diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 1268afa3a..7b073397f 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -13,6 +13,20 @@ jar + + + org.apache.hadoop + hadoop-common + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + commons-cli commons-cli diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/FunctionalInterfaceSupport.java new file mode 100644 index 000000000..d78520f55 --- /dev/null +++ b/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 + */ + @FunctionalInterface + public interface SerializableSupplier extends Supplier, Serializable { + } + + /** + * Extension of consumer accepting functions throwing an exception. + * + * @param + * @param + */ + @FunctionalInterface + public interface ThrowingConsumer { + void accept(T t) throws E; + } + + /** + * Extension of supplier accepting functions throwing an exception. + * + * @param + * @param + */ + @FunctionalInterface + public interface ThrowingSupplier { + T get() throws E; + } + + /** + * Extension of runnable accepting functions throwing an exception. + * + * @param + */ + @FunctionalInterface + public interface ThrowingRunnable { + void run() throws E; + } + +} \ No newline at end of file diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java new file mode 100644 index 000000000..05beaa51e --- /dev/null +++ b/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 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())); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java new file mode 100644 index 000000000..43c18a956 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java @@ -0,0 +1,71 @@ +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 fn) { + runWithSparkSession(c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn); + } + + /** + * Runs a given function using SparkSession created with hive support and 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 runWithSparkHiveSession(SparkConf conf, + Boolean isSparkSessionManaged, + ThrowingConsumer fn) { + runWithSparkSession(c -> SparkSession.builder().config(c).enableHiveSupport().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 sparkSessionBuilder, + SparkConf conf, + Boolean isSparkSessionManaged, + ThrowingConsumer 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(); + } + } + } +} \ No newline at end of file diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java new file mode 100644 index 000000000..b32803c37 --- /dev/null +++ b/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 Type of exception thrown + */ + public static void rethrowAsRuntimeException(ThrowingRunnable 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 Type of exception thrown + */ + public static void rethrowAsRuntimeException(ThrowingRunnable 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 Type of returned value + * @param Type of exception thrown + * @return Result of supplier execution + */ + public static T rethrowAsRuntimeException(ThrowingSupplier 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 Type of returned value + * @param Type of exception thrown + * @return Result of supplier execution + */ + public static T rethrowAsRuntimeException(ThrowingSupplier fn, String msg) { + try { + return fn.get(); + } catch (Exception e) { + throw new RuntimeException(msg, e); + } + } + +} \ No newline at end of file diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java new file mode 100644 index 000000000..f1e790ee7 --- /dev/null +++ b/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 paths = HdfsSupport.listFiles(tempDir.toString(), new Configuration()); + + // then + assertEquals(2, paths.size()); + List expecteds = Arrays.stream(new String[]{subDir1.toString(), subDir2.toString()}) + .sorted().collect(Collectors.toList()); + List actuals = paths.stream().sorted().collect(Collectors.toList()); + assertTrue(actuals.get(0).contains(expecteds.get(0))); + assertTrue(actuals.get(1).contains(expecteds.get(1))); + } + } +} \ No newline at end of file diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java new file mode 100644 index 000000000..bc2dce3cf --- /dev/null +++ b/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 sparkSessionBuilder = mock(Function.class); + when(sparkSessionBuilder.apply(conf)).thenReturn(spark); + ThrowingConsumer 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 sparkSessionBuilder = mock(Function.class); + when(sparkSessionBuilder.apply(conf)).thenReturn(spark); + ThrowingConsumer 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(); + } + } +} \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java new file mode 100644 index 000000000..9e4fa7d8a --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java @@ -0,0 +1,23 @@ +package eu.dnetlib.dhp.schema.common; + +import eu.dnetlib.dhp.schema.oaf.OafEntity; + +/** + * Actual entity types in the Graph + */ +public enum EntityType { + + publication, dataset, otherresearchproduct, software, datasource, organization, project; + + /** + * Resolves the EntityType, given the relative class name + * @param clazz the given class name + * @param actual OafEntity subclass + * @return the EntityType associated to the given class + */ + public static EntityType fromClass(Class clazz) { + + return EntityType.valueOf(clazz.getSimpleName().toLowerCase()); + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java new file mode 100644 index 000000000..7d65e39c0 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java @@ -0,0 +1,9 @@ +package eu.dnetlib.dhp.schema.common; + +/** + * Main entity types in the Graph + */ +public enum MainEntityType { + + result, datasource, organization, project +} \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java new file mode 100644 index 000000000..48f711a03 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java @@ -0,0 +1,151 @@ +package eu.dnetlib.dhp.schema.common; + +import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.oaf.*; + +import java.util.Map; + +/** + * Oaf model utility methods. + */ +public class ModelSupport { + + /** + * Defines the mapping between the actual entity type and the main entity type + */ + private static Map entityMapping = Maps.newHashMap(); + + static { + entityMapping.put(EntityType.publication, MainEntityType.result); + entityMapping.put(EntityType.dataset, MainEntityType.result); + entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); + entityMapping.put(EntityType.software, MainEntityType.result); + entityMapping.put(EntityType.datasource, MainEntityType.datasource); + entityMapping.put(EntityType.organization, MainEntityType.organization); + entityMapping.put(EntityType.project, MainEntityType.project); + } + + /** + * Defines the mapping between the actual entity types and the relative classes implementing them + */ + public final static Map 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 final static Map oafTypes = Maps.newHashMap(); + + static { + oafTypes.put("datasource", Datasource.class); + oafTypes.put("organization", Organization.class); + oafTypes.put("project", Project.class); + oafTypes.put("dataset", Dataset.class); + oafTypes.put("otherresearchproduct", OtherResearchProduct.class); + oafTypes.put("software", Software.class); + oafTypes.put("publication", Publication.class); + oafTypes.put("relation", Relation.class); + } + + private static final String schemeTemplate = "dnet:%s_%s_relations"; + + private ModelSupport() { + } + + /** + * Checks subclass-superclass relationship. + * + * @param subClazzObject Subclass object instance + * @param superClazzObject Superclass object instance + * @param Subclass type + * @param Superclass type + * @return True if X is a subclass of Y + */ + public static 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 Subclass type + * @param Superclass type + * @return True if X is a subclass of Y + */ + public static Boolean isSubClass(X subClazzObject, Class superClazz) { + return isSubClass(subClazzObject.getClass(), superClazz); + } + + /** + * Checks subclass-superclass relationship. + * + * @param subClazz Subclass class + * @param superClazz Superclass class + * @param Subclass type + * @param Superclass type + * @return True if X is a subclass of Y + */ + public static Boolean isSubClass(Class subClazz, Class superClazz) { + return superClazz.isAssignableFrom(subClazz); + } + + /** + * Lists all the OAF model classes + * + * @param + * @return + */ + public static Class[] getOafModelClasses() { + return new Class[]{ + Author.class, + Context.class, + Country.class, + DataInfo.class, + 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 + }; + } + + public static String getMainType(final EntityType type) { + return entityMapping.get(type).name(); + } + + public static boolean isResult(EntityType type) { + return MainEntityType.result.name().equals(getMainType(type)); + } + + public static String getScheme(final String sourceType, final String targetType) { + return String.format(schemeTemplate, + entityMapping.get(EntityType.valueOf(sourceType)).name(), + entityMapping.get(EntityType.valueOf(targetType)).name()); + } + +} \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java index 3e6621e3f..93ab60b05 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Author implements Serializable { @@ -64,4 +65,22 @@ public class Author implements Serializable { public void setAffiliation(List> affiliation) { this.affiliation = affiliation; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Author author = (Author) o; + return Objects.equals(fullname, author.fullname) && + Objects.equals(name, author.name) && + Objects.equals(surname, author.surname) && + Objects.equals(rank, author.rank) && + Objects.equals(pid, author.pid) && + Objects.equals(affiliation, author.affiliation); + } + + @Override + public int hashCode() { + return Objects.hash(fullname, name, surname, rank, pid, affiliation); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java index e81120e42..b2da92c43 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java @@ -1,5 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; +import java.util.Objects; + public class Country extends Qualifier { private DataInfo dataInfo; @@ -12,4 +14,17 @@ public class Country extends Qualifier { this.dataInfo = dataInfo; } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Country country = (Country) o; + return Objects.equals(dataInfo, country.dataInfo); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), dataInfo); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java index 16683cf30..49a186701 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class DataInfo implements Serializable { @@ -60,4 +61,22 @@ public class DataInfo implements Serializable { public void setProvenanceaction(Qualifier provenanceaction) { this.provenanceaction = provenanceaction; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + DataInfo dataInfo = (DataInfo) o; + return Objects.equals(invisible, dataInfo.invisible) && + Objects.equals(inferred, dataInfo.inferred) && + Objects.equals(deletedbyinference, dataInfo.deletedbyinference) && + Objects.equals(trust, dataInfo.trust) && + Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) && + Objects.equals(provenanceaction, dataInfo.provenanceaction); + } + + @Override + public int hashCode() { + return Objects.hash(invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java index 27bee998e..70a6d1f31 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Dataset extends Result implements Serializable { @@ -78,6 +79,11 @@ public class Dataset extends Result implements Serializable { @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); + + if (!Dataset.class.isAssignableFrom(e.getClass())){ + return; + } + final Dataset d = (Dataset) e; storagedate = d.getStoragedate() != null && compareTrust(this, e)<0? d.getStoragedate() : storagedate; @@ -96,4 +102,24 @@ public class Dataset extends Result implements Serializable { mergeOAFDataInfo(d); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Dataset dataset = (Dataset) o; + return Objects.equals(storagedate, dataset.storagedate) && + Objects.equals(device, dataset.device) && + Objects.equals(size, dataset.size) && + Objects.equals(version, dataset.version) && + Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate) && + Objects.equals(metadataversionnumber, dataset.metadataversionnumber) && + Objects.equals(geolocation, dataset.geolocation); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), storagedate, device, size, version, lastmetadataupdate, metadataversionnumber, geolocation); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java index 032468de2..c8d9736c5 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Datasource extends OafEntity implements Serializable { @@ -366,6 +367,10 @@ public class Datasource extends OafEntity implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); + if (!Datasource.class.isAssignableFrom(e.getClass())){ + return; + } + Datasource d = (Datasource)e; datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e)<0? d.getDatasourcetype() : datasourcetype; @@ -424,4 +429,52 @@ public class Datasource extends OafEntity implements Serializable { mergeOAFDataInfo(e); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Datasource that = (Datasource) o; + return Objects.equals(datasourcetype, that.datasourcetype) && + Objects.equals(openairecompatibility, that.openairecompatibility) && + Objects.equals(officialname, that.officialname) && + Objects.equals(englishname, that.englishname) && + Objects.equals(websiteurl, that.websiteurl) && + Objects.equals(logourl, that.logourl) && + Objects.equals(contactemail, that.contactemail) && + Objects.equals(namespaceprefix, that.namespaceprefix) && + Objects.equals(latitude, that.latitude) && + Objects.equals(longitude, that.longitude) && + Objects.equals(dateofvalidation, that.dateofvalidation) && + Objects.equals(description, that.description) && + Objects.equals(subjects, that.subjects) && + Objects.equals(odnumberofitems, that.odnumberofitems) && + Objects.equals(odnumberofitemsdate, that.odnumberofitemsdate) && + Objects.equals(odpolicies, that.odpolicies) && + Objects.equals(odlanguages, that.odlanguages) && + Objects.equals(odcontenttypes, that.odcontenttypes) && + Objects.equals(accessinfopackage, that.accessinfopackage) && + Objects.equals(releasestartdate, that.releasestartdate) && + Objects.equals(releaseenddate, that.releaseenddate) && + Objects.equals(missionstatementurl, that.missionstatementurl) && + Objects.equals(dataprovider, that.dataprovider) && + Objects.equals(serviceprovider, that.serviceprovider) && + Objects.equals(databaseaccesstype, that.databaseaccesstype) && + Objects.equals(datauploadtype, that.datauploadtype) && + Objects.equals(databaseaccessrestriction, that.databaseaccessrestriction) && + Objects.equals(datauploadrestriction, that.datauploadrestriction) && + Objects.equals(versioning, that.versioning) && + Objects.equals(citationguidelineurl, that.citationguidelineurl) && + Objects.equals(qualitymanagementkind, that.qualitymanagementkind) && + Objects.equals(pidsystems, that.pidsystems) && + Objects.equals(certificates, that.certificates) && + Objects.equals(policies, that.policies) && + Objects.equals(journal, that.journal); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), datasourcetype, openairecompatibility, officialname, englishname, websiteurl, logourl, contactemail, namespaceprefix, latitude, longitude, dateofvalidation, description, subjects, odnumberofitems, odnumberofitemsdate, odpolicies, odlanguages, odcontenttypes, accessinfopackage, releasestartdate, releaseenddate, missionstatementurl, dataprovider, serviceprovider, databaseaccesstype, datauploadtype, databaseaccessrestriction, datauploadrestriction, versioning, citationguidelineurl, qualitymanagementkind, pidsystems, certificates, policies, journal); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java index 006658133..24c94065b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class ExternalReference implements Serializable { // source @@ -90,4 +91,24 @@ public class ExternalReference implements Serializable { public void setDataInfo(DataInfo dataInfo) { this.dataInfo = dataInfo; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + ExternalReference that = (ExternalReference) o; + return Objects.equals(sitename, that.sitename) && + Objects.equals(label, that.label) && + Objects.equals(url, that.url) && + Objects.equals(description, that.description) && + Objects.equals(qualifier, that.qualifier) && + Objects.equals(refidentifier, that.refidentifier) && + Objects.equals(query, that.query) && + Objects.equals(dataInfo, that.dataInfo); + } + + @Override + public int hashCode() { + return Objects.hash(sitename, label, url, description, qualifier, refidentifier, query, dataInfo); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java index 028b812a5..46107b214 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class ExtraInfo implements Serializable { private String name; @@ -53,4 +54,21 @@ public class ExtraInfo implements Serializable { public void setValue(String value) { this.value = value; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + ExtraInfo extraInfo = (ExtraInfo) o; + return Objects.equals(name, extraInfo.name) && + Objects.equals(typology, extraInfo.typology) && + Objects.equals(provenance, extraInfo.provenance) && + Objects.equals(trust, extraInfo.trust) && + Objects.equals(value, extraInfo.value); + } + + @Override + public int hashCode() { + return Objects.hash(name, typology, provenance, trust, value); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java index 06e5ca7dc..e3c80b120 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class Journal implements Serializable { @@ -123,4 +124,28 @@ public class Journal implements Serializable { public void setDataInfo(DataInfo dataInfo) { this.dataInfo = dataInfo; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Journal journal = (Journal) o; + return Objects.equals(name, journal.name) && + Objects.equals(issnPrinted, journal.issnPrinted) && + Objects.equals(issnOnline, journal.issnOnline) && + Objects.equals(issnLinking, journal.issnLinking) && + Objects.equals(ep, journal.ep) && + Objects.equals(iss, journal.iss) && + Objects.equals(sp, journal.sp) && + Objects.equals(vol, journal.vol) && + Objects.equals(edition, journal.edition) && + Objects.equals(conferenceplace, journal.conferenceplace) && + Objects.equals(conferencedate, journal.conferencedate) && + Objects.equals(dataInfo, journal.dataInfo); + } + + @Override + public int hashCode() { + return Objects.hash(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, conferenceplace, conferencedate, dataInfo); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java index bb97654b9..52ddf27d8 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class OAIProvenance implements Serializable { @@ -13,4 +14,17 @@ public class OAIProvenance implements Serializable { public void setOriginDescription(OriginDescription originDescription) { this.originDescription = originDescription; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OAIProvenance that = (OAIProvenance) o; + return Objects.equals(originDescription, that.originDescription); + } + + @Override + public int hashCode() { + return Objects.hash(originDescription); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java index cc2ab8428..64217e5d8 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public abstract class Oaf implements Serializable { @@ -43,4 +44,18 @@ public abstract class Oaf implements Serializable { return extractTrust(a).compareTo(extractTrust(b)); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + Oaf oaf = (Oaf) o; + return Objects.equals(dataInfo, oaf.dataInfo) && + Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); + } + + @Override + public int hashCode() { + return Objects.hash(dataInfo, lastupdatetimestamp); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java index 8a86f822d..cd196243a 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java @@ -116,5 +116,24 @@ public abstract class OafEntity extends Oaf implements Serializable { return Arrays.stream(lists).filter(Objects::nonNull).flatMap(List::stream).distinct().collect(Collectors.toList()); } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + OafEntity oafEntity = (OafEntity) o; + return Objects.equals(id, oafEntity.id) && + Objects.equals(originalId, oafEntity.originalId) && + Objects.equals(collectedfrom, oafEntity.collectedfrom) && + Objects.equals(pid, oafEntity.pid) && + Objects.equals(dateofcollection, oafEntity.dateofcollection) && + Objects.equals(dateoftransformation, oafEntity.dateoftransformation) && + Objects.equals(extraInfo, oafEntity.extraInfo) && + Objects.equals(oaiprovenance, oafEntity.oaiprovenance); + } + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), id, originalId, collectedfrom, pid, dateofcollection, dateoftransformation, extraInfo, oaiprovenance); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java index b0dffb485..a73a7f845 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Organization extends OafEntity implements Serializable { @@ -169,6 +170,11 @@ public class Organization extends OafEntity implements Serializable { @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); + + if (!Organization.class.isAssignableFrom(e.getClass())){ + return; + } + final Organization o = (Organization) e; legalshortname = o.getLegalshortname() != null && compareTrust(this, e)<0? o.getLegalshortname() : legalshortname; legalname = o.getLegalname() != null && compareTrust(this, e)<0 ? o.getLegalname() : legalname; @@ -188,4 +194,33 @@ public class Organization extends OafEntity implements Serializable { country = o.getCountry() != null && compareTrust(this, e)<0 ? o.getCountry() :country; mergeOAFDataInfo(o); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Organization that = (Organization) o; + return Objects.equals(legalshortname, that.legalshortname) && + Objects.equals(legalname, that.legalname) && + Objects.equals(alternativeNames, that.alternativeNames) && + Objects.equals(websiteurl, that.websiteurl) && + Objects.equals(logourl, that.logourl) && + Objects.equals(eclegalbody, that.eclegalbody) && + Objects.equals(eclegalperson, that.eclegalperson) && + Objects.equals(ecnonprofit, that.ecnonprofit) && + Objects.equals(ecresearchorganization, that.ecresearchorganization) && + Objects.equals(echighereducation, that.echighereducation) && + Objects.equals(ecinternationalorganizationeurinterests, that.ecinternationalorganizationeurinterests) && + Objects.equals(ecinternationalorganization, that.ecinternationalorganization) && + Objects.equals(ecenterprise, that.ecenterprise) && + Objects.equals(ecsmevalidated, that.ecsmevalidated) && + Objects.equals(ecnutscode, that.ecnutscode) && + Objects.equals(country, that.country); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), legalshortname, legalname, alternativeNames, websiteurl, logourl, eclegalbody, eclegalperson, ecnonprofit, ecresearchorganization, echighereducation, ecinternationalorganizationeurinterests, ecinternationalorganization, ecenterprise, ecsmevalidated, ecnutscode, country); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java index a990cee6f..8038242ca 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class OriginDescription implements Serializable { @@ -63,4 +64,22 @@ public class OriginDescription implements Serializable { public void setMetadataNamespace(String metadataNamespace) { this.metadataNamespace = metadataNamespace; } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + OriginDescription that = (OriginDescription) o; + return Objects.equals(harvestDate, that.harvestDate) && + Objects.equals(altered, that.altered) && + Objects.equals(baseURL, that.baseURL) && + Objects.equals(identifier, that.identifier) && + Objects.equals(datestamp, that.datestamp) && + Objects.equals(metadataNamespace, that.metadataNamespace); + } + + @Override + public int hashCode() { + return Objects.hash(harvestDate, altered, baseURL, identifier, datestamp, metadataNamespace); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java index 72bec727e..cc36817bb 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class OtherResearchProduct extends Result implements Serializable { @@ -39,6 +40,10 @@ public class OtherResearchProduct extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); + if (!OtherResearchProduct.class.isAssignableFrom(e.getClass())){ + return; + } + OtherResearchProduct o = (OtherResearchProduct)e; contactperson = mergeLists(contactperson, o.getContactperson()); @@ -46,4 +51,20 @@ public class OtherResearchProduct extends Result implements Serializable { tool = mergeLists(tool, o.getTool()); mergeOAFDataInfo(e); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + OtherResearchProduct that = (OtherResearchProduct) o; + return Objects.equals(contactperson, that.contactperson) && + Objects.equals(contactgroup, that.contactgroup) && + Objects.equals(tool, that.tool); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), contactperson, contactgroup, tool); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java index 0bc11bb41..023be8fc0 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Project extends OafEntity implements Serializable { @@ -269,6 +270,11 @@ public class Project extends OafEntity implements Serializable { @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); + + if (!Project.class.isAssignableFrom(e.getClass())){ + return; + } + Project p = (Project)e; websiteurl= p.getWebsiteurl()!= null && compareTrust(this,e)<0?p.getWebsiteurl():websiteurl; @@ -299,4 +305,43 @@ public class Project extends OafEntity implements Serializable { fundedamount= p.getFundedamount()!= null && compareTrust(this,e)<0?p.getFundedamount():fundedamount; mergeOAFDataInfo(e); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Project project = (Project) o; + return Objects.equals(websiteurl, project.websiteurl) && + Objects.equals(code, project.code) && + Objects.equals(acronym, project.acronym) && + Objects.equals(title, project.title) && + Objects.equals(startdate, project.startdate) && + Objects.equals(enddate, project.enddate) && + Objects.equals(callidentifier, project.callidentifier) && + Objects.equals(keywords, project.keywords) && + Objects.equals(duration, project.duration) && + Objects.equals(ecsc39, project.ecsc39) && + Objects.equals(oamandatepublications, project.oamandatepublications) && + Objects.equals(ecarticle29_3, project.ecarticle29_3) && + Objects.equals(subjects, project.subjects) && + Objects.equals(fundingtree, project.fundingtree) && + Objects.equals(contracttype, project.contracttype) && + Objects.equals(optional1, project.optional1) && + Objects.equals(optional2, project.optional2) && + Objects.equals(jsonextrainfo, project.jsonextrainfo) && + Objects.equals(contactfullname, project.contactfullname) && + Objects.equals(contactfax, project.contactfax) && + Objects.equals(contactphone, project.contactphone) && + Objects.equals(contactemail, project.contactemail) && + Objects.equals(summary, project.summary) && + Objects.equals(currency, project.currency) && + Objects.equals(totalcost, project.totalcost) && + Objects.equals(fundedamount, project.fundedamount); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), websiteurl, code, acronym, title, startdate, enddate, callidentifier, keywords, duration, ecsc39, oamandatepublications, ecarticle29_3, subjects, fundingtree, contracttype, optional1, optional2, jsonextrainfo, contactfullname, contactfax, contactphone, contactemail, summary, currency, totalcost, fundedamount); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java index bb6990c1d..20a0b2121 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; +import java.util.Objects; public class Publication extends Result implements Serializable { @@ -19,6 +20,10 @@ public class Publication extends Result implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); + if (!Publication.class.isAssignableFrom(e.getClass())){ + return; + } + Publication p = (Publication) e; if (p.getJournal() != null && compareTrust(this, e)<0) @@ -26,5 +31,17 @@ public class Publication extends Result implements Serializable { mergeOAFDataInfo(e); } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Publication that = (Publication) o; + return Objects.equals(journal, that.journal); + } + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), journal); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java index 6738b8693..6871c0197 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java @@ -1,8 +1,6 @@ package eu.dnetlib.dhp.schema.oaf; -import java.util.ArrayList; -import java.util.List; -import java.util.Objects; +import java.util.*; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -78,9 +76,12 @@ public class Relation extends Oaf { checkArgument(Objects.equals(getSubRelType(), r.getSubRelType()),"subRelType(s) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()),"relClass(es) must be equal"); - setCollectedFrom(Stream.concat(getCollectedFrom().stream(), r.getCollectedFrom().stream()) - .distinct() // relies on KeyValue.equals - .collect(Collectors.toList())); + setCollectedFrom( + Stream + .concat(Optional.ofNullable(getCollectedFrom()).map(Collection::stream).orElse(Stream.empty()), + Optional.ofNullable(r.getCollectedFrom()).map(Collection::stream).orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); } @Override @@ -92,8 +93,7 @@ public class Relation extends Oaf { subRelType.equals(relation.subRelType) && relClass.equals(relation.relClass) && source.equals(relation.source) && - target.equals(relation.target) && - Objects.equals(collectedFrom, relation.collectedFrom); + target.equals(relation.target); } @Override diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java index b6c73e84a..f98bcec93 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java @@ -3,6 +3,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.Comparator; import java.util.List; +import java.util.Objects; public class Result extends OafEntity implements Serializable { @@ -222,6 +223,10 @@ public class Result extends OafEntity implements Serializable { public void mergeFrom(OafEntity e) { super.mergeFrom(e); + if (!Result.class.isAssignableFrom(e.getClass())){ + return; + } + Result r = (Result) e; instance = mergeLists(instance, r.getInstance()); @@ -278,4 +283,37 @@ public class Result extends OafEntity implements Serializable { return a.size() > b.size() ? a : b; } + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Result result = (Result) o; + return Objects.equals(author, result.author) && + Objects.equals(resulttype, result.resulttype) && + Objects.equals(language, result.language) && + Objects.equals(country, result.country) && + Objects.equals(subject, result.subject) && + Objects.equals(title, result.title) && + Objects.equals(relevantdate, result.relevantdate) && + Objects.equals(description, result.description) && + Objects.equals(dateofacceptance, result.dateofacceptance) && + Objects.equals(publisher, result.publisher) && + Objects.equals(embargoenddate, result.embargoenddate) && + Objects.equals(source, result.source) && + Objects.equals(fulltext, result.fulltext) && + Objects.equals(format, result.format) && + Objects.equals(contributor, result.contributor) && + Objects.equals(resourcetype, result.resourcetype) && + Objects.equals(coverage, result.coverage) && + Objects.equals(bestaccessright, result.bestaccessright) && + Objects.equals(context, result.context) && + Objects.equals(externalReference, result.externalReference) && + Objects.equals(instance, result.instance); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), author, resulttype, language, country, subject, title, relevantdate, description, dateofacceptance, publisher, embargoenddate, source, fulltext, format, contributor, resourcetype, coverage, bestaccessright, context, externalReference, instance); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java index 7f835fdf8..6b51a6ada 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.schema.oaf; import java.io.Serializable; import java.util.List; +import java.util.Objects; public class Software extends Result implements Serializable { @@ -48,6 +49,11 @@ public class Software extends Result implements Serializable { @Override public void mergeFrom(OafEntity e) { super.mergeFrom(e); + + if (!Software.class.isAssignableFrom(e.getClass())){ + return; + } + final Software s = (Software) e; documentationUrl = mergeLists(documentationUrl, s.getDocumentationUrl()); @@ -59,4 +65,21 @@ public class Software extends Result implements Serializable { mergeOAFDataInfo(e); } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + if (!super.equals(o)) return false; + Software software = (Software) o; + return Objects.equals(documentationUrl, software.documentationUrl) && + Objects.equals(license, software.license) && + Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl) && + Objects.equals(programmingLanguage, software.programmingLanguage); + } + + @Override + public int hashCode() { + return Objects.hash(super.hashCode(), documentationUrl, license, codeRepositoryUrl, programmingLanguage); + } } diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java new file mode 100644 index 000000000..1a45b64ff --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java @@ -0,0 +1,15 @@ +package eu.dnetlib.dhp.schema.scholexplorer; + +import eu.dnetlib.dhp.schema.oaf.Relation; + +public class DLIRelation extends Relation { + private String dateOfCollection; + + public String getDateOfCollection() { + return dateOfCollection; + } + + public void setDateOfCollection(String dateOfCollection) { + this.dateOfCollection = dateOfCollection; + } +} diff --git a/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java new file mode 100644 index 000000000..21583cd44 --- /dev/null +++ b/dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java @@ -0,0 +1,35 @@ +package eu.dnetlib.dhp.schema.common; + +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); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml new file mode 100644 index 000000000..aa2078be5 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/pom.xml @@ -0,0 +1,62 @@ + + + 4.0.0 + + eu.dnetlib.dhp + dhp-workflows + 1.1.7-SNAPSHOT + + dhp-actionmanager + + + + org.apache.spark + spark-core_2.11 + + + + org.apache.spark + spark-sql_2.11 + + + + eu.dnetlib.dhp + dhp-common + ${project.version} + + + net.sf.saxon + Saxon-HE + + + + + + dom4j + dom4j + + + + xml-apis + xml-apis + + + + jaxen + jaxen + + + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + + + eu.dnetlib + dnet-actionmanager-api + + + + diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java new file mode 100644 index 000000000..994108b1c --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java @@ -0,0 +1,126 @@ +package eu.dnetlib.dhp.actionmanager; + +import com.google.common.base.Splitter; +import com.google.common.collect.Iterables; +import com.google.common.collect.Lists; +import eu.dnetlib.actionmanager.rmi.ActionManagerException; +import eu.dnetlib.actionmanager.set.ActionManagerSet; +import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes; +import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJob; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import org.dom4j.Document; +import org.dom4j.Element; +import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.Serializable; +import java.io.StringReader; +import java.util.ArrayList; +import java.util.List; +import java.util.NoSuchElementException; +import java.util.stream.Collectors; + +public class ISClient implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); + + private static final String INPUT_ACTION_SET_ID_SEPARATOR = ","; + + private ISLookUpService isLookup; + + public ISClient(String isLookupUrl) { + isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + } + + public List getLatestRawsetPaths(String setIds) { + + List ids = Lists.newArrayList(Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR) + .omitEmptyStrings() + .trimResults() + .split(setIds)); + + return ids.stream() + .map(id -> getSet(isLookup, id)) + .map(as -> as.getPathToLatest()) + .collect(Collectors.toCollection(ArrayList::new)); + } + + private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) { + + final String q = "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') " + + "where $x//SET/@id = '" + setId + "' return $x"; + + try { + final String basePath = getBasePathHDFS(isLookup); + final String setProfile = isLookup.getResourceProfileByQuery(q); + return getActionManagerSet(basePath, setProfile); + } catch (ISLookUpException | ActionManagerException e) { + throw new RuntimeException("Error accessing Sets, using query: " + q); + } + } + + private ActionManagerSet getActionManagerSet(final String basePath, final String profile) throws ActionManagerException { + final SAXReader reader = new SAXReader(); + final ActionManagerSet set = new ActionManagerSet(); + + try { + final Document doc = reader.read(new StringReader(profile)); + + set.setId(doc.valueOf("//SET/@id").trim()); + set.setName(doc.valueOf("//SET").trim()); + set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim())); + set.setLatest(doc.valueOf("//RAW_SETS/LATEST/@id"), doc.valueOf("//RAW_SETS/LATEST/@creationDate"), doc.valueOf("//RAW_SETS/LATEST/@lastUpdate")); + set.setDirectory(doc.valueOf("//SET/@directory")); + final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED"); + if (expiredNodes != null) { + for (int i = 0; i < expiredNodes.size(); i++) { + Element ex = (Element) expiredNodes.get(i); + set.addExpired(ex.attributeValue("id"), ex.attributeValue("creationDate"), ex.attributeValue("lastUpdate")); + } + } + + final StringBuilder sb = new StringBuilder(); + sb.append(basePath); + sb.append("/"); + sb.append(doc.valueOf("//SET/@directory")); + sb.append("/"); + sb.append(doc.valueOf("//RAW_SETS/LATEST/@id")); + set.setPathToLatest(sb.toString()); + + return set; + } catch (Exception e) { + throw new ActionManagerException("Error creating set from profile: " + profile, e); + } + } + + private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException { + return queryServiceProperty(isLookup, "basePath"); + } + + private String queryServiceProperty(ISLookUpService isLookup, final String propertyName) throws ActionManagerException { + final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='" + + propertyName + "']/@value/string()"; + log.debug("quering for service property: " + q); + try { + final List value = isLookup.quickSearchProfile(q); + return Iterables.getOnlyElement(value); + } catch (ISLookUpException e) { + String msg = "Error accessing service profile, using query: " + q; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } catch (NoSuchElementException e) { + String msg = "missing service property: " + propertyName; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } catch (IllegalArgumentException e) { + String msg = "found more than one service property: " + propertyName; + log.error(msg, e); + throw new ActionManagerException(msg, e); + } + } + + +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java new file mode 100644 index 000000000..31a4da190 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJob.java @@ -0,0 +1,140 @@ +package eu.dnetlib.dhp.actionmanager.partition; + +import eu.dnetlib.dhp.actionmanager.ISClient; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.*; +import org.apache.spark.sql.types.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; +import java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static org.apache.spark.sql.functions.*; + +/** + * Partitions given set of action sets by payload type. + */ +public class PartitionActionSetsByPayloadTypeJob { + + private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); + + private static final StructType KV_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty()) + )); + + private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) + )); + + private ISClient isClient; + + public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) { + this.isClient = new ISClient(isLookupUrl); + } + + public PartitionActionSetsByPayloadTypeJob() { + } + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils.toString( + PromoteActionPayloadForGraphTableJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputActionSetIds = parser.get("inputActionSetIds"); + logger.info("inputActionSetIds: {}", inputActionSetIds); + + String outputPath = parser.get("outputPath"); + logger.info("outputPath: {}", outputPath); + + String isLookupUrl = parser.get("isLookupUrl"); + logger.info("isLookupUrl: {}", isLookupUrl); + + new PartitionActionSetsByPayloadTypeJob(isLookupUrl).run(isSparkSessionManaged, inputActionSetIds, outputPath); + } + + protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) { + + List inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds); + logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths)); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath); + }); + } + + private static void removeOutputDir(SparkSession spark, + String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void readAndWriteActionSetsFromPaths(SparkSession spark, + List inputActionSetPaths, + String outputPath) { + inputActionSetPaths + .forEach(inputActionSetPath -> { + Dataset actionDS = readActionSetFromPath(spark, inputActionSetPath); + saveActions(actionDS, outputPath); + }); + } + + private static Dataset readActionSetFromPath(SparkSession spark, + String path) { + logger.info("Reading actions from path: {}", path); + + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD rdd = sc + .sequenceFile(path, Text.class, Text.class) + .map(x -> RowFactory.create(x._1().toString(), x._2().toString())); + + return spark.createDataFrame(rdd, KV_SCHEMA) + .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) + .select(expr("atomic_action.*")); + } + + private static void saveActions(Dataset actionDS, + String path) { + logger.info("Saving actions to path: {}", path); + actionDS + .write() + .partitionBy("clazz") + .mode(SaveMode.Append) + .parquet(path); + } + + public ISClient getIsClient() { + return isClient; + } + + public void setIsClient(ISClient isClient) { + this.isClient = isClient; + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java new file mode 100644 index 000000000..19b2104bc --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java @@ -0,0 +1,74 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Relation; + +import java.util.function.BiFunction; + +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + +/** + * OAF model merging support. + */ +public class MergeAndGet { + + private MergeAndGet() { + } + + /** + * Strategy for merging OAF model objects. + *

+ * MERGE_FROM_AND_GET: use OAF 'mergeFrom' method + * SELECT_NEWER_AND_GET: use last update timestamp to return newer instance + */ + public enum Strategy { + MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET + } + + /** + * Returns a function for merging OAF model objects. + * + * @param strategy Strategy to be used to merge objects + * @param Graph table type + * @param Action payload type + * @return BiFunction to be used to merge OAF objects + */ + public static SerializableSupplier> functionFor(Strategy strategy) { + switch (strategy) { + case MERGE_FROM_AND_GET: + return () -> MergeAndGet::mergeFromAndGet; + case SELECT_NEWER_AND_GET: + return () -> MergeAndGet::selectNewerAndGet; + } + throw new RuntimeException(); + } + + private static G mergeFromAndGet(G x, A y) { + if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { + ((Relation) x).mergeFrom((Relation) y); + return x; + } else if (isSubClass(x, OafEntity.class) && isSubClass(y, OafEntity.class) && isSubClass(x, y)) { + ((OafEntity) x).mergeFrom((OafEntity) y); + return x; + } + throw new RuntimeException(String.format("MERGE_FROM_AND_GET incompatible types: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + } + + private static G selectNewerAndGet(G x, A y) { + if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { + return x; + } else if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { + return (G) y; + } else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { + return x; + } else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { + throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + } + throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s", + x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java new file mode 100644 index 000000000..20b75842c --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java @@ -0,0 +1,254 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelSupport; +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.Row; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.util.Objects; +import java.util.Optional; +import java.util.function.BiFunction; +import java.util.function.Function; + +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +/** + * Applies a given action payload file to graph table of compatible type. + */ +public class PromoteActionPayloadForGraphTableJob { + private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils.toString( + PromoteActionPayloadForGraphTableJob.class + .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + logger.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputGraphTablePath = parser.get("inputGraphTablePath"); + logger.info("inputGraphTablePath: {}", inputGraphTablePath); + + String graphTableClassName = parser.get("graphTableClassName"); + logger.info("graphTableClassName: {}", graphTableClassName); + + String inputActionPayloadPath = parser.get("inputActionPayloadPath"); + logger.info("inputActionPayloadPath: {}", inputActionPayloadPath); + + String actionPayloadClassName = parser.get("actionPayloadClassName"); + logger.info("actionPayloadClassName: {}", actionPayloadClassName); + + String outputGraphTablePath = parser.get("outputGraphTablePath"); + logger.info("outputGraphTablePath: {}", outputGraphTablePath); + + MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase()); + logger.info("strategy: {}", strategy); + + Class rowClazz = (Class) Class.forName(graphTableClassName); + Class actionPayloadClazz = (Class) Class.forName(actionPayloadClassName); + + throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputGraphTablePath); + promoteActionPayloadForGraphTable(spark, + inputGraphTablePath, + inputActionPayloadPath, + outputGraphTablePath, + strategy, + rowClazz, + actionPayloadClazz); + }); + } + + private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(Class rowClazz, + Class actionPayloadClazz) { + if (!isSubClass(rowClazz, actionPayloadClazz)) { + String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s", + rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); + throw new RuntimeException(msg); + } + } + + private static void removeOutputDir(SparkSession spark, + String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static void promoteActionPayloadForGraphTable(SparkSession spark, + String inputGraphTablePath, + String inputActionPayloadPath, + String outputGraphTablePath, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + Dataset rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz); + Dataset actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); + + Dataset result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz) + .map((MapFunction) value -> value, Encoders.bean(rowClazz)); + + saveGraphTable(result, outputGraphTablePath); + } + + private static Dataset readGraphTable(SparkSession spark, + String path, + Class rowClazz) { + logger.info("Reading graph table from path: {}", path); + + return spark.read() + .textFile(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz)); + + /* + return spark + .read() + .parquet(path) + .as(Encoders.bean(rowClazz)); + */ + } + + private static Dataset readActionPayload(SparkSession spark, + String path, + Class actionPayloadClazz) { + logger.info("Reading action payload from path: {}", path); + return spark + .read() + .parquet(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), + actionPayloadClazz), Encoders.bean(actionPayloadClazz)); + } + + private static Dataset promoteActionPayloadForGraphTable(Dataset rowDS, + Dataset actionPayloadDS, + MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName()); + + SerializableSupplier> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn; + SerializableSupplier> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy); + SerializableSupplier zeroFn = zeroFn(rowClazz); + SerializableSupplier> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource; + + Dataset joinedAndMerged = PromoteActionPayloadFunctions + .joinGraphTableWithActionPayloadAndMerge( + rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeRowWithActionPayloadAndGetFn, + rowClazz, + actionPayloadClazz); + + return PromoteActionPayloadFunctions + .groupGraphTableByIdAndMerge( + joinedAndMerged, + rowIdFn, + mergeRowsAndGetFn, + zeroFn, + isNotZeroFn, + rowClazz); + } + + private static Function idFn() { + return x -> { + if (isSubClass(x, Relation.class)) { + return idFnForRelation(x); + } + return idFnForOafEntity(x); + }; + } + + private static String idFnForRelation(T t) { + Relation r = (Relation) t; + return Optional.ofNullable(r.getSource()) + .map(source -> Optional.ofNullable(r.getTarget()) + .map(target -> Optional.ofNullable(r.getRelType()) + .map(relType -> Optional.ofNullable(r.getSubRelType()) + .map(subRelType -> Optional.ofNullable(r.getRelClass()) + .map(relClass -> String.join(source, target, relType, subRelType, relClass)) + .orElse(String.join(source, target, relType, subRelType)) + ) + .orElse(String.join(source, target, relType)) + ) + .orElse(String.join(source, target)) + ) + .orElse(source) + ) + .orElse(null); + } + + private static String idFnForOafEntity(T t) { + return ((OafEntity) t).getId(); + } + + private static SerializableSupplier zeroFn(Class clazz) { + switch (clazz.getCanonicalName()) { + case "eu.dnetlib.dhp.schema.oaf.Dataset": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Dataset()); + case "eu.dnetlib.dhp.schema.oaf.Datasource": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Datasource()); + case "eu.dnetlib.dhp.schema.oaf.Organization": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Organization()); + case "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.OtherResearchProduct()); + case "eu.dnetlib.dhp.schema.oaf.Project": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Project()); + case "eu.dnetlib.dhp.schema.oaf.Publication": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Publication()); + case "eu.dnetlib.dhp.schema.oaf.Relation": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Relation()); + case "eu.dnetlib.dhp.schema.oaf.Software": + return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Software()); + default: + throw new RuntimeException("unknown class: " + clazz.getCanonicalName()); + } + } + + private static Function isNotZeroFnUsingIdOrSource() { + return t -> { + if (isSubClass(t, Relation.class)) { + return Objects.nonNull(((Relation) t).getSource()); + } + return Objects.nonNull(((OafEntity) t).getId()); + }; + } + + private static void saveGraphTable(Dataset result, + String path) { + logger.info("Saving graph table to path: {}", path); + result + .toJSON() + .write() + .option("compression", "gzip") + .text(path); + } +} diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java new file mode 100644 index 000000000..fda86cb19 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java @@ -0,0 +1,170 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.Oaf; +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.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.TypedColumn; +import org.apache.spark.sql.expressions.Aggregator; +import scala.Tuple2; + +import java.util.Objects; +import java.util.Optional; +import java.util.function.BiFunction; +import java.util.function.Function; + +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + +/** + * Promote action payload functions. + */ +public class PromoteActionPayloadFunctions { + + private PromoteActionPayloadFunctions() { + } + + /** + * Joins dataset representing graph table with dataset representing action payload using supplied functions. + * + * @param rowDS Dataset representing graph table + * @param actionPayloadDS Dataset representing action payload + * @param rowIdFn Function used to get the id of graph table row + * @param actionPayloadIdFn Function used to get id of action payload instance + * @param mergeAndGetFn Function used to merge graph table row and action payload instance + * @param rowClazz Class of graph table + * @param actionPayloadClazz Class of action payload + * @param Type of graph table row + * @param Type of action payload instance + * @return Dataset of merged graph table rows and action payload instances + */ + public static Dataset joinGraphTableWithActionPayloadAndMerge(Dataset rowDS, + Dataset actionPayloadDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> actionPayloadIdFn, + SerializableSupplier> mergeAndGetFn, + Class rowClazz, + Class actionPayloadClazz) { + if (!isSubClass(rowClazz, actionPayloadClazz)) { + throw new RuntimeException("action payload type must be the same or be a super type of table row type"); + } + + Dataset> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz); + Dataset> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz); + + return rowWithIdDS + .joinWith(actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "full_outer") + .map((MapFunction, Tuple2>, G>) value -> { + Optional rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2); + Optional actionPayloadOpt = Optional.ofNullable(value._2()).map(Tuple2::_2); + return rowOpt + .map(row -> actionPayloadOpt + .map(actionPayload -> mergeAndGetFn.get().apply(row, actionPayload)) + .orElse(row)) + .orElseGet(() -> actionPayloadOpt + .filter(actionPayload -> actionPayload.getClass().equals(rowClazz)) + .map(rowClazz::cast) + .orElse(null)); + }, Encoders.kryo(rowClazz)) + .filter((FilterFunction) Objects::nonNull); + } + + private static Dataset> mapToTupleWithId(Dataset ds, + SerializableSupplier> idFn, + Class clazz) { + return ds + .map((MapFunction>) value -> new Tuple2<>(idFn.get().apply(value), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + } + + /** + * Groups graph table by id and aggregates using supplied functions. + * + * @param rowDS Dataset representing graph table + * @param rowIdFn Function used to get the id of graph table row + * @param mergeAndGetFn Function used to merge graph table rows + * @param zeroFn Function to create a zero/empty instance of graph table row + * @param isNotZeroFn Function to check if graph table row is not zero/empty + * @param rowClazz Class of graph table + * @param Type of graph table row + * @return Dataset of aggregated graph table rows + */ + public static Dataset groupGraphTableByIdAndMerge(Dataset rowDS, + SerializableSupplier> rowIdFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier zeroFn, + SerializableSupplier> isNotZeroFn, + Class rowClazz) { + TypedColumn aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn(); + return rowDS + .groupByKey((MapFunction) x -> rowIdFn.get().apply(x), Encoders.STRING()) + .agg(aggregator) + .map((MapFunction, G>) Tuple2::_2, Encoders.kryo(rowClazz)); + } + + /** + * Aggregator to be used for aggregating graph table rows during grouping. + * + * @param Type of graph table row + */ + public static class TableAggregator extends Aggregator { + private SerializableSupplier zeroFn; + private SerializableSupplier> mergeAndGetFn; + private SerializableSupplier> isNotZeroFn; + private Class rowClazz; + + public TableAggregator(SerializableSupplier zeroFn, + SerializableSupplier> mergeAndGetFn, + SerializableSupplier> isNotZeroFn, + Class rowClazz) { + this.zeroFn = zeroFn; + this.mergeAndGetFn = mergeAndGetFn; + this.isNotZeroFn = isNotZeroFn; + this.rowClazz = rowClazz; + } + + @Override + public G zero() { + return zeroFn.get(); + } + + @Override + public G reduce(G b, G a) { + return zeroSafeMergeAndGet(b, a); + } + + @Override + public G merge(G b1, G b2) { + return zeroSafeMergeAndGet(b1, b2); + } + + private G zeroSafeMergeAndGet(G left, G right) { + Function isNotZero = isNotZeroFn.get(); + if (isNotZero.apply(left) && isNotZero.apply(right)) { + return mergeAndGetFn.get().apply(left, right); + } else if (isNotZero.apply(left) && !isNotZero.apply(right)) { + return left; + } else if (!isNotZero.apply(left) && isNotZero.apply(right)) { + return right; + } + throw new RuntimeException("internal aggregation error: left and right objects are zero"); + } + + @Override + public G finish(G reduction) { + return reduction; + } + + @Override + public Encoder bufferEncoder() { + return Encoders.kryo(rowClazz); + } + + @Override + public Encoder outputEncoder() { + return Encoders.kryo(rowClazz); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json new file mode 100644 index 000000000..ad58fe754 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "iasi", + "paramLongName": "inputActionSetIds", + "paramDescription": "comma separated list of action set ids to partition by payload type", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "root output location for partitioned action sets", + "paramRequired": true + }, + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json new file mode 100644 index 000000000..e111f156e --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json @@ -0,0 +1,44 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "igtp", + "paramLongName": "inputGraphTablePath", + "paramDescription": "location of graph table to promote", + "paramRequired": true + }, + { + "paramName": "gtcn", + "paramLongName": "graphTableClassName", + "paramDescription": "canonical name of graph table row class", + "paramRequired": true + }, + { + "paramName": "iapp", + "paramLongName": "inputActionPayloadPath", + "paramDescription": "location of action payload to promote", + "paramRequired": true + }, + { + "paramName": "apcn", + "paramLongName": "actionPayloadClassName", + "paramDescription": "canonical name of action payload class", + "paramRequired": true + }, + { + "paramName": "ogtp", + "paramLongName": "outputGraphTablePath", + "paramDescription": "location of promoted graph table", + "paramRequired": true + }, + { + "paramName": "mags", + "paramLongName": "mergeAndGetStrategy", + "paramDescription": "strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml new file mode 100644 index 000000000..27c272aea --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml @@ -0,0 +1,178 @@ + + + + activePromoteDatasetActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Dataset payload + + + activePromoteResultActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteDatasetActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'dataset')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Dataset')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteDatasetActionPayloadForDatasetTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${inputGraphRootPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Dataset + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputGraphTablePath${workingDir}/dataset + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/dataset + ${workingDir}/dataset + + + + + + + + + ${(activePromoteResultActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteResultActionPayloadForDatasetTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${workingDir}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result + --outputGraphTablePath${outputGraphRootPath}/dataset + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${workingDir}/dataset + ${outputGraphRootPath}/dataset + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml new file mode 100644 index 000000000..800f29b17 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml @@ -0,0 +1,125 @@ + + + + activePromoteDatasourceActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Datasource payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteDatasourceActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'datasource')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Datasource')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteDatasourceActionPayloadForDatasourceTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputGraphTablePath${inputGraphRootPath}/datasource + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Datasource + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputGraphTablePath${outputGraphRootPath}/datasource + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/datasource + ${outputGraphRootPath}/datasource + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt new file mode 100644 index 000000000..dd8f5e14e --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt @@ -0,0 +1,9 @@ +## This is a classpath-based import file (this header is required) +promote_action_payload_for_dataset_table classpath eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app +promote_action_payload_for_datasource_table classpath eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app +promote_action_payload_for_organization_table classpath eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app +promote_action_payload_for_otherresearchproduct_table classpath eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app +promote_action_payload_for_project_table classpath eu/dnetlib/dhp/actionmanager/wf/project/oozie_app +promote_action_payload_for_publication_table classpath eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app +promote_action_payload_for_relation_table classpath eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app +promote_action_payload_for_software_table classpath eu/dnetlib/dhp/actionmanager/wf/software/oozie_app diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml new file mode 100644 index 000000000..25afc34c9 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml @@ -0,0 +1,270 @@ + + + + activePromoteDatasetActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Dataset payload + + + activePromoteDatasourceActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Datasource payload + + + activePromoteOrganizationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Organization payload + + + activePromoteOtherResearchProductActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload + + + activePromoteProjectActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Project payload + + + activePromotePublicationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Publication payload + + + activePromoteRelationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Relation payload + + + activePromoteResultActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload + + + activePromoteSoftwareActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Software payload + + + inputGraphRootPath + root location of input materialized graph + + + isLookupUrl + URL of the ISLookupService + + + inputActionSetIds + comma separated list of action set ids to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn-cluster + cluster + PartitionActionSetsByPayloadType + eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputActionSetIds${inputActionSetIds} + --outputPath${workingDir}/action_payload_by_type + --isLookupUrl${isLookupUrl} + + + + + + + + + + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_dataset_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_datasource_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_organization_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_otherresearchproduct_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_project_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_publication_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_relation_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + ${wf:appPath()}/promote_action_payload_for_software_table + + + + inputActionPayloadRootPath + ${workingDir}/action_payload_by_type + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml new file mode 100644 index 000000000..a6c6220e4 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml @@ -0,0 +1,125 @@ + + + + activePromoteOrganizationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Organization payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteOrganizationActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'organization')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Organization')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteOrganizationActionPayloadForOrganizationTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputGraphTablePath${inputGraphRootPath}/organization + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Organization + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Organization + --outputGraphTablePath${outputGraphRootPath}/organization + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/organization + ${outputGraphRootPath}/organization + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml new file mode 100644 index 000000000..4b65de3df --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml @@ -0,0 +1,177 @@ + + + + activePromoteOtherResearchProductActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload + + + activePromoteResultActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteOtherResearchProductActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'otherresearchproduct')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.OtherResearchProduct')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteOtherResearchProductActionPayloadForOtherResearchProductTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputGraphTablePath${inputGraphRootPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputGraphTablePath${workingDir}/otherresearchproduct + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/otherresearchproduct + ${workingDir}/otherresearchproduct + + + + + + + + + ${(activePromoteResultActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteResultActionPayloadForOtherResearchProductTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${workingDir}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result + --outputGraphTablePath${outputGraphRootPath}/otherresearchproduct + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${workingDir}/otherresearchproduct + ${outputGraphRootPath}/otherresearchproduct + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml new file mode 100644 index 000000000..c73fea96e --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml @@ -0,0 +1,125 @@ + + + + activePromoteProjectActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteProjectActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'project')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Project')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteProjectActionPayloadForProjectTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputGraphTablePath${inputGraphRootPath}/project + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Project + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Project + --outputGraphTablePath${outputGraphRootPath}/project + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/project + ${outputGraphRootPath}/project + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml new file mode 100644 index 000000000..35be128da --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml @@ -0,0 +1,178 @@ + + + + activePromotePublicationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Publication payload + + + activePromoteResultActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromotePublicationActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'publication')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Publication')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromotePublicationActionPayloadForPublicationTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${inputGraphRootPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Publication + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Publication + --outputGraphTablePath${workingDir}/publication + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/publication + ${workingDir}/publication + + + + + + + + + ${(activePromoteResultActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteResultActionPayloadForPublicationTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${workingDir}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result + --outputGraphTablePath${outputGraphRootPath}/publication + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${workingDir}/publication + ${outputGraphRootPath}/publication + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml new file mode 100644 index 000000000..f64301c70 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml @@ -0,0 +1,126 @@ + + + + activePromoteRelationActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Relation payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteRelationActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'relation')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Relation')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteRelationActionPayloadForRelationTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${inputGraphRootPath}/relation + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Relation + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Relation + --outputGraphTablePath${outputGraphRootPath}/relation + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/relation + ${outputGraphRootPath}/relation + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml new file mode 100644 index 000000000..397184c91 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml @@ -0,0 +1,177 @@ + + + + activePromoteSoftwareActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Software payload + + + activePromoteResultActionPayload + when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload + + + inputGraphRootPath + root location of input materialized graph + + + inputActionPayloadRootPath + root location of action payloads to promote + + + outputGraphRootPath + root location for output materialized graph + + + mergeAndGetStrategy + strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + ${(activePromoteSoftwareActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'software')) eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Software')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteSoftwareActionPayloadForSoftwareTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --inputGraphTablePath${inputGraphRootPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Software + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Software + --outputGraphTablePath${workingDir}/software + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${inputGraphRootPath}/software + ${workingDir}/software + + + + + + + + + ${(activePromoteResultActionPayload eq "true") and + (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")} + + + + + + + + yarn-cluster + cluster + PromoteResultActionPayloadForSoftwareTable + eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob + dhp-actionmanager-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=2560 + + --inputGraphTablePath${workingDir}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --inputActionPayloadPath${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result + --actionPayloadClassNameeu.dnetlib.dhp.schema.oaf.Result + --outputGraphTablePath${outputGraphRootPath}/software + --mergeAndGetStrategy${mergeAndGetStrategy} + + + + + + + + -pb + ${workingDir}/software + ${outputGraphRootPath}/software + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java new file mode 100644 index 000000000..bd5dc9a5d --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java @@ -0,0 +1,221 @@ +package eu.dnetlib.dhp.actionmanager.partition; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; +import eu.dnetlib.dhp.actionmanager.ISClient; +import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapreduce.Job; +import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat; +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.Row; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.types.*; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.junit.jupiter.api.io.TempDir; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; +import scala.Tuple2; +import scala.collection.mutable.Seq; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException; +import static org.apache.spark.sql.functions.*; +import static org.junit.jupiter.api.Assertions.assertIterableEquals; +import static scala.collection.JavaConversions.mutableSeqAsJavaList; + +@ExtendWith(MockitoExtension.class) +public class PartitionActionSetsByPayloadTypeJobTest { + private static final ClassLoader cl = PartitionActionSetsByPayloadTypeJobTest.class.getClassLoader(); + + private static Configuration configuration; + private static SparkSession spark; + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( + Arrays.asList( + StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), + StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) + )); + + @BeforeAll + public static void beforeAll() throws IOException { + configuration = Job.getInstance().getConfiguration(); + SparkConf conf = new SparkConf(); + conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + + @DisplayName("Job") + @Nested + class Main { + + @Mock + private ISClient isClient; + + @Test + public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception { + // given + Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets"); + Path outputDir = workingDir.resolve("output"); + + Map> oafsByClassName = createActionSets(inputActionSetsBaseDir); + + List inputActionSetsPaths = resolveInputActionSetPaths(inputActionSetsBaseDir); + + // when + Mockito.when(isClient.getLatestRawsetPaths(Mockito.anyString())).thenReturn(inputActionSetsPaths); + + PartitionActionSetsByPayloadTypeJob job = new PartitionActionSetsByPayloadTypeJob(); + job.setIsClient(isClient); + job.run( + Boolean.FALSE, + "", // it can be empty we're mocking the response from isClient to resolve the paths + outputDir.toString() + ); + + // then + Files.exists(outputDir); + + assertForOafType(outputDir, oafsByClassName, eu.dnetlib.dhp.schema.oaf.Dataset.class); + assertForOafType(outputDir, oafsByClassName, Datasource.class); + assertForOafType(outputDir, oafsByClassName, Organization.class); + assertForOafType(outputDir, oafsByClassName, OtherResearchProduct.class); + assertForOafType(outputDir, oafsByClassName, Project.class); + assertForOafType(outputDir, oafsByClassName, Publication.class); + assertForOafType(outputDir, oafsByClassName, Result.class); + assertForOafType(outputDir, oafsByClassName, Relation.class); + assertForOafType(outputDir, oafsByClassName, Software.class); + } + } + + private List resolveInputActionSetPaths(Path inputActionSetsBaseDir) throws IOException { + Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); + return Files + .list(inputActionSetJsonDumpsDir) + .map(path -> { + String inputActionSetId = path.getFileName().toString(); + return inputActionSetsBaseDir.resolve(inputActionSetId).toString(); + }) + .collect(Collectors.toCollection(ArrayList::new)); + } + + private static Map> createActionSets(Path inputActionSetsDir) throws IOException { + Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir(); + + Map> oafsByType = new HashMap<>(); + Files + .list(inputActionSetJsonDumpsDir) + .forEach(inputActionSetJsonDumpFile -> { + String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString(); + Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId); + + Dataset actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString()) + .cache(); + + writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString()); + + Map> actionSetOafsByType = actionDS + .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) + .select(expr("atomic_action.*")) + .groupBy(col("clazz")) + .agg(collect_list(col("payload")).as("payload_list")) + .collectAsList() + .stream() + .map(row -> new AbstractMap.SimpleEntry<>(row.getAs("clazz"), + mutableSeqAsJavaList(row.>getAs("payload_list")))) + .collect(Collectors.toMap(AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue)); + + actionSetOafsByType.keySet() + .forEach(x -> { + if (oafsByType.containsKey(x)) { + List collected = new ArrayList<>(); + collected.addAll(oafsByType.get(x)); + collected.addAll(actionSetOafsByType.get(x)); + oafsByType.put(x, collected); + } else { + oafsByType.put(x, actionSetOafsByType.get(x)); + } + }); + }); + + return oafsByType; + } + + private static Path getInputActionSetJsonDumpsDir() { + return Paths + .get(Objects.requireNonNull(cl.getResource("eu/dnetlib/dhp/actionmanager/partition/input/")) + .getFile()); + } + + private static Dataset readActionsFromJsonDump(String path) { + return spark + .read() + .textFile(path); + } + + private static void writeActionsAsJobInput(Dataset actionDS, + String inputActionSetId, + String path) { + actionDS + .javaRDD() + .mapToPair(json -> new Tuple2<>(new Text(inputActionSetId), new Text(json))) + .saveAsNewAPIHadoopFile(path, + Text.class, + Text.class, + SequenceFileOutputFormat.class, + configuration); + } + + private static void assertForOafType(Path outputDir, Map> oafsByClassName, Class clazz) { + Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName())); + Files.exists(outputDatasetDir); + + List actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList(); + actuals.sort(Comparator.comparingInt(Object::hashCode)); + + List expecteds = oafsByClassName.get(clazz.getCanonicalName()).stream() + .map(json -> mapToOaf(json, clazz)) + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + assertIterableEquals(expecteds, actuals); + } + + private static Dataset readActionPayloadFromJobOutput(String path, + Class clazz) { + return spark + .read() + .parquet(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value.getAs("payload"), clazz), + Encoders.bean(clazz)); + } + + private static T mapToOaf(String json, Class clazz) { + return rethrowAsRuntimeException( + () -> OBJECT_MAPPER.readValue(json, clazz), + String.format("failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName()) + ); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java new file mode 100644 index 000000000..154e0a331 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java @@ -0,0 +1,268 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.*; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; + +import java.util.function.BiFunction; + +import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.Strategy; +import static eu.dnetlib.dhp.actionmanager.promote.MergeAndGet.functionFor; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.*; + +public class MergeAndGetTest { + + @Nested + class MergeFromAndGetStrategy { + + @Test + public void shouldThrowForOafAndOaf() { + // given + Oaf a = mock(Oaf.class); + Oaf b = mock(Oaf.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForOafAndRelation() { + // given + Oaf a = mock(Oaf.class); + Relation b = mock(Relation.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForOafAndOafEntity() { + // given + Oaf a = mock(Oaf.class); + OafEntity b = mock(OafEntity.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForRelationAndOaf() { + // given + Relation a = mock(Relation.class); + Oaf b = mock(Oaf.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForRelationAndOafEntity() { + // given + Relation a = mock(Relation.class); + OafEntity b = mock(OafEntity.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldBehaveProperlyForRelationAndRelation() { + // given + Relation a = mock(Relation.class); + Relation b = mock(Relation.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + Oaf x = fn.get().apply(a, b); + assertTrue(Relation.class.isAssignableFrom(x.getClass())); + verify(a).mergeFrom(b); + assertEquals(a, x); + } + + @Test + public void shouldThrowForOafEntityAndOaf() { + // given + OafEntity a = mock(OafEntity.class); + Oaf b = mock(Oaf.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForOafEntityAndRelation() { + // given + OafEntity a = mock(OafEntity.class); + Relation b = mock(Relation.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() { + // given + class OafEntitySub1 extends OafEntity { + } + class OafEntitySub2 extends OafEntity { + } + + OafEntitySub1 a = mock(OafEntitySub1.class); + OafEntitySub2 b = mock(OafEntitySub2.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldBehaveProperlyForOafEntityAndOafEntity() { + // given + OafEntity a = mock(OafEntity.class); + OafEntity b = mock(OafEntity.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.MERGE_FROM_AND_GET); + + // then + Oaf x = fn.get().apply(a, b); + assertTrue(OafEntity.class.isAssignableFrom(x.getClass())); + verify(a).mergeFrom(b); + assertEquals(a, x); + } + } + + @Nested + class SelectNewerAndGetStrategy { + + @Test + public void shouldThrowForOafEntityAndRelation() { + // given + OafEntity a = mock(OafEntity.class); + Relation b = mock(Relation.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForRelationAndOafEntity() { + // given + Relation a = mock(Relation.class); + OafEntity b = mock(OafEntity.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowForOafEntityAndResult() { + // given + OafEntity a = mock(OafEntity.class); + Result b = mock(Result.class); + + // when + SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() { + // given + // real types must be used because subclass-superclass resolution does not work for mocks + Dataset a = new Dataset(); + a.setLastupdatetimestamp(1L); + Result b = new Result(); + b.setLastupdatetimestamp(2L); + + // when + SerializableSupplier> fn = functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + assertThrows(RuntimeException.class, () -> + fn.get().apply(a, b)); + } + + @Test + public void shouldShouldReturnLeftForOafEntityAndOafEntity() { + // given + OafEntity a = mock(OafEntity.class); + when(a.getLastupdatetimestamp()).thenReturn(1L); + OafEntity b = mock(OafEntity.class); + when(b.getLastupdatetimestamp()).thenReturn(2L); + + // when + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + Oaf x = fn.get().apply(a, b); + assertTrue(OafEntity.class.isAssignableFrom(x.getClass())); + assertEquals(b, x); + } + + @Test + public void shouldShouldReturnRightForOafEntityAndOafEntity() { + // given + OafEntity a = mock(OafEntity.class); + when(a.getLastupdatetimestamp()).thenReturn(2L); + OafEntity b = mock(OafEntity.class); + when(b.getLastupdatetimestamp()).thenReturn(1L); + + // when + SerializableSupplier> fn = + functionFor(Strategy.SELECT_NEWER_AND_GET); + + // then + Oaf x = fn.get().apply(a, b); + assertTrue(OafEntity.class.isAssignableFrom(x.getClass())); + assertEquals(a, x); + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java new file mode 100644 index 000000000..6f53fbec2 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -0,0 +1,239 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.FileUtils; +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.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.Arguments; +import org.junit.jupiter.params.provider.MethodSource; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.Comparator; +import java.util.List; +import java.util.Objects; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import static org.junit.jupiter.api.Assertions.*; +import static org.junit.jupiter.params.provider.Arguments.arguments; + +public class PromoteActionPayloadForGraphTableJobTest { + private static final ClassLoader cl = PromoteActionPayloadForGraphTableJobTest.class.getClassLoader(); + + private static SparkSession spark; + + private Path workingDir; + private Path inputDir; + private Path inputGraphRootDir; + private Path inputActionPayloadRootDir; + private Path outputDir; + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + @BeforeAll + public static void beforeAll() { + SparkConf conf = new SparkConf(); + conf.setAppName(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); + conf.setMaster("local"); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @BeforeEach + public void beforeEach() throws IOException { + workingDir = Files.createTempDirectory(PromoteActionPayloadForGraphTableJobTest.class.getSimpleName()); + inputDir = workingDir.resolve("input"); + inputGraphRootDir = inputDir.resolve("graph"); + inputActionPayloadRootDir = inputDir.resolve("action_payload"); + outputDir = workingDir.resolve("output"); + } + + @AfterEach + public void afterEach() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + + @DisplayName("Job") + @Nested + class Main { + + @Test + public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() { + // given + Class rowClazz = Relation.class; + Class actionPayloadClazz = OafEntity.class; + + // when + RuntimeException exception = assertThrows(RuntimeException.class, () -> + PromoteActionPayloadForGraphTableJob.main(new String[]{ + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputGraphTablePath", "", + "-graphTableClassName", rowClazz.getCanonicalName(), + "-inputActionPayloadPath", "", + "-actionPayloadClassName", actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", "", + "-mergeAndGetStrategy", MergeAndGet.Strategy.SELECT_NEWER_AND_GET.name() + })); + + // then + String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s", + rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); + assertTrue(exception.getMessage().contains(msg)); + } + + @ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}") + @MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams") + public void shouldPromoteActionPayloadForGraphTable(MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) throws Exception { + // given + Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); + Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + + // when + PromoteActionPayloadForGraphTableJob.main(new String[]{ + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputGraphTablePath", inputGraphTableDir.toString(), + "-graphTableClassName", rowClazz.getCanonicalName(), + "-inputActionPayloadPath", inputActionPayloadDir.toString(), + "-actionPayloadClassName", actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", outputGraphTableDir.toString(), + "-mergeAndGetStrategy", strategy.name() + }); + + // then + assertTrue(Files.exists(outputGraphTableDir)); + + List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + String expectedOutputGraphTableJsonDumpPath = resultFileLocation(strategy, rowClazz, actionPayloadClazz); + Path expectedOutputGraphTableJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(expectedOutputGraphTableJsonDumpPath)).getFile()); + List expectedOutputRows = readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + assertIterableEquals(expectedOutputRows, actualOutputRows); + } + } + + public static Stream promoteJobTestParams() { + return Stream.of( + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Dataset.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, eu.dnetlib.dhp.schema.oaf.Dataset.class, eu.dnetlib.dhp.schema.oaf.Result.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Datasource.class, Datasource.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Organization.class, Organization.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, OtherResearchProduct.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, OtherResearchProduct.class, Result.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Project.class, Project.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Publication.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Publication.class, Result.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Relation.class, Relation.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Software.class), + arguments(MergeAndGet.Strategy.MERGE_FROM_AND_GET, Software.class, Result.class) + ); + } + + private static Path createGraphTable(Path inputGraphRootDir, + Class rowClazz) { + String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz); + Path inputGraphTableJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile()); + Dataset rowDS = readGraphTableFromJsonDump(inputGraphTableJsonDumpFile.toString(), rowClazz); + String inputGraphTableName = rowClazz.getSimpleName().toLowerCase(); + Path inputGraphTableDir = inputGraphRootDir.resolve(inputGraphTableName); + writeGraphTableAaJobInput(rowDS, inputGraphTableDir.toString()); + return inputGraphTableDir; + } + + private static String inputGraphTableJsonDumpLocation(Class rowClazz) { + return String.format( + "%s/%s.json", "eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase()); + } + + private static Dataset readGraphTableFromJsonDump(String path, + Class rowClazz) { + return spark + .read() + .textFile(path) + .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + } + + private static void writeGraphTableAaJobInput(Dataset rowDS, + String path) { + rowDS + .write() + .option("compression", "gzip") + .json(path); + } + + private static Path createActionPayload(Path inputActionPayloadRootDir, + Class rowClazz, + Class actionPayloadClazz) { + String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz); + Path inputActionPayloadJsonDumpFile = Paths + .get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile()); + Dataset actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString()); + Path inputActionPayloadDir = inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase()); + writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString()); + return inputActionPayloadDir; + } + + private static String inputActionPayloadJsonDumpLocation(Class rowClazz, + Class actionPayloadClazz) { + + return String.format("eu/dnetlib/dhp/actionmanager/promote/input/action_payload/%s_table/%s.json", + rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase()); + } + + private static Dataset readActionPayloadFromJsonDump(String path) { + return spark + .read() + .textFile(path); + } + + private static void writeActionPayloadAsJobInput(Dataset actionPayloadDS, + String path) { + actionPayloadDS + .withColumnRenamed("value", "payload") + .write() + .parquet(path); + } + + private static Dataset readGraphTableFromJobOutput(String path, + Class rowClazz) { + return spark + .read() + .textFile(path) + .map((MapFunction) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz)); + } + + private static String resultFileLocation(MergeAndGet.Strategy strategy, + Class rowClazz, + Class actionPayloadClazz) { + return String + .format("eu/dnetlib/dhp/actionmanager/promote/output/graph/%s/%s/%s_action_payload/result.json", + strategy.name().toLowerCase(), rowClazz.getSimpleName().toLowerCase(), actionPayloadClazz.getSimpleName().toLowerCase()); + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java new file mode 100644 index 000000000..e3fc7db48 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java @@ -0,0 +1,314 @@ +package eu.dnetlib.dhp.actionmanager.promote; + +import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Nested; +import org.junit.jupiter.api.Test; + +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.function.BiFunction; +import java.util.function.Function; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertThrows; + +public class PromoteActionPayloadFunctionsTest { + + private static SparkSession spark; + + @BeforeAll + public static void beforeAll() { + SparkConf conf = new SparkConf(); + conf.setMaster("local"); + conf.setAppName(PromoteActionPayloadFunctionsTest.class.getSimpleName()); + conf.set("spark.driver.host", "localhost"); + spark = SparkSession.builder().config(conf).getOrCreate(); + } + + @AfterAll + public static void afterAll() { + spark.stop(); + } + + @Nested + class JoinTableWithActionPayloadAndMerge { + + @Test + public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() { + // given + class OafImpl extends Oaf { + } + + // when + assertThrows(RuntimeException.class, () -> + PromoteActionPayloadFunctions + .joinGraphTableWithActionPayloadAndMerge(null, + null, + null, + null, + null, + OafImplSubSub.class, + OafImpl.class + )); + } + + @Test + public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() { + // given + String id0 = "id0"; + String id1 = "id1"; + String id2 = "id2"; + String id3 = "id3"; + String id4 = "id4"; + List rowData = Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + List actionPayloadData = Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), createOafImplSubSub(id2), + createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3), + createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4) + ); + Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + + // when + List results = PromoteActionPayloadFunctions + .joinGraphTableWithActionPayloadAndMerge(rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeAndGetFn, + OafImplSubSub.class, + OafImplSubSub.class + ) + .collectAsList(); + + // then + assertEquals(11, results.size()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count()); + assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count()); + assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count()); + assertEquals(4, results.stream().filter(x -> x.getId().equals(id4)).count()); + + results.forEach(result -> { + switch (result.getId()) { + case "id0": + assertEquals(1, result.getMerged()); + break; + case "id1": + case "id2": + case "id3": + assertEquals(2, result.getMerged()); + break; + case "id4": + assertEquals(1, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); + } + + @Test + public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() { + // given + String id0 = "id0"; + String id1 = "id1"; + String id2 = "id2"; + String id3 = "id3"; + String id4 = "id4"; + List rowData = Arrays.asList( + createOafImplSubSub(id0), + createOafImplSubSub(id1), + createOafImplSubSub(id2), + createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + List actionPayloadData = Arrays.asList( + createOafImplSub(id1), + createOafImplSub(id2), createOafImplSub(id2), + createOafImplSub(id3), createOafImplSub(id3), createOafImplSub(id3), + createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4) + ); + Dataset actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> actionPayloadIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + + // when + List results = PromoteActionPayloadFunctions + .joinGraphTableWithActionPayloadAndMerge(rowDS, + actionPayloadDS, + rowIdFn, + actionPayloadIdFn, + mergeAndGetFn, + OafImplSubSub.class, + OafImplSub.class + ) + .collectAsList(); + + // then + assertEquals(7, results.size()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id0)).count()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count()); + assertEquals(2, results.stream().filter(x -> x.getId().equals(id2)).count()); + assertEquals(3, results.stream().filter(x -> x.getId().equals(id3)).count()); + assertEquals(0, results.stream().filter(x -> x.getId().equals(id4)).count()); + + results.forEach(result -> { + switch (result.getId()) { + case "id0": + assertEquals(1, result.getMerged()); + break; + case "id1": + case "id2": + case "id3": + assertEquals(2, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); + } + + } + + @Nested + class GroupTableByIdAndMerge { + + @Test + public void shouldRunProperly() { + // given + String id1 = "id1"; + String id2 = "id2"; + String id3 = "id3"; + List rowData = Arrays.asList( + createOafImplSubSub(id1), + createOafImplSubSub(id2), createOafImplSubSub(id2), + createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3) + ); + Dataset rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class)); + + SerializableSupplier> rowIdFn = () -> OafImplRoot::getId; + SerializableSupplier> mergeAndGetFn = () -> (x, y) -> { + x.merge(y); + return x; + }; + SerializableSupplier zeroFn = OafImplSubSub::new; + SerializableSupplier> isNotZeroFn = () -> x -> Objects.nonNull(x.getId()); + + // when + List results = PromoteActionPayloadFunctions + .groupGraphTableByIdAndMerge(rowDS, + rowIdFn, + mergeAndGetFn, + zeroFn, + isNotZeroFn, + OafImplSubSub.class) + .collectAsList(); + + // then + assertEquals(3, results.size()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id1)).count()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id2)).count()); + assertEquals(1, results.stream().filter(x -> x.getId().equals(id3)).count()); + + results.forEach(result -> { + switch (result.getId()) { + case "id1": + assertEquals(1, result.getMerged()); + break; + case "id2": + assertEquals(2, result.getMerged()); + break; + case "id3": + assertEquals(3, result.getMerged()); + break; + default: + throw new RuntimeException(); + } + }); + } + + } + + public static class OafImplRoot extends Oaf { + private String id; + private int merged = 1; + + public void merge(OafImplRoot e) { + merged += e.merged; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public int getMerged() { + return merged; + } + + public void setMerged(int merged) { + this.merged = merged; + } + } + + public static class OafImplSub extends OafImplRoot { + + @Override + public void merge(OafImplRoot e) { + super.merge(e); + } + } + + private static OafImplSub createOafImplSub(String id) { + OafImplSub x = new OafImplSub(); + x.setId(id); + return x; + } + + public static class OafImplSubSub extends OafImplSub { + + @Override + public void merge(OafImplRoot e) { + super.merge(e); + } + } + + private static OafImplSubSub createOafImplSubSub(String id) { + OafImplSubSub x = new OafImplSubSub(); + x.setId(id); + return x; + } + +} diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json new file mode 100644 index 000000000..7a8778172 --- /dev/null +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/partition/input/action_set_1_payload.json @@ -0,0 +1,90 @@ +{"clazz":"eu.dnetlib.dhp.schema.oaf.Dataset","payload":{"author":[{"affiliation":[],"fullname":"Boža, Pal","name":"Pal","pid":[],"rank":1,"surname":"Boža"},{"affiliation":[],"fullname":"Anačkov, Goran","name":"Goran","pid":[],"rank":2,"surname":"Anačkov"},{"affiliation":[],"fullname":"Karaman, 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title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"PFSQL, version 2.0"}]} diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 8d4d880b3..3e7b1a375 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -99,23 +99,11 @@ jaxen jaxen - - - org.mongodb - mongo-java-driver - - org.apache.hadoop hadoop-distcp - - - org.postgresql - postgresql - 42.2.10 - diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step3/DispatchEntitiesApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step3/DispatchEntitiesApplication.java deleted file mode 100644 index 4ee24cba0..