package eu.dnetlib.dhp.bulktag.eosc; import static eu.dnetlib.dhp.PropagationConstant.readPath; import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir; import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*; import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; import java.io.Serializable; import java.util.*; import java.util.stream.Collectors; import javax.print.attribute.DocAttributeSet; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.ForeachFunction; 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.SparkBulkTagJob; import eu.dnetlib.dhp.bulktag.community.*; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; /** * @author miriam.baglioni * @Date 21/07/22 */ public class SparkEoscBulkTag implements Serializable { private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class); public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkEoscBulkTag.class .getResourceAsStream( "/eu/dnetlib/dhp/bulktag/input_eosc_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); final String inputPath = parser.get("sourcePath"); log.info("inputPath: {}", inputPath); final String workingPath = parser.get("workingPath"); log.info("workingPath: {}", workingPath); String datasourceMapPath = parser.get("datasourceMapPath"); log.info("datasourceMapPath: {}", datasourceMapPath); final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); Class resultClazz = (Class) Class.forName(resultClassName); SparkConf conf = new SparkConf(); CommunityConfiguration cc; runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, workingPath); execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz); }); } private static void execBulkTag( SparkSession spark, String inputPath, String workingPath, String datasourceMapPath, Class resultClazz) { List hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class) .map((MapFunction) dm -> dm.getMaster(), Encoders.STRING()) .collectAsList(); readPath(spark, inputPath, resultClazz) .map(patchResult(), Encoders.bean(resultClazz)) .filter(Objects::nonNull) .map( (MapFunction) value -> enrich(value, hostedByList), Encoders.bean(resultClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(workingPath); readPath(spark, workingPath, resultClazz) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(inputPath); } private static R enrich(R value, List hostedByList) { if (value .getInstance() .stream() .anyMatch( i -> (hostedByList.contains(i.getHostedby().getKey()))) && !value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) { Context context = new Context(); context.setId("eosc"); context .setDataInfo( Arrays .asList( OafMapperUtils .dataInfo( false, BULKTAG_DATA_INFO_TYPE, true, false, OafMapperUtils .qualifier( CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE, DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST))); value.getContext().add(context); } return value; } 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; }; } }