package eu.dnetlib.dhp.bulktag; import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.ArrayList; import java.util.Objects; import java.util.Optional; 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 com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.bulktag.community.*; import eu.dnetlib.dhp.schema.oaf.Result; public class SparkBulkTagJob { private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkBulkTagJob.class .getResourceAsStream( "/eu/dnetlib/dhp/bulktag/input_bulkTag_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); Boolean isTest = Optional .ofNullable(parser.get("isTest")) .map(Boolean::valueOf) .orElse(Boolean.FALSE); log.info("isTest: {} ", isTest); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class); log.info("pathMap: {}", new Gson().toJson(protoMappingParams)); final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); final Boolean saveGraph = Optional .ofNullable(parser.get("saveGraph")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("saveGraph: {}", saveGraph); Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); CommunityConfiguration cc; String taggingConf = parser.get("taggingConf"); if (isTest) { cc = CommunityConfigurationFactory.newInstance(taggingConf); } else { cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); } runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc); }); } private static void execBulkTag( SparkSession spark, String inputPath, String outputPath, ProtoMap protoMappingParams, Class resultClazz, CommunityConfiguration communityConfiguration) { ResultTagger resultTagger = new ResultTagger(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) .filter(Objects::nonNull) .map( (MapFunction) value -> resultTagger .enrichContextCriteria( value, communityConfiguration, protoMappingParams), Encoders.bean(resultClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); } public static Dataset readPath( SparkSession spark, String inputPath, Class clazz) { return spark .read() .textFile(inputPath) .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); } // TODO remove this hack as soon as the values fixed by this method will be provided as NON null private static MapFunction patchResult() { return r -> { if (r.getDataInfo().getDeletedbyinference() == null) { r.getDataInfo().setDeletedbyinference(false); } if (r.getContext() == null) { r.setContext(new ArrayList<>()); } return r; }; } }