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step3/DispatchEntitiesApplication.java +++ /dev/null @@ -1,71 +0,0 @@ -package eu.dnetlib.dhp.migration.step3; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; - -public class DispatchEntitiesApplication { - - private static final Log log = LogFactory.getLog(DispatchEntitiesApplication.class); - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json"))); - parser.parseArgument(args); - - try (final SparkSession spark = newSparkSession(parser); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) { - - final String sourcePath = parser.get("sourcePath"); - final String targetPath = parser.get("graphRawPath"); - - processEntity(sc, Publication.class, sourcePath, targetPath); - processEntity(sc, Dataset.class, sourcePath, targetPath); - processEntity(sc, Software.class, sourcePath, targetPath); - processEntity(sc, OtherResearchProduct.class, sourcePath, targetPath); - processEntity(sc, Datasource.class, sourcePath, targetPath); - processEntity(sc, Organization.class, sourcePath, targetPath); - processEntity(sc, Project.class, sourcePath, targetPath); - processEntity(sc, Relation.class, sourcePath, targetPath); - } - } - - private static SparkSession newSparkSession(final ArgumentApplicationParser parser) { - return SparkSession - .builder() - .appName(DispatchEntitiesApplication.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - } - - private static void processEntity(final JavaSparkContext sc, final Class clazz, final String sourcePath, final String targetPath) { - final String type = clazz.getSimpleName().toLowerCase(); - - log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); - - sc.textFile(sourcePath) - .filter(l -> isEntityType(l, type)) - .map(l -> StringUtils.substringAfter(l, "|")) - .saveAsTextFile(targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? - } - - private static boolean isEntityType(final String line, final String type) { - return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type); - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/workflow.xml deleted file mode 100644 index 42ab59822..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/workflow.xml +++ /dev/null @@ -1,197 +0,0 @@ - - - - - workingPath - /tmp/dhp_migration - the base path to store temporary intermediate data - - - graphBasePath - the target path to store raw graph - - - reuseContent - false - should import content from the aggregator or reuse a previous version - - - postgresURL - the postgres URL to access to the database - - - postgresUser - the user postgres - - - postgresPassword - the password postgres - - - mongoURL - mongoDB url, example: mongodb://[username:password@]host[:port] - - - mongoDb - mongo database - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - ${jobTracker} - ${nameNode} - - - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${wf:conf('reuseContent') eq false} - ${wf:conf('reuseContent') eq true} - - - - - - - - - - - - - - - - eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication - -p${workingPath}/db_records - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} - - - - - - - - eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication - -p${workingPath}/odf_records - -mongourl${mongoURL} - -mongodb${mongoDb} - -fODF - -lstore - -icleaned - - - - - - - - eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication - -p${workingPath}/oaf_records - -mongourl${mongoURL} - -mongodb${mongoDb} - -fOAF - -lstore - -icleaned - - - - - - - - - - - - - - - - yarn - cluster - GenerateEntities - eu.dnetlib.dhp.migration.step2.GenerateEntitiesApplication - dhp-aggregation-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" - - -mt yarn-cluster - -s${workingPath}/db_records,${workingPath}/oaf_records,${workingPath}/odf_records - -t${workingPath}/all_entities - -pgurl${postgresURL} - -pguser${postgresUser} - -pgpasswd${postgresPassword} - - - - - - - - - - - - - - - - - yarn - cluster - GenerateGraph - eu.dnetlib.dhp.migration.step3.DispatchEntitiesApplication - dhp-aggregation-${projectVersion}.jar - - --executor-memory ${sparkExecutorMemory} - --executor-cores ${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" - --conf spark.sql.warehouse.dir="/user/hive/warehouse" - - -mt yarn-cluster - -s${workingPath}/all_entities - -g${graphBasePath}/graph_raw - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 9876edc16..d25446bbc 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -40,6 +40,7 @@ dhp-schemas ${project.version} + com.jayway.jsonpath json-path @@ -48,6 +49,18 @@ org.mongodb mongo-java-driver + + dom4j + dom4j + + + jaxen + jaxen + + + org.postgresql + postgresql + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java new file mode 100644 index 000000000..0270076dd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJob.java @@ -0,0 +1,69 @@ +package eu.dnetlib.dhp.oa.graph; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +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 java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class GraphHiveImporterJob { + + private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class); + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(GraphHiveImporterJob.class.getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.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 hiveMetastoreUris = parser.get("hiveMetastoreUris"); + log.info("hiveMetastoreUris: {}", hiveMetastoreUris); + + String hiveDbName = parser.get("hiveDbName"); + log.info("hiveDbName: {}", hiveDbName); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", hiveMetastoreUris); + + runWithSparkHiveSession(conf, isSparkSessionManaged, + spark -> loadGraphAsHiveDB(spark, inputPath, hiveDbName)); + } + + // protected for testing + private static void loadGraphAsHiveDB(SparkSession spark, String inputPath, String hiveDbName) { + + spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName)); + spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName)); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + // Read the input file and convert it into RDD of serializable object + ModelSupport.oafTypes.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name) + .map(s -> new ObjectMapper().readValue(s, clazz)) + .rdd(), Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .saveAsTable(hiveDbName + "." + name)); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphMappingUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphMappingUtils.java deleted file mode 100644 index 81fde7e29..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/GraphMappingUtils.java +++ /dev/null @@ -1,31 +0,0 @@ -package eu.dnetlib.dhp.oa.graph; - -import java.util.Map; - -import com.google.common.collect.Maps; - -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; - -public class GraphMappingUtils { - - public final static Map types = Maps.newHashMap(); - - static { - types.put("datasource", Datasource.class); - types.put("organization", Organization.class); - types.put("project", Project.class); - types.put("dataset", Dataset.class); - types.put("otherresearchproduct", OtherResearchProduct.class); - types.put("software", Software.class); - types.put("publication", Publication.class); - types.put("relation", Relation.class); - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJob.java deleted file mode 100644 index e78635a81..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJob.java +++ /dev/null @@ -1,61 +0,0 @@ -package eu.dnetlib.dhp.oa.graph; - -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import org.apache.commons.io.IOUtils; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -public class SparkGraphImporterJob { - - public static void main(String[] args) throws Exception { - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(SparkGraphImporterJob.class.getResourceAsStream( - "/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json"))); - parser.parseArgument(args); - - new SparkGraphImporterJob().run(parser); - } - - private void run(ArgumentApplicationParser parser) { - try(SparkSession spark = getSparkSession(parser)) { - - final String inputPath = parser.get("sourcePath"); - final String hiveDbName = parser.get("hive_db_name"); - - runWith(spark, inputPath, hiveDbName); - } - } - - // protected for testing - protected void runWith(SparkSession spark, String inputPath, String hiveDbName) { - - spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName)); - spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName)); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - // Read the input file and convert it into RDD of serializable object - GraphMappingUtils.types.forEach((name, clazz) -> spark.createDataset(sc.textFile(inputPath + "/" + name) - .map(s -> new ObjectMapper().readValue(s, clazz)) - .rdd(), Encoders.bean(clazz)) - .write() - .mode(SaveMode.Overwrite) - .saveAsTable(hiveDbName + "." + name)); - } - - private static SparkSession getSparkSession(ArgumentApplicationParser parser) { - SparkConf conf = new SparkConf(); - conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); - return SparkSession - .builder() - .appName(SparkGraphImporterJob.class.getSimpleName()) - .master(parser.get("master")) - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 18a62124b..7d99a4774 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,45 +1,15 @@ -package eu.dnetlib.dhp.migration.step2; - -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.journal; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.keyValue; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.oaiIProvenance; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty; - -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +package eu.dnetlib.dhp.oa.graph.raw; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import java.util.*; + +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; public abstract class AbstractMdRecordToOafMapper { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java new file mode 100644 index 000000000..4812f1c30 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/DispatchEntitiesApplication.java @@ -0,0 +1,94 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; +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 java.util.Optional; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +public class DispatchEntitiesApplication { + + private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(MigrateMongoMdstoresApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json"))); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String sourcePath = parser.get("sourcePath"); + final String targetPath = parser.get("graphRawPath"); + + SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, targetPath); + + processEntity(spark, Publication.class, sourcePath, targetPath); + processEntity(spark, Dataset.class, sourcePath, targetPath); + processEntity(spark, Software.class, sourcePath, targetPath); + processEntity(spark, OtherResearchProduct.class, sourcePath, targetPath); + processEntity(spark, Datasource.class, sourcePath, targetPath); + processEntity(spark, Organization.class, sourcePath, targetPath); + processEntity(spark, Project.class, sourcePath, targetPath); + processEntity(spark, Relation.class, sourcePath, targetPath); + }); + } + + private static void processEntity(final SparkSession spark, final Class clazz, final String sourcePath, final String targetPath) { + final String type = clazz.getSimpleName().toLowerCase(); + + log.info(String.format("Processing entities (%s) in file: %s", type, sourcePath)); + + /* + spark.read() + .textFile(sourcePath) + .filter((FilterFunction) value -> isEntityType(value, type)) + .map((MapFunction) value -> StringUtils.substringAfter(value, "|"), Encoders.STRING()) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)) + .write() + .mode(SaveMode.Overwrite) + .parquet(targetPath + "/" + type); + + */ + + JavaSparkContext.fromSparkContext(spark.sparkContext()) + .textFile(sourcePath) + .filter(l -> isEntityType(l, type)) + .map(l -> StringUtils.substringAfter(l, "|")) + .saveAsTextFile(targetPath + "/" + type, GzipCodec.class); // use repartition(XXX) ??? + } + + private static boolean isEntityType(final String line, final String type) { + return StringUtils.substringBefore(line, "|").equalsIgnoreCase(type); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java similarity index 70% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/GenerateEntitiesApplication.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 7f907b0c8..a9f331f53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.migration.step2; - -import java.io.IOException; -import java.sql.SQLException; -import java.util.Arrays; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.stream.Collectors; +package eu.dnetlib.dhp.oa.graph.raw; +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -16,37 +13,38 @@ import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication; -import eu.dnetlib.dhp.migration.utils.DbClient; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import scala.Tuple2; +import java.io.IOException; +import java.sql.SQLException; +import java.util.*; +import java.util.stream.Collectors; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + public class GenerateEntitiesApplication { - private static final Log log = LogFactory.getLog(GenerateEntitiesApplication.class); + private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class); public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString(MigrateMongoMdstoresApplication.class - .getResourceAsStream("/eu/dnetlib/dhp/migration/generate_entities_parameters.json"))); + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json"))); parser.parseArgument(args); + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + final String sourcePaths = parser.get("sourcePaths"); final String targetPath = parser.get("targetPath"); @@ -56,31 +54,27 @@ public class GenerateEntitiesApplication { final Map code2name = loadClassNames(dbUrl, dbUser, dbPassword); - try (final SparkSession spark = newSparkSession(parser); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext())) { - final List existingSourcePaths = Arrays.stream(sourcePaths.split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList()); - generateEntities(sc, code2name, existingSourcePaths, targetPath); - } + SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + removeOutputDir(spark, targetPath); + generateEntities(spark, code2name, sourcePaths, targetPath); + }); } - private static SparkSession newSparkSession(final ArgumentApplicationParser parser) { - return SparkSession - .builder() - .appName(GenerateEntitiesApplication.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - } - - private static void generateEntities(final JavaSparkContext sc, + private static void generateEntities(final SparkSession spark, final Map code2name, - final List sourcePaths, + final String sourcePaths, final String targetPath) { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final List existingSourcePaths = Arrays.stream(sourcePaths.split(",")).filter(p -> exists(sc, p)).collect(Collectors.toList()); + log.info("Generate entities from files:"); - sourcePaths.forEach(log::info); + existingSourcePaths.forEach(log::info); JavaRDD inputRdd = sc.emptyRDD(); - for (final String sp : sourcePaths) { + for (final String sp : existingSourcePaths) { inputRdd = inputRdd.union(sc.sequenceFile(sp, Text.class, Text.class) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> convertToListOaf(k._1(), k._2(), code2name)) @@ -88,7 +82,8 @@ public class GenerateEntitiesApplication { .map(oaf -> oaf.getClass().getSimpleName().toLowerCase() + "|" + convertToJson(oaf))); } - inputRdd.saveAsTextFile(targetPath, GzipCodec.class); + inputRdd + .saveAsTextFile(targetPath, GzipCodec.class); } @@ -163,11 +158,15 @@ public class GenerateEntitiesApplication { private static boolean exists(final JavaSparkContext context, final String pathToFile) { try { - final FileSystem hdfs = org.apache.hadoop.fs.FileSystem.get(context.hadoopConfiguration()); + final FileSystem hdfs = FileSystem.get(context.hadoopConfiguration()); final Path path = new Path(pathToFile); return hdfs.exists(path); } catch (final IOException e) { throw new RuntimeException(e); } } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java new file mode 100644 index 000000000..4b209c68a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java @@ -0,0 +1,159 @@ +package eu.dnetlib.dhp.oa.graph.raw; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +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 scala.reflect.ClassTag; +import scala.reflect.ClassTag$; + +import java.util.Objects; +import java.util.Optional; +import java.util.function.Function; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; + +public class MergeClaimsApplication { + + private static final Logger log = LoggerFactory.getLogger(MergeClaimsApplication.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils.toString(MigrateMongoMdstoresApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json"))); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String rawGraphPath = parser.get("rawGraphPath"); + log.info("rawGraphPath: {}", rawGraphPath); + + final String claimsGraphPath = parser.get("claimsGraphPath"); + log.info("claimsGraphPath: {}", claimsGraphPath); + + final String outputRawGaphPath = parser.get("outputRawGaphPath"); + log.info("outputRawGaphPath: {}", outputRawGaphPath); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class clazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + String type = clazz.getSimpleName().toLowerCase(); + + String rawPath = rawGraphPath + "/" + type; + String claimPath = claimsGraphPath + "/" + type; + String outPath = outputRawGaphPath + "/" + type; + + removeOutputDir(spark, outPath); + mergeByType(spark, rawPath, claimPath, outPath, clazz); + }); + } + + private static void mergeByType(SparkSession spark, String rawPath, String claimPath, String outPath, Class clazz) { + Dataset> raw = readFromPath(spark, rawPath, clazz) + .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + + final JavaSparkContext jsc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + Dataset> claim = jsc.broadcast(readFromPath(spark, claimPath, clazz)) + .getValue() + .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + + /* + Dataset> claim = readFromPath(spark, claimPath, clazz) + .map((MapFunction>) value -> new Tuple2<>(idFn().apply(value), value), Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); + */ + + raw.joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer") + .map((MapFunction, Tuple2>, T>) value -> { + + Optional> opRaw = Optional.ofNullable(value._1()); + Optional> opClaim = Optional.ofNullable(value._2()); + + return opRaw.isPresent() ? opRaw.get()._2() : opClaim.isPresent() ? opClaim.get()._2() : null; + }, Encoders.bean(clazz)) + .filter(Objects::nonNull) + .map((MapFunction) value -> OBJECT_MAPPER.writeValueAsString(value), Encoders.STRING()) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .text(outPath); + } + + private static Dataset readFromPath(SparkSession spark, String path, Class clazz) { + return spark.read() + .textFile(path) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)) + .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); + /* + return spark.read() + .load(path) + .as(Encoders.bean(clazz)) + .filter((FilterFunction) value -> Objects.nonNull(idFn().apply(value))); + */ + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static Function idFn() { + return x -> { + if (isSubClass(x, Relation.class)) { + return idFnForRelation(x); + } + return idFnForOafEntity(x); + }; + } + + private static String idFnForRelation(T t) { + Relation r = (Relation) t; + return Optional.ofNullable(r.getSource()) + .map(source -> Optional.ofNullable(r.getTarget()) + .map(target -> Optional.ofNullable(r.getRelType()) + .map(relType -> Optional.ofNullable(r.getSubRelType()) + .map(subRelType -> Optional.ofNullable(r.getRelClass()) + .map(relClass -> String.join(source, target, relType, subRelType, relClass)) + .orElse(String.join(source, target, relType, subRelType)) + ) + .orElse(String.join(source, target, relType)) + ) + .orElse(String.join(source, target)) + ) + .orElse(source) + ) + .orElse(null); + } + + private static String idFnForOafEntity(T t) { + return ((OafEntity) t).getId(); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java similarity index 91% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplication.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 7db2b1772..f8f6b58cc 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,14 +1,13 @@ -package eu.dnetlib.dhp.migration.step1; +package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.asString; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.journal; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.listKeyValues; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.oa.graph.raw.common.DbClient; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import java.io.Closeable; import java.io.IOException; @@ -22,31 +21,7 @@ import java.util.List; import java.util.function.Consumer; import java.util.function.Function; -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.migration.utils.AbstractMigrationApplication; -import eu.dnetlib.dhp.migration.utils.DbClient; -import eu.dnetlib.dhp.schema.oaf.Context; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable { @@ -61,7 +36,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json"))); + IOUtils.toString(MigrateDbEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json"))); parser.parseArgument(args); @@ -111,7 +86,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } public void execute(final String sqlFile, final Function> producer) throws Exception { - final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/migration/sql/" + sqlFile)); + final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateMongoMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java similarity index 89% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateMongoMdstoresApplication.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java index b1de31326..585209ac9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateMongoMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java @@ -1,18 +1,17 @@ -package eu.dnetlib.dhp.migration.step1; +package eu.dnetlib.dhp.oa.graph.raw; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.oa.graph.raw.common.MdstoreClient; +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; import java.io.Closeable; import java.io.IOException; import java.util.Map; import java.util.Map.Entry; -import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.migration.utils.AbstractMigrationApplication; -import eu.dnetlib.dhp.migration.utils.MdstoreClient; - public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication implements Closeable { private static final Log log = LogFactory.getLog(MigrateMongoMdstoresApplication.class); @@ -21,7 +20,7 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json"))); + IOUtils.toString(MigrateMongoMdstoresApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json"))); parser.parseArgument(args); final String mongoBaseUrl = parser.get("mongoBaseUrl"); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java similarity index 91% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OafToOafMapper.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index 110abc486..aed582d8f 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,27 +1,17 @@ -package eu.dnetlib.dhp.migration.step2; +package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field; +import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson; +import eu.dnetlib.dhp.schema.oaf.*; +import org.dom4j.Document; +import org.dom4j.Node; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; -import org.dom4j.Document; -import org.dom4j.Node; - -import eu.dnetlib.dhp.migration.utils.PacePerson; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; public class OafToOafMapper extends AbstractMdRecordToOafMapper { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java similarity index 93% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OdfToOafMapper.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index b4868b8f9..6a6def977 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step2/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -1,28 +1,16 @@ -package eu.dnetlib.dhp.migration.step2; +package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.field; -import static eu.dnetlib.dhp.migration.utils.OafMapperUtils.structuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.lang3.StringUtils; +import org.dom4j.Document; +import org.dom4j.Node; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; -import org.apache.commons.lang3.StringUtils; -import org.dom4j.Document; -import org.dom4j.Node; - -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/AbstractMigrationApplication.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index e1a5e5fa7..aec1ea50d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -1,9 +1,6 @@ -package eu.dnetlib.dhp.migration.utils; - -import java.io.Closeable; -import java.io.IOException; -import java.util.concurrent.atomic.AtomicInteger; +package eu.dnetlib.dhp.oa.graph.raw.common; +import eu.dnetlib.dhp.schema.oaf.Oaf; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; @@ -12,7 +9,9 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import org.codehaus.jackson.map.ObjectMapper; -import eu.dnetlib.dhp.schema.oaf.Oaf; +import java.io.Closeable; +import java.io.IOException; +import java.util.concurrent.atomic.AtomicInteger; public class AbstractMigrationApplication implements Closeable { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/DbClient.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/DbClient.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java index 8e9784346..9c0562946 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/DbClient.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java @@ -1,18 +1,14 @@ -package eu.dnetlib.dhp.migration.utils; - -import java.io.Closeable; -import java.io.IOException; -import java.sql.Connection; -import java.sql.DriverManager; -import java.sql.ResultSet; -import java.sql.SQLException; -import java.sql.Statement; -import java.util.function.Consumer; +package eu.dnetlib.dhp.oa.graph.raw.common; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; +import java.io.Closeable; +import java.io.IOException; +import java.sql.*; +import java.util.function.Consumer; + public class DbClient implements Closeable { private static final Log log = LogFactory.getLog(DbClient.class); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/MdstoreClient.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/MdstoreClient.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java index 612503da7..ac700ef63 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/MdstoreClient.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/MdstoreClient.java @@ -1,4 +1,14 @@ -package eu.dnetlib.dhp.migration.utils; +package eu.dnetlib.dhp.oa.graph.raw.common; + +import com.google.common.collect.Iterables; +import com.mongodb.MongoClient; +import com.mongodb.MongoClientURI; +import com.mongodb.client.MongoCollection; +import com.mongodb.client.MongoDatabase; +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.bson.Document; import java.io.Closeable; import java.io.IOException; @@ -7,17 +17,6 @@ import java.util.HashMap; import java.util.Map; import java.util.stream.StreamSupport; -import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.bson.Document; - -import com.google.common.collect.Iterables; -import com.mongodb.MongoClient; -import com.mongodb.MongoClientURI; -import com.mongodb.client.MongoCollection; -import com.mongodb.client.MongoDatabase; - public class MdstoreClient implements Closeable { private final MongoClient client; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/OafMapperUtils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java similarity index 92% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/OafMapperUtils.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java index 8e51c1858..d02070a8b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/OafMapperUtils.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java @@ -1,4 +1,8 @@ -package eu.dnetlib.dhp.migration.utils; +package eu.dnetlib.dhp.oa.graph.raw.common; + +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.utils.DHPUtils; +import org.apache.commons.lang3.StringUtils; import java.util.ArrayList; import java.util.Arrays; @@ -6,19 +10,6 @@ import java.util.List; import java.util.Objects; import java.util.stream.Collectors; -import org.apache.commons.lang3.StringUtils; - -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.ExtraInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.OriginDescription; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.utils.DHPUtils; - public class OafMapperUtils { public static KeyValue keyValue(final String k, final String v) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/PacePerson.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java similarity index 97% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/PacePerson.java rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java index 69e128e63..a72788728 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/PacePerson.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java @@ -1,19 +1,18 @@ -package eu.dnetlib.dhp.migration.utils; - -import java.nio.charset.Charset; -import java.text.Normalizer; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.text.WordUtils; +package eu.dnetlib.dhp.oa.graph.raw.common; import com.google.common.base.Joiner; import com.google.common.base.Splitter; import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.hash.Hashing; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.text.WordUtils; + +import java.nio.charset.Charset; +import java.text.Normalizer; +import java.util.HashSet; +import java.util.List; +import java.util.Set; public class PacePerson { @@ -105,7 +104,7 @@ public class PacePerson { private List splitTerms(final String s) { if (particles == null) { - particles = loadFromClasspath("/eu/dnetlib/dhp/migration/pace/name_particles.txt"); + particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt"); } final List list = Lists.newArrayList(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java index 806140160..aa2f2cc58 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.sx.graph; import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.utils.DHPUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.api.java.JavaPairRDD; @@ -49,15 +50,15 @@ public class SparkSXGeneratePidSimlarity { .equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::"))) .distinct(); - JavaRDD simRel = datasetSimRel.union(publicationSimRel).map(s -> { - final Relation r = new Relation(); + JavaRDD simRel = datasetSimRel.union(publicationSimRel).map(s -> { + final DLIRelation r = new DLIRelation(); r.setSource(s._1()); r.setTarget(s._2()); r.setRelType("similar"); return r; } ); - spark.createDataset(simRel.rdd(), Encoders.bean(Relation.class)).distinct().write() + spark.createDataset(simRel.rdd(), Encoders.bean(DLIRelation.class)).distinct().write() .mode(SaveMode.Overwrite).save(targetPath+"/pid_simRel"); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java index 36d3cf540..36c94f595 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java @@ -7,6 +7,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; +import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.utils.DHPUtils; import net.minidev.json.JSONArray; @@ -135,19 +136,19 @@ public class SparkScholexplorerCreateRawGraphJob { SparkSXGeneratePidSimlarity.generateDataFrame(spark, sc, inputPath.replace("/relation",""),targetPath.replace("/relation","") ); - RDD rdd = union.mapToPair((PairFunction) f -> { + RDD rdd = union.mapToPair((PairFunction) f -> { final String source = getJPathString(SOURCEJSONPATH, f); final String target = getJPathString(TARGETJSONPATH, f); final String reltype = getJPathString(RELJSONPATH, f); ObjectMapper mapper = new ObjectMapper(); mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - return new Tuple2<>(DHPUtils.md5(String.format("%s::%s::%s", source.toLowerCase(), reltype.toLowerCase(), target.toLowerCase())), mapper.readValue(f, Relation.class)); + return new Tuple2<>(DHPUtils.md5(String.format("%s::%s::%s", source.toLowerCase(), reltype.toLowerCase(), target.toLowerCase())), mapper.readValue(f, DLIRelation.class)); }).reduceByKey((a, b) -> { a.mergeFrom(b); return a; }).map(Tuple2::_2).rdd(); - spark.createDataset(rdd, Encoders.bean(Relation.class)).write().mode(SaveMode.Overwrite).save(targetPath); + spark.createDataset(rdd, Encoders.bean(DLIRelation.class)).write().mode(SaveMode.Overwrite).save(targetPath); Dataset rel_ds =spark.read().load(targetPath).as(Encoders.bean(Relation.class)); System.out.println("LOADING PATH :"+targetPath.replace("/relation","")+"/pid_simRel"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index ca20c0aba..9eeff9613 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -2,10 +2,13 @@ package eu.dnetlib.dhp.sx.graph.parser; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; +import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; +import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; +import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo; import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.scholexplorer.relation.RelInfo; import eu.dnetlib.scholexplorer.relation.RelationMapper; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; @@ -15,6 +18,7 @@ import javax.xml.stream.XMLStreamReader; import java.util.