package eu.dnetlib.dhp.oa.graph.clean; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; 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 java.io.Serializable; import java.util.List; import java.util.Optional; import java.util.stream.Collectors; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; public class CleanContextSparkJob implements Serializable { private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( CleanContextSparkJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String inputPath = parser.get("inputPath"); log.info("inputPath: {}", inputPath); String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); String contextId = parser.get("contextId"); log.info("contextId: {}", contextId); String verifyParam = parser.get("verifyParam"); log.info("verifyParam: {}", verifyParam); String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); Class entityClazz = (Class) Class.forName(graphTableClassName); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); }); } private static void cleanContext(SparkSession spark, String contextId, String verifyParam, String inputPath, Class entityClazz, String workingPath) { Dataset res = spark .read() .textFile(inputPath) .map( (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)); res.map((MapFunction) r -> { if(!r.getTitle() .stream() .filter(t -> t.getQualifier().getClassid() .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))){ return r; } r.setContext(r.getContext().stream().filter(c -> !c.getId().split("::")[0] .equalsIgnoreCase(contextId)).collect(Collectors.toList())); return r; } ,Encoders.bean(entityClazz)) .write() .mode(SaveMode.Overwrite) .option("compression","gzip") .json(workingPath); spark.read().textFile(workingPath).map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)) .write() .mode(SaveMode.Overwrite) .option("compression","gzip") .json(inputPath); } }