package eu.dnetlib.dhp.oa.dedup; import java.io.IOException; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; 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.dom4j.DocumentException; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkCopyOpenorgsMergeRels.class); public SparkCopyOpenorgsMergeRels(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); } public static void main(String[] args) throws Exception { ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( SparkCopyOpenorgsMergeRels.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json"))); parser.parseArgument(args); SparkConf conf = new SparkConf(); new SparkCopyOpenorgsMergeRels(parser, getSparkSession(conf)) .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl"))); } @Override public void run(ISLookUpService isLookUpService) throws DocumentException, IOException, ISLookUpException { // read oozie parameters final String graphBasePath = parser.get("graphBasePath"); final String actionSetId = parser.get("actionSetId"); final String workingPath = parser.get("workingPath"); final int numPartitions = Optional .ofNullable(parser.get("numPartitions")) .map(Integer::valueOf) .orElse(NUM_PARTITIONS); log.info("numPartitions: '{}'", numPartitions); log.info("graphBasePath: '{}'", graphBasePath); log.info("actionSetId: '{}'", actionSetId); log.info("workingPath: '{}'", workingPath); log.info("Copying OpenOrgs Merge Rels"); final String outputPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization"); final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation"); // collect organization merge relations from openorgs database JavaRDD mergeRelsRDD = spark .read() .textFile(relationPath) .map(patchRelFn(), Encoders.bean(Relation.class)) .toJavaRDD() .filter(this::isOpenorgs) // take only openorgs relations .filter(this::isMergeRel); // take merges and isMergedIn relations log.info("Number of Openorgs Merge Relations collected: {}", mergeRelsRDD.count()); final Dataset relations = spark .createDataset( mergeRelsRDD.rdd(), Encoders.bean(Relation.class)); saveParquet(relations, outputPath, SaveMode.Append); } private boolean isMergeRel(Relation rel) { return (rel.getRelClass().equals(ModelConstants.MERGES) || rel.getRelClass().equals(ModelConstants.IS_MERGED_IN)) && rel.getRelType().equals(ModelConstants.ORG_ORG_RELTYPE) && rel.getSubRelType().equals(ModelConstants.DEDUP); } }