tuple2<String, R>, Tuple2<String, ResultCountrySet>>, R>) value -> {
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.joinWith(potentialUpdates, result_pair.col("_1").equalTo(potentialUpdates.col("resultId")), "left_outer")
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.map((MapFunction<Tuple2<Tuple2<String, R>, ResultCountrySet>, R>) value -> {
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R r = value._1()._2();
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Optional<ResultCountrySet> potentialNewCountries = Optional.ofNullable(value._2()).map(Tuple2::_2);
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Optional<ResultCountrySet> potentialNewCountries = Optional.ofNullable(value._2());
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if (potentialNewCountries.isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : r.getCountry()) {
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countries.add(country.getClassid());
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}
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for (Country country : potentialNewCountries.get().getCountrySet()) {
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for (CountrySbs country : potentialNewCountries.get().getCountrySet()) {
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if (!countries.contains(country.getClassid())) {
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r.getCountry().add(getCountry(country.getClassid(), country.getClassname()));
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}
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}
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}
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return r;
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}, Encoders.bean(resultClazz));
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log.info("Saving graph table to path: {}", outputPath);
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//log.info("number of saved recordsa: {}", new_table.count());
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new_table
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.toJSON()
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.write()
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.option("compression", "gzip")
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.text(outputPath);
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.toJavaRDD()
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath , GzipCodec.class);
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}
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@ -133,6 +161,7 @@ public class SparkCountryPropagationJob2 {
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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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result.createOrReplaceTempView("result");
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//log.info("number of results: {}", result.count());
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createCfHbforresult(spark);
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return countryPropagationAssoc(spark, broadcast_datasourcecountryassoc);
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}
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@ -147,6 +176,7 @@ public class SparkCountryPropagationJob2 {
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"LATERAL VIEW EXPLODE(instance) i AS inst";
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Dataset<Row> cfhb = spark.sql(query);
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cfhb.createOrReplaceTempView("cfhb");
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log.info("cfhb_number : {}", cfhb.count());
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}
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@ -155,19 +185,22 @@ public class SparkCountryPropagationJob2 {
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Dataset<DatasourceCountry> datasource_country = broadcast_datasourcecountryassoc.value();
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datasource_country.createOrReplaceTempView("datasource_country");
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log.info("datasource_country number : {}",datasource_country.count());
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String query = "SELECT id, collect_set(country) country "+
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String query = "SELECT id resultId, collect_set(country) countrySet "+
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"FROM ( SELECT id, country " +
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"FROM rels " +
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"FROM datasource_country " +
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"JOIN cfhb " +
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" ON cf = ds " +
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" ON cf = dataSourceId " +
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"UNION ALL " +
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"SELECT id , country " +
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"FROM rels " +
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"FROM datasource_country " +
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"JOIN cfhb " +
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" ON hb = ds ) tmp " +
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" ON hb = dataSourceId ) tmp " +
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"GROUP BY id";
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return spark.sql(query);
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Dataset<Row> potentialUpdates = spark.sql(query);
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log.info("potential update number : {}", potentialUpdates.count());
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return potentialUpdates;
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}
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private static <R extends Result> Dataset<R> readPathEntity(SparkSession spark, String inputEntityPath, Class<R> resultClazz) {
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@ -180,14 +213,15 @@ public class SparkCountryPropagationJob2 {
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}
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private static Dataset<DatasourceCountry> readAssocDatasourceCountry(SparkSession spark, String relationPath) {
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return spark.read()
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.load(relationPath)
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.as(Encoders.bean(DatasourceCountry.class));
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return spark
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.read()
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.textFile(relationPath)
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.map(value -> OBJECT_MAPPER.readValue(value, DatasourceCountry.class), Encoders.bean(DatasourceCountry.class));
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}
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private static void writeUpdates(JavaRDD<ResultCountrySet> potentialUpdates, String outputPath){
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potentialUpdates.map(u -> OBJECT_MAPPER.writeValueAsString(u))
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.saveAsTextFile(outputPath);
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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