*; import java.util.regex.Matcher; import java.util.regex.Pattern; +import java.util.stream.Collectors; public abstract class AbstractScholexplorerParser { @@ -104,6 +108,74 @@ public abstract class AbstractScholexplorerParser { return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); } + protected DLIUnknown createUnknownObject(final String pid, final String pidType, final KeyValue cf, final DataInfo di, final String dateOfCollection) { + final DLIUnknown uk = new DLIUnknown(); + uk.setId(generateId(pid, pidType, "unknown")); + ProvenaceInfo pi = new ProvenaceInfo(); + pi.setId(cf.getKey()); + pi.setName(cf.getValue()); + pi.setCompletionStatus("incomplete"); + uk.setDataInfo(di); + uk.setDlicollectedfrom(Collections.singletonList(pi)); + final StructuredProperty sourcePid = new StructuredProperty(); + sourcePid.setValue(pid); + final Qualifier pt = new Qualifier(); + pt.setClassname(pidType); + pt.setClassid(pidType); + pt.setSchemename("dnet:pid_types"); + pt.setSchemeid("dnet:pid_types"); + sourcePid.setQualifier(pt); + uk.setPid(Collections.singletonList(sourcePid)); + uk.setDateofcollection(dateOfCollection); + return uk; + } + + protected void generateRelations(RelationMapper relationMapper, Result parsedObject, List result, DataInfo di, String dateOfCollection, List relatedIdentifiers) { + if(relatedIdentifiers!= null) { + result.addAll(relatedIdentifiers.stream() + .flatMap(n -> { + final List rels = new ArrayList<>(); + DLIRelation r = new DLIRelation(); + r.setSource(parsedObject.getId()); + final String relatedPid = n.getTextValue(); + final String relatedPidType = n.getAttributes().get("relatedIdentifierType"); + final String relatedType = n.getAttributes().getOrDefault("entityType", "unknown"); + String relationSemantic = n.getAttributes().get("relationType"); + String inverseRelation; + final String targetId = generateId(relatedPid, relatedPidType, relatedType); + r.setDateOfCollection(dateOfCollection); + if (relationMapper.containsKey(relationSemantic.toLowerCase())) + { + RelInfo relInfo = relationMapper.get(relationSemantic.toLowerCase()); + relationSemantic = relInfo.getOriginal(); + inverseRelation = relInfo.getInverse(); + } + else { + relationSemantic = "Unknown"; + inverseRelation = "Unknown"; + } + r.setTarget(targetId); + r.setRelType(relationSemantic); + r.setRelClass("datacite"); + r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setDataInfo(di); + rels.add(r); + r = new DLIRelation(); + r.setDataInfo(di); + r.setSource(targetId); + r.setTarget(parsedObject.getId()); + r.setRelType(inverseRelation); + r.setRelClass("datacite"); + r.setCollectedFrom(parsedObject.getCollectedfrom()); + r.setDateOfCollection(dateOfCollection); + rels.add(r); + if("unknown".equalsIgnoreCase(relatedType)) + result.add(createUnknownObject(relatedPid, relatedPidType, parsedObject.getCollectedfrom().get(0), di, dateOfCollection)); + return rels.stream(); + }).collect(Collectors.toList())); + } + } + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java index 2ba2bd519..f1915c5cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java @@ -42,7 +42,8 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { parsedObject.setOriginalId(Collections.singletonList(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='recordIdentifier']"))); parsedObject.setOriginalObjIdentifier(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='objIdentifier']")); - parsedObject.setDateofcollection(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']")); + String dateOfCollection = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); + parsedObject.setDateofcollection(dateOfCollection); final String resolvedDate = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); @@ -123,7 +124,7 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { List descs = VtdUtilityParser.getTextValue(ap, vn, "//*[local-name()='description']"); if (descs != null && descs.size() > 0) parsedObject.setDescription(descs.stream() - .map(it -> it.length() < 512 ? it : it.substring(0, 512)) + .map(it -> it.length() < 10000 ? it : it.substring(0, 10000)) .map(it -> { final Field d = new Field<>(); d.setValue(it); @@ -137,48 +138,7 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { Arrays.asList("relatedIdentifierType", "relationType", "entityType", "inverseRelationType")); - if(relatedIdentifiers!= null) { - result.addAll(relatedIdentifiers.stream() - .flatMap(n -> { - final List rels = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(parsedObject.getId()); - final String relatedPid = n.getTextValue(); - final String relatedPidType = n.getAttributes().get("relatedIdentifierType"); - final String relatedType = n.getAttributes().getOrDefault("entityType", "unknown"); - String relationSemantic = n.getAttributes().get("relationType"); - String inverseRelation = n.getAttributes().get("inverseRelationType"); - final String targetId = generateId(relatedPid, relatedPidType, relatedType); - - if (relationMapper.containsKey(relationSemantic.toLowerCase())) - { - RelInfo relInfo = relationMapper.get(relationSemantic.toLowerCase()); - relationSemantic = relInfo.getOriginal(); - inverseRelation = relInfo.getInverse(); - } - else { - relationSemantic = "Unknown"; - inverseRelation = "Unknown"; - } - r.setTarget(targetId); - r.setRelType(relationSemantic); - r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - r.setDataInfo(di); - rels.add(r); - r = new Relation(); - r.setDataInfo(di); - r.setSource(targetId); - r.setTarget(parsedObject.getId()); - r.setRelType(inverseRelation); - r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - rels.add(r); - if("unknown".equalsIgnoreCase(relatedType)) - result.add(createUnknownObject(relatedPid, relatedPidType, parsedObject.getCollectedfrom().get(0), di)); - return rels.stream(); - }).collect(Collectors.toList())); - } + generateRelations(relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); final List hostedBy = @@ -199,7 +159,7 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { } - List subjects = extractSubject(VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resource']//*[local-name()='subject']", Arrays.asList("subjectScheme"))); + List subjects = extractSubject(VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='resource']//*[local-name()='subject']", Collections.singletonList("subjectScheme"))); parsedObject.setSubject(subjects); @@ -265,24 +225,6 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { } - private DLIUnknown createUnknownObject(final String pid, final String pidType, final KeyValue cf, final DataInfo di) { - final DLIUnknown uk = new DLIUnknown(); - uk.setId(generateId(pid, pidType, "unknown")); - ProvenaceInfo pi = new ProvenaceInfo(); - pi.setId(cf.getKey()); - pi.setName(cf.getValue()); - pi.setCompletionStatus("incomplete"); - uk.setDataInfo(di); - uk.setDlicollectedfrom(Collections.singletonList(pi)); - final StructuredProperty sourcePid = new StructuredProperty(); - sourcePid.setValue(pid); - final Qualifier pt = new Qualifier(); - pt.setClassname(pidType); - pt.setClassid(pidType); - pt.setSchemename("dnet:pid_types"); - pt.setSchemeid("dnet:pid_types"); - sourcePid.setQualifier(pt); - uk.setPid(Collections.singletonList(sourcePid)); - return uk; - } + + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java index b8b38515b..aa2f86076 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/PublicationScholexplorerParser.java @@ -38,7 +38,8 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser di.setDeletedbyinference(false); di.setInvisible(false); - parsedObject.setDateofcollection(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']")); + String dateOfCollection = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='dateOfCollection']"); + parsedObject.setDateofcollection(dateOfCollection); final String resolvedDate = VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='resolvedDate']"); parsedObject.setOriginalId(Collections.singletonList(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='recordIdentifier']"))); @@ -118,48 +119,7 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser final List relatedIdentifiers = VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='relatedIdentifier']", Arrays.asList("relatedIdentifierType", "relationType", "entityType", "inverseRelationType")); - - - if (relatedIdentifiers != null) { - result.addAll(relatedIdentifiers.stream() - .flatMap(n -> { - final List rels = new ArrayList<>(); - Relation r = new Relation(); - r.setSource(parsedObject.getId()); - final String relatedPid = n.getTextValue(); - final String relatedPidType = n.getAttributes().get("relatedIdentifierType"); - final String relatedType = n.getAttributes().getOrDefault("entityType", "unknown"); - String relationSemantic = n.getAttributes().get("relationType"); - String inverseRelation = "Unknown"; - final String targetId = generateId(relatedPid, relatedPidType, relatedType); - - if (relationMapper.containsKey(relationSemantic.toLowerCase())) - { - RelInfo relInfo = relationMapper.get(relationSemantic.toLowerCase()); - relationSemantic = relInfo.getOriginal(); - inverseRelation = relInfo.getInverse(); - } - else { - relationSemantic = "Unknown"; - } - r.setTarget(targetId); - r.setRelType(relationSemantic); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - r.setRelClass("datacite"); - r.setDataInfo(di); - rels.add(r); - r = new Relation(); - r.setDataInfo(di); - r.setSource(targetId); - r.setTarget(parsedObject.getId()); - r.setRelType(inverseRelation); - r.setRelClass("datacite"); - r.setCollectedFrom(parsedObject.getCollectedfrom()); - rels.add(r); - - return rels.stream(); - }).collect(Collectors.toList())); - } + generateRelations(relationMapper, parsedObject, result, di, dateOfCollection, relatedIdentifiers); final List hostedBy = VtdUtilityParser.getTextValuesWithAttributes(ap, vn, "//*[local-name()='hostedBy']", Arrays.asList("id", "name")); @@ -206,8 +166,8 @@ public class PublicationScholexplorerParser extends AbstractScholexplorerParser description.setValue(VtdUtilityParser.getSingleValue(ap, vn, "//*[local-name()='description']")); - if (StringUtils.isNotBlank(description.getValue()) && description.getValue().length() > 512) { - description.setValue(description.getValue().substring(0, 512)); + if (StringUtils.isNotBlank(description.getValue()) && description.getValue().length() > 10000) { + description.setValue(description.getValue().substring(0, 10000)); } parsedObject.setDescription(Collections.singletonList(description)); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json similarity index 61% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json index 8c81290ca..7d995f39a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/dispatch_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dispatch_entities_parameters.json @@ -1,16 +1,16 @@ [ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, { "paramName": "s", "paramLongName": "sourcePath", "paramDescription": "the source path", "paramRequired": true }, - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "g", "paramLongName": "graphRawPath", diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/generate_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json similarity index 82% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/generate_entities_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json index 53ee010c4..293bf041b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/generate_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json @@ -1,16 +1,16 @@ [ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, { "paramName": "s", "paramLongName": "sourcePaths", "paramDescription": "the HDFS source paths which contains the sequential file (comma separated)", "paramRequired": true }, - { - "paramName": "mt", - "paramLongName": "master", - "paramDescription": "should be local or yarn", - "paramRequired": true - }, { "paramName": "t", "paramLongName": "targetPath", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/lib/scripts/postprocessing.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/lib/scripts/postprocessing.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/lib/scripts/postprocessing.sql diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml similarity index 97% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml index b523ca17a..271c7040f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml @@ -49,7 +49,7 @@ yarn cluster MapGraphAsHiveDB - eu.dnetlib.dhp.oa.graph.SparkGraphImporterJob + eu.dnetlib.dhp.oa.graph.GraphHiveImporterJob dhp-graph-mapper-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json new file mode 100644 index 000000000..d6c13773a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_hive_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "hmu", + "paramLongName": "hiveMetastoreUris", + "paramDescription": "the hive metastore uris", + "paramRequired": true + }, + { + "paramName": "db", + "paramLongName": "hiveDbName", + "paramDescription": "the target hive database name", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json deleted file mode 100644 index 13c7abd51..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_graph_parameters.json +++ /dev/null @@ -1,6 +0,0 @@ -[ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"h", "paramLongName":"hive_metastore_uris","paramDescription": "the hive metastore uris", "paramRequired": true}, - {"paramName":"db", "paramLongName":"hive_db_name", "paramDescription": "the target hive database name", "paramRequired": true} -] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json new file mode 100644 index 000000000..686fea643 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "rgp", + "paramLongName": "rawGraphPath", + "paramDescription": "the raw graph path", + "paramRequired": true + }, + { + "paramName": "cgp", + "paramLongName": "claimsGraphPath", + "paramDescription": "the path of the claims graph", + "paramRequired": true + }, + { + "paramName": "ogp", + "paramLongName": "outputRawGaphPath", + "paramDescription": "the path of output graph, combining raw and claims", + "paramRequired": true + }, + { + "paramName": "clazz", + "paramLongName": "graphTableClassName", + "paramDescription": "class name associated to the input entity path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json new file mode 100644 index 000000000..c4910ec61 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_actionsets_parameters.json @@ -0,0 +1,10 @@ +[ + {"paramName":"is", "paramLongName":"isLookupUrl", "paramDescription": "URL of the isLookUp Service", "paramRequired": true}, + {"paramName":"sn", "paramLongName":"sourceNameNode", "paramDescription": "nameNode of the source cluster", "paramRequired": true}, + {"paramName":"tn", "paramLongName":"targetNameNode", "paramDescription": "namoNode of the target cluster", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingDirectory", "paramDescription": "working directory", "paramRequired": true}, + {"paramName":"nm", "paramLongName":"distcp_num_maps", "paramDescription": "maximum number of map tasks used in the distcp process", "paramRequired": true}, + {"paramName":"mm", "paramLongName":"distcp_memory_mb", "paramDescription": "memory for distcp action copying actionsets from remote cluster", "paramRequired": true}, + {"paramName":"tt", "paramLongName":"distcp_task_timeout", "paramDescription": "timeout for distcp copying actions from remote cluster", "paramRequired": true}, + {"paramName":"tr", "paramLongName":"transform_only", "paramDescription": "activate tranform-only mode. Only apply transformation step", "paramRequired": true} +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/pace/name_particles.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/pace/name_particles.txt rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml new file mode 100644 index 000000000..9f91380ab --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -0,0 +1,542 @@ + + + + + graphOutputPath + the target path to store raw graph + + + reuseContent + false + should import content from the aggregator or reuse a previous version + + + contentPath + path location to store (or reuse) content from the aggregator + + + postgresURL + the postgres URL to access to the database + + + postgresUser + the user postgres + + + postgresPassword + the password postgres + + + mongoURL + mongoDB url, example: mongodb://[username:password@]host[:port] + + + mongoDb + mongo database + + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:conf('reuseContent') eq false} + ${wf:conf('reuseContent') eq true} + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication + -p${contentPath}/db_claims + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + -aclaims + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication + -p${contentPath}/odf_claims + -mongourl${mongoURL} + -mongodb${mongoDb} + -fODF + -lstore + -iclaim + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication + -p${contentPath}/oaf_claims + -mongourl${mongoURL} + -mongodb${mongoDb} + -fOAF + -lstore + -iclaim + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateDbEntitiesApplication + -p${contentPath}/db_records + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication + -p${contentPath}/odf_records + -mongourl${mongoURL} + -mongodb${mongoDb} + -fODF + -lstore + -icleaned + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication + -p${contentPath}/oaf_records + -mongourl${mongoURL} + -mongodb${mongoDb} + -fOAF + -lstore + -icleaned + + + + + + + + + + + + + + + yarn + cluster + GenerateEntities_claim + eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + -s${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims + -t${workingDir}/entities_claim + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + + + + + + + + yarn + cluster + GenerateGraph_claims + eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + -s${workingDir}/entities_claim + -g${workingDir}/graph_claims + + + + + + + + yarn + cluster + GenerateEntities + eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + -s${contentPath}/db_records,${contentPath}/oaf_records,${contentPath}/odf_records + -t${workingDir}/entities + -pgurl${postgresURL} + -pguser${postgresUser} + -pgpasswd${postgresPassword} + + + + + + + + yarn + cluster + GenerateGraph + eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + -s${workingDir}/entities + -g${workingDir}/graph_raw + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + MergeClaims_publication + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + + + + + + + + yarn + cluster + MergeClaims_dataset + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + + + + + + + + yarn + cluster + MergeClaims_relation + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation + + + + + + + + yarn + cluster + MergeClaims_software + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=1920 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + + + + + + + + yarn + cluster + MergeClaims_otherresearchproduct + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=1920 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + + + + + + + + yarn + cluster + MergeClaims_datasource + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=200 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource + + + + + + + + yarn + cluster + MergeClaims_organization + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=200 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization + + + + + + + + yarn + cluster + MergeClaims_project + eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=200 + + --rawGraphPath${workingDir}/graph_raw + --claimsGraphPath${workingDir}/graph_claims + --outputRawGaphPath${graphOutputPath} + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1_onlydb/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1_onlydb/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1_onlydb/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1_onlydb/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step2/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step2/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step2/oozie_app/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step2/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step3/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step3/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step3/oozie_app/workflow.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/workflow.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step3/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryClaims.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryClaims.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasourceOrganization.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql similarity index 97% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql index 8c587f34e..9a0a45f78 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryDatasources.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql @@ -8,6 +8,9 @@ SELECT WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire-cris_1.1']) THEN 'openaire-cris_1.1@@@OpenAIRE CRIS v1.1@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' + WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) + THEN + 'openaire4.0@@@OpenAIRE 4.0@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN 'driver-openaire2.0@@@OpenAIRE 2.0+ (DRIVER OA, EC funding)@@@dnet:datasourceCompatibilityLevel@@@dnet:datasourceCompatibilityLevel' diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizations.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizationsFromOpenOrgsDB.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryOrganizationsFromOpenOrgsDB.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizationsFromOpenOrgsDB.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjectOrganization.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects_production.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/querySimilarityFromOpenOrgsDB.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/querySimilarityFromOpenOrgsDB.sql similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/querySimilarityFromOpenOrgsDB.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/querySimilarityFromOpenOrgsDB.sql diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json new file mode 100644 index 000000000..6fa10f739 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/transform_actionsets_parameters.json @@ -0,0 +1,20 @@ +[ + { + "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": "i", + "paramLongName": "inputPaths", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java new file mode 100644 index 000000000..ecadbe981 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java @@ -0,0 +1,83 @@ +package eu.dnetlib.dhp.oa.graph; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import org.apache.commons.io.FileUtils; +import org.apache.commons.lang3.RandomStringUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +public class GraphHiveImporterJobTest { + + private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJobTest.class); + + public static final String JDBC_DERBY_TEMPLATE = "jdbc:derby:;databaseName=%s/junit_metastore_db;create=true"; + + private static SparkSession spark; + + private static Path workingDir; + + private static String dbName; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(GraphHiveImporterJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + dbName = RandomStringUtils.randomAlphabetic(5); + log.info("using DB name {}", "test_" + dbName); + + SparkConf conf = new SparkConf(); + conf.setAppName(GraphHiveImporterJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + conf.set("javax.jdo.option.ConnectionURL", String.format(JDBC_DERBY_TEMPLATE, workingDir.resolve("warehouse").toString())); + + spark = SparkSession + .builder() + .appName(GraphHiveImporterJobTest.class.getSimpleName()) + .config(conf) + .enableHiveSupport() + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testImportGraphAsHiveDB() throws Exception { + + GraphHiveImporterJob.main(new String[]{ + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-inputPath", getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(), + "-hiveMetastoreUris", "", + "-hiveDbName", dbName + }); + + ModelSupport.oafTypes.forEach((name, clazz) -> { + long count = spark.read().table(dbName + "." + name).count(); + int expected = name.equals("relation") ? 100 : 10; + + Assertions.assertEquals(expected, count, String.format("%s should be %s", name, expected)); + }); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJobTest.java deleted file mode 100644 index 302cef8d6..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/SparkGraphImporterJobTest.java +++ /dev/null @@ -1,54 +0,0 @@ -package eu.dnetlib.dhp.oa.graph; - -import org.apache.spark.SparkConf; -import org.apache.spark.sql.SparkSession; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; -import org.junit.jupiter.api.io.TempDir; - -import java.nio.file.Path; - -public class SparkGraphImporterJobTest { - - private final static String TEST_DB_NAME = "test"; - - @Test - public void testImport(@TempDir Path outPath) { - try(SparkSession spark = testSparkSession(outPath.toString())) { - - new SparkGraphImporterJob().runWith( - spark, - getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(), - TEST_DB_NAME); - - GraphMappingUtils.types.forEach((name, clazz) -> { - final long count = spark.read().table(TEST_DB_NAME + "." + name).count(); - if (name.equals("relation")) { - Assertions.assertEquals(100, count, String.format("%s should be 100", name)); - } else { - Assertions.assertEquals(10, count, String.format("%s should be 10", name)); - } - }); - } - } - - private SparkSession testSparkSession(final String inputPath) { - SparkConf conf = new SparkConf(); - - conf.set("spark.driver.host", "localhost"); - conf.set("hive.metastore.local", "true"); - conf.set("hive.metastore.warehouse.dir", inputPath + "/warehouse"); - conf.set("spark.sql.warehouse.dir", inputPath); - conf.set("javax.jdo.option.ConnectionURL", String.format("jdbc:derby:;databaseName=%s/junit_metastore_db;create=true", inputPath)); - conf.set("spark.ui.enabled", "false"); - - return SparkSession - .builder() - .appName(SparkGraphImporterJobTest.class.getSimpleName()) - .master("local[*]") - .config(conf) - .enableHiveSupport() - .getOrCreate(); - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java similarity index 91% rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java rename to dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 894355bcb..63d7d50db 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step2/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,27 +1,24 @@ -package eu.dnetlib.dhp.migration.step2; - -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.anyString; -import static org.mockito.Mockito.when; - -import java.io.IOException; -import java.util.List; -import java.util.Map; +package eu.dnetlib.dhp.oa.graph.raw; +import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; +import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; +import java.io.IOException; +import java.util.List; +import java.util.Map; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.ArgumentMatchers.anyString; +import static org.mockito.Mockito.when; @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -30,7 +27,7 @@ public class MappersTest { private Map code2name; @BeforeEach - void setUp() throws Exception { + public void setUp() throws Exception { when(code2name.get(anyString())).thenAnswer(invocation -> invocation.getArgument(0)); } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java similarity index 99% rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplicationTest.java rename to dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index d63bb3ee3..b1fc9131f 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.migration.step1; +package eu.dnetlib.dhp.oa.graph.raw; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/claimscontext_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimscontext_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/claimscontext_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimscontext_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/claimsrel_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/claimsrel_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/datasourceorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/datasourceorganization_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/datasources_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/oaf_record.xml rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_dataset.xml rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_software.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step2/odf_software.xml rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/organizations_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/organizations_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/projectorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/projectorganization_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projectorganization_resultset_entry.json diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/projects_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/migration/step1/projects_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/projects_resultset_entry.json diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index de38a01b3..03604f431 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -69,6 +69,11 @@ + + org.apache.httpcomponents + httpclient + + diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java index 49b891e65..f29722eb8 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/ScholixResource.java @@ -3,7 +3,6 @@ package eu.dnetlib.dhp.provision.scholix; import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; import java.io.Serializable; -import java.util.Arrays; import java.util.Collections; import java.util.List; import java.util.stream.Collectors; @@ -20,10 +19,6 @@ public class ScholixResource implements Serializable { private List publisher; private List collectedFrom; - - - - public static ScholixResource fromSummary(ScholixSummary summary) { final ScholixResource resource = new ScholixResource(); @@ -38,7 +33,7 @@ public class ScholixResource implements Serializable { resource.setObjectType(summary.getTypology().toString()); - if (summary.getTitle() != null && summary.getTitle().size()>0) + if (summary.getTitle() != null && summary.getTitle().size() > 0) resource.setTitle(summary.getTitle().get(0)); if (summary.getAuthor() != null) @@ -47,7 +42,7 @@ public class ScholixResource implements Serializable { .collect(Collectors.toList()) ); - if (summary.getDate() != null && summary.getDate().size()>0) + if (summary.getDate() != null && summary.getDate().size() > 0) resource.setPublicationDate(summary.getDate().get(0)); if (summary.getPublisher() != null) resource.setPublisher(summary.getPublisher().stream() @@ -65,6 +60,7 @@ public class ScholixResource implements Serializable { } + public List getIdentifier() { return identifier; } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java new file mode 100644 index 000000000..828d8f9b5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java @@ -0,0 +1,108 @@ +package eu.dnetlib.dhp.provision.update; + +import com.google.gson.JsonArray; +import com.google.gson.JsonElement; +import com.google.gson.JsonObject; +import com.google.gson.JsonParser; +import eu.dnetlib.dhp.provision.scholix.ScholixCollectedFrom; +import eu.dnetlib.dhp.provision.scholix.ScholixEntityId; +import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier; +import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import eu.dnetlib.dhp.utils.DHPUtils; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; + +public class CrossRefParserJSON { + + private static List collectedFrom =generateCrossrefCollectedFrom("complete"); + + public static ScholixResource parseRecord(final String record) { + if (record == null) return null; + JsonElement jElement = new JsonParser().parse(record); + JsonElement source = null; + if (jElement.getAsJsonObject().has("_source")) { + source = jElement.getAsJsonObject().get("_source"); + if (source == null || !source.isJsonObject()) + return null; + } + else if(jElement.getAsJsonObject().has("DOI")){ + source = jElement; + } else { + return null; + } + + final JsonObject message = source.getAsJsonObject(); + ScholixResource currentObject = new ScholixResource(); + + if (message.get("DOI") != null) { + final String doi = message.get("DOI").getAsString(); + currentObject.