package eu.dnetlib.dhp.actionmanager.project; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.HashMap; import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme; import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject; import eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.action.AtomicAction; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.H2020Classification; import eu.dnetlib.dhp.schema.oaf.H2020Programme; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; /** * Class that makes the ActionSet. To prepare the AS two joins are needed * * 1. join betweem the collected project subset and the programme extenden with the classification on the grant agreement. * For each entry a * eu.dnetlib.dhp.Project entity is created and the information about H2020Classification is set together with the * h2020topiccode variable * 2. join between the output of the previous step and the topic information on the topic code. Each time a match is * found the h2020topicdescription variable is set. * * To produce one single entry for each project code a step of groupoing is needed: each project can be associated to more * than one programme. * * */ public class SparkAtomicActionJob { private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final HashMap programmeMap = new HashMap<>(); public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( SparkAtomicActionJob.class .getResourceAsStream( "/eu/dnetlib/dhp/actionmanager/project/action_set_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 projectPath = parser.get("projectPath"); log.info("projectPath: {}", projectPath); final String outputPath = parser.get("outputPath"); log.info("outputPath {}: ", outputPath); final String programmePath = parser.get("programmePath"); log.info("programmePath {}: ", programmePath); final String topicPath = parser.get("topicPath"); log.info("topic path {}: ", topicPath); SparkConf conf = new SparkConf(); runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); getAtomicActions( spark, projectPath, programmePath, topicPath, outputPath); }); } private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } private static void getAtomicActions(SparkSession spark, String projectPatH, String programmePath, String topicPath, String outputPath) { Dataset project = readPath(spark, projectPatH, CSVProject.class); Dataset programme = readPath(spark, programmePath, CSVProgramme.class); Dataset topic = readPath(spark, topicPath, EXCELTopic.class); Dataset aaproject = project .joinWith(programme, project.col("programme").equalTo(programme.col("code")), "left") .map((MapFunction, Project>) c -> { CSVProject csvProject = c._1(); return Optional .ofNullable(c._2()) .map(csvProgramme -> { Project pp = new Project(); pp .setId( createOpenaireId( ModelSupport.entityIdPrefix.get("project"), "corda__h2020", csvProject.getId())); pp.setH2020topiccode(csvProject.getTopics()); H2020Programme pm = new H2020Programme(); H2020Classification h2020classification = new H2020Classification(); pm.setCode(csvProject.getProgramme()); h2020classification.setClassification(csvProgramme.getClassification()); h2020classification.setH2020Programme(pm); setLevelsandProgramme(h2020classification, csvProgramme.getClassification_short()); // setProgramme(h2020classification, ocsvProgramme.get().getClassification()); pp.setH2020classification(Arrays.asList(h2020classification)); return pp; }) .orElse(null); }, Encoders.bean(Project.class)) .filter(Objects::nonNull); aaproject .joinWith(topic, aaproject.col("h2020topiccode").equalTo(topic.col("code")), "left") .map((MapFunction, Project>) p -> { Optional op = Optional.ofNullable(p._2()); Project rp = p._1(); if (op.isPresent()) { rp.setH2020topicdescription(op.get().getTitle()); } return rp; }, Encoders.bean(Project.class)) .filter(Objects::nonNull) .groupByKey( (MapFunction) p -> p.getId(), Encoders.STRING()) .mapGroups((MapGroupsFunction) (s, it) -> { Project first = it.next(); it.forEachRemaining(p -> { first.mergeFrom(p); }); return first; }, Encoders.bean(Project.class)) .toJavaRDD() .map(p -> new AtomicAction(Project.class, p)) .mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), new Text(OBJECT_MAPPER.writeValueAsString(aa)))) .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); } private static void setLevelsandProgramme(H2020Classification h2020Classification, String classification_short) { String[] tmp = classification_short.split(" \\| "); h2020Classification.setLevel1(tmp[0]); if (tmp.length > 1) { h2020Classification.setLevel2(tmp[1]); } if (tmp.length > 2) { h2020Classification.setLevel3(tmp[2]); } h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]); } // private static void setProgramme(H2020Classification h2020Classification, String classification) { // String[] tmp = classification.split(" \\| "); // // h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]); // } 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)); } public static String createOpenaireId( final String prefix, final String nsPrefix, final String id) { return String.format("%s|%s::%s", prefix, nsPrefix, DHPUtils.md5(id)); } }