classes for dumping of the graph as ttl file

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ttl/OrganizationInfo.java

@@ -1,4 +1,62 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.ttl;
 
-public class OrganizationInfo {
+import java.io.Serializable;
+import java.util.List;
+
+public class OrganizationInfo implements Serializable {
+	private String name;
+	private String shortName;
+	private String country;
+	private String websiteUrl;
+	private List<Pids> pidsList;
+	private String id;
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getShortName() {
+		return shortName;
+	}
+
+	public void setShortName(String shortName) {
+		this.shortName = shortName;
+	}
+
+	public String getCountry() {
+		return country;
+	}
+
+	public void setCountry(String country) {
+		this.country = country;
+	}
+
+	public String getWebsiteUrl() {
+		return websiteUrl;
+	}
+
+	public void setWebsiteUrl(String webciteUrl) {
+		this.websiteUrl = webciteUrl;
+	}
+
+	public List<Pids> getPidsList() {
+		return pidsList;
+	}
+
+	public void setPidsList(List<Pids> pidsList) {
+		this.pidsList = pidsList;
+	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ttl/Pids.java

@@ -1,4 +1,25 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.ttl;
 
-public class Pids {
+import java.io.Serializable;
+
+public class Pids implements Serializable {
+	private String type;
+	private String value;
+
+	public String getType() {
+		return type;
+	}
+
+	public void setType(String type) {
+		this.type = type;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ttl/SparkPrepareOrganizationInfo.java

@@ -1,4 +1,88 @@
+
 package eu.dnetlib.dhp.oa.graph.dump.ttl;
 
-public class SparkPrepareOrganizationInfo {
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.compress.GzipCodec;
+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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.Utils;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import scala.Tuple2;
+
+public class SparkPrepareOrganizationInfo implements Serializable {
+	private static final Logger log = LoggerFactory.getLogger(SparkPrepareOrganizationInfo.class);
+
+	public static void main(String[] args) throws Exception {
+		String jsonConfiguration = IOUtils
+			.toString(
+				SparkPrepareOrganizationInfo.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_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 outputPath = parser.get("outputPath");
+		log.info("outputPath: {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+
+		runWithSparkHiveSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				Utils.removeOutputDir(spark, outputPath);
+				prepareOrganization(spark, inputPath, outputPath);
+
+			});
+
+	}
+
+	private static void prepareOrganization(SparkSession spark, String inputPath, String outputPath) {
+		Dataset<Organization> orgs = Utils.readPath(spark, inputPath, Organization.class);
+
+		orgs.createOrReplaceTempView("organization");
+
+		String query = "select country.classname country, legalname.value name, legalshortname.value shortName, websiteurl.value websiteUrl, "
+			+
+			"collect_set(named_struct(\"pidtype\", pIde.qualifier.classid, \"pid\", pIde.value)) as pidsList, id " +
+			"from organization " +
+			"lateral view explode( pid) p as pIde " +
+			"group by country.classname, legalname.value, legalshortname.value, websiteurl.value, id";
+
+		spark
+			.sql(query)
+			.as(Encoders.bean(OrganizationInfo.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(outputPath);
+
+	}
+
 }