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi"))); + } + + if ((!message.get("created").isJsonNull()) && (message.getAsJsonObject("created").get("date-time") != null)) { + currentObject.setPublicationDate(message.getAsJsonObject("created").get("date-time").getAsString()); + } + + if (message.get("title")!= null && !message.get("title").isJsonNull() && message.get("title").isJsonArray() ) { + + JsonArray array = message.get("title").getAsJsonArray(); + currentObject.setTitle(array.get(0).getAsString()); + } + if (message.get("author") != null && !message.get("author").isJsonNull()) { + JsonArray author = message.getAsJsonArray("author"); + List authorList = new ArrayList<>(); + for (JsonElement anAuthor : author) { + JsonObject currentAuth = anAuthor.getAsJsonObject(); + + String family = ""; + String given = ""; + if (currentAuth != null && currentAuth.get("family") != null && !currentAuth.get("family").isJsonNull()) { + family = currentAuth.get("family").getAsString(); + } + if (currentAuth != null && currentAuth.get("given") != null && !currentAuth.get("given").isJsonNull()) { + given = currentAuth.get("given").getAsString(); + } + authorList.add(new ScholixEntityId(String.format("%s %s", family, given), null)); + } + currentObject.setCreator(authorList); + } + if (message.get("publisher") != null && !message.get("publisher").isJsonNull()) { + currentObject.setPublisher(Collections.singletonList(new ScholixEntityId(message.get("publisher").getAsString(), null))); + } + currentObject.setCollectedFrom(collectedFrom); + currentObject.setObjectType("publication"); + currentObject.setDnetIdentifier(generateId(message.get("DOI").getAsString(), "doi", "publication")); + + return currentObject; + } + + private static List generateCrossrefCollectedFrom(final String completionStatus) { + final ScholixEntityId scholixEntityId = new ScholixEntityId("Crossref", + Collections.singletonList(new ScholixIdentifier("dli_________::crossref", "dnet_identifier"))); + return Collections.singletonList( + new ScholixCollectedFrom( + scholixEntityId,"resolved", completionStatus)); + } + + private static String generateId(final String pid, final String pidType, final String entityType) { + String type; + switch (entityType){ + case "publication": + type = "50|"; + break; + case "dataset": + type = "60|"; + break; + case "unknown": + type = "70|"; + break; + default: + throw new IllegalArgumentException("unexpected value "+entityType); + } + return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); + } + + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java new file mode 100644 index 000000000..3190ee516 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossrefClient.java @@ -0,0 +1,88 @@ +package eu.dnetlib.dhp.provision.update; + +import com.google.gson.JsonElement; +import com.google.gson.JsonParser; +import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import org.apache.commons.codec.binary.Base64; +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; + +import java.io.ByteArrayOutputStream; +import java.util.zip.Inflater; + +public class CrossrefClient { + + private String host; + private String index ="crossref"; + private String indexType = "item"; + + + public CrossrefClient(String host) { + this.host = host; + } + + public String getHost() { + return host; + } + + public void setHost(String host) { + this.host = host; + } + + public String getIndex() { + return index; + } + + public void setIndex(String index) { + this.index = index; + } + + public String getIndexType() { + return indexType; + } + + public void setIndexType(String indexType) { + this.indexType = indexType; + } + + private static String decompressBlob(final String blob) { + try { + byte[] byteArray = Base64.decodeBase64(blob.getBytes()); + final Inflater decompresser = new Inflater(); + decompresser.setInput(byteArray); + final ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length); + byte[] buffer = new byte[8192]; + while (!decompresser.finished()) { + int size = decompresser.inflate(buffer); + bos.write(buffer, 0, size); + } + byte[] unzippeddata = bos.toByteArray(); + decompresser.end(); + return new String(unzippeddata); + } catch (Throwable e) { + throw new RuntimeException("Wrong record:" + blob,e); + } + } + + + + public ScholixResource getResourceByDOI(final String doi) { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F"))); + CloseableHttpResponse response = client.execute(httpGet); + String json = IOUtils.toString(response.getEntity().getContent()); + if (json.contains("blob")) { + JsonParser p = new JsonParser(); + final JsonElement root = p.parse(json); + json =decompressBlob(root.getAsJsonObject().get("_source").getAsJsonObject().get("blob").getAsString()); + } + return CrossRefParserJSON.parseRecord(json); + } catch (Throwable e) { + return null; + } + + } +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/Datacite2Scholix.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java similarity index 88% rename from dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/Datacite2Scholix.java rename to dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java index 809186a50..ac05a8350 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/Datacite2Scholix.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/Datacite2Scholix.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.provision; +package eu.dnetlib.dhp.provision.update; import com.jayway.jsonpath.JsonPath; import eu.dnetlib.dhp.provision.scholix.*; @@ -15,16 +15,14 @@ import java.util.stream.Collectors; public class Datacite2Scholix { - + private String rootPath = "$.attributes"; final RelationMapper relationMapper; public Datacite2Scholix(RelationMapper relationMapper) { this.relationMapper = relationMapper; } - public List generateScholixFromJson(final String dJson) { - List> relIds = getRelatedIendtifiers(dJson); relIds = relIds!= null ? relIds.stream().filter(m-> m.containsKey("relatedIdentifierType") && m.containsKey("relationType" ) && m.containsKey( "relatedIdentifier") @@ -32,22 +30,24 @@ public class Datacite2Scholix { if(relIds== null || relIds.size() ==0 ) return null; - - - final String updated = JsonPath.read(dJson,"$.attributes.updated" ); + final String updated = JsonPath.read(dJson, rootPath + ".updated"); ScholixResource resource = generateDataciteScholixResource(dJson); return relIds.stream().flatMap(s-> { final List result = generateScholix(resource, s.get("relatedIdentifier"), s.get("relatedIdentifierType"), s.get("relationType"), updated); return result.stream(); }).collect(Collectors.toList()); - } + public String getRootPath() { + return rootPath; + } + + public void setRootPath(String rootPath) { + this.rootPath = rootPath; + } private List generateScholix(ScholixResource source, final String pid, final String pidtype, final String relType, final String updated) { - - if ("doi".equalsIgnoreCase(pidtype)) { ScholixResource target = new ScholixResource(); target.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, pidtype))); @@ -92,20 +92,17 @@ public class Datacite2Scholix { result.add(s2); return result; } - - - } public ScholixResource generateDataciteScholixResource(String dJson) { ScholixResource resource = new ScholixResource(); - String DOI_PATH = "$.attributes.doi"; + String DOI_PATH = rootPath + ".doi"; final String doi = JsonPath.read(dJson, DOI_PATH); resource.setIdentifier(Collections.singletonList(new ScholixIdentifier(doi, "doi"))); resource.setObjectType(getType(dJson)); resource.setDnetIdentifier(generateId(doi, "doi", resource.getObjectType())); resource.setCollectedFrom(generateDataciteCollectedFrom("complete")); - final String publisher = JsonPath.read(dJson, "$.attributes.publisher"); + final String publisher = JsonPath.read(dJson, rootPath + ".publisher"); if (StringUtils.isNotBlank(publisher)) resource.setPublisher(Collections.singletonList(new ScholixEntityId(publisher, null))); final String date = getDate(dJson); @@ -119,7 +116,7 @@ public class Datacite2Scholix { } private List getCreators(final String json) { - final List creatorName = JsonPath.read(json, "$.attributes.creators[*].name"); + final List creatorName = JsonPath.read(json, rootPath + ".creators[*].name"); if (creatorName!= null && creatorName.size() >0) { return creatorName.stream().map(s-> new ScholixEntityId(s, null)).collect(Collectors.toList()); } @@ -127,12 +124,12 @@ public class Datacite2Scholix { } private String getTitle(final String json){ - final List titles = JsonPath.read(json, "$.attributes.titles[*].title"); + final List titles = JsonPath.read(json, rootPath + ".titles[*].title"); return titles!= null && titles.size()>0?titles.get(0): null; } private String getDate(final String json) { - final List> dates = JsonPath.read(json,"$.attributes.dates"); + final List> dates = JsonPath.read(json, rootPath + ".dates"); if(dates!= null && dates.size()>0){ List> issued = dates.stream().filter(s -> "issued".equalsIgnoreCase(s.get("dateType"))).collect(Collectors.toList()); @@ -152,7 +149,7 @@ public class Datacite2Scholix { private String getType(final String json) { try { - final String bibtext = JsonPath.read(json, "$.attributes.types.bibtex"); + final String bibtext = JsonPath.read(json, rootPath + ".types.bibtex"); if ("article".equalsIgnoreCase(bibtext)) { return "publication"; } @@ -162,17 +159,13 @@ public class Datacite2Scholix { } } - - - private List> getRelatedIendtifiers(final String json) { - String REL_IDENTIFIER_PATH = "$.attributes.relatedIdentifiers[*]"; + String REL_IDENTIFIER_PATH = rootPath + ".relatedIdentifiers[*]"; List> res = JsonPath.read(json, REL_IDENTIFIER_PATH); return res; - } - protected String generateId(final String pid, final String pidType, final String entityType) { + public static String generateId(final String pid, final String pidType, final String entityType) { String type; switch (entityType){ case "publication": @@ -186,18 +179,7 @@ public class Datacite2Scholix { break; default: throw new IllegalArgumentException("unexpected value "+entityType); - } - return type+ DHPUtils.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidType.toLowerCase().trim())); } - - - - - - - - - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java new file mode 100644 index 000000000..e1d25bf2e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java @@ -0,0 +1,75 @@ +package eu.dnetlib.dhp.provision.update; + +import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; + +import java.io.IOException; + +public class DataciteClient { + + + private String host; + private String index ="datacite"; + private String indexType = "dump"; + private Datacite2Scholix d2s; + + public DataciteClient(String host) { + this.host = host; + + d2s = new Datacite2Scholix(null); + d2s.setRootPath("$._source.attributes"); + } + + public Iterable getDatasetsFromTs(final Long timestamp) { + return ()-> { + try { + return new DataciteClientIterator(host, index, timestamp); + } catch (IOException e) { + throw new RuntimeException(e); + } + }; + + + } + + public String getHost() { + return host; + } + + public void setHost(String host) { + this.host = host; + } + + public String getIndex() { + return index; + } + + public void setIndex(String index) { + this.index = index; + } + + public String getIndexType() { + return indexType; + } + + public void setIndexType(String indexType) { + this.indexType = indexType; + } + + public ScholixResource getDatasetByDOI(final String doi) { + try (CloseableHttpClient client = HttpClients.createDefault()) { + HttpGet httpGet = new HttpGet(String.format("http://%s:9200/%s/%s/%s", host, index,indexType, doi.replaceAll("/","%2F"))); + CloseableHttpResponse response = client.execute(httpGet); + final String json =IOUtils.toString(response.getEntity().getContent()); + return d2s.generateDataciteScholixResource(json); + } catch (Throwable e) { + return null; + } + } + + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DataciteClient.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java similarity index 91% rename from dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DataciteClient.java rename to dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java index 37a0bb23b..61c1aa39f 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DataciteClient.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClientIterator.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.provision; +package eu.dnetlib.dhp.provision.update; import com.fasterxml.jackson.databind.ObjectMapper; import com.jayway.jsonpath.JsonPath; import net.minidev.json.JSONArray; @@ -14,7 +14,7 @@ import java.util.Iterator; import java.util.List; import java.util.stream.Collectors; -public class DataciteClient implements Iterator { +public class DataciteClientIterator implements Iterator { final static String blobPath = "$.hits.hits[*]._source"; final static String scrollIdPath = "$._scroll_id"; @@ -27,10 +27,12 @@ public class DataciteClient implements Iterator { final String esIndex; final ObjectMapper mapper = new ObjectMapper(); - public DataciteClient(final String esHost, final String esIndex, final long timestamp) throws IOException { + public DataciteClientIterator(final String esHost, final String esIndex, long timestamp) throws IOException { this.esHost = esHost; this.esIndex = esIndex; + // THIS FIX IS NECESSARY to avoid different timezone + timestamp -= (60 *60 *2); final String body =getResponse(String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), String.format("{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}", timestamp)); scrollId= getJPathString(scrollIdPath, body); buffer = getBlobs(body); diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RetrieveUpdateFromDatacite.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java similarity index 52% rename from dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RetrieveUpdateFromDatacite.java rename to dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java index ad0034733..ea659dbb1 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/RetrieveUpdateFromDatacite.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/RetrieveUpdateFromDatacite.java @@ -1,8 +1,10 @@ -package eu.dnetlib.dhp.provision; +package eu.dnetlib.dhp.provision.update; +import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.provision.scholix.Scholix; +import eu.dnetlib.scholexplorer.relation.RelationMapper; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; @@ -11,17 +13,19 @@ import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; import java.net.URI; +import java.util.List; import java.util.concurrent.atomic.AtomicInteger; public class RetrieveUpdateFromDatacite { public static void main(String[] args) throws Exception{ - final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(RetrieveUpdateFromDatacite.class.getResourceAsStream("/eu/dnetlib/dhp/provision/retrieve_update_parameters.json"))); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(RetrieveUpdateFromDatacite.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json"))); parser.parseArgument(args); final String hdfsuri = parser.get("namenode"); Path hdfswritepath = new Path(parser.get("targetPath")); - final String timestamp = parser.get("timestamp"); - + final long timestamp = Long.parseLong(parser.get("timestamp")); + final String host = parser.get("indexHost"); + final String index = parser.get("indexName"); // ====== Init HDFS File System Object Configuration conf = new Configuration(); @@ -32,13 +36,28 @@ public class RetrieveUpdateFromDatacite { conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); FileSystem.get(URI.create(hdfsuri), conf); - - final AtomicInteger counter = new AtomicInteger(0); + final Datacite2Scholix d2s = new Datacite2Scholix(RelationMapper.load()); + final ObjectMapper mapper = new ObjectMapper(); try (SequenceFile.Writer writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfswritepath), SequenceFile.Writer.keyClass(IntWritable.class), SequenceFile.Writer.valueClass(Text.class))) { + final Text value = new Text(); + final IntWritable key = new IntWritable(); + int i = 0; + for(String dataset: new DataciteClient(host).getDatasetsFromTs(timestamp)) { + i++; + List scholix = d2s.generateScholixFromJson(dataset); + if (scholix!= null) + for(Scholix s: scholix) { + key.set(i); + value.set(mapper.writeValueAsString(s)); + writer.append(key, value); + if (i % 10000 == 0) { + System.out.println("wrote "+i); + } + } + } } } - } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java new file mode 100644 index 000000000..35020ecdf --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/SparkResolveScholixTarget.java @@ -0,0 +1,134 @@ +package eu.dnetlib.dhp.provision.update; + +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.provision.scholix.Scholix; +import eu.dnetlib.dhp.provision.scholix.ScholixIdentifier; +import eu.dnetlib.dhp.provision.scholix.ScholixRelationship; +import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.scholexplorer.relation.RelationMapper; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.hadoop.io.IntWritable; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +import scala.Tuple2; + +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; +import java.util.stream.Collectors; + +public class SparkResolveScholixTarget { + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResolveScholixTarget.class.getResourceAsStream("/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json"))); + parser.parseArgument(args); + + final SparkConf conf = new SparkConf(); + + final String master = parser.get("master"); + final String sourcePath = parser.get("sourcePath"); + final String workingDirPath= parser.get("workingDirPath"); + final String indexHost= parser.get("indexHost"); + try (SparkSession spark = getSession(conf, master)){ + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + + spark.createDataset(sc.sequenceFile(sourcePath, IntWritable.class,Text.class) + .map(Tuple2::_2) + .map(s-> new ObjectMapper().readValue(s.toString(), Scholix.class)).rdd(), Encoders.bean(Scholix.class)) + .write().save(workingDirPath+"/stepA"); + + + + Dataset s1 = spark.read().load(workingDirPath+"/stepA").as(Encoders.bean(Scholix.class)); + + s1.where(s1.col("target.dnetIdentifier").isNull()).select(s1.col("target.identifier")).distinct() + .map((MapFunction) f-> { + final String pid = ((Row) f.getList(0).get(0)).getString(0); + ScholixResource publication = new CrossrefClient(indexHost).getResourceByDOI(pid); + if (publication != null) { + return publication; + } + ScholixResource dataset = new DataciteClient(indexHost).getDatasetByDOI(pid); + if (dataset!= null) { + return dataset; + } + ScholixResource r = new ScholixResource(); + r.setIdentifier(Collections.singletonList(new ScholixIdentifier(pid, "doi"))); + r.setObjectType("unknown"); + r.setDnetIdentifier("70|"+DHPUtils.md5(String.format("%s::doi", pid.toLowerCase().trim()))); + + return r; + }, Encoders.bean(ScholixResource.class)).write().mode(SaveMode.Overwrite).save(workingDirPath+"/stepB"); + + + Dataset s2 = spark.read().load(workingDirPath+"/stepB").as(Encoders.bean(ScholixResource.class)); + + + s1.joinWith(s2, s1.col("target.identifier.identifier").equalTo(s2.col("identifier.identifier")), "left") + + .flatMap((FlatMapFunction, Scholix>) f -> + { + + final List res = new ArrayList<>(); + final Scholix s = f._1(); + final ScholixResource target = f._2(); + if (StringUtils.isNotBlank(s.getIdentifier())) + res.add(s); + else if (target == null) { + ScholixResource currentTarget = s.getTarget(); + currentTarget.setObjectType("unknown"); + currentTarget.setDnetIdentifier(Datacite2Scholix.generateId(currentTarget.getIdentifier().get(0).getIdentifier(),currentTarget.getIdentifier().get(0).getSchema(), currentTarget.getObjectType())); + + s.generateIdentifier(); + res.add(s); + final Scholix inverse = new Scholix(); + inverse.setTarget(s.getSource()); + inverse.setSource(s.getTarget()); + inverse.setLinkprovider(s.getLinkprovider()); + inverse.setPublicationDate(s.getPublicationDate()); + inverse.setPublisher(s.getPublisher()); + inverse.setRelationship(new ScholixRelationship(s.getRelationship().getInverse(), s.getRelationship().getSchema(), s.getRelationship().getName())); + inverse.generateIdentifier(); + res.add(inverse); + + } else + { + target.setIdentifier(target.getIdentifier().stream().map(d -> new ScholixIdentifier(d.getIdentifier().toLowerCase(), d.getSchema().toLowerCase())).collect(Collectors.toList())); + s.setTarget(target); + s.generateIdentifier(); + res.add(s); + final Scholix inverse = new Scholix(); + inverse.setTarget(s.getSource()); + inverse.setSource(s.getTarget()); + inverse.setLinkprovider(s.getLinkprovider()); + inverse.setPublicationDate(s.getPublicationDate()); + inverse.setPublisher(s.getPublisher()); + inverse.setRelationship(new ScholixRelationship(s.getRelationship().getInverse(), s.getRelationship().getSchema(), s.getRelationship().getName())); + inverse.generateIdentifier(); + res.add(inverse); + } + + return res.iterator(); + }, Encoders.bean(Scholix.class)).javaRDD().map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(workingDirPath+"/resolved_json"); + } + } + + private static SparkSession getSession(SparkConf conf, String master) { + return SparkSession + .builder() + .config(conf) + .appName(SparkResolveScholixTarget.class.getSimpleName()) + .master(master) + .getOrCreate(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json new file mode 100644 index 000000000..e4b6b9dfd --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_resolve_scholix_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the name node", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the source path", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingDirPath", + "paramDescription": "the working Dir Path", + "paramRequired": true + }, + { + "paramName": "h", + "paramLongName": "indexHost", + "paramDescription": "the working Dir Path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json new file mode 100644 index 000000000..5c11aca8d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/input_retrieve_update_parameters.json @@ -0,0 +1,33 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the name node", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the working path where generated files", + "paramRequired": true + }, + { + "paramName": "ts", + "paramLongName": "timestamp", + "paramDescription": "the timestamp for incremental harvesting", + "paramRequired": true + }, + { + "paramName": "ih", + "paramLongName": "indexHost", + "paramDescription": "the ip name of the index", + "paramRequired": true + }, + { + "paramName": "in", + "paramLongName": "indexName", + "paramDescription": "the name of the index", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/retrieve_update_parameters.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/retrieve_update_parameters.json deleted file mode 100644 index e69de29bb..000000000 diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/config-default.xml new file mode 100644 index 000000000..6fb2a1253 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml new file mode 100644 index 000000000..9fc86e014 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml @@ -0,0 +1,68 @@ + + + + workingDirPath + the source path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + index + index name + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + index Summary + eu.dnetlib.dhp.provision.SparkIndexCollectionOnES + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" + -mt yarn-cluster + --sourcePath${workingDirPath}/summary + --index${index}_object + --idPathid + --typesummary + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + index scholix + eu.dnetlib.dhp.provision.SparkIndexCollectionOnES + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" + -mt yarn-cluster + --sourcePath${workingDirPath}/scholix_json + --index${index}_scholix + --idPathidentifier + --typescholix + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml index abdc69097..68543e3f2 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml @@ -16,21 +16,21 @@ sparkExecutorMemory memory for individual executor - - index - index name - - - idScholix - the identifier name of the scholix - - - idSummary - the identifier name of the summary - + + + + + + + + + + + + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] @@ -98,45 +98,45 @@ - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - index Summary - eu.dnetlib.dhp.provision.SparkIndexCollectionOnES - dhp-graph-provision-scholexplorer-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" - -mt yarn-cluster - --sourcePath${workingDirPath}/summary - --index${index}_object - --idPathid - --typesummary - - - - + + + + + + + + + + + + + + + + + + + - - - ${jobTracker} - ${nameNode} - yarn-cluster - cluster - index scholix - eu.dnetlib.dhp.provision.SparkIndexCollectionOnES - dhp-graph-provision-scholexplorer-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" - -mt yarn-cluster - --sourcePath${workingDirPath}/scholix_json - --index${index}_scholix - --idPathidentifier - --typescholix - - - - + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/config-default.xml new file mode 100644 index 000000000..6fb2a1253 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/config-default.xml @@ -0,0 +1,10 @@ + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/workflow.xml new file mode 100644 index 000000000..c004eafe6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/synch/oozie_app/workflow.xml @@ -0,0 +1,97 @@ + + + + workingDirPath + the source path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + index + index name + + + timestamp + timestamp from incremental harvesting + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.provision.update.RetrieveUpdateFromDatacite + -t${workingDirPath}/synch/input_json + -n${nameNode} + -ts${timestamp} + -ihip-90-147-167-25.ct1.garrservices.it + -indatacite + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + resolve and generate Scholix + eu.dnetlib.dhp.provision.update.SparkResolveScholixTarget + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" + -m yarn-cluster + -s${workingDirPath}/synch/input_json + -w${workingDirPath}/synch + -hip-90-147-167-25.ct1.garrservices.it + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + index scholix + eu.dnetlib.dhp.provision.SparkIndexCollectionOnES + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" + -mt yarn-cluster + --sourcePath${workingDirPath}/synch/resolved_json + --index${index}_scholix + --idPathidentifier + --typescholix + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java index 780d4a2d6..f4a480163 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DataciteClientTest.java @@ -2,24 +2,21 @@ package eu.dnetlib.dhp.provision; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.provision.scholix.Scholix; +import eu.dnetlib.dhp.provision.scholix.ScholixResource; +import eu.dnetlib.dhp.provision.update.CrossrefClient; +import eu.dnetlib.dhp.provision.update.Datacite2Scholix; +import eu.dnetlib.dhp.provision.update.DataciteClient; +import eu.dnetlib.dhp.provision.update.DataciteClientIterator; import eu.dnetlib.scholexplorer.relation.RelationMapper; import org.apache.commons.io.IOUtils; -import org.apache.http.client.methods.CloseableHttpResponse; -import org.apache.http.client.methods.HttpPost; -import org.apache.http.entity.StringEntity; -import org.apache.http.impl.client.CloseableHttpClient; -import org.apache.http.impl.client.HttpClients; +import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; -import java.io.BufferedWriter; -import java.io.FileWriter; import java.io.IOException; import java.util.List; public class DataciteClientTest { - - @Test public void dataciteSCholixTest() throws Exception { final String json = IOUtils.toString(getClass().getResourceAsStream("datacite.json")); @@ -27,83 +24,19 @@ public class DataciteClientTest { Datacite2Scholix ds = new Datacite2Scholix(mapper); final List s = ds.generateScholixFromJson(json); - - System.out.println(new ObjectMapper().writeValueAsString(s)); - } - - @Test - public void testClient() throws Exception { - DataciteClient client = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it","datacite",1585454082); - int i = 0; - final RelationMapper mapper = RelationMapper.load(); - - Datacite2Scholix ds = new Datacite2Scholix(mapper); - BufferedWriter writer = new BufferedWriter(new FileWriter("/Users/sandro/new_s.txt")); - - final ObjectMapper m = new ObjectMapper(); + public void testResolveDataset() throws Exception { + DataciteClient dc = new DataciteClient("ip-90-147-167-25.ct1.garrservices.it"); + ScholixResource datasetByDOI = dc.getDatasetByDOI("10.17182/hepdata.15392.v1/t5"); + Assertions.assertNotNull(datasetByDOI); + System.out.println(new ObjectMapper().writeValueAsString(datasetByDOI)); - - - - while (client.hasNext()){ - i ++; - - - final String next = client.next(); - try { - final List res = ds.generateScholixFromJson(next); - if (res!= null) - res - .forEach( - s -> { - try { - - writer.write(m.writeValueAsString(s)); - writer.write("\n"); - } catch (Throwable e) { - throw new RuntimeException(e); - } - } - - - ); - }catch (Throwable t) { - System.out.println(next); - throw new RuntimeException(t); - } - if(i %1000 == 0) { - System.out.println("added "+i); - } - } - } - - private String getResponse(final String url,final String json ) { - CloseableHttpClient client = HttpClients.createDefault(); - try { - - HttpPost httpPost = new HttpPost(url); - if (json!