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 java.util.*; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FlatMapFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; 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.actionmanager.createunresolvedentities.model.FOSDataModel; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.utils.DHPUtils; public class PrepareFOSSparkJob 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/prepare_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 -> { distributeFOSdois( spark, sourcePath, outputPath); }); } private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) { Dataset fosDataset = readPath(spark, sourcePath, FOSDataModel.class); fosDataset.flatMap((FlatMapFunction) v -> { List fosList = new ArrayList<>(); final String level1 = v.getLevel1(); final String level2 = v.getLevel2(); final String level3 = v.getLevel3(); Arrays .stream(v.getDoi().split("\u0002")) .forEach(d -> fosList.add(FOSDataModel.newInstance(d, level1, level2, level3))); return fosList.iterator(); }, Encoders.bean(FOSDataModel.class)) .map((MapFunction) value -> { Result r = new Result(); r.setId(DHPUtils.generateUnresolvedIdentifier(value.getDoi(), DOI)); r.setSubject(getSubjects(value)); return r; }, Encoders.bean(Result.class)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath + "/fos"); } private static List 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)) return null; StructuredProperty sp = new StructuredProperty(); sp.setValue(sbj); sp .setQualifier( 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; } }