dataset based provision WIP

dhp-common/pom.xml

@@ -13,6 +13,26 @@
 	<packaging>jar</packaging>
 
 	<dependencies>
+
+		<dependency>
+			<groupId>eu.dnetlib.dhp</groupId>
+			<artifactId>dhp-schemas</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-common</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.spark</groupId>
+			<artifactId>spark-core_2.11</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.spark</groupId>
+			<artifactId>spark-sql_2.11</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>commons-cli</groupId>
 			<artifactId>commons-cli</artifactId>

dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java

@@ -0,0 +1,56 @@
+package eu.dnetlib.dhp.common;
+
+import java.io.Serializable;
+import java.util.function.Supplier;
+
+/**
+ * Provides serializable and throwing extensions to standard functional interfaces.
+ */
+public class FunctionalInterfaceSupport {
+
+    private FunctionalInterfaceSupport() {
+    }
+
+    /**
+     * Serializable supplier of any kind of objects. To be used withing spark processing pipelines when supplying
+     * functions externally.
+     *
+     * @param <T>
+     */
+    @FunctionalInterface
+    public interface SerializableSupplier<T> extends Supplier<T>, Serializable {
+    }
+
+    /**
+     * Extension of consumer accepting functions throwing an exception.
+     *
+     * @param <T>
+     * @param <E>
+     */
+    @FunctionalInterface
+    public interface ThrowingConsumer<T, E extends Exception> {
+        void accept(T t) throws E;
+    }
+
+    /**
+     * Extension of supplier accepting functions throwing an exception.
+     *
+     * @param <T>
+     * @param <E>
+     */
+    @FunctionalInterface
+    public interface ThrowingSupplier<T, E extends Exception> {
+        T get() throws E;
+    }
+
+    /**
+     * Extension of runnable accepting functions throwing an exception.
+     *
+     * @param <E>
+     */
+    @FunctionalInterface
+    public interface ThrowingRunnable<E extends Exception> {
+        void run() throws E;
+    }
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java

@@ -0,0 +1,57 @@
+package eu.dnetlib.dhp.common;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileStatus;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
+
+/**
+ * HDFS utility methods.
+ */
+public class HdfsSupport {
+    private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class);
+
+    private HdfsSupport() {
+    }
+
+    /**
+     * Removes a path (file or dir) from HDFS.
+     *
+     * @param path          Path to be removed
+     * @param configuration Configuration of hadoop env
+     */
+    public static void remove(String path, Configuration configuration) {
+        logger.info("Removing path: {}", path);
+        rethrowAsRuntimeException(() -> {
+            Path f = new Path(path);
+            FileSystem fileSystem = FileSystem.get(configuration);
+            if (fileSystem.exists(f)) {
+                fileSystem.delete(f, true);
+            }
+        });
+    }
+
+    /**
+     * Lists hadoop files located below path or alternatively lists subdirs under path.
+     *
+     * @param path          Path to be listed for hadoop files
+     * @param configuration Configuration of hadoop env
+     * @return List with string locations of hadoop files
+     */
+    public static List<String> listFiles(String path, Configuration configuration) {
+        logger.info("Listing files in path: {}", path);
+        return rethrowAsRuntimeException(() -> Arrays
+                .stream(FileSystem.get(configuration).listStatus(new Path(path)))
+                .filter(FileStatus::isDirectory)
+                .map(x -> x.getPath().toString())
+                .collect(Collectors.toList()));
+    }
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java

@@ -0,0 +1,57 @@
+package eu.dnetlib.dhp.common;
+
+import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.SparkSession;
+
+import java.util.Objects;
+import java.util.function.Function;
+
+/**
+ * SparkSession utility methods.
+ */
+public class SparkSessionSupport {
+
+    private SparkSessionSupport() {
+    }
+
+    /**
+     * Runs a given function using SparkSession created using default builder and supplied SparkConf. Stops SparkSession
+     * when SparkSession is managed. Allows to reuse SparkSession created externally.
+     *
+     * @param conf                  SparkConf instance
+     * @param isSparkSessionManaged When true will stop SparkSession
+     * @param fn                    Consumer to be applied to constructed SparkSession
+     */
+    public static void runWithSparkSession(SparkConf conf,
+                                           Boolean isSparkSessionManaged,
+                                           ThrowingConsumer<SparkSession, Exception> fn) {
+        runWithSparkSession(c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn);
+    }
+
+    /**
+     * Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops SparkSession
+     * when SparkSession is managed. Allows to reuse SparkSession created externally.
+     *
+     * @param sparkSessionBuilder   Builder of SparkSession
+     * @param conf                  SparkConf instance
+     * @param isSparkSessionManaged When true will stop SparkSession
+     * @param fn                    Consumer to be applied to constructed SparkSession
+     */
+    public static void runWithSparkSession(Function<SparkConf, SparkSession> sparkSessionBuilder,
+                                           SparkConf conf,
+                                           Boolean isSparkSessionManaged,
+                                           ThrowingConsumer<SparkSession, Exception> fn) {
+        SparkSession spark = null;
+        try {
+            spark = sparkSessionBuilder.apply(conf);
+            fn.accept(spark);
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        } finally {
+            if (Objects.nonNull(spark) && isSparkSessionManaged) {
+                spark.stop();
+            }
+        }
+    }
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java

@@ -0,0 +1,76 @@
+package eu.dnetlib.dhp.common;
+
+import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingRunnable;
+import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingSupplier;
+
+/**
+ * Exception handling utility methods.
+ */
+public class ThrowingSupport {
+
+    private ThrowingSupport() {
+    }
+
+    /**
+     * Executes given runnable and rethrows any exceptions as RuntimeException.
+     *
+     * @param fn  Runnable to be executed
+     * @param <E> Type of exception thrown
+     */
+    public static <E extends Exception> void rethrowAsRuntimeException(ThrowingRunnable<E> fn) {
+        try {
+            fn.run();
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    /**
+     * Executes given runnable and rethrows any exceptions as RuntimeException with custom message.
+     *
+     * @param fn  Runnable to be executed
+     * @param msg Message to be set for rethrown exception
+     * @param <E> Type of exception thrown
+     */
+    public static <E extends Exception> void rethrowAsRuntimeException(ThrowingRunnable<E> fn, String msg) {
+        try {
+            fn.run();
+        } catch (Exception e) {
+            throw new RuntimeException(msg, e);
+        }
+    }
+
+    /**
+     * Executes given supplier and rethrows any exceptions as RuntimeException.
+     *
+     * @param fn  Supplier to be executed
+     * @param <T> Type of returned value
+     * @param <E> Type of exception thrown
+     * @return Result of supplier execution
+     */
+    public static <T, E extends Exception> T rethrowAsRuntimeException(ThrowingSupplier<T, E> fn) {
+        try {
+            return fn.get();
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    /**
+     * Executes given supplier and rethrows any exceptions as RuntimeException with custom message.
+     *
+     * @param fn  Supplier to be executed
+     * @param msg Message to be set for rethrown exception
+     * @param <T> Type of returned value
+     * @param <E> Type of exception thrown
+     * @return Result of supplier execution
+     */
+    public static <T, E extends Exception> T rethrowAsRuntimeException(ThrowingSupplier<T, E> fn, String msg) {
+        try {
+            return fn.get();
+        } catch (Exception e) {
+            throw new RuntimeException(msg, e);
+        }
+    }
+
+}

dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java

@@ -0,0 +1,78 @@
+package eu.dnetlib.dhp.common;
+
+import org.apache.hadoop.conf.Configuration;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Arrays;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+public class HdfsSupportTest {
+
+    @Nested
+    class Remove {
+
+        @Test
+        public void shouldThrowARuntimeExceptionOnError() {
+            // when
+            assertThrows(RuntimeException.class, () ->
+                    HdfsSupport.remove(null, new Configuration()));
+        }
+
+        @Test
+        public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
+            // when
+            HdfsSupport.remove(tempDir.toString(), new Configuration());
+
+            // then
+            assertFalse(Files.exists(tempDir));
+        }
+
+        @Test
+        public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
+            // given
+            Path file = Files.createTempFile(tempDir, "p", "s");
+
+            // when
+            HdfsSupport.remove(file.toString(), new Configuration());
+
+            // then
+            assertFalse(Files.exists(file));
+        }
+    }
+
+    @Nested
+    class ListFiles {
+
+        @Test
+        public void shouldThrowARuntimeExceptionOnError() {
+            // when
+            assertThrows(RuntimeException.class, () ->
+                    HdfsSupport.listFiles(null, new Configuration()));
+        }
+
+        @Test
+        public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
+            Path subDir1 = Files.createTempDirectory(tempDir, "list_me");
+            Path subDir2 = Files.createTempDirectory(tempDir, "list_me");
+
+            // when
+            List<String> paths = HdfsSupport.listFiles(tempDir.toString(), new Configuration());
+
+            // then
+            assertEquals(2, paths.size());
+            List<String> expecteds = Arrays.stream(new String[]{subDir1.toString(), subDir2.toString()})
+                    .sorted().collect(Collectors.toList());
+            List<String> actuals = paths.stream().sorted().collect(Collectors.toList());
+            assertTrue(actuals.get(0).contains(expecteds.get(0)));
+            assertTrue(actuals.get(1).contains(expecteds.get(1)));
+        }
+    }
+}

dhp-common/src/test/java/eu/dnetlib/dhp/common/ModelSupportTest.java

@@ -0,0 +1,36 @@
+package eu.dnetlib.dhp.common;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class ModelSupportTest {
+
+    @Nested
+    class IsSubClass {
+
+        @Test
+        public void shouldReturnFalseWhenSubClassDoesNotExtendSuperClass() {
+            // when
+            Boolean result = ModelSupport.isSubClass(Relation.class, OafEntity.class);
+
+            // then
+            assertFalse(result);
+        }
+
+        @Test
+        public void shouldReturnTrueWhenSubClassExtendsSuperClass() {
+            // when
+            Boolean result = ModelSupport.isSubClass(Result.class, OafEntity.class);
+
+            // then
+            assertTrue(result);
+        }
+    }
+}

dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java

@@ -0,0 +1,54 @@
+package eu.dnetlib.dhp.common;
+
+import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.Nested;
+import org.junit.jupiter.api.Test;
+
+import java.util.function.Function;
+
+import static org.mockito.Mockito.*;
+
+public class SparkSessionSupportTest {
+
+    @Nested
+    class RunWithSparkSession {
+
+        @Test
+        public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged() throws Exception {
+            // given
+            SparkSession spark = mock(SparkSession.class);
+            SparkConf conf = mock(SparkConf.class);
+            Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
+            when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
+            ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
+
+            // when
+            SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, false, fn);
+
+            // then
+            verify(sparkSessionBuilder).apply(conf);
+            verify(fn).accept(spark);
+            verify(spark, never()).stop();
+        }
+
+        @Test
+        public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged() throws Exception {
+            // given
+            SparkSession spark = mock(SparkSession.class);
+            SparkConf conf = mock(SparkConf.class);
+            Function<SparkConf, SparkSession> sparkSessionBuilder = mock(Function.class);
+            when(sparkSessionBuilder.apply(conf)).thenReturn(spark);
+            ThrowingConsumer<SparkSession, Exception> fn = mock(ThrowingConsumer.class);
+
+            // when
+            SparkSessionSupport.runWithSparkSession(sparkSessionBuilder, conf, true, fn);
+
+            // then
+            verify(sparkSessionBuilder).apply(conf);
+            verify(fn).accept(spark);
+            verify(spark, times(1)).stop();
+        }
+    }
+}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java