= null) { - StringEntity entity = new StringEntity(json); - httpPost.setEntity(entity); - httpPost.setHeader("Accept", "application/json"); - httpPost.setHeader("Content-type", "application/json"); - } - CloseableHttpResponse response = client.execute(httpPost); - - return IOUtils.toString(response.getEntity().getContent()); - } catch (Throwable e) { - throw new RuntimeException("Error on executing request ",e); - } finally { - try { - client.close(); - } catch (IOException e) { - throw new RuntimeException("Unable to close client ",e); - } - } - + CrossrefClient cr = new CrossrefClient("ip-90-147-167-25.ct1.garrservices.it"); + ScholixResource crossrefByDOI = cr.getResourceByDOI("10.26850/1678-4618eqj.v35.1.2010.p41-46"); + Assertions.assertNotNull(crossrefByDOI); + System.out.println(new ObjectMapper().writeValueAsString(crossrefByDOI)); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java new file mode 100644 index 000000000..8162927b8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/AdjacencyListBuilderJob.java @@ -0,0 +1,122 @@ +package eu.dnetlib.dhp.oa.provision; + +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.JoinedEntity; +import eu.dnetlib.dhp.oa.provision.model.Tuple2; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +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: + * (phase 1): prepare tuples [relation - target entity] (R - T): + * for each entity type E_i + * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information + * join (R.target = T_i.id) + * save the tuples (R_i, T_i) + * (phase 2): + * create the union of all the entity types E, hash by id + * read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S + * save the tuples (S, R, T) + * + * 3) AdjacencyListBuilderJob: + * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + * + * 4) XmlConverterJob: + * convert the JoinedEntities as XML records + */ +public class AdjacencyListBuilderJob { + + private static final Logger log = LoggerFactory.getLogger(AdjacencyListBuilderJob.class); + + public static final int MAX_LINKS = 100; + + 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(ModelSupport.getOafModelClasses()); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + createAdjacencyLists(spark, inputPath, outputPath); + }); + } + + private static void createAdjacencyLists(SparkSession spark, String inputPath, String outputPath) { + + log.info("Reading joined entities from: {}", inputPath); + spark.read() + .load(inputPath) + .as(Encoders.bean(EntityRelEntity.class)) + .groupByKey((MapFunction) value -> value.getEntity().getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (key, values) -> { + JoinedEntity j = new JoinedEntity(); + List links = new ArrayList<>(); + while (values.hasNext() && links.size() < MAX_LINKS) { + EntityRelEntity curr = values.next(); + if (j.getEntity() == null) { + j.setEntity(curr.getEntity()); + } + links.add(new Tuple2(curr.getRelation(), curr.getTarget())); + } + j.setLinks(links); + return j; + }, Encoders.bean(JoinedEntity.class)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java new file mode 100644 index 000000000..d0035fa78 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -0,0 +1,158 @@ +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.RelatedEntity; +import eu.dnetlib.dhp.oa.provision.model.SortableRelation; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +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) JoinRelationEntityByTargetJob: + * (phase 1): prepare tuples [relation - target entity] (R - T): + * for each entity type E_i + * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information + * join (R.target = T_i.id) + * save the tuples (R_i, T_i) + * (phase 2): + * create the union of all the entity types E, hash by id + * read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S + * save the tuples (S, R, T) + * + * 3) AdjacencyListBuilderJob: + * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + * + * 4) 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 entityClazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath); + }); + } + + private static void joinRelationEntity(SparkSession spark, String inputRelationsPath, String inputEntityPath, Class entityClazz, String outputPath) { + + Dataset> relsByTarget = readPathRelation(spark, inputRelationsPath) + .filter((FilterFunction) value -> value.getDataInfo().getDeletedbyinference() == false) + .map((MapFunction>) r -> new Tuple2<>(r.getTarget(), r), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(SortableRelation.class))) + .cache(); + + Dataset> entities = readPathEntity(spark, inputEntityPath, entityClazz) + .map((MapFunction) value -> asRelatedEntity(value, entityClazz), Encoders.bean(RelatedEntity.class)) + .map((MapFunction>) e -> new Tuple2<>(e.getId(), e), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(RelatedEntity.class))) + .cache(); + + relsByTarget + .joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner") + .map((MapFunction, Tuple2>, EntityRelEntity>) + t -> new EntityRelEntity(t._1()._2(), t._2()._2()), + Encoders.bean(EntityRelEntity.class)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath + "/" + EntityType.fromClass(entityClazz)); + } + + private static Dataset readPathEntity(SparkSession spark, String inputEntityPath, Class entityClazz) { + + log.info("Reading Graph table from: {}", inputEntityPath); + return spark + .read() + .textFile(inputEntityPath) + .map((MapFunction) 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 containing all the relationships + */ + private static Dataset 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()); + } + + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java new file mode 100644 index 000000000..0a9235cc9 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java @@ -0,0 +1,194 @@ +package eu.dnetlib.dhp.oa.provision; + +import com.fasterxml.jackson.core.JsonProcessingException; +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.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +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 scala.collection.JavaConverters; +import scala.collection.Seq; + +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: + * (phase 1): prepare tuples [relation - target entity] (R - T): + * for each entity type E_i + * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information + * join (R.target = T_i.id) + * save the tuples (R_i, T_i) + * (phase 2): + * create the union of all the entity types E, hash by id + * read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S + * save the tuples (S, R, T) + * + * 3) AdjacencyListBuilderJob: + * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + * + * 4) 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_pahase2.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 inputGraphRootPath = parser.get("inputGraphRootPath"); + log.info("inputGraphRootPath: {}", inputGraphRootPath); + + String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + int numPartitions = Integer.parseInt(parser.get("numPartitions")); + log.info("numPartitions: {}", numPartitions); + + SparkConf conf = new SparkConf(); + conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + conf.registerKryoClasses(ModelSupport.getOafModelClasses()); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + joinAllEntities(spark, inputRelatedEntitiesPath, inputGraphRootPath, outputPath, numPartitions); + }); + } + + private static void joinAllEntities(SparkSession spark, String inputRelatedEntitiesPath, String inputGraphRootPath, String outputPath, int numPartitions) { + + Dataset> entities = readAllEntities(spark, inputGraphRootPath, numPartitions); + Dataset> relsBySource = readRelatedEntities(spark, inputRelatedEntitiesPath); + + entities + .joinWith(relsBySource, entities.col("_1").equalTo(relsBySource.col("_1")), "left_outer") + .map((MapFunction, Tuple2>, EntityRelEntity>) value -> { + EntityRelEntity re = new EntityRelEntity(); + re.setEntity(value._1()._2()); + Optional 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)) + .repartition(numPartitions) + .filter((FilterFunction) value -> value.getEntity() != null && StringUtils.isNotBlank(value.getEntity().getId())) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + + private static Dataset> readAllEntities(SparkSession spark, String inputGraphPath, int numPartitions) { + Dataset publication = readPathEntity(spark, inputGraphPath + "/publication", Publication.class); + Dataset dataset = readPathEntity(spark, inputGraphPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset other = readPathEntity(spark, inputGraphPath + "/otherresearchproduct", OtherResearchProduct.class); + Dataset software = readPathEntity(spark, inputGraphPath + "/software", Software.class); + Dataset datasource = readPathEntity(spark, inputGraphPath + "/datasource", Datasource.class); + Dataset organization = readPathEntity(spark, inputGraphPath + "/organization", Organization.class); + Dataset project = readPathEntity(spark, inputGraphPath + "/project", Project.class); + + return publication + .union(dataset) + .union(other) + .union(software) + .union(datasource) + .union(organization) + .union(project) + .map((MapFunction>) + value -> new Tuple2<>(value.getId(), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(TypedRow.class))) + .repartition(numPartitions); + } + + private static Dataset> readRelatedEntities(SparkSession spark, String inputRelatedEntitiesPath) { + + log.info("Reading related entities from: {}", inputRelatedEntitiesPath); + + final List paths = HdfsSupport.listFiles(inputRelatedEntitiesPath, spark.sparkContext().hadoopConfiguration()); + + log.info("Found paths: {}", String.join(",", paths)); + + return spark.read() + .load(toSeq(paths)) + .as(Encoders.bean(EntityRelEntity.class)) + .map((MapFunction>) + value -> new Tuple2<>(value.getRelation().getSource(), value), + Encoders.tuple(Encoders.STRING(), Encoders.kryo(EntityRelEntity.class))); + } + + private static Dataset readPathEntity(SparkSession spark, String inputEntityPath, Class entityClazz) { + + log.info("Reading Graph table from: {}", inputEntityPath); + return spark + .read() + .textFile(inputEntityPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), Encoders.bean(entityClazz)) + .map((MapFunction) value -> getTypedRow(StringUtils.substringAfterLast(inputEntityPath, "/"), value), Encoders.bean(TypedRow.class)); + } + + private static TypedRow getTypedRow(String type, OafEntity entity) throws JsonProcessingException { + TypedRow t = new TypedRow(); + t.setType(type); + t.setDeleted(entity.getDataInfo().getDeletedbyinference()); + t.setId(entity.getId()); + t.setOaf(OBJECT_MAPPER.writeValueAsString(entity)); + return t; + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + private static Seq toSeq(List list) { + return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/GraphJoiner.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/GraphJoiner.java deleted file mode 100644 index def757da3..000000000 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/GraphJoiner.java +++ /dev/null @@ -1,291 +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.Iterables; -import com.google.common.collect.Maps; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; -import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; -import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils; -import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner; -import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory; -import eu.dnetlib.dhp.oa.provision.model.*; -import eu.dnetlib.dhp.schema.oaf.*; -import org.apache.hadoop.io.Text; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.hadoop.mapred.SequenceFileOutputFormat; -import org.apache.spark.SparkContext; -import org.apache.spark.api.java.JavaPairRDD; -import org.apache.spark.api.java.JavaRDD; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.PairFunction; -import org.apache.spark.sql.SparkSession; -import org.apache.spark.util.LongAccumulator; -import scala.Tuple2; - -import java.io.IOException; -import java.io.Serializable; -import java.util.Map; - -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 -> [ ] - */ -public class GraphJoiner implements Serializable { - - private Map 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(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 adjacencyLists() { - final JavaSparkContext jsc = new JavaSparkContext(getSpark().sparkContext()); - - // read each entity - JavaPairRDD datasource = readPathEntity(jsc, getInputPath(), "datasource"); - JavaPairRDD organization = readPathEntity(jsc, getInputPath(), "organization"); - JavaPairRDD project = readPathEntity(jsc, getInputPath(), "project"); - JavaPairRDD dataset = readPathEntity(jsc, getInputPath(), "dataset"); - JavaPairRDD otherresearchproduct = readPathEntity(jsc, getInputPath(), "otherresearchproduct"); - JavaPairRDD software = readPathEntity(jsc, getInputPath(), "software"); - JavaPairRDD publication = readPathEntity(jsc, getInputPath(), "publication"); - - // create the union between all the entities - final String entitiesPath = getOutPath() + "/entities"; - datasource - .union(organization) - .union(project) - .union(dataset) - .union(otherresearchproduct) - .union(software) - .union(publication) - .map(e -> new EntityRelEntity().setSource(e._2())) - .map(GraphMappingUtils::serialize) - .saveAsTextFile(entitiesPath, GzipCodec.class); - - JavaPairRDD entities = jsc.textFile(entitiesPath) - .map(t -> new ObjectMapper().readValue(t, EntityRelEntity.class)) - .mapToPair(t -> new Tuple2<>(t.getSource().getSourceId(), t)); - - final String relationPath = getOutPath() + "/relation"; - // reads the relationships - final JavaPairRDD rels = readPathRelation(jsc, getInputPath()) - .filter(rel -> !rel.getDeleted()) //only consider those that are not virtually deleted - .map(p -> new EntityRelEntity().setRelation(p)) - .mapToPair(p -> new Tuple2<>(SortableRelationKey.from(p), p)); - rels - .groupByKey(new RelationPartitioner(rels.getNumPartitions())) - .map(p -> Iterables.limit(p._2(), MAX_RELS)) - .flatMap(p -> p.iterator()) - .map(s -> new ObjectMapper().writeValueAsString(s)) - .saveAsTextFile(relationPath, GzipCodec.class); - - final JavaPairRDD relation = jsc.textFile(relationPath) - .map(s -> new ObjectMapper().readValue(s, EntityRelEntity.class)) - .mapToPair(p -> new Tuple2<>(p.getRelation().getTargetId(), p)); - - final String bySourcePath = getOutPath() + "/join_by_source"; - relation - .join(entities - .filter(e -> !e._2().getSource().getDeleted()) - .mapToPair(e -> new Tuple2<>(e._1(), asRelatedEntity(e._2())))) - .map(s -> new EntityRelEntity() - .setRelation(s._2()._1().getRelation()) - .setTarget(s._2()._2().getSource())) - .map(j -> new ObjectMapper().writeValueAsString(j)) - .saveAsTextFile(bySourcePath, GzipCodec.class); - - JavaPairRDD bySource = jsc.textFile(bySourcePath) - .map(e -> getObjectMapper().readValue(e, EntityRelEntity.class)) - .mapToPair(t -> new Tuple2<>(t.getRelation().getSourceId(), t)); - - final XmlRecordFactory recordFactory = new XmlRecordFactory(accumulators, contextMapper, false, schemaLocation, otherDsTypeId); - entities - .union(bySource) - .groupByKey() // by source id - .map(l -> toJoinedEntity(l)) - .mapToPair(je -> new Tuple2<>( - new Text(je.getEntity().getId()), - new Text(recordFactory.build(je)))) - .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 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, 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); - } - } - - private JoinedEntity toJoinedEntity(Tuple2> p) { - final ObjectMapper mapper = getObjectMapper(); - final JoinedEntity j = new JoinedEntity(); - final Links links = new Links(); - for(EntityRelEntity rel : p._2()) { - if (rel.hasMainEntity() & j.getEntity() == null) { - j.setType(rel.getSource().getType()); - j.setEntity(parseOaf(rel.getSource().getOaf(), rel.getSource().getType(), mapper)); - } - if (rel.hasRelatedEntity()) { - try { - links.add( - new eu.dnetlib.dhp.oa.provision.model.Tuple2() - .setRelation(mapper.readValue(rel.getRelation().getOaf(), Relation.class)) - .setRelatedEntity(mapper.readValue(rel.getTarget().getOaf(), RelatedEntity.class))); - } catch (IOException e) { - throw new IllegalArgumentException(e); - } - } - } - j.setLinks(links); - if (j.getEntity() == null) { - throw new IllegalStateException("missing main entity on '" + p._1() + "'"); - } - return j; - } - - /** - * Reads a set of eu.dnetlib.dhp.schema.oaf.OafEntity objects from a sequence 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 indexed by entity identifier - */ - private JavaPairRDD readPathEntity(final JavaSparkContext sc, final String inputPath, final String type) { - return sc.textFile(inputPath + "/" + type) - .mapToPair((PairFunction) s -> { - final DocumentContext json = JsonPath.parse(s); - final String id = json.read("$.id"); - return new Tuple2<>(id, new TypedRow() - .setSourceId(id) - .setDeleted(json.read("$.dataInfo.deletedbyinference")) - .setType(type) - .setOaf(s)); - }); - } - - /** - * Reads a set of eu.dnetlib.dhp.schema.oaf.Relation objects from a sequence file , - * extracts necessary information using json path, wraps the oaf object in a eu.dnetlib.dhp.graph.model.TypedRow - * @param sc - * @param inputPath - * @return the JavaRDD containing all the relationships - */ - private JavaRDD readPathRelation(final JavaSparkContext sc, final String inputPath) { - return sc.textFile(inputPath + "/relation") - .map(s -> { - final DocumentContext json = JsonPath.parse(s); - return new TypedRow() - .setSourceId(json.read("$.source")) - .setTargetId(json.read("$.target")) - .setDeleted(json.read("$.dataInfo.deletedbyinference")) - .setType("relation") - .setRelType("$.relType") - .setSubRelType("$.subRelType") - .setRelClass("$.relClass") - .setOaf(s); - }); - } - - 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")); - } - -} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java new file mode 100644 index 000000000..95d2263b5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java @@ -0,0 +1,152 @@ +package eu.dnetlib.dhp.oa.provision; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Iterables; +import com.google.common.collect.Iterators; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.provision.model.SortableRelation; +import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +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.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; + +/** + * 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: + * (phase 1): prepare tuples [relation - target entity] (R - T): + * for each entity type E_i + * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information + * join (R.target = T_i.id) + * save the tuples (R_i, T_i) + * (phase 2): + * create the union of all the entity types E, hash by id + * read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S + * save the tuples (S, R, T) + * + * 3) AdjacencyListBuilderJob: + * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping 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); + + int numPartitions = Integer.parseInt(parser.get("relPartitions")); + log.info("relPartitions: {}", numPartitions); + + SparkConf conf = new SparkConf(); + + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareRelationsFromPaths(spark, inputRelationsPath, outputPath, numPartitions); + }); + } + + private static void prepareRelationsFromPaths(SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + readPathRelation(spark, inputRelationsPath) + .filter((FilterFunction) value -> value.getDataInfo().getDeletedbyinference() == false) + .groupByKey((MapFunction) value -> value.getSource(), Encoders.STRING()) + .flatMapGroups((FlatMapGroupsFunction) (key, values) -> Iterators.limit(values, MAX_RELS), Encoders.bean(SortableRelation.class)) + .repartition(numPartitions) + .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 containing all the relationships + */ + private static Dataset readPathRelation(SparkSession spark, final String inputPath) { + return spark.read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, SortableRelation.class), Encoders.bean(SortableRelation.class)); + } + + //TODO work in progress + private static void prepareRelationsRDDFromPaths(SparkSession spark, String inputRelationsPath, String outputPath, int numPartitions) { + JavaRDD rels = readPathRelationRDD(spark, inputRelationsPath) + .repartition(numPartitions); + + RDD d = rels + .filter(rel -> !rel.getDataInfo().getDeletedbyinference()) //only consider those that are not virtually deleted + .mapToPair((PairFunction) rel -> new Tuple2<>(rel, rel)) + .groupByKey(new RelationPartitioner(rels.getNumPartitions())) + .map(p -> Iterables.limit(p._2(), MAX_RELS)) + .flatMap(p -> p.iterator()) + .rdd(); + + spark.createDataset(d, Encoders.bean(SortableRelation.class)) + .write() + .mode(SaveMode.Overwrite) + .parquet(outputPath); + } + + private static JavaRDD readPathRelationRDD(SparkSession spark, final String inputPath) { + JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + return sc.textFile(inputPath) + .map(s -> OBJECT_MAPPER.readValue(s, SortableRelation.class)); + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlRecordBuilderJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlRecordBuilderJob.java deleted file mode 100644 index 0a898c0fc..000000000 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlRecordBuilderJob.java +++ /dev/null @@ -1,47 +0,0 @@ -package eu.dnetlib.dhp.oa.provision; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.oa.provision.utils.ContextMapper; -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.fs.FileSystem; -import org.apache.hadoop.fs.Path; -import org.apache.spark.SparkConf; -import org.apache.spark.sql.SparkSession; - -public class SparkXmlRecordBuilderJob { - - public static void main(String[] args) throws Exception { - - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils.toString( - SparkXmlRecordBuilderJob.class.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json"))); - parser.parseArgument(args); - - final String master = parser.get("master"); - final SparkConf conf = new SparkConf() - .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - - try(SparkSession spark = getSession(conf, master)) { - - final String inputPath = parser.get("sourcePath"); - final String outputPath = parser.get("outputPath"); - final String isLookupUrl = parser.get("isLookupUrl"); - final String otherDsTypeId = parser.get("otherDsTypeId"); - - final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration()); - - new GraphJoiner(spark, ContextMapper.fromIS(isLookupUrl), otherDsTypeId, inputPath, outputPath) - .adjacencyLists(); - } - } - - private static SparkSession getSession(SparkConf conf, String master) { - return SparkSession - .builder() - .config(conf) - .appName(SparkXmlRecordBuilderJob.class.getSimpleName()) - .master(master) - .getOrCreate(); - } - -} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java new file mode 100644 index 000000000..059cb31f2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlConverterJob.java @@ -0,0 +1,166 @@ +package eu.dnetlib.dhp.oa.provision; + +import com.fasterxml.jackson.databind.ObjectMapper; +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.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.Optional; +import java.util.stream.Collectors; + +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 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: + * (phase 1): prepare tuples [relation - target entity] (R - T): + * for each entity type E_i + * map E_i as RelatedEntity T_i to simplify the model and extracting only the necessary information + * join (R.target = T_i.id) + * save the tuples (R_i, T_i) + * (phase 2): + * create the union of all the entity types E, hash by id + * read the tuples (R, T), hash by R.source + * join E.id = (R, T).source, where E becomes the Source Entity S + * save the tuples (S, R, T) + * + * 3) AdjacencyListBuilderJob: + * given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mapping the result as JoinedEntity + * + * 4) XmlConverterJob: + * convert the JoinedEntities as XML records + */ +public class XmlConverterJob { + + private static final Logger log = LoggerFactory.getLogger(XmlConverterJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + 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) j -> { + if (j.getLinks() != null) { + j.setLinks(j.getLinks() + .stream() + .filter(t -> t.getRelation() != null & t.getRelatedEntity() != null) + .collect(Collectors.toCollection(ArrayList::new))); + } + return j; + }, Encoders.bean(JoinedEntity.class)) + .map((MapFunction>) je -> new Tuple2<>( + je.getEntity().getId(), + recordFactory.build(je) + ), Encoders.tuple(Encoders.STRING(), Encoders.STRING())) + .javaRDD() + .mapToPair((PairFunction, Text, Text>) t -> new Tuple2<>(new Text(t._1()), new Text(t._2()))) + .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 prepareAccumulators(SparkContext sc) { + Map 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; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java similarity index 75% rename from dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlIndexingJob.java rename to dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index cafbc8653..84538c924 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SparkXmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -10,14 +10,13 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.Text; import org.apache.solr.common.SolrInputDocument; 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; @@ -28,65 +27,79 @@ import java.io.StringReader; import java.io.StringWriter; import java.text.SimpleDateFormat; import java.util.Date; +import java.util.Optional; -public class SparkXmlIndexingJob { +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; - private static final Log log = LogFactory.getLog(SparkXmlIndexingJob.class); +public class XmlIndexingJob { + + private static final Logger log = LoggerFactory.getLogger(XmlIndexingJob.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 { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils.toString( - SparkXmlIndexingJob.class.getResourceAsStream( + XmlIndexingJob.class.getResourceAsStream( "/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"); - final SparkConf conf = new SparkConf() - .set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); + runWithSparkSession(conf, isSparkSessionManaged, + spark -> { + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); - try(SparkSession spark = getSession(conf, master)) { + RDD 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()); - - RDD 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(SparkXmlRecordBuilderJob.class.getSimpleName()) - .master(master) - .getOrCreate(); + final String collection = format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION; + SolrSupport.indexDocs(zkHost, collection, batchSize, docs); + }); } private static String toIndexRecord(Transformer tr, final String record) { @@ -95,7 +108,7 @@ 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 +140,7 @@ 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()); } /** diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java index ba89eaa38..e1ca8e316 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/EntityRelEntity.java @@ -1,54 +1,64 @@ package eu.dnetlib.dhp.oa.provision.model; +import com.google.common.base.Objects; + import java.io.Serializable; public class EntityRelEntity implements Serializable { - private TypedRow source; - private TypedRow relation; - private TypedRow target; + private TypedRow entity; + private SortableRelation relation; + private RelatedEntity target; public EntityRelEntity() { } - public EntityRelEntity(TypedRow source) { - this.source = source; + public EntityRelEntity(SortableRelation relation, RelatedEntity target) { + this(null, relation, target); } - //helpers - public Boolean hasMainEntity() { - return getSource() != null & getRelation() == null & getTarget() == null; + public EntityRelEntity(TypedRow entity, SortableRelation relation, RelatedEntity target) { + this.entity = entity; + this.relation = relation; + this.target = target; } - public Boolean hasRelatedEntity() { - return getSource() == null & getRelation() != null & getTarget() != null; + public TypedRow getEntity() { + return entity; } - - public TypedRow getSource() { - return source; + public void setEntity(TypedRow entity) { + this.entity = entity; } - public EntityRelEntity setSource(TypedRow source) { - this.source = source; - return this; - } - - public TypedRow getRelation() { + public SortableRelation getRelation() { return relation; } - public EntityRelEntity setRelation(TypedRow relation) { + public void setRelation(SortableRelation relation) { this.relation = relation; - return this; } - public TypedRow getTarget() { + public RelatedEntity getTarget() { return target; } - public EntityRelEntity setTarget(TypedRow target) { + public void setTarget(RelatedEntity target) { this.target = target; - return this; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + EntityRelEntity that = (EntityRelEntity) o; + return Objects.equal(entity, that.entity) && + Objects.equal(relation, that.relation) && + Objects.equal(target, that.target); + } + + @Override + public int hashCode() { + return Objects.hashCode(entity, relation, target); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java index 80b15a4d6..b6e97a503 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java @@ -1,41 +1,30 @@ package eu.dnetlib.dhp.oa.provision.model; -import eu.dnetlib.dhp.schema.oaf.OafEntity; - import java.io.Serializable; +import java.util.List; public class JoinedEntity implements Serializable { - private String type; + private TypedRow entity; - private OafEntity entity; + private List links; - private Links links; - - public String getType() { - return type; + public JoinedEntity() { } - public JoinedEntity setType(String type) { - this.type = type; - return this; - } - - public OafEntity getEntity() { + public TypedRow getEntity() { return entity; } - public JoinedEntity setEntity(OafEntity entity) { + public void setEntity(TypedRow entity) { this.entity = entity; - return this; } - public Links getLinks() { + public List getLinks() { return links; } - public JoinedEntity setLinks(Links links) { + public void setLinks(List links) { this.links = links; - return this; } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Links.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Links.java deleted file mode 100644 index 0cb4617ec..000000000 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Links.java +++ /dev/null @@ -1,6 +0,0 @@ -package eu.dnetlib.dhp.oa.provision.model; - -import java.util.ArrayList; - -public class Links extends ArrayList { -} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java index 75e9045e8..011d9276d 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.oa.provision.model; +import com.google.common.base.Objects; import eu.dnetlib.dhp.schema.oaf.Instance; import eu.dnetlib.dhp.schema.oaf.KeyValue; import eu.dnetlib.dhp.schema.oaf.Qualifier; @@ -49,207 +50,218 @@ public class RelatedEntity implements Serializable { return id; } - public RelatedEntity setId(String id) { + public void setId(String id) { this.id = id; - return this; - } - - public StructuredProperty getTitle() { - return title; - } - - public RelatedEntity setTitle(StructuredProperty title) { - this.title = title; - return this; - } - - public String getDateofacceptance() { - return dateofacceptance; - } - - public RelatedEntity setDateofacceptance(String dateofacceptance) { - this.dateofacceptance = dateofacceptance; - return this; - } - - public String getPublisher() { - return publisher; - } - - public RelatedEntity setPublisher(String publisher) { - this.publisher = publisher; - return this; - } - - public List getPid() { - return pid; - } - - public RelatedEntity setPid(List pid) { - this.pid = pid; - return this; - } - - public String getCodeRepositoryUrl() { - return codeRepositoryUrl; - } - - public RelatedEntity setCodeRepositoryUrl(String codeRepositoryUrl) { - this.codeRepositoryUrl = codeRepositoryUrl; - return this; - } - - public Qualifier getResulttype() { - return resulttype; - } - - public RelatedEntity setResulttype(Qualifier resulttype) { - this.resulttype = resulttype; - return this; - } - - public List getCollectedfrom() { - return collectedfrom; - } - - public RelatedEntity setCollectedfrom(List collectedfrom) { - this.collectedfrom = collectedfrom; - return this; - } - - public List getInstances() { - return instances; - } - - public RelatedEntity setInstances(List instances) { - this.instances = instances; - return this; - } - - public String getOfficialname() { - return officialname; - } - - public RelatedEntity setOfficialname(String officialname) { - this.officialname = officialname; - return this; - } - - public String getWebsiteurl() { - return websiteurl; - } - - public RelatedEntity setWebsiteurl(String websiteurl) { - this.websiteurl = websiteurl; - return this; - } - - public Qualifier getDatasourcetype() { - return datasourcetype; - } - - public RelatedEntity setDatasourcetype(Qualifier datasourcetype) { - this.datasourcetype = datasourcetype; - return this; - } - - public Qualifier getDatasourcetypeui() { - return datasourcetypeui; - } - - public RelatedEntity setDatasourcetypeui(Qualifier datasourcetypeui) { - this.datasourcetypeui = datasourcetypeui; - return this; - } - - public Qualifier getOpenairecompatibility() { - return openairecompatibility; - } - - public RelatedEntity setOpenairecompatibility(Qualifier openairecompatibility) { - this.openairecompatibility = openairecompatibility; - return this; - } - - public String getLegalname() { - return legalname; - } - - public RelatedEntity setLegalname(String legalname) { - this.legalname = legalname; - return this; - } - - public String getLegalshortname() { - return legalshortname; - } - - public RelatedEntity setLegalshortname(String legalshortname) { - this.legalshortname = legalshortname; - return this; - } - - public Qualifier getCountry() { - return country; - } - - public RelatedEntity setCountry(Qualifier country) { - this.country = country; - return this; - } - - public String getCode() { - return code; - } - - public RelatedEntity setCode(String code) { - this.code = code; - return this; - } - - public String getAcronym() { - return acronym; - } - - public RelatedEntity setAcronym(String acronym) { - this.acronym = acronym; - return this; - } - - public Qualifier getContracttype() { - return contracttype; - } - - public RelatedEntity setContracttype(Qualifier contracttype) { - this.contracttype = contracttype; - return this; - } - - public List getFundingtree() { - return fundingtree; - } - - public RelatedEntity setFundingtree(List fundingtree) { - this.fundingtree = fundingtree; - return this; - } - - public String getProjectTitle() { - return projectTitle; - } - - public RelatedEntity setProjectTitle(String projectTitle) { - this.projectTitle = projectTitle; - return this; } public String getType() { return type; } - public RelatedEntity setType(String type) { + public void setType(String type) { this.type = type; - return this; } + public StructuredProperty getTitle() { + return title; + } + + public void setTitle(StructuredProperty title) { + this.title = title; + } + + public String getWebsiteurl() { + return websiteurl; + } + + public void setWebsiteurl(String websiteurl) { + this.websiteurl = websiteurl; + } + + public String getDateofacceptance() { + return dateofacceptance; + } + + public void setDateofacceptance(String dateofacceptance) { + this.dateofacceptance = dateofacceptance; + } + + public String getPublisher() { + return publisher; + } + + public void setPublisher(String publisher) { + this.publisher = publisher; + } + + public List getPid() { + return pid; + } + + public void setPid(List pid) { + this.pid = pid; + } + + public String getCodeRepositoryUrl() { + return codeRepositoryUrl; + } + + public void setCodeRepositoryUrl(String codeRepositoryUrl) { + this.codeRepositoryUrl = codeRepositoryUrl; + } + + public Qualifier getResulttype() { + return resulttype; + } + + public void setResulttype(Qualifier resulttype) { + this.resulttype = resulttype; + } + + public List getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + } + + public List getInstances() { + return instances; + } + + public void setInstances(List instances) { + this.instances = instances; + } + + public String getOfficialname() { + return officialname; + } + + public void setOfficialname(String officialname) { + this.officialname = officialname; + } + + public Qualifier getDatasourcetype() { + return datasourcetype; + } + + public void setDatasourcetype(Qualifier datasourcetype) { + this.datasourcetype = datasourcetype; + } + + public Qualifier getDatasourcetypeui() { + return datasourcetypeui; + } + + public void setDatasourcetypeui(Qualifier datasourcetypeui) { + this.datasourcetypeui = datasourcetypeui; + } + + public Qualifier getOpenairecompatibility() { + return openairecompatibility; + } + + public void setOpenairecompatibility(Qualifier openairecompatibility) { + this.openairecompatibility = openairecompatibility; + } + + public String getLegalname() { + return legalname; + } + + public void setLegalname(String legalname) { + this.legalname = legalname; + } + + public String getLegalshortname() { + return legalshortname; + } + + public void setLegalshortname(String legalshortname) { + this.legalshortname = legalshortname; + } + + public Qualifier getCountry() { + return country; + } + + public void setCountry(Qualifier country) { + this.country = country; + } + + public String getProjectTitle() { + return projectTitle; + } + + public void setProjectTitle(String projectTitle) { + this.projectTitle = projectTitle; + } + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public Qualifier getContracttype() { + return contracttype; + } + + public void setContracttype(Qualifier contracttype) { + this.contracttype = contracttype; + } + + public List getFundingtree() { + return fundingtree; + } + + public void setFundingtree(List fundingtree) { + this.fundingtree = fundingtree; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + RelatedEntity that = (RelatedEntity) o; + return Objects.equal(id, that.id) && + Objects.equal(type, that.type) && + Objects.equal(title, that.title) && + Objects.equal(websiteurl, that.websiteurl) && + Objects.equal(dateofacceptance, that.dateofacceptance) && + Objects.equal(publisher, that.publisher) && + Objects.equal(pid, that.pid) && + Objects.equal(codeRepositoryUrl, that.codeRepositoryUrl) && + Objects.equal(resulttype, that.resulttype) && + Objects.equal(collectedfrom, that.collectedfrom) && + Objects.equal(instances, that.instances) && + Objects.equal(officialname, that.officialname) && + Objects.equal(datasourcetype, that.datasourcetype) && + Objects.equal(datasourcetypeui, that.datasourcetypeui) && + Objects.equal(openairecompatibility, that.openairecompatibility) && + Objects.equal(legalname, that.legalname) && + Objects.equal(legalshortname, that.legalshortname) && + Objects.equal(country, that.country) && + Objects.equal(projectTitle, that.projectTitle) && + Objects.equal(code, that.code) && + Objects.equal(acronym, that.acronym) && + Objects.equal(contracttype, that.contracttype) && + Objects.equal(fundingtree, that.fundingtree); + } + + @Override + public int hashCode() { + return Objects.hashCode(id, type, title, websiteurl, dateofacceptance, publisher, pid, codeRepositoryUrl, resulttype, collectedfrom, instances, officialname, datasourcetype, datasourcetypeui, openairecompatibility, legalname, legalshortname, country, projectTitle, code, acronym, contracttype, fundingtree); + } } \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java new file mode 100644 index 000000000..b294a6633 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelation.java @@ -0,0 +1,35 @@ +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.io.Serializable; +import java.util.Map; + +public class SortableRelation extends Relation implements Comparable, Serializable { + + private final static Map 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(); + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelationKey.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelationKey.java deleted file mode 100644 index 8169e57e0..000000000 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SortableRelationKey.java +++ /dev/null @@ -1,99 +0,0 @@ -package eu.dnetlib.dhp.oa.provision.model; - -import com.google.common.collect.ComparisonChain; -import com.google.common.collect.Maps; - -import java.io.Serializable; -import java.util.Map; - -/** - * Allows to sort relationships according to the priority defined in weights map. - */ -public class SortableRelationKey implements Comparable, Serializable { - - private String sourceId; - private String targetId; - - private String relType; - private String subRelType; - private String relClass; - - private final static Map 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); - } - - public static SortableRelationKey from(final EntityRelEntity e) { - return new SortableRelationKey() - .setSourceId(e.getRelation().getSourceId()) - .setTargetId(e.getRelation().getTargetId()) - .setRelType(e.getRelation().getRelType()) - .setSubRelType(e.getRelation().getSubRelType()) - .setRelClass(e.getRelation().getRelClass()); - } - - public String getSourceId() { - return sourceId; - } - - public SortableRelationKey setSourceId(String sourceId) { - this.sourceId = sourceId; - return this; - } - - public String getTargetId() { - return targetId; - } - - public SortableRelationKey setTargetId(String targetId) { - this.targetId = targetId; - return this; - } - - public String getRelType() { - return relType; - } - - public SortableRelationKey setRelType(String relType) { - this.relType = relType; - return this; - } - - public String getSubRelType() { - return subRelType; - } - - public SortableRelationKey setSubRelType(String subRelType) { - this.subRelType = subRelType; - return this; - } - - public String getRelClass() { - return relClass; - } - - public SortableRelationKey setRelClass(String relClass) { - this.relClass = relClass; - return this; - } - - @Override - public int compareTo(SortableRelationKey o) { - return ComparisonChain.start() - .compare(weights.get(getSubRelType()), weights.get(o.getSubRelType())) - .compare(getSourceId(), o.getSourceId()) - .compare(getTargetId(), o.getTargetId()) - .result(); - } - -} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java index ded976eea..942acaea1 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/Tuple2.java @@ -2,27 +2,50 @@ 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; private RelatedEntity relatedEntity; + public Tuple2() { + } + + public Tuple2(Relation relation, RelatedEntity relatedEntity) { + this.relation = relation; + this.relatedEntity = relatedEntity; + } + public Relation getRelation() { return relation; } - public Tuple2 setRelation(Relation relation) { + public void setRelation(Relation relation) { this.relation = relation; - return this; } public RelatedEntity getRelatedEntity() { return relatedEntity; } - public Tuple2 setRelatedEntity(RelatedEntity relatedEntity) { + public void setRelatedEntity(RelatedEntity relatedEntity) { this.relatedEntity = relatedEntity; - return this; } + + @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()); + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java index e275fd9da..54f34802f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java @@ -1,92 +1,61 @@ package eu.dnetlib.dhp.oa.provision.model; +import com.google.common.base.Objects; + import java.io.Serializable; public class TypedRow implements Serializable { - private String sourceId; - - private String targetId; + private String id; private Boolean deleted; private String type; - private String relType; - private String subRelType; - private String relClass; - private String oaf; - public String getSourceId() { - return sourceId; + public String getId() { + return id; } - public TypedRow setSourceId(String sourceId) { - this.sourceId = sourceId; - return this; - } - - public String getTargetId() { - return targetId; - } - - public TypedRow setTargetId(String targetId) { - this.targetId = targetId; - return this; + public void setId(String id) { + this.id = id; } public Boolean getDeleted() { return deleted; } - public TypedRow setDeleted(Boolean deleted) { + public void setDeleted(Boolean deleted) { this.deleted = deleted; - return this; } public String getType() { return type; } - public TypedRow setType(String type) { + public void setType(String type) { this.type = type; - return this; - } - - public String getRelType() { - return relType; - } - - public TypedRow setRelType(String relType) { - this.relType = relType; - return this; - } - - public String getSubRelType() { - return subRelType; - } - - public TypedRow setSubRelType(String subRelType) { - this.subRelType = subRelType; - return this; - } - - public String getRelClass() { - return relClass; - } - - public TypedRow setRelClass(String relClass) { - this.relClass = relClass; - return this; } public String getOaf() { return oaf; } - public TypedRow setOaf(String oaf) { + public void setOaf(String oaf) { this.oaf = oaf; - return this; + } + + @Override + public boolean equals(Object o) { + if (this == o) return true; + if (o == null || getClass() != o.getClass()) return false; + TypedRow typedRow2 = (TypedRow) o; + return Objects.equal(id, typedRow2.id); + } + + @Override + public int hashCode() { + return Objects.hashCode(id); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java index a48c812fc..42174ac94 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/GraphMappingUtils.java @@ -1,220 +1,99 @@ 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.base.Predicate; -import com.google.common.collect.Maps; import com.google.common.collect.Sets; -import com.jayway.jsonpath.DocumentContext; -import com.jayway.jsonpath.JsonPath; -import eu.dnetlib.dhp.oa.provision.model.EntityRelEntity; import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; -import eu.dnetlib.dhp.oa.provision.model.TypedRow; +import eu.dnetlib.dhp.schema.common.EntityType; import eu.dnetlib.dhp.schema.oaf.*; -import net.minidev.json.JSONArray; -import org.apache.commons.lang3.StringUtils; -import java.util.LinkedHashMap; -import java.util.Map; +import java.util.List; +import java.util.Objects; +import java.util.Optional; 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 enum EntityType { - publication, dataset, otherresearchproduct, software, datasource, organization, project - } - - public enum MainEntityType { - result, datasource, organization, project - } - public static Set authorPidTypes = Sets.newHashSet("orcid", "magidentifier"); - public static Set instanceFieldFilter = Sets.newHashSet("instancetype", "hostedby", "license", "accessright", "collectedfrom", "dateofacceptance", "distributionlocation"); + public static RelatedEntity asRelatedEntity(E entity, Class clazz) { - private static final String schemeTemplate = "dnet:%s_%s_relations"; + final RelatedEntity re = new RelatedEntity(); + re.setId(entity.getId()); + re.setType(EntityType.fromClass(clazz).name()); - private static Map entityMapping = Maps.newHashMap(); + re.setPid(entity.getPid()); + re.setCollectedfrom(entity.getCollectedfrom()); - static { - entityMapping.put(EntityType.publication, MainEntityType.result); - entityMapping.put(EntityType.dataset, MainEntityType.result); - entityMapping.put(EntityType.otherresearchproduct, MainEntityType.result); - entityMapping.put(EntityType.software, MainEntityType.result); - entityMapping.put(EntityType.datasource, MainEntityType.datasource); - entityMapping.put(EntityType.organization, MainEntityType.organization); - entityMapping.put(EntityType.project, MainEntityType.project); - } - - public static String getScheme(final String sourceType, final String targetType) { - return String.format(schemeTemplate, - entityMapping.get(EntityType.valueOf(sourceType)).name(), - entityMapping.get(EntityType.valueOf(targetType)).name()); - } - - public static String getMainType(final String type) { - return entityMapping.get(EntityType.valueOf(type)).name(); - } - - public static boolean isResult(String type) { - return MainEntityType.result.name().equals(getMainType(type)); - } - - public static Predicate instanceFilter = s -> instanceFieldFilter.contains(s); - - public static EntityRelEntity asRelatedEntity(EntityRelEntity e) { - - final DocumentContext j = JsonPath.parse(e.getSource().getOaf()); - final RelatedEntity re = new RelatedEntity().setId(j.read("$.id")).setType(e.getSource().getType()); - - switch (EntityType.valueOf(e.getSource().getType())) { + switch (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("$.pid"); - re.setPid(pids.stream() - .map(p -> asStructuredProperty((LinkedHashMap) p)) - .collect(Collectors.toList())); + Result result = (Result) entity; - re.setResulttype(asQualifier(j.read("$.resulttype"))); + if (result.getTitle() == null && !result.getTitle().isEmpty()) { + re.setTitle(result.getTitle().stream().findFirst().get()); + } - JSONArray collfrom = j.read("$.collectedfrom"); - re.setCollectedfrom(collfrom.stream() - .map(c -> asKV((LinkedHashMap) c)) - .collect(Collectors.toList())); - - // will throw exception when the instance is not found - JSONArray instances = j.read("$.instance"); - re.setInstances(instances.stream() - .map(i -> { - final LinkedHashMap p = (LinkedHashMap) i; - final Field license = new Field(); - license.setValue((String) ((LinkedHashMap) p.get("license")).get("value")); - final Instance instance = new Instance(); - instance.setLicense(license); - instance.setAccessright(asQualifier((LinkedHashMap) p.get("accessright"))); - instance.setInstancetype(asQualifier((LinkedHashMap) p.get("instancetype"))); - instance.setHostedby(asKV((LinkedHashMap) p.get("hostedby"))); - //TODO mapping of distributionlocation - instance.setCollectedfrom(asKV((LinkedHashMap) p.get("collectedfrom"))); - - Field dateofacceptance = new Field(); - dateofacceptance.setValue((String) ((LinkedHashMap) p.get("dateofacceptance")).get("value")); - instance.setDateofacceptance(dateofacceptance); - return instance; - }).collect(Collectors.toList())); + re.setDateofacceptance(getValue(result.getDateofacceptance())); + re.setPublisher(getValue(result.getPublisher())); + re.setResulttype(result.getResulttype()); + re.setInstances(result.getInstance()); //TODO still to be mapped //re.setCodeRepositoryUrl(j.read("$.coderepositoryurl")); break; case datasource: - re.setOfficialname(j.read("$.officialname.value")); - re.setWebsiteurl(j.read("$.websiteurl.value")); - re.setDatasourcetype(asQualifier(j.read("$.datasourcetype"))); - re.setOpenairecompatibility(asQualifier(j.read("$.openairecompatibility"))); + Datasource d = (Datasource) entity; + + re.setOfficialname(getValue(d.getOfficialname())); + re.setWebsiteurl(getValue(d.getWebsiteurl())); + re.setDatasourcetype(d.getDatasourcetype()); + re.setOpenairecompatibility(d.getOpenairecompatibility()); break; case organization: - re.setLegalname(j.read("$.legalname.value")); - re.setLegalshortname(j.read("$.legalshortname.value")); - re.setCountry(asQualifier(j.read("$.country"))); - re.setWebsiteurl(j.read("$.websiteurl.value")); + Organization o = (Organization) entity; + + re.setLegalname(getValue(o.getLegalname())); + re.setLegalshortname(getValue(o.getLegalshortname())); + re.setCountry(o.getCountry()); + re.setWebsiteurl(getValue(o.getWebsiteurl())); break; case project: - re.setProjectTitle(j.read("$.title.value")); - re.setCode(j.read("$.code.value")); - re.setAcronym(j.read("$.acronym.value")); - re.setContracttype(asQualifier(j.read("$.contracttype"))); + Project p = (Project) entity; - JSONArray f = j.read("$.fundingtree"); + re.setProjectTitle(getValue(p.getTitle())); + re.setCode(getValue(p.getCode())); + re.setAcronym(getValue(p.getAcronym())); + re.setContracttype(p.getContracttype()); + + List> f = p.getFundingtree(); if (!f.isEmpty()) { re.setFundingtree(f.stream() - .map(s -> ((LinkedHashMap) s).get("value")) + .map(s -> s.getValue()) .collect(Collectors.toList())); } - break; } - return new EntityRelEntity().setSource( - new TypedRow() - .setSourceId(e.getSource().getSourceId()) - .setDeleted(e.getSource().getDeleted()) - .setType(e.getSource().getType()) - .setOaf(serialize(re))); + return re; } - private static KeyValue asKV(LinkedHashMap j) { - final KeyValue kv = new KeyValue(); - kv.setKey((String) j.get("key")); - kv.setValue((String) j.get("value")); - return kv; + private static String getValue(Field field) { + return getFieldValueWithDefault(field, ""); } - private static void mapTitle(DocumentContext j, RelatedEntity re) { - final JSONArray a = j.read("$.title"); - if (!a.isEmpty()) { - final StructuredProperty sp = asStructuredProperty((LinkedHashMap) a.get(0)); - if (StringUtils.isNotBlank(sp.getValue())) { - re.setTitle(sp); - } - } - } - - private static StructuredProperty asStructuredProperty(LinkedHashMap 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) j.get("qualifier"))); - } - return sp; - } - - public static Qualifier asQualifier(LinkedHashMap 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); - } + private static T getFieldValueWithDefault(Field f, T defaultValue) { + return Optional.ofNullable(f) + .filter(Objects::nonNull) + .map(x -> x.getValue()) + .orElse(defaultValue); } public static String removePrefix(final String s) { diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java index 9714830d3..c8e7a2429 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java @@ -1,6 +1,6 @@ package eu.dnetlib.dhp.oa.provision.utils; -import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey; +import eu.dnetlib.dhp.oa.provision.model.SortableRelation; import org.apache.spark.Partitioner; import org.apache.spark.util.Utils; @@ -23,7 +23,7 @@ public class RelationPartitioner extends Partitioner { @Override public int getPartition(Object key) { - return Utils.nonNegativeMod(((SortableRelationKey) key).getSourceId().hashCode(), numPartitions()); + return Utils.nonNegativeMod(((SortableRelation) key).getSource().hashCode(), numPartitions()); } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index ffbe54904..aced9ac0a 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.oa.provision.utils; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.base.Joiner; import com.google.common.base.Splitter; import com.google.common.collect.Lists; @@ -7,13 +8,15 @@ import com.google.common.collect.Maps; import com.google.common.collect.Sets; import com.mycila.xmltool.XMLDoc; import com.mycila.xmltool.XMLTag; -import eu.dnetlib.dhp.oa.provision.model.JoinedEntity; -import eu.dnetlib.dhp.oa.provision.model.RelatedEntity; -import eu.dnetlib.dhp.oa.provision.model.Tuple2; +import eu.dnetlib.dhp.oa.provision.model.*; +import eu.dnetlib.dhp.schema.common.EntityType; +import eu.dnetlib.dhp.schema.common.MainEntityType; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.*; import org.apache.commons.lang3.StringUtils; import org.apache.spark.util.LongAccumulator; +import org.codehaus.janino.Mod; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Element; @@ -50,6 +53,8 @@ public class XmlRecordFactory implements Serializable { private boolean indent = false; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public XmlRecordFactory( final ContextMapper contextMapper, final boolean indent, final String schemaLocation, final String otherDatasourceTypesUForUI) { @@ -74,22 +79,24 @@ public class XmlRecordFactory implements Serializable { final Set contexts = Sets.newHashSet(); - final OafEntity entity = je.getEntity(); + final OafEntity entity = toOafEntity(je.getEntity()); TemplateFactory templateFactory = new TemplateFactory(); try { - final List metadata = metadata(je.getType(), entity, contexts); + final EntityType type = EntityType.valueOf(je.getEntity().getType()); + final List metadata = metadata(type, entity, contexts); // rels has to be processed before the contexts because they enrich the contextMap with the funding info. final List relations = listRelations(je, templateFactory, contexts); - metadata.addAll(buildContexts(getMainType(je.getType()), contexts)); + final String mainType = ModelSupport.getMainType(type); + metadata.addAll(buildContexts(mainType, contexts)); metadata.add(XmlSerializationUtils.parseDataInfo(entity.getDataInfo())); final String body = templateFactory.buildBody( - getMainType(je.getType()), + mainType, metadata, relations, - listChildren(je, templateFactory), listExtraInfo(je)); + listChildren(entity, je.getEntity().getType(), templateFactory), listExtraInfo(entity)); return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent); } catch (final Throwable e) { @@ -97,6 +104,35 @@ public class XmlRecordFactory implements Serializable { } } + private static OafEntity toOafEntity(TypedRow typedRow) { + return parseOaf(typedRow.getOaf(), typedRow.getType()); + } + + private static OafEntity parseOaf(final String json, final String type) { + try { + switch (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 String printXML(String xml, boolean indent) { try { final Document doc = new SAXReader().read(new StringReader(xml)); @@ -112,7 +148,7 @@ public class XmlRecordFactory implements Serializable { } } - private List metadata(final String type, final OafEntity entity, final Set contexts) { + private List metadata(final EntityType type, final OafEntity entity, final Set contexts) { final List metadata = Lists.newArrayList(); @@ -136,7 +172,7 @@ public class XmlRecordFactory implements Serializable { .collect(Collectors.toList())); } - if (GraphMappingUtils.isResult(type)) { + if (ModelSupport.isResult(type)) { final Result r = (Result) entity; if (r.getContext() != null) { @@ -260,11 +296,9 @@ public class XmlRecordFactory implements Serializable { if (r.getResourcetype() != null) { metadata.add(XmlSerializationUtils.mapQualifier("resourcetype", r.getResourcetype())); } - - metadata.add(XmlSerializationUtils.mapQualifier("bestaccessright", getBestAccessright(r))); } - switch (EntityType.valueOf(type)) { + switch (type) { case publication: final Publication pub = (Publication) entity; @@ -662,7 +696,7 @@ public class XmlRecordFactory implements Serializable { if (isNotBlank(re.getCodeRepositoryUrl())) { metadata.add(XmlSerializationUtils.asXmlElement("coderepositoryurl", re.getCodeRepositoryUrl())); } - if (re.getResulttype() != null & !re.getResulttype().isBlank()) { + if (re.getResulttype() != null & re.getResulttype().isBlank()) { metadata.add(XmlSerializationUtils.mapQualifier("resulttype", re.getResulttype())); } if (re.getCollectedfrom() != null) { @@ -726,7 +760,7 @@ public class XmlRecordFactory implements Serializable { } final DataInfo info = rel.getDataInfo(); - final String scheme = getScheme(re.getType(), targetType); + final String scheme = ModelSupport.getScheme(re.getType(), targetType); if (StringUtils.isBlank(scheme)) { throw new IllegalArgumentException(String.format("missing scheme for: <%s - %s>", re.getType(), targetType)); @@ -748,14 +782,14 @@ public class XmlRecordFactory implements Serializable { return rels; } - private List listChildren(final JoinedEntity je, TemplateFactory templateFactory) { + private List listChildren(final OafEntity entity, String type, TemplateFactory templateFactory) { final List children = Lists.newArrayList(); - - if (MainEntityType.result.toString().equals(getMainType(je.getType()))) { - final List instances = ((Result) je.getEntity()).getInstance(); + EntityType entityType = EntityType.valueOf(type); + if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) { + final List instances = ((Result) entity).getInstance(); if (instances != null) { - for (final Instance instance : ((Result) je.getEntity()).getInstance()) { + for (final Instance instance : ((Result) entity).getInstance()) { final List fields = Lists.newArrayList(); @@ -790,9 +824,9 @@ public class XmlRecordFactory implements Serializable { children.add(templateFactory.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl())); } } - final List ext = ((Result) je.getEntity()).getExternalReference(); + final List ext = ((Result) entity).getExternalReference(); if (ext != null) { - for (final ExternalReference er : ((Result) je.getEntity()).getExternalReference()) { + for (final ExternalReference er : ((Result) entity).getExternalReference()) { final List fields = Lists.newArrayList(); @@ -826,8 +860,8 @@ public class XmlRecordFactory implements Serializable { return children; } - private List listExtraInfo(JoinedEntity je) { - final List extraInfo = je.getEntity().getExtraInfo(); + private List listExtraInfo(OafEntity entity) { + final List extraInfo = entity.getExtraInfo(); return extraInfo != null ? extraInfo .stream() .map(e -> XmlSerializationUtils.mapExtraInfo(e)) diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json index a5d20a55f..e57df9b09 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json @@ -1,7 +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":"o", "paramLongName":"outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true}, - {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequence file to read", "paramRequired": true}, - {"paramName":"t", "paramLongName":"otherDsTypeId", "paramDescription": "list of datasource types to populate field datasourcetypeui", "paramRequired": true} + { + "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 + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json new file mode 100644 index 000000000..bfb248d01 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_prepare_relations.json @@ -0,0 +1,26 @@ +[ + { + "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 + }, + { + "paramName": "rp", + "paramLongName": "relPartitions", + "paramDescription": "number or partitions for the relations Dataset", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase1.json new file mode 100644 index 000000000..0090716d6 --- /dev/null +++ b/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 + } +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json new file mode 100644 index 000000000..2727f153b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_related_entities_pahase2.json @@ -0,0 +1,32 @@ +[ + { + "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": "inputGraphRootPath", + "paramDescription": "root graph path", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "root output location for prepared relations", + "paramRequired": true + }, + { + "paramName": "np", + "paramLongName": "numPartitions", + "paramDescription": "number of partitions to use for the output", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json index 0d45e9e29..3396020e0 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json @@ -1,7 +1,26 @@ [ - {"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":"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} + { + "paramName": "is", + "paramLongName": "isLookupUrl", + "paramDescription": "URL of the isLookUp Service", + "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 + } ] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json new file mode 100644 index 000000000..32720514e --- /dev/null +++ b/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 + } +] diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/config-default.xml index 624d3ea76..c070d8338 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/config-default.xml @@ -19,16 +19,24 @@ hive_metastore_uris thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - hive_db_name - openaire - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18088 + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 spark2EventLogDir - /user/spark/applicationHistory + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + + oozieActionShareLibForSpark2 + spark2 \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index a28174cce..e6587ef5e 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -2,21 +2,52 @@ - hive_db_name - the target hive database name + inputGraphRootPath + root location of input materialized graph - sparkDriverMemory + isLookupUrl + URL for the isLookup service + + + + sparkDriverMemoryForJoining memory for driver process - sparkExecutorMemory + sparkExecutorMemoryForJoining memory for individual executor - sparkExecutorCores + sparkExecutorCoresForJoining number of cores used by single executor + + sparkDriverMemoryForIndexing + memory for driver process + + + sparkExecutorMemoryForIndexing + memory for individual executor + + + sparkExecutorCoresForIndexing + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + spark2YarnHistoryServerAddress spark 2.* yarn history server address @@ -32,12 +63,8 @@ ${nameNode} - mapreduce.job.queuename - ${queueName} - - - oozie.launcher.mapred.job.queue.name - ${oozieLauncherQueueName} + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} @@ -46,9 +73,9 @@ - ${wf:conf('reuseRecords') eq false} + ${wf:conf('reuseRecords') eq false} ${wf:conf('reuseRecords') eq true} - + @@ -56,31 +83,306 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - - - - yarn cluster - build_adjacency_lists - eu.dnetlib.dhp.oa.provision.SparkXmlRecordBuilderJob + PrepareRelations + eu.dnetlib.dhp.oa.provision.PrepareRelationsJob dhp-graph-provision-${projectVersion}.jar - --executor-cores ${sparkExecutorCoresForJoining} - --executor-memory ${sparkExecutorMemoryForJoining} + --executor-cores=${sparkExecutorCoresForJoining} + --executor-memory=${sparkExecutorMemoryForJoining} --driver-memory=${sparkDriverMemoryForJoining} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -mt yarn - -is ${isLookupUrl} - -t ${otherDsTypeId} - --sourcePath${sourcePath} - --outputPath${outputPath} + --inputRelationsPath${inputGraphRootPath}/relation + --outputPath${workingDir}/relation + --relPartitions3000 + + + + + + + + + + + + + + + + + + yarn + cluster + Join[relation.target = publication.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --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=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = dataset.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = otherresearchproduct.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --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 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = software.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = datasource.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --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 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/datasource + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = organization.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/organization + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Organization + --outputPath${workingDir}/join_partial + + + + + + + + yarn + cluster + Join[relation.target = project.id] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1 + dhp-graph-provision-${projectVersion}.jar + + --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 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputRelationsPath${workingDir}/relation + --inputEntityPath${inputGraphRootPath}/project + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/join_partial + + + + + + + + + + + yarn + cluster + Join[entities.id = relatedEntity.source] + eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2 + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputGraphRootPath${inputGraphRootPath} + --inputRelatedEntitiesPath${workingDir}/join_partial + --outputPath${workingDir}/join_entities + --numPartitions12000 + + + + + + + + yarn + cluster + build_adjacency_lists + eu.dnetlib.dhp.oa.provision.AdjacencyListBuilderJob + dhp-graph-provision-${projectVersion}.jar + + --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=7680 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath ${workingDir}/join_entities + --outputPath${workingDir}/joined + + + + + + + + yarn + cluster + convert_to_xml + eu.dnetlib.dhp.oa.provision.XmlConverterJob + dhp-graph-provision-${projectVersion}.jar + + --executor-cores=${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.network.timeout=${sparkNetworkTimeout} + + --inputPath${workingDir}/joined + --outputPath${workingDir}/xml + --isLookupUrl${isLookupUrl} + --otherDsTypeId${otherDsTypeId} @@ -91,21 +393,20 @@ yarn cluster to_solr_index - eu.dnetlib.dhp.oa.provision.SparkXmlIndexingJob + eu.dