dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateRelationsJson.java

package eu.dnetlib.dhp.actionmanager.opencitations;

import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;

import java.io.IOException;
import java.io.Serializable;
import java.util.*;

import org.apache.commons.cli.ParseException;
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.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import scala.Tuple2;

public class CreateRelationsJson implements Serializable {
	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
	private static final String ID_PREFIX = "50|doi_________::";
	private static final String TRUST = "0.91";

	private static final Logger log = LoggerFactory.getLogger(CreateRelationsJson.class);
	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

	public static void main(final String[] args) throws IOException, ParseException {

		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
			IOUtils
				.toString(
					Objects
						.requireNonNull(
							CreateRelationsJson.class
								.getResourceAsStream(
									"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));

		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("inputPath");
		log.info("inputPath {}", inputPath.toString());

		final String outputPath = parser.get("outputPath");
		log.info("outputPath {}", outputPath);

		SparkConf conf = new SparkConf();
		runWithSparkSession(
			conf,
			isSparkSessionManaged,
			spark -> {
				extractContent(spark, inputPath, outputPath);
			});

	}

	private static void extractContent(SparkSession spark, String inputPath, String outputPath) {
		spark
			.sqlContext()
			.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
			.flatMap(
				(FlatMapFunction<String, Relation>) value -> createRelation(value).iterator(),
				Encoders.bean(Relation.class))
			.filter((FilterFunction<Relation>) value -> value != null)
			.write()
			.mode(SaveMode.Overwrite)
			.option("compression", "gzip")
			.json(outputPath);

	}

	private static List<Relation> createRelation(String value) {
		String[] line = value.split(",");
		if (!line[1].startsWith("10.")) {
			return new ArrayList<>();
		}
		List<Relation> relationList = new ArrayList<>();

		String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
		final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));

		relationList
			.addAll(
				getRelations(
					citing,
					cited));

		if (line[1].endsWith(".refs")) {
			citing = ID_PREFIX + IdentifierFactory
				.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
			relationList.addAll(getRelations(citing, cited));
		}

		return relationList;
	}

	private static Collection<Relation> getRelations(String citing, String cited) {

		return Arrays
			.asList(
				getRelation(citing, cited, ModelConstants.CITES),
				getRelation(cited, citing, ModelConstants.IS_CITED_BY));
	}

	public static Relation getRelation(
		String source,
		String target,
		String relclass) {
		Relation r = new Relation();
		r.setCollectedfrom(getCollectedFrom());
		r.setSource(source);
		r.setTarget(target);
		r.setRelClass(relclass);
		r.setRelType(ModelConstants.RESULT_RESULT);
		r.setSubRelType(ModelConstants.CITATION);
		r
			.setDataInfo(
				getDataInfo());
		return r;
	}

	public static List<KeyValue> getCollectedFrom() {
		KeyValue kv = new KeyValue();
		kv.setKey(ModelConstants.OPENOCITATIONS_ID);
		kv.setValue(ModelConstants.OPENOCITATIONS_NAME);

		return Arrays.asList(kv);
	}

	public static DataInfo getDataInfo() {
		DataInfo di = new DataInfo();
		di.setInferred(false);
		di.setDeletedbyinference(false);
		di.setTrust(TRUST);

		di
			.setProvenanceaction(
				getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
		return di;
	}

	public static Qualifier getQualifier(String class_id, String class_name,
		String qualifierSchema) {
		Qualifier pa = new Qualifier();
		pa.setClassid(class_id);
		pa.setClassname(class_name);
		pa.setSchemeid(qualifierSchema);
		pa.setSchemename(qualifierSchema);
		return pa;
	}

}