@@ -0,0 +1,51 @@
+package eu.dnetlib.dhp.schema.common;
+
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+
+/**
+ * Inheritance utility methods.
+ */
+public class ModelSupport {
+
+    private ModelSupport() {
+    }
+
+    /**
+     * Checks subclass-superclass relationship.
+     *
+     * @param subClazzObject   Subclass object instance
+     * @param superClazzObject Superclass object instance
+     * @param <X>              Subclass type
+     * @param <Y>              Superclass type
+     * @return True if X is a subclass of Y
+     */
+    public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Y superClazzObject) {
+        return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
+    }
+
+    /**
+     * Checks subclass-superclass relationship.
+     *
+     * @param subClazzObject Subclass object instance
+     * @param superClazz     Superclass class
+     * @param <X>            Subclass type
+     * @param <Y>            Superclass type
+     * @return True if X is a subclass of Y
+     */
+    public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Class<Y> superClazz) {
+        return isSubClass(subClazzObject.getClass(), superClazz);
+    }
+
+    /**
+     * Checks subclass-superclass relationship.
+     *
+     * @param subClazz   Subclass class
+     * @param superClazz Superclass class
+     * @param <X>        Subclass type
+     * @param <Y>        Superclass type
+     * @return True if X is a subclass of Y
+     */
+    public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(Class<X> subClazz, Class<Y> superClazz) {
+        return superClazz.isAssignableFrom(subClazz);
+    }
+}

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java

@@ -92,8 +92,7 @@ public class Relation extends Oaf {
 				subRelType.equals(relation.subRelType) &&
 				relClass.equals(relation.relClass) &&
 				source.equals(relation.source) &&
-				target.equals(relation.target) &&
+				target.equals(relation.target);
-				Objects.equals(collectedFrom, relation.collectedFrom);
 	}
 
 	@Override

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java

@@ -0,0 +1,167 @@
+package eu.dnetlib.dhp.oa.provision;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.*;
+import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
+import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.Function;
+import org.apache.spark.api.java.function.Function2;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.rdd.RDD;
+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 scala.Tuple2;
+
+import java.io.IOException;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*;
+
+/**
+ * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
+ * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
+ * and all the possible relationships (similarity links produced by the Dedup process are excluded).
+ *
+ * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
+ * by E, finally grouped by E.id;
+ *
+ * The workflow is organized in different parts aimed to to reduce the complexity of the operation
+ *  1) PrepareRelationsJob:
+ *      only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
+ *      can be linked at most to 100 other objects
+ *
+ *  2) JoinRelationEntityByTargetJob:
+ *      prepare tuples [source entity - relation - target entity] (S - R - T):
+ *      for each entity type E_i
+ *          join (R.target = E_i.id),
+ *          map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
+ *          join (E_i.id = [R - T_i].source), where E_i becomes the source entity S
+ *
+ *  3) AdjacencyListBuilderJob:
+ *      given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
+ *
+ *  4) XmlConverterJob:
+ *      convert the JoinedEntities as XML records
+ */
+public class AdjacencyListBuilderJob {
+
+    private static final Logger log = LoggerFactory.getLogger(AdjacencyListBuilderJob.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                IOUtils.toString(
+                        AdjacencyListBuilderJob.class
+                                .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        String inputPath = parser.get("inputPath");
+        log.info("inputPath: {}", inputPath);
+
+        String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        SparkConf conf = new SparkConf();
+        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+        conf.registerKryoClasses(getKryoClasses());
+
+        runWithSparkSession(conf, isSparkSessionManaged,
+                spark -> {
+                    removeOutputDir(spark, outputPath);
+                    createAdjacencyLists(spark, inputPath, outputPath);
+                });
+
+    }
+
+    private static void createAdjacencyLists(SparkSession spark, String inputPath, String outputPath) {
+
+        RDD<JoinedEntity> joined = spark.read()
+                .load(inputPath)
+                .as(Encoders.kryo(EntityRelEntity.class))
+                .javaRDD()
+                .map(e -> getJoinedEntity(e))
+                .mapToPair(e -> new Tuple2<>(e.getEntity().getId(), e))
+                .reduceByKey((j1, j2) -> getJoinedEntity(j1, j2))
+                .map(Tuple2::_2)
+                .rdd();
+
+        spark.createDataset(joined, Encoders.bean(JoinedEntity.class))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .parquet(outputPath);
+
+    }
+
+    private static JoinedEntity getJoinedEntity(JoinedEntity j1, JoinedEntity j2) {
+        JoinedEntity je = new JoinedEntity();
+        je.setEntity(je.getEntity());
+        je.setType(j1.getType());
+
+        Links links = new Links();
+        links.addAll(j1.getLinks());
+        links.addAll(j2.getLinks());
+
+        return je;
+    }
+
+    private static JoinedEntity getJoinedEntity(EntityRelEntity e) {
+        JoinedEntity j = new JoinedEntity();
+        j.setEntity(toOafEntity(e.getEntity()));
+        j.setType(EntityType.valueOf(e.getEntity().getType()));
+        Links links = new Links();
+        links.add(new eu.dnetlib.dhp.oa.provision.model.Tuple2(e.getRelation(), e.getTarget()));
+        j.setLinks(links);
+        return j;
+    }
+
+    private static OafEntity toOafEntity(TypedRow typedRow) {
+        return parseOaf(typedRow.getOaf(), typedRow.getType());
+    }
+
+    private static OafEntity parseOaf(final String json, final String type) {
+        try {
+            switch (GraphMappingUtils.EntityType.valueOf(type)) {
+                case publication:
+                    return OBJECT_MAPPER.readValue(json, Publication.class);
+                case dataset:
+                    return OBJECT_MAPPER.readValue(json, Dataset.class);
+                case otherresearchproduct:
+                    return OBJECT_MAPPER.readValue(json, OtherResearchProduct.class);
+                case software:
+                    return OBJECT_MAPPER.readValue(json, Software.class);
+                case datasource:
+                    return OBJECT_MAPPER.readValue(json, Datasource.class);
+                case organization:
+                    return OBJECT_MAPPER.readValue(json, Organization.class);
+                case project:
+                    return OBJECT_MAPPER.readValue(json, Project.class);
+                default:
+                    throw new IllegalArgumentException("invalid type: " + type);
+            }
+        } catch (IOException e) {
+            throw new IllegalArgumentException(e);
+        }
+    }
+
+    private static void removeOutputDir(SparkSession spark, String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java

