[BIP! Scores integration] merged missing classes from bipFinder branch

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/BipDeserialize.java

@@ -0,0 +1,28 @@
+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+/**
+ * Class that maps the model of the bipFinder! input data.
+ * Only needed for deserialization purposes
+ */
+
+public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
+
+	public BipDeserialize() {
+		super();
+	}
+
+	public List<Score> get(String key) {
+
+		if (super.get(key) == null) {
+			return new ArrayList<>();
+		}
+		return super.get(key);
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java

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+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+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.JavaSparkContext;
+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.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+/**
+ * Just collects all the atomic actions produced for the different results and saves them in
+ * outputpath for the ActionSet
+ */
+public class CollectAndSave implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				CollectAndSave.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.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("inputPath");
+		log.info("inputPath {}: ", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}: ", outputPath);
+
+		SparkConf conf = new SparkConf();
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				removeOutputDir(spark, outputPath);
+				collectAndSave(spark, inputPath, outputPath);
+			});
+	}
+
+	private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
+		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		sc
+			.sequenceFile(inputPath + "/publication", Text.class, Text.class)
+			.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
+			.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
+			.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+		;
+	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/KeyValue.java

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+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.Serializable;
+
+public class KeyValue implements Serializable {
+
+	private String key;
+	private String value;
+
+	public String getKey() {
+		return key;
+	}
+
+	public void setKey(String key) {
+		this.key = key;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/PreparedResult.java

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+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.Serializable;
+
+/**
+ * Subset of the information of the generic results that are needed to create the atomic action
+ */
+public class PreparedResult implements Serializable {
+	private String id; // openaire id
+	private String value; // doi
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/Score.java

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+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.Serializable;
+import java.util.List;
+
+/**
+ * represents the score in the input file
+ */
+public class Score implements Serializable {
+
+	private String id;
+	private List<KeyValue> unit;
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public List<KeyValue> getUnit() {
+		return unit;
+	}
+
+	public void setUnit(List<KeyValue> unit) {
+		this.unit = unit;
+	}
+}