@@ -0,0 +1,157 @@
+package eu.dnetlib.dhp.oa.provision;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity;
+import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
+import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+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 scala.Tuple2;
+
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*;
+
+/**
+ * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
+ * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
+ * and all the possible relationships (similarity links produced by the Dedup process are excluded).
+ *
+ * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
+ * by E, finally grouped by E.id;
+ *
+ * The workflow is organized in different parts aimed to to reduce the complexity of the operation
+ *  1) PrepareRelationsJob:
+ *      only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
+ *      can be linked at most to 100 other objects
+ *
+ *  2) CreateRelatedEntitiesJob_phase1:
+ *      prepare tuples [relation - target entity] (R - T):
+ *      for each entity type E_i
+ *          join (R.target = E_i.id),
+ *          map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
+ *          save the tuples [R - T_i] in append mode
+ *
+ *  3) CreateRelatedEntitiesJob_phase2:
+ *      prepare tuples [source entity - relation - target entity] (S - R - T):
+ *      create the union of the each entity type, hash by id (S)
+ *      for each [R - T_i] produced in phase1
+ *          join S.id = [R - T_i].source to produce (S_i - R - T_i)
+ *          save in append mode
+ *
+ *  4) AdjacencyListBuilderJob:
+ *      given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
+ *
+ *  5) XmlConverterJob:
+ *      convert the JoinedEntities as XML records
+ */
+public class CreateRelatedEntitiesJob_phase1 {
+
+    private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase1.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+
+        String jsonConfiguration = IOUtils.toString(
+                PrepareRelationsJob.class
+                        .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.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 inputRelationsPath = parser.get("inputRelationsPath");
+        log.info("inputRelationsPath: {}", inputRelationsPath);
+
+        String inputEntityPath = parser.get("inputEntityPath");
+        log.info("inputEntityPath: {}", inputEntityPath);
+
+        String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        String graphTableClassName = parser.get("graphTableClassName");
+        log.info("graphTableClassName: {}", graphTableClassName);
+
+        Class<? extends OafEntity> entityClazz = (Class<? extends OafEntity>) Class.forName(graphTableClassName);
+
+        SparkConf conf = new SparkConf();
+        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+        conf.registerKryoClasses(getKryoClasses());
+
+        runWithSparkSession(conf, isSparkSessionManaged,
+                spark -> {
+                    removeOutputDir(spark, outputPath);
+                    joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
+                });
+    }
+
+    private static <E extends OafEntity> void joinRelationEntity(SparkSession spark, String inputRelationsPath, String inputEntityPath, Class<E> entityClazz, String outputPath) {
+
+        Dataset<Tuple2<String, SortableRelation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
+                .map((MapFunction<SortableRelation, Tuple2<String, SortableRelation>>) r -> new Tuple2<>(r.getTarget(), r),
+                        Encoders.tuple(Encoders.STRING(), Encoders.kryo(SortableRelation.class)));
+
+        Dataset<Tuple2<String, E>> entities = readPathEntity(spark, inputEntityPath, entityClazz)
+                .map((MapFunction<E, Tuple2<String, E>>) e -> new Tuple2<>(e.getId(), e),
+                        Encoders.tuple(Encoders.STRING(), Encoders.kryo(entityClazz)))
+                .cache();
+
+        relsByTarget
+                .joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner")
+                .filter((FilterFunction<Tuple2<Tuple2<String, SortableRelation>, Tuple2<String, E>>>)
+                        value -> value._2()._2().getDataInfo().getDeletedbyinference() == false)
+                .map((MapFunction<Tuple2<Tuple2<String, SortableRelation>, Tuple2<String, E>>, EntityRelEntity>)
+                        t -> new EntityRelEntity(t._1()._2(), GraphMappingUtils.asRelatedEntity(t._2()._2(), entityClazz)),
+                        Encoders.bean(EntityRelEntity.class))
+                .write()
+                .mode(SaveMode.Append)
+                .parquet(outputPath);
+    }
+
+    private static <E extends OafEntity> Dataset<E> readPathEntity(SparkSession spark, String inputEntityPath, Class<E> entityClazz) {
+
+        log.info("Reading Graph table from: {}", inputEntityPath);
+        return spark
+                .read()
+                .textFile(inputEntityPath)
+                .map((MapFunction<String, E>) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz));
+    }
+
+    /**
+     * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file,
+     *
+     * @param spark
+     * @param relationPath
+     * @return the Dataset<SortableRelation> containing all the relationships
+     */
+    private static Dataset<SortableRelation> readPathRelation(SparkSession spark, final String relationPath) {
+
+        log.info("Reading relations from: {}", relationPath);
+        return spark.read()
+                .load(relationPath)
+                .as(Encoders.bean(SortableRelation.class));
+    }
+
+    private static void removeOutputDir(SparkSession spark, String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java

@@ -0,0 +1,168 @@
+package eu.dnetlib.dhp.oa.provision;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity;
+import eu.dnetlib.dhp.oa.provision.model.TypedRow;
+import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+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 scala.Tuple2;
+
+import java.util.Map;
+import java.util.Optional;
+import java.util.function.Function;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*;
+
+/**
+ * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
+ * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
+ * and all the possible relationships (similarity links produced by the Dedup process are excluded).
+ *
+ * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
+ * by E, finally grouped by E.id;
+ *
+ * The workflow is organized in different parts aimed to to reduce the complexity of the operation
+ *  1) PrepareRelationsJob:
+ *      only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
+ *      can be linked at most to 100 other objects
+ *
+ *  2) CreateRelatedEntitiesJob_phase1:
+ *      prepare tuples [relation - target entity] (R - T):
+ *      for each entity type E_i
+ *          join (R.target = E_i.id),
+ *          map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
+ *          save the tuples [R - T_i] in append mode
+ *
+ *  3) CreateRelatedEntitiesJob_phase2:
+ *      prepare tuples [source entity - relation - target entity] (S - R - T):
+ *      create the union of the each entity type, hash by id (S)
+ *      for each [R - T_i] produced in phase1
+ *          join S.id = [R - T_i].source to produce (S_i - R - T_i)
+ *          save in append mode
+ *
+ *  4) AdjacencyListBuilderJob:
+ *      given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
+ *
+ *  5) XmlConverterJob:
+ *      convert the JoinedEntities as XML records
+ */
+public class CreateRelatedEntitiesJob_phase2 {
+
+    private static final Logger log = LoggerFactory.getLogger(CreateRelatedEntitiesJob_phase2.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+
+        String jsonConfiguration = IOUtils.toString(
+                PrepareRelationsJob.class
+                        .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.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 inputRelatedEntitiesPath = parser.get("inputRelatedEntitiesPath");
+        log.info("inputRelatedEntitiesPath: {}", inputRelatedEntitiesPath);
+
+        String inputGraphPath = parser.get("inputGraphPath");
+        log.info("inputGraphPath: {}", inputGraphPath);
+
+        String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        String graphTableClassName = parser.get("graphTableClassName");
+        log.info("graphTableClassName: {}", graphTableClassName);
+
+        SparkConf conf = new SparkConf();
+        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+        conf.registerKryoClasses(getKryoClasses());
+
+        runWithSparkSession(conf, isSparkSessionManaged,
+                spark -> {
+                    removeOutputDir(spark, outputPath);
+                    joinAllEntities(spark, inputRelatedEntitiesPath, inputGraphPath, outputPath);
+                });
+    }
+
+    private static void joinAllEntities(SparkSession spark, String inputRelatedEntitiesPath, String inputGraphPath, String outputPath) {
+
+        Dataset<Tuple2<String, EntityRelEntity>> relsBySource = readRelatedEntities(spark, inputRelatedEntitiesPath);
+        Dataset<Tuple2<String, TypedRow>> entities = readAllEntities(spark, inputGraphPath);
+
+        entities
+                .joinWith(relsBySource, entities.col("_1").equalTo(relsBySource.col("_1")), "left_outer")
+                .map((MapFunction<Tuple2<Tuple2<String, TypedRow>, Tuple2<String, EntityRelEntity>>, EntityRelEntity>) value -> {
+                    EntityRelEntity re = new EntityRelEntity();
+                    re.setEntity(value._1()._2());
+                    Optional<EntityRelEntity> related = Optional.ofNullable(value._2()).map(Tuple2::_2);
+                    if (related.isPresent()) {
+                        re.setRelation(related.get().getRelation());
+                        re.setTarget(related.get().getTarget());
+                    }
+                    return re;
+                }, Encoders.bean(EntityRelEntity.class))
+                .write()
+                .mode(SaveMode.Append)
+                .parquet(outputPath);
+    }
+
+    private static Dataset<Tuple2<String, TypedRow>> readAllEntities(SparkSession spark, String inputGraphPath) {
+        return GraphMappingUtils.entityTypes.entrySet()
+                .stream()
+                .map((Function<Map.Entry<GraphMappingUtils.EntityType, Class>, Dataset<TypedRow>>)
+                        e -> readPathEntity(spark, inputGraphPath + "/" + e.getKey().name(), e.getValue())
+                        .map((MapFunction<OafEntity, TypedRow>) entity -> {
+                            TypedRow t = new TypedRow();
+                            t.setType(e.getKey().name());
+                            t.setDeleted(entity.getDataInfo().getDeletedbyinference());
+                            t.setId(entity.getId());
+                            t.setOaf(OBJECT_MAPPER.writeValueAsString(entity));
+                            return t;
+                        }, Encoders.bean(TypedRow.class)))
+                .reduce(spark.emptyDataset(Encoders.bean(TypedRow.class)), Dataset::union)
+                .map((MapFunction<TypedRow, Tuple2<String, TypedRow>>)
+                        value -> new Tuple2<>(value.getId(), value),
+                        Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class)));
+    }
+
+    private static Dataset<Tuple2<String, EntityRelEntity>> readRelatedEntities(SparkSession spark, String inputRelatedEntitiesPath) {
+        return spark.read()
+                .load(inputRelatedEntitiesPath)
+                .as(Encoders.kryo(EntityRelEntity.class))
+                .map((MapFunction<EntityRelEntity, Tuple2<String, EntityRelEntity>>)
+                        value -> new Tuple2<>(value.getRelation().getSource(), value),
+                    Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class)));
+    }
+
+
+    private static <E extends OafEntity> Dataset<E> readPathEntity(SparkSession spark, String inputEntityPath, Class<E> entityClazz) {
+
+        log.info("Reading Graph table from: {}", inputEntityPath);
+        return spark
+                .read()
+                .textFile(inputEntityPath)
+                .map((MapFunction<String, E>) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz));
+    }
+
+    private static void removeOutputDir(SparkSession spark, String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/GraphJoiner_v2.java

@@ -1,346 +0,0 @@
-package eu.dnetlib.dhp.oa.provision;
-
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.collect.Iterators;
-import com.google.common.collect.Maps;
-import com.jayway.jsonpath.DocumentContext;
-import com.jayway.jsonpath.JsonPath;
-import eu.dnetlib.dhp.oa.provision.model.*;
-import eu.dnetlib.dhp.oa.provision.utils.*;
-import eu.dnetlib.dhp.schema.oaf.*;
-import org.apache.spark.SparkContext;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.*;
-import org.apache.spark.rdd.RDD;
-import org.apache.spark.sql.*;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.types.*;
-import org.apache.spark.util.LongAccumulator;
-import scala.Tuple2;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.*;
-
-import static org.apache.spark.sql.functions.*;
-
-import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.asRelatedEntity;
-
-/**
- * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
- * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
- * and all the possible relationships (similarity links produced by the Dedup process are excluded).
- *
- * The operation is implemented creating the union between the entity types (E), joined by the relationships (R), and again
- * by E, finally grouped by E.id;
- *
- * Different manipulations of the E and R sets are introduced to reduce the complexity of the operation
- * 1) treat the object payload as string, extracting only the necessary information beforehand using json path,
- *      it seems that deserializing it with jackson's object mapper has higher memory footprint.
- *
- * 2) only consider rels that are not virtually deleted ($.dataInfo.deletedbyinference == false)
- * 3) we only need a subset of fields from the related entities, so we introduce a distinction between E_source = S
- *      and E_target = T. Objects in T are heavily pruned by all the unnecessary information
- *
- * 4) perform the join as (((T.id join R.target) union S) groupby S.id) yield S -> [ <T, R> ]
- */
-public class GraphJoiner_v2 implements Serializable {
-
-    private Map<String, LongAccumulator> accumulators = Maps.newHashMap();
-
-    public static final int MAX_RELS = 100;
-
-    public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd";
-
-    private SparkSession spark;
-
-    private ContextMapper contextMapper;
-
-    private String inputPath;
-
-    private String outPath;
-
-    private String otherDsTypeId;
-
-    public GraphJoiner_v2(SparkSession spark, ContextMapper contextMapper, String otherDsTypeId, String inputPath, String outPath) {
-        this.spark = spark;
-        this.contextMapper = contextMapper;
-        this.otherDsTypeId = otherDsTypeId;
-        this.inputPath = inputPath;
-        this.outPath = outPath;
-
-        final SparkContext sc = spark.sparkContext();
-        prepareAccumulators(sc);
-    }
-
-    public GraphJoiner_v2 adjacencyLists() throws IOException {
-
-        final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(getSpark().sparkContext());
-
-        // read each entity
-        Dataset<TypedRow> datasource = readPathEntity(jsc, getInputPath(), "datasource");
-        Dataset<TypedRow> organization = readPathEntity(jsc, getInputPath(), "organization");
-        Dataset<TypedRow> project = readPathEntity(jsc, getInputPath(), "project");
-        Dataset<TypedRow> dataset = readPathEntity(jsc, getInputPath(), "dataset");
-        Dataset<TypedRow> otherresearchproduct = readPathEntity(jsc, getInputPath(), "otherresearchproduct");
-        Dataset<TypedRow> software = readPathEntity(jsc, getInputPath(), "software");
-        Dataset<TypedRow> publication = readPathEntity(jsc, getInputPath(), "publication");
-
-        // create the union between all the entities
-         datasource
-                .union(organization)
-                .union(project)
-                .union(dataset)
-                .union(otherresearchproduct)
-                .union(software)
-                .union(publication)
-                .repartition(7000)
-                .write()
-                .partitionBy("id")
-                .parquet(getOutPath() + "/entities");
-
-        Dataset<Tuple2<String, TypedRow>> entities = getSpark()
-                .read()
-                .load(getOutPath() + "/entities")
-                .map((MapFunction<Row, Tuple2<String, TypedRow>>) r -> {
-                    TypedRow t = new TypedRow();
-                    t.setId(r.getAs("id"));
-                    t.setDeleted(r.getAs("deleted"));
-                    t.setType(r.getAs("type"));
-                    t.setOaf(r.getAs("oaf"));
-
-                    return new Tuple2<>(t.getId(), t);
-                }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class)))
-                .cache();
-
-        System.out.println("Entities, number of partitions: " + entities.rdd().getNumPartitions());
-        System.out.println("Entities schema:");
-        entities.printSchema();
-        System.out.println("Entities count:" + entities.count());
-
-        // reads the relationships
-        readPathRelation(jsc, getInputPath())
-                .groupByKey((MapFunction<Relation, SortableRelationKey>) t -> SortableRelationKey.from(t), Encoders.kryo(SortableRelationKey.class))
-                .flatMapGroups((FlatMapGroupsFunction<SortableRelationKey, Relation, Relation>) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.kryo(Relation.class))
-                .repartition(3000)
-                .write()
-                .partitionBy("source", "target")
-                .parquet(getOutPath() + "/relations");
-
-        Dataset<Relation> rels = getSpark()
-                .read()
-                .load(getOutPath() + "/relations")
-                .map((MapFunction<Row, Relation>) r -> {
-                    Relation rel = new Relation();
-                    rel.setSource(r.getAs("source"));
-                    rel.setTarget(r.getAs("target"));
-                    rel.setRelType(r.getAs("relType"));
-                    rel.setSubRelType(r.getAs("subRelType"));
-                    rel.setRelClass(r.getAs("relClass"));
-                    rel.setDataInfo(r.getAs("dataInfo"));
-                    rel.setCollectedFrom(r.getList(r.fieldIndex("collectedFrom")));
-                    return rel;
-                }, Encoders.kryo(Relation.class))
-                .cache();
-
-        System.out.println("Relation schema:");
-        System.out.println("Relation, number of partitions: " + rels.rdd().getNumPartitions());
-        System.out.println("Relation schema:");
-        entities.printSchema();
-        System.out.println("Relation count:" + rels.count());
-
-                /*
-        Dataset<Tuple2<String, Relation>> relsByTarget = rels
-                .map((MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(), r), Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)));
-
-
-        relsByTarget
-                .joinWith(entities, relsByTarget.col("_1").equalTo(entities.col("_1")), "inner")
-                .filter((FilterFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, TypedRow>>>) value -> value._2()._2().getDeleted() == false)
-                .map((MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, TypedRow>>, EntityRelEntity>) t -> {
-                    EntityRelEntity e = new EntityRelEntity();
-                    e.setRelation(t._1()._2());
-                    e.setTarget(asRelatedEntity(t._2()._2()));
-                    return e;
-                }, Encoders.kryo(EntityRelEntity.class))
-                .repartition(20000)
-                .write()
-                .parquet(getOutPath() + "/bySource");
-
-        Dataset<Tuple2<String, EntityRelEntity>> bySource = getSpark()
-                .read()
-                .load(getOutPath() + "/bySource")
-                .map(new MapFunction<Row, EntityRelEntity>() {
-                    @Override
-                    public EntityRelEntity call(Row value) throws Exception {
-                        return null;
-                    }
-                }, Encoders.kryo(EntityRelEntity.class))
-                .map((MapFunction<EntityRelEntity, Tuple2<String, EntityRelEntity>>) e -> new Tuple2<>(e.getRelation().getSource(), e),
-                        Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class)))
-
-                System.out.println("bySource schema");
-        bySource.printSchema();
-
-
-
-
-        Dataset<EntityRelEntity> joined = entities
-                .joinWith(bySource, entities.col("_1").equalTo(bySource.col("_1")), "left")
-                .map((MapFunction<Tuple2<Tuple2<String, TypedRow>, Tuple2<String, EntityRelEntity>>, EntityRelEntity>) value -> {
-                    EntityRelEntity re = new EntityRelEntity();
-                    re.setEntity(value._1()._2());
-                    Optional<EntityRelEntity> related = Optional.ofNullable(value._2()).map(Tuple2::_2);
-                    if (related.isPresent()) {
-                        re.setRelation(related.get().getRelation());
-                        re.setTarget(related.get().getTarget());
-                    }
-                    return re;
-                }, Encoders.kryo(EntityRelEntity.class));
-
-        System.out.println("joined schema");
-        joined.printSchema();
-        //joined.write().json(getOutPath() + "/joined");
-
-        final Dataset<JoinedEntity> grouped = joined
-                .groupByKey((MapFunction<EntityRelEntity, TypedRow>) e -> e.getEntity(), Encoders.kryo(TypedRow.class))
-                .mapGroups((MapGroupsFunction<TypedRow, EntityRelEntity, JoinedEntity>) (key, values) -> toJoinedEntity(key, values), Encoders.kryo(JoinedEntity.class));
-
-        System.out.println("grouped schema");
-        grouped.printSchema();
-
-        final XmlRecordFactory recordFactory = new XmlRecordFactory(accumulators, contextMapper, false, schemaLocation, otherDsTypeId);
-        grouped
-                .map((MapFunction<JoinedEntity, String>) value -> recordFactory.build(value), Encoders.STRING())
-                .javaRDD()
-                .mapToPair((PairFunction<Tuple2<String, String>, String, String>) t -> new Tuple2<>(t._1(), t._2()))
-                .saveAsHadoopFile(getOutPath() + "/xml", Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
-
-
-*/
-
-        return this;
-    }
-
-    public SparkSession getSpark() {
-        return spark;
-    }
-
-    public String getInputPath() {
-        return inputPath;
-    }
-
-    public String getOutPath() {
-        return outPath;
-    }
-
-    // HELPERS
-
-    private JoinedEntity toJoinedEntity(TypedRow key, Iterator<EntityRelEntity> values) {
-        final ObjectMapper mapper = getObjectMapper();
-        final JoinedEntity j = new JoinedEntity();
-        j.setType(key.getType());
-        j.setEntity(parseOaf(key.getOaf(), key.getType(), mapper));
-        final Links links = new Links();
-        values.forEachRemaining(rel -> links.add(
-                new eu.dnetlib.dhp.oa.provision.model.Tuple2(
-                        rel.getRelation(),
-                        rel.getTarget()
-                )));
-        j.setLinks(links);
-        return j;
-    }
-
-    private OafEntity parseOaf(final String json, final String type, final ObjectMapper mapper) {
-        try {
-            switch (GraphMappingUtils.EntityType.valueOf(type)) {
-                case publication:
-                    return mapper.readValue(json, Publication.class);
-                case dataset:
-                    return mapper.readValue(json, eu.dnetlib.dhp.schema.oaf.Dataset.class);
-                case otherresearchproduct:
-                    return mapper.readValue(json, OtherResearchProduct.class);
-                case software:
-                    return mapper.readValue(json, Software.class);
-                case datasource:
-                    return mapper.readValue(json, Datasource.class);
-                case organization:
-                    return mapper.readValue(json, Organization.class);
-                case project:
-                    return mapper.readValue(json, Project.class);
-                default:
-                    throw new IllegalArgumentException("invalid type: " + type);
-            }
-        } catch (IOException e) {
-            throw new IllegalArgumentException(e);
-        }
-    }
-
-    /**
-     * Reads a set of eu.dnetlib.dhp.schema.oaf.OafEntity objects from a new line delimited json file,
-     * extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
-     * @param sc
-     * @param inputPath
-     * @param type
-     * @return the JavaPairRDD<String, TypedRow> indexed by entity identifier
-     */
-    private Dataset<TypedRow> readPathEntity(final JavaSparkContext sc, final String inputPath, final String type) {
-        RDD<String> rdd = sc.textFile(inputPath + "/" + type)
-                .rdd();
-
-        return getSpark().createDataset(rdd, Encoders.STRING())
-                .map((MapFunction<String, TypedRow>) s -> {
-                    final DocumentContext json = JsonPath.parse(s);
-                    final TypedRow t = new TypedRow();
-                    t.setId(json.read("$.id"));
-                    t.setDeleted(json.read("$.dataInfo.deletedbyinference"));
-                    t.setType(type);
-                    t.setOaf(s);
-                    return t;
-                }, Encoders.bean(TypedRow.class));
-    }
-
-    /**
-     * Reads a set of eu.dnetlib.dhp.schema.oaf.Relation objects from a sequence file <className, relation json serialization>,
-     * extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow
-     * @param sc
-     * @param inputPath
-     * @return the JavaRDD<TypedRow> containing all the relationships
-     */
-    private Dataset<Relation> readPathRelation(final JavaSparkContext sc, final String inputPath) {
-        final RDD<String> rdd = sc.textFile(inputPath + "/relation")
-                .rdd();
-
-        return getSpark().createDataset(rdd, Encoders.STRING())
-                .map((MapFunction<String, Relation>) s -> new ObjectMapper().readValue(s, Relation.class), Encoders.bean(Relation.class));
-    }
-
-    private ObjectMapper getObjectMapper() {
-        return new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-    }
-
-    private void prepareAccumulators(SparkContext sc) {
-        accumulators.put("resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments"));
-        accumulators.put("resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments"));
-        accumulators.put("resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo"));
-        accumulators.put("resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy"));
-        accumulators.put("resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn"));
-        accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges"));
-
-        accumulators.put("resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo"));
-        accumulators.put("resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo"));
-        accumulators.put("resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy"));
-        accumulators.put("resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces"));
-        accumulators.put("resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf"));
-
-        accumulators.put("resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution"));
-        accumulators.put("projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant"));
-        accumulators.put("projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant"));
-        accumulators.put("organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn"));
-        accumulators.put("organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces"));
-        accumulators.put("datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy"));
-        accumulators.put("datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides"));
-    }
-
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java

@@ -0,0 +1,132 @@
+package eu.dnetlib.dhp.oa.provision;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.rdd.RDD;
+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 scala.Tuple2;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+/**
+ * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
+ * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
+ * and all the possible relationships (similarity links produced by the Dedup process are excluded).
+ *
+ * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
+ * by E, finally grouped by E.id;
+ *
+ * The workflow is organized in different parts aimed to to reduce the complexity of the operation
+ *  1) PrepareRelationsJob:
+ *      only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
+ *      can be linked at most to 100 other objects
+ *
+ *  2) JoinRelationEntityByTargetJob:
+ *      prepare tuples [source entity - relation - target entity] (S - R - T):
+ *      for each entity type E_i
+ *          join (R.target = E_i.id),
+ *          map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
+ *          join (E_i.id = [R - T_i].source), where E_i becomes the source entity S
+ *
+ *  3) AdjacencyListBuilderJob:
+ *      given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
+ *
+ *  4) XmlConverterJob:
+ *      convert the JoinedEntities as XML records
+ */
+public class PrepareRelationsJob {
+
+    private static final Logger log = LoggerFactory.getLogger(PrepareRelationsJob.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static final int MAX_RELS = 100;
+
+    public static void main(String[] args) throws Exception {
+        String jsonConfiguration = IOUtils.toString(
+                PrepareRelationsJob.class
+                        .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.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 inputRelationsPath = parser.get("inputRelationsPath");
+        log.info("inputRelationsPath: {}", inputRelationsPath);
+
+        String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        SparkConf conf = new SparkConf();
+
+        runWithSparkSession(conf, isSparkSessionManaged,
+                spark -> {
+                    removeOutputDir(spark, outputPath);
+                    prepareRelationsFromPaths(spark, inputRelationsPath, outputPath);
+                });
+    }
+
+    private static void prepareRelationsFromPaths(SparkSession spark, String inputRelationsPath, String outputPath) {
+        RDD<SortableRelation> rels = readPathRelation(spark, inputRelationsPath)
+                .filter((FilterFunction<SortableRelation>) r -> r.getDataInfo().getDeletedbyinference() == false)
+                .javaRDD()
+                .mapToPair((PairFunction<SortableRelation, String, List<SortableRelation>>) rel -> new Tuple2<>(
+                        rel.getSource(),
+                        Lists.newArrayList(rel)))
+                .reduceByKey((v1, v2) -> {
+                    v1.addAll(v2);
+                    v1.sort(SortableRelation::compareTo);
+                    if (v1.size() > MAX_RELS) {
+                        return v1.subList(0, MAX_RELS);
+                    }
+                    return new ArrayList<>(v1.subList(0, MAX_RELS));
+                })
+                .flatMap(r -> r._2().iterator())
+                .rdd();
+
+        spark.createDataset(rels, Encoders.bean(SortableRelation.class))
+                .write()
+                .mode(SaveMode.Overwrite)
+                .parquet(outputPath);
+    }
+
+    /**
+     * Reads a Dataset of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text file,
+     *
+     * @param spark
+     * @param inputPath
+     * @return the Dataset<SortableRelation> containing all the relationships
+     */
+    private static Dataset<SortableRelation> readPathRelation(SparkSession spark, final String inputPath) {
+        return spark.read()
+                .textFile(inputPath)
+                .map((MapFunction<String, SortableRelation>) s -> OBJECT_MAPPER.readValue(s, SortableRelation.class),
+                        Encoders.bean(SortableRelation.class));
+    }
+
+    private static void removeOutputDir(SparkSession spark, String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlIndexingJob.java

@@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.provision;
 
 import com.lucidworks.spark.util.SolrSupport;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
@@ -18,6 +19,8 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.rdd.RDD;
 import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerException;
@@ -28,14 +31,20 @@ import java.io.StringReader;
 import java.io.StringWriter;
 import java.text.SimpleDateFormat;
 import java.util.Date;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 public class SparkXmlIndexingJob {
 
-    private static final Log log = LogFactory.getLog(SparkXmlIndexingJob.class);
+    private static final Logger log = LoggerFactory.getLogger(SparkXmlIndexingJob.class);
 
     private static final Integer DEFAULT_BATCH_SIZE = 1000;
 
     private static final String LAYOUT = "index";
+    private static final String INTERPRETATION = "openaire";
+    private static final String SEPARATOR = "-";
+    public static final String DATE_FORMAT = "yyyy-MM-dd'T'hh:mm:ss'Z'";
 
     public static void main(String[] args) throws Exception {
 
@@ -45,48 +54,56 @@ public class SparkXmlIndexingJob {
                                 "/eu/dnetlib/dhp/oa/provision/input_params_update_index.json")));
         parser.parseArgument(args);
 
-        final String inputPath = parser.get("sourcePath");
+        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 isLookupUrl = parser.get("isLookupUrl");
+        log.info("isLookupUrl: {}", isLookupUrl);
+
         final String format = parser.get("format");
+        log.info("format: {}", format);
+
         final Integer batchSize = parser.getObjectMap().containsKey("batchSize") ? Integer.valueOf(parser.get("batchSize")) : DEFAULT_BATCH_SIZE;
+        log.info("batchSize: {}", batchSize);
 
         final ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
         final String fields = getLayoutSource(isLookup, format);
+        log.info("fields: {}", fields);
+
         final String xslt = getLayoutTransformer(isLookup);
 
         final String dsId = getDsId(format, isLookup);
+        log.info("dsId: {}", dsId);
+
         final String zkHost = getZkHost(isLookup);
+        log.info("zkHost: {}", zkHost);
+
         final String version = getRecordDatestamp();
 
         final String indexRecordXslt = getLayoutTransformer(format, fields, xslt);
+        log.info("indexRecordTransformer {}", indexRecordXslt);
 
-        log.info("indexRecordTransformer: " + indexRecordXslt);
+        final SparkConf conf = new SparkConf();
 
-        final String master = parser.get("master");
+        runWithSparkSession(conf, isSparkSessionManaged,
-        final SparkConf conf = new SparkConf()
+                spark -> {
-                .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+                    final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
-        try(SparkSession spark = getSession(conf, master)) {
+                    RDD<SolrInputDocument> docs = sc.sequenceFile(inputPath, Text.class, Text.class)
+                            .map(t -> t._2().toString())
+                            .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s))
+                            .map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s))
+                            .rdd();
 
-            final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+                    final String collection = format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
-
+                    SolrSupport.indexDocs(zkHost, collection, batchSize, docs);
-            RDD<SolrInputDocument> docs = sc.sequenceFile(inputPath, Text.class, Text.class)
+                });
-                    .map(t -> t._2().toString())
-                    .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s))
-                    .map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s))
-                    .rdd();
-
-            SolrSupport.indexDocs(zkHost, format + "-" + LAYOUT + "-openaire", batchSize, docs);
-        }
-    }
-
-    private static SparkSession getSession(SparkConf conf, String master) {
-        return SparkSession
-                .builder()
-                .config(conf)
-                .appName(SparkXmlIndexingJob.class.getSimpleName())
-                .master(master)
-                .getOrCreate();
     }
 
     private static String toIndexRecord(Transformer tr, final String record) {
@@ -95,7 +112,7 @@ public class SparkXmlIndexingJob {
             tr.transform(new StreamSource(new StringReader(record)), res);
             return res.getWriter().toString();
         } catch (Throwable e) {
-            System.out.println("XPathException on record:\n" + record);
+            log.error("XPathException on record: \n {}", record, e);
             throw new IllegalArgumentException(e);
         }
     }
@@ -127,7 +144,7 @@ public class SparkXmlIndexingJob {
      * @return the parsed date
      */
     public static String getRecordDatestamp() {
-        return new SimpleDateFormat("yyyy-MM-dd'T'hh:mm:ss'Z'").format(new Date());
+        return new SimpleDateFormat(DATE_FORMAT).format(new Date());
     }
 
     /**

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlRecordBuilderJob_v2.java

@@ -1,81 +0,0 @@
-package eu.dnetlib.dhp.oa.provision;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.provision.model.*;
-import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
-import eu.dnetlib.dhp.schema.oaf.*;
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.sql.SparkSession;
-
-public class SparkXmlRecordBuilderJob_v2 {
-
-    public static void main(String[] args) throws Exception {
-
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-                IOUtils.toString(
-                        SparkXmlRecordBuilderJob_v2.class.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
-        parser.parseArgument(args);
-
-        try(SparkSession spark = getSession(parser)) {
-
-            final String inputPath = parser.get("sourcePath");
-            final String outputPath = parser.get("outputPath");
-            final String isLookupUrl = parser.get("isLookupUrl");
-            final String otherDsTypeId = parser.get("otherDsTypeId");
-
-
-            new GraphJoiner_v2(spark, ContextMapper.fromIS(isLookupUrl), otherDsTypeId, inputPath, outputPath)
-                    .adjacencyLists();
-        }
-    }
-
-    private static SparkSession getSession(ArgumentApplicationParser parser) {
-        final SparkConf conf = new SparkConf();
-        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
-        conf.set("spark.sql.shuffle.partitions", parser.get("sparkSqlShufflePartitions"));
-        conf.registerKryoClasses(new Class[]{
-                Author.class,
-                Context.class,
-                Country.class,
-                DataInfo.class,
-                eu.dnetlib.dhp.schema.oaf.Dataset.class,
-                Datasource.class,
-                ExternalReference.class,
-                ExtraInfo.class,
-                Field.class,
-                GeoLocation.class,
-                Instance.class,
-                Journal.class,
-                KeyValue.class,
-                Oaf.class,
-                OafEntity.class,
-                OAIProvenance.class,
-                Organization.class,
-                OriginDescription.class,
-                OtherResearchProduct.class,
-                Project.class,
-                Publication.class,
-                Qualifier.class,
-                Relation.class,
-                Result.class,
-                Software.class,
-                StructuredProperty.class,
-
-                TypedRow.class,
-                EntityRelEntity.class,
-                JoinedEntity.class,
-                SortableRelationKey.class,
-                Tuple2.class,
-                Links.class,
-                RelatedEntity.class
-        });
-        return SparkSession
-                .builder()
-                .config(conf)
-                .appName(SparkXmlRecordBuilderJob_v2.class.getSimpleName())
-                .master(parser.get("master"))
-                .getOrCreate();
-    }
-
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java

@@ -0,0 +1,149 @@
+package eu.dnetlib.dhp.oa.provision;
+
+import com.google.common.collect.Maps;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.*;
+import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
+import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
+import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.SparkContext;
+import org.apache.spark.api.java.function.Function;
+import org.apache.spark.api.java.function.Function2;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.rdd.RDD;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.apache.spark.util.LongAccumulator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import scala.Tuple2;
+
+import java.util.Map;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+/**
+ * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
+ * The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
+ * and all the possible relationships (similarity links produced by the Dedup process are excluded).
+ *
+ * The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
+ * by E, finally grouped by E.id;
+ *
+ * The workflow is organized in different parts aimed to to reduce the complexity of the operation
+ *  1) PrepareRelationsJob:
+ *      only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
+ *      can be linked at most to 100 other objects
+ *
+ *  2) JoinRelationEntityByTargetJob:
+ *      prepare tuples [source entity - relation - target entity] (S - R - T):
+ *      for each entity type E_i
+ *          join (R.target = E_i.id),
+ *          map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
+ *          join (E_i.id = [R - T_i].source), where E_i becomes the source entity S
+ *
+ *  3) AdjacencyListBuilderJob:
+ *      given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
+ *
+ *  4) XmlConverterJob:
+ *      convert the JoinedEntities as XML records
+ */
+public class XmlConverterJob {
+
+    private static final Logger log = LoggerFactory.getLogger(XmlConverterJob.class);
+
+    public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd";
+
+    public static void main(String[] args) throws Exception {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                IOUtils.toString(
+                        XmlConverterJob.class
+                                .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json")));
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        String inputPath = parser.get("inputPath");
+        log.info("inputPath: {}", inputPath);
+
+        String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        String isLookupUrl = parser.get("isLookupUrl");
+        log.info("isLookupUrl: {}", isLookupUrl);
+
+        String otherDsTypeId = parser.get("otherDsTypeId");
+        log.info("otherDsTypeId: {}", otherDsTypeId);
+
+        SparkConf conf = new SparkConf();
+
+        runWithSparkSession(conf, isSparkSessionManaged,
+                spark -> {
+                    removeOutputDir(spark, outputPath);
+                    convertToXml(spark, inputPath, outputPath, ContextMapper.fromIS(isLookupUrl), otherDsTypeId);
+                });
+
+    }
+
+    private static void convertToXml(SparkSession spark, String inputPath, String outputPath, ContextMapper contextMapper, String otherDsTypeId) {
+
+        final XmlRecordFactory recordFactory = new XmlRecordFactory(prepareAccumulators(spark.sparkContext()), contextMapper, false, schemaLocation, otherDsTypeId);
+
+        spark.read()
+                .load(inputPath)
+                .as(Encoders.bean(JoinedEntity.class))
+                .map((MapFunction<JoinedEntity, Tuple2<String, String>>) je -> new Tuple2<>(
+                        je.getEntity().getId(),
+                        recordFactory.build(je)
+                ), Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
+                .javaRDD()
+                .mapToPair((PairFunction<Tuple2<String, String>, String, String>) t -> t)
+                .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+    }
+
+    private static void removeOutputDir(SparkSession spark, String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+    private static Map<String, LongAccumulator> prepareAccumulators(SparkContext sc) {
+        Map<String, LongAccumulator> accumulators = Maps.newHashMap();
+        accumulators.put("resultResult_similarity_isAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_isAmongTopNSimilarDocuments"));
+        accumulators.put("resultResult_similarity_hasAmongTopNSimilarDocuments", sc.longAccumulator("resultResult_similarity_hasAmongTopNSimilarDocuments"));
+        accumulators.put("resultResult_supplement_isSupplementTo", sc.longAccumulator("resultResult_supplement_isSupplementTo"));
+        accumulators.put("resultResult_supplement_isSupplementedBy", sc.longAccumulator("resultResult_supplement_isSupplementedBy"));
+        accumulators.put("resultResult_dedup_isMergedIn", sc.longAccumulator("resultResult_dedup_isMergedIn"));
+        accumulators.put("resultResult_dedup_merges", sc.longAccumulator("resultResult_dedup_merges"));
+
+        accumulators.put("resultResult_publicationDataset_isRelatedTo", sc.longAccumulator("resultResult_publicationDataset_isRelatedTo"));
+        accumulators.put("resultResult_relationship_isRelatedTo", sc.longAccumulator("resultResult_relationship_isRelatedTo"));
+        accumulators.put("resultProject_outcome_isProducedBy", sc.longAccumulator("resultProject_outcome_isProducedBy"));
+        accumulators.put("resultProject_outcome_produces", sc.longAccumulator("resultProject_outcome_produces"));
+        accumulators.put("resultOrganization_affiliation_isAuthorInstitutionOf", sc.longAccumulator("resultOrganization_affiliation_isAuthorInstitutionOf"));
+
+        accumulators.put("resultOrganization_affiliation_hasAuthorInstitution", sc.longAccumulator("resultOrganization_affiliation_hasAuthorInstitution"));
+        accumulators.put("projectOrganization_participation_hasParticipant", sc.longAccumulator("projectOrganization_participation_hasParticipant"));
+        accumulators.put("projectOrganization_participation_isParticipant", sc.longAccumulator("projectOrganization_participation_isParticipant"));
+        accumulators.put("organizationOrganization_dedup_isMergedIn", sc.longAccumulator("organizationOrganization_dedup_isMergedIn"));
+        accumulators.put("organizationOrganization_dedup_merges", sc.longAccumulator("resultProject_outcome_produces"));
+        accumulators.put("datasourceOrganization_provision_isProvidedBy", sc.longAccumulator("datasourceOrganization_provision_isProvidedBy"));
+        accumulators.put("datasourceOrganization_provision_provides", sc.longAccumulator("datasourceOrganization_provision_provides"));
+
+        return accumulators;
+    }
+
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java

@@ -1,15 +1,26 @@
 package eu.dnetlib.dhp.oa.provision.model;
 
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
 import java.io.Serializable;
 
 public class EntityRelEntity implements Serializable {
 
     private TypedRow entity;
-    private Relation relation;
+    private SortableRelation relation;
     private RelatedEntity target;
 
+    public EntityRelEntity() {
+    }
+
+    public EntityRelEntity(SortableRelation relation, RelatedEntity target) {
+        this(null, relation, target);
+    }
+
+    public EntityRelEntity(TypedRow entity, SortableRelation relation, RelatedEntity target) {
+        this.entity = entity;
+        this.relation = relation;
+        this.target = target;
+    }
+
     public TypedRow getEntity() {
         return entity;
     }
@@ -18,11 +29,11 @@ public class EntityRelEntity implements Serializable {
         this.entity = entity;
     }
 
-    public Relation getRelation() {
+    public SortableRelation getRelation() {
         return relation;
     }
 
-    public void setRelation(Relation relation) {
+    public void setRelation(SortableRelation relation) {
         this.relation = relation;
     }
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java

@@ -1,22 +1,23 @@
 package eu.dnetlib.dhp.oa.provision.model;
 
+import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 
 import java.io.Serializable;
 
 public class JoinedEntity implements Serializable {
 
-    private String type;
+    private GraphMappingUtils.EntityType type;
 
     private OafEntity entity;
 
     private Links links;
 
-    public String getType() {
+    public GraphMappingUtils.EntityType getType() {
         return type;
     }
 
-    public void setType(String type) {
+    public void setType(GraphMappingUtils.EntityType type) {
         this.type = type;
     }
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Links.java

@@ -1,6 +1,6 @@
 package eu.dnetlib.dhp.oa.provision.model;
 
-import java.util.ArrayList;
+import java.util.HashSet;
 
-public class Links extends ArrayList<Tuple2> {
+public class Links extends HashSet<Tuple2> {
 }

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java

@@ -0,0 +1,34 @@
+package eu.dnetlib.dhp.oa.provision.model;
+
+import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.Maps;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+import java.util.Map;
+
+public class SortableRelation extends Relation implements Comparable<Relation> {
+
+    private final static Map<String, Integer> weights = Maps.newHashMap();
+
+    static {
+        weights.put("outcome", 0);
+        weights.put("supplement", 1);
+        weights.put("publicationDataset", 2);
+        weights.put("relationship", 3);
+        weights.put("similarity", 4);
+        weights.put("affiliation", 5);
+
+        weights.put("provision", 6);
+        weights.put("participation", 7);
+        weights.put("dedup", 8);
+    }
+
+    @Override
+    public int compareTo(Relation o) {
+        return ComparisonChain.start()
+                .compare(weights.get(getSubRelType()), weights.get(o.getSubRelType()))
+                .compare(getSource(), o.getSource())
+                .compare(getTarget(), o.getTarget())
+                .result();
+    }
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java

@@ -2,7 +2,10 @@ package eu.dnetlib.dhp.oa.provision.model;
 
 import eu.dnetlib.dhp.schema.oaf.Relation;
 
-public class Tuple2 {
+import java.io.Serializable;
+import java.util.Objects;
+
+public class Tuple2 implements Serializable {
 
     private Relation relation;
 
@@ -28,4 +31,18 @@ public class Tuple2 {
     public void setRelatedEntity(RelatedEntity relatedEntity) {
         this.relatedEntity = relatedEntity;
     }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Tuple2 t2 = (Tuple2) o;
+        return getRelation().equals(t2.getRelation());
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(getRelation().hashCode());
+    }
+
 }

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java

@@ -1,30 +1,47 @@
 package eu.dnetlib.dhp.oa.provision.utils;
 
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
-import com.jayway.jsonpath.DocumentContext;
+import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
-import com.jayway.jsonpath.JsonPath;
+import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
-import eu.dnetlib.dhp.oa.provision.model.*;
 import eu.dnetlib.dhp.schema.oaf.*;
-import net.minidev.json.JSONArray;
-import org.apache.commons.lang3.StringUtils;
 
-import java.util.LinkedHashMap;
+import java.util.*;
-import java.util.Map;
-import java.util.Set;
 import java.util.stream.Collectors;
 
-import static org.apache.commons.lang3.StringUtils.*;
+import static org.apache.commons.lang3.StringUtils.substringAfter;
 
 public class GraphMappingUtils {
 
     public static final String SEPARATOR = "_";
 
+    public final static Map<EntityType, Class> entityTypes = Maps.newHashMap();
+
+    static {
+        entityTypes.put(EntityType.datasource, Datasource.class);
+        entityTypes.put(EntityType.organization, Organization.class);
+        entityTypes.put(EntityType.project, Project.class);
+        entityTypes.put(EntityType.dataset, Dataset.class);
+        entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
+        entityTypes.put(EntityType.software, Software.class);
+        entityTypes.put(EntityType.publication, Publication.class);
+    }
+
     public enum EntityType {
-        publication, dataset, otherresearchproduct, software, datasource, organization, project
+        publication, dataset, otherresearchproduct, software, datasource, organization, project;
+
+        public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
+            switch (clazz.getName()) {
+                case "eu.dnetlib.dhp.schema.oaf.Publication"            : return publication;
+                case "eu.dnetlib.dhp.schema.oaf.Dataset"                : return dataset;
+                case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct"   : return otherresearchproduct;
+                case "eu.dnetlib.dhp.schema.oaf.Software"               : return software;
+                case "eu.dnetlib.dhp.schema.oaf.Datasource"             : return datasource;
+                case "eu.dnetlib.dhp.schema.oaf.Organization"           : return organization;
+                case "eu.dnetlib.dhp.schema.oaf.Project"                : return project;
+                default: throw new IllegalArgumentException("Unknown OafEntity class: " + clazz.getName());
+            }
+        }
     }
 
     public enum MainEntityType {
@@ -33,8 +50,6 @@ public class GraphMappingUtils {
 
     public static Set<String> authorPidTypes = Sets.newHashSet("orcid", "magidentifier");
 
-    public static Set<String> instanceFieldFilter = Sets.newHashSet("instancetype", "hostedby", "license", "accessright", "collectedfrom", "dateofacceptance", "distributionlocation");
-
     private static final String schemeTemplate = "dnet:%s_%s_relations";
 
     private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
@@ -49,6 +64,38 @@ public class GraphMappingUtils {
         entityMapping.put(EntityType.project,                MainEntityType.project);
     }
 
+    public static Class[] getKryoClasses() {
+        return new Class[]{
+                Author.class,
+                Context.class,
+                Country.class,
+                DataInfo.class,
+                eu.dnetlib.dhp.schema.oaf.Dataset.class,
+                Datasource.class,
+                ExternalReference.class,
+                ExtraInfo.class,
+                Field.class,
+                GeoLocation.class,
+                Instance.class,
+                Journal.class,
+                KeyValue.class,
+                Oaf.class,
+                OafEntity.class,
+                OAIProvenance.class,
+                Organization.class,
+                OriginDescription.class,
+                OtherResearchProduct.class,
+                Project.class,
+                Publication.class,
+                Qualifier.class,
+                Relation.class,
+                SortableRelation.class, //SUPPORT
+                Result.class,
+                Software.class,
+                StructuredProperty.class
+        };
+    }
+
     public static String getScheme(final String sourceType, final String targetType) {
         return String.format(schemeTemplate,
                 entityMapping.get(EntityType.valueOf(sourceType)).name(),
@@ -63,152 +110,81 @@ public class GraphMappingUtils {
         return MainEntityType.result.name().equals(getMainType(type));
     }
 
-    public static RelatedEntity asRelatedEntity(TypedRow e) {
+    public static <E extends OafEntity> RelatedEntity asRelatedEntity(E entity, Class<E> clazz) {
 
-        final DocumentContext j = JsonPath.parse(e.getOaf());
         final RelatedEntity re = new RelatedEntity();
-        re.setId(j.read("$.id"));
+        re.setId(entity.getId());
-        re.setType(e.getType());
+        re.setType(clazz.getName());
 
-        switch (EntityType.valueOf(e.getType())) {
+        re.setPid(entity.getPid());
+        re.setCollectedfrom(entity.getCollectedfrom());
+
+        switch (GraphMappingUtils.EntityType.fromClass(clazz)) {
             case publication:
             case dataset:
             case otherresearchproduct:
             case software:
-                mapTitle(j, re);
-                re.setDateofacceptance(j.read("$.dateofacceptance.value"));
-                re.setPublisher(j.read("$.publisher.value"));
 
-                JSONArray pids = j.read("$.pid");
+                Result r = (Result) entity;
-                re.setPid(pids.stream()
-                        .map(p -> asStructuredProperty((LinkedHashMap<String, Object>) p))
-                        .collect(Collectors.toList()));
 
-                re.setResulttype(asQualifier(j.read("$.resulttype")));
+                if (r.getTitle() == null && !r.getTitle().isEmpty()) {
+                    re.setTitle(r.getTitle().stream().findFirst().get());
+                }
 
-                JSONArray collfrom = j.read("$.collectedfrom");
+                re.setDateofacceptance(getValue(r.getDateofacceptance()));
-                re.setCollectedfrom(collfrom.stream()
+                re.setPublisher(getValue(r.getPublisher()));
-                        .map(c -> asKV((LinkedHashMap<String, Object>) c))
+                re.setResulttype(re.getResulttype());
-                        .collect(Collectors.toList()));
+                re.setInstances(re.getInstances());
-
-                // will throw exception when the instance is not found
-                JSONArray instances = j.read("$.instance");
-                re.setInstances(instances.stream()
-                        .map(i -> {
-                            final LinkedHashMap<String, Object> p = (LinkedHashMap<String, Object>) i;
-                            final Field<String> license = new Field<String>();
-                            license.setValue((String) ((LinkedHashMap<String, Object>) p.get("license")).get("value"));
-                            final Instance instance = new Instance();
-                            instance.setLicense(license);
-                            instance.setAccessright(asQualifier((LinkedHashMap<String, String>) p.get("accessright")));
-                            instance.setInstancetype(asQualifier((LinkedHashMap<String, String>) p.get("instancetype")));
-                            instance.setHostedby(asKV((LinkedHashMap<String, Object>) p.get("hostedby")));
-                            //TODO mapping of distributionlocation
-                            instance.setCollectedfrom(asKV((LinkedHashMap<String, Object>) p.get("collectedfrom")));
-
-                            Field<String> dateofacceptance = new Field<String>();
-                            dateofacceptance.setValue((String) ((LinkedHashMap<String, Object>) p.get("dateofacceptance")).get("value"));
-                            instance.setDateofacceptance(dateofacceptance);
-                            return instance;
-                        }).collect(Collectors.toList()));
 
                 //TODO still to be mapped
                 //re.setCodeRepositoryUrl(j.read("$.coderepositoryurl"));
 
                 break;
             case datasource:
-                re.setOfficialname(j.read("$.officialname.value"));
+                Datasource d = (Datasource) entity;
-                re.setWebsiteurl(j.read("$.websiteurl.value"));
+
-                re.setDatasourcetype(asQualifier(j.read("$.datasourcetype")));
+                re.setOfficialname(getValue(d.getOfficialname()));
-                re.setOpenairecompatibility(asQualifier(j.read("$.openairecompatibility")));
+                re.setWebsiteurl(getValue(d.getWebsiteurl()));
+                re.setDatasourcetype(d.getDatasourcetype());
+                re.setOpenairecompatibility(d.getOpenairecompatibility());
 
                 break;
             case organization:
-                re.setLegalname(j.read("$.legalname.value"));
+                Organization o = (Organization) entity;
-                re.setLegalshortname(j.read("$.legalshortname.value"));
+
-                re.setCountry(asQualifier(j.read("$.country")));
+                re.setLegalname(getValue(o.getLegalname()));
-                re.setWebsiteurl(j.read("$.websiteurl.value"));
+                re.setLegalshortname(getValue(o.getLegalshortname()));
+                re.setCountry(o.getCountry());
+                re.setWebsiteurl(getValue(o.getWebsiteurl()));
                 break;
             case project:
-                re.setProjectTitle(j.read("$.title.value"));
+                Project p = (Project) entity;
-                re.setCode(j.read("$.code.value"));
-                re.setAcronym(j.read("$.acronym.value"));
-                re.setContracttype(asQualifier(j.read("$.contracttype")));
 
-                JSONArray f = j.read("$.fundingtree");
+                re.setProjectTitle(getValue(p.getTitle()));
+                re.setCode(getValue(p.getCode()));
+                re.setAcronym(getValue(p.getAcronym()));
+                re.setContracttype(p.getContracttype());
+
+                List<Field<String>> f = p.getFundingtree();
                 if (!f.isEmpty()) {
                     re.setFundingtree(f.stream()
-                            .map(s -> ((LinkedHashMap<String, String>) s).get("value"))
+                            .map(s -> s.getValue())
                             .collect(Collectors.toList()));
                 }
-
                 break;
         }
-
         return re;
     }
 
-
+    private static String getValue(Field<String> field) {
-    private static KeyValue asKV(LinkedHashMap<String, Object> j) {
+        return getFieldValueWithDefault(field, "");
-        final KeyValue kv = new KeyValue();
-        kv.setKey((String) j.get("key"));
-        kv.setValue((String) j.get("value"));
-        return kv;
     }
 
-    private static void mapTitle(DocumentContext j, RelatedEntity re) {
+    private static <T> T getFieldValueWithDefault(Field<T> f, T defaultValue) {
-        final JSONArray a = j.read("$.title");
+        return Optional.ofNullable(f)
-        if (!a.isEmpty()) {
+                .filter(Objects::nonNull)
-            final StructuredProperty sp = asStructuredProperty((LinkedHashMap<String, Object>) a.get(0));
+                .map(x -> x.getValue())
-            if (StringUtils.isNotBlank(sp.getValue())) {
+                .orElse(defaultValue);
-                re.setTitle(sp);
-            }
-        }
-    }
-
-    private static StructuredProperty asStructuredProperty(LinkedHashMap<String, Object> j) {
-        final StructuredProperty sp = new StructuredProperty();
-        final String value = (String) j.get("value");
-        if (StringUtils.isNotBlank(value)) {
-            sp.setValue((String) j.get("value"));
-            sp.setQualifier(asQualifier((LinkedHashMap<String, String>) j.get("qualifier")));
-        }
-        return sp;
-    }
-
-    public static Qualifier asQualifier(LinkedHashMap<String, String> j) {
-        final Qualifier q = new Qualifier();
-
-        final String classid = j.get("classid");
-        if (StringUtils.isNotBlank(classid)) {
-            q.setClassid(classid);
-        }
-
-        final String classname = j.get("classname");
-        if (StringUtils.isNotBlank(classname)) {
-            q.setClassname(classname);
-        }
-
-        final String schemeid = j.get("schemeid");
-        if (StringUtils.isNotBlank(schemeid)) {
-            q.setSchemeid(schemeid);
-        }
-
-        final String schemename = j.get("schemename");
-        if (StringUtils.isNotBlank(schemename)) {
-            q.setSchemename(schemename);
-        }
-        return q;
-    }
-
-    public static String serialize(final Object o) {
-        try {
-            return new ObjectMapper()
-                    .setSerializationInclusion(JsonInclude.Include.NON_NULL)
-                    .writeValueAsString(o);
-        } catch (JsonProcessingException e) {
-            throw new IllegalArgumentException("unable to serialize: " + o.toString(), e);
-        }
     }
 
     public static String removePrefix(final String s) {

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json

@@ -1,8 +1,14 @@
 [
-  {"paramName":"mt",  "paramLongName":"master",          "paramDescription": "should be local or yarn",                                     "paramRequired": true},
+  {
-  {"paramName":"is",  "paramLongName":"isLookupUrl",     "paramDescription": "URL of the isLookUp Service",                                 "paramRequired": true},
+    "paramName": "in",
-  {"paramName":"o",   "paramLongName":"outputPath",      "paramDescription": "the path used to store temporary output files",               "paramRequired": true},
+    "paramLongName": "inputPath",
-  {"paramName":"s",   "paramLongName":"sourcePath",      "paramDescription": "the path of the sequence file to read",                       "paramRequired": true},
+    "paramDescription": "the path of the sequence file to read",
-  {"paramName":"t",   "paramLongName":"otherDsTypeId",   "paramDescription": "list of datasource types to populate field datasourcetypeui", "paramRequired": true},
+    "paramRequired": true
-  {"paramName":"sp",  "paramLongName":"sparkSqlShufflePartitions",   "paramDescription": "Configures the number of partitions to use when shuffling data for joins or aggregations", "paramRequired": true}
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path used to store temporary output files",
+    "paramRequired": true
+  }
 ]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "irp",
+    "paramLongName": "inputRelationsPath",
+    "paramDescription": "path to input relations prepare",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "root output location for prepared relations",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "irp",
+    "paramLongName": "inputRelationsPath",
+    "paramDescription": "path to input relations from the graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "iep",
+    "paramLongName": "inputEntityPath",
+    "paramDescription": "path to input entity from the graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "clazz",
+    "paramLongName": "graphTableClassName",
+    "paramDescription": "class name associated to the input entity path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "root output location for prepared relations",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "irp",
+    "paramLongName": "inputRelatedEntitiesPath",
+    "paramDescription": "path to input relations from the graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "iep",
+    "paramLongName": "inputGraphPath",
+    "paramDescription": "root graph path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "root output location for prepared relations",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json

@@ -1,7 +1,7 @@
 [
   {"paramName":"mt",  "paramLongName":"master",             "paramDescription": "should be local or yarn",                                  "paramRequired": true},
   {"paramName":"is",  "paramLongName":"isLookupUrl",        "paramDescription": "URL of the isLookUp Service",                              "paramRequired": true},
-  {"paramName":"s",   "paramLongName":"sourcePath",         "paramDescription": "the path of the sequence file to read the XML records",    "paramRequired": true},
+  {"paramName":"i",   "paramLongName":"inputPath",         "paramDescription": "the path of the sequence file to read the XML records",    "paramRequired": true},
   {"paramName":"f",   "paramLongName":"format",             "paramDescription": "MDFormat name found in the IS profile",                    "paramRequired": true},
   {"paramName":"b",   "paramLongName":"batchSize",          "paramDescription": "size of the batch of documents sent to solr",              "paramRequired": false}
 ]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "in",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path of the sequence file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path used to store temporary output files",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ilu",
+    "paramLongName": "isLookupUrl",
+    "paramDescription": "URL of the isLookUp Service",
+    "paramRequired": true
+  },
+  {
+    "paramName": "odt",
+    "paramLongName": "otherDsTypeId",
+    "paramDescription": "list of datasource types to populate field datasourcetypeui",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml

@@ -1,6 +1,11 @@
 <workflow-app name="index_infospace_graph" xmlns="uri:oozie:workflow:0.5">
 
     <parameters>
+        <property>
+            <name>inputGraphRootPath</name>
+            <description>root location of input materialized graph</description>
+        </property>
+
         <property>
             <name>sparkDriverMemoryForJoining</name>
             <description>memory for driver process</description>
@@ -64,7 +69,7 @@
 
     <decision name="reuse_records">
         <switch>
-            <case to="adjancency_lists">${wf:conf('reuseRecords') eq false}</case>
+            <case to="prepare_relations">${wf:conf('reuseRecords') eq false}</case>
             <case to="to_solr_index">${wf:conf('reuseRecords') eq true}</case>
             <default to="adjancency_lists"/>
         </switch>
@@ -74,16 +79,12 @@
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="adjancency_lists">
+    <action name="prepare_relations">
         <spark xmlns="uri:oozie:spark-action:0.2">
-            <prepare>
-                <delete path="${outputPath}"/>
-                <mkdir path="${outputPath}"/>
-            </prepare>
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>build_adjacency_lists</name>
+            <name>PrepareRelations</name>
-            <class>eu.dnetlib.dhp.oa.provision.SparkXmlRecordBuilderJob_v2</class>
+            <class>eu.dnetlib.dhp.oa.provision.PrepareRelationsJob</class>
             <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCoresForJoining}
@@ -94,12 +95,135 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>-mt</arg> <arg>yarn</arg>
+            <arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
-            <arg>-is</arg> <arg>${isLookupUrl}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
-            <arg>-t</arg> <arg>${otherDsTypeId}</arg>
+        </spark>
-            <arg>-s</arg><arg>${sourcePath}</arg>
+        <ok to="prepare_publication_table"/>
-            <arg>-o</arg><arg>${outputPath}</arg>
+        <error to="Kill"/>
-            <arg>-sp</arg><arg>${sparkSqlShufflePartitions}</arg>
+    </action>
+
+    <action name="join_relation_publication">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Join[relation.target = publication.id]</name>
+            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputRelationsPath</arg><arg>${workingDir}/relations</arg>
+            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/publication</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/join_partial</arg>
+        </spark>
+        <ok to="join_relation_dataset"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_relation_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Join[relation.target = dataset.id]</name>
+            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputRelationsPath</arg><arg>${workingDir}/relations</arg>
+            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/dataset</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/join_partial</arg>
+        </spark>
+        <ok to="join_all_entities"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_all_entities">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Join[relation.target = dataset.id]</name>
+            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
+            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/join_entities</arg>
+        </spark>
+        <ok to="adjancency_lists"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="adjancency_lists">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>build_adjacency_lists</name>
+            <class>eu.dnetlib.dhp.oa.provision.AdjacencyListBuilderJob</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputPath</arg> <arg>${${workingDir}/join_entities</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/joined</arg>
+        </spark>
+        <ok to="convert_to_xml"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="convert_to_xml">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>build_adjacency_lists</name>
+            <class>eu.dnetlib.dhp.oa.provision.XmlConverterJob</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${${workingDir}/joined</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/xml</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--otherDsTypeId</arg><arg>${otherDsTypeId}</arg>
         </spark>
         <ok to="to_solr_index"/>
         <error to="Kill"/>
@@ -122,9 +246,8 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>-mt</arg> <arg>yarn</arg>
+            <arg>--isLookupUrl</arg> <arg>${isLookupUrl}</arg>
-            <arg>-is</arg> <arg>${isLookupUrl}</arg>
+            <arg>--inputPath</arg><arg>${workingDir}/xml</arg>
-            <arg>--sourcePath</arg><arg>${outputPath}/xml</arg>
             <arg>--format</arg><arg>${format}</arg>
             <arg>--batchSize</arg><arg>${batchSize}</arg>
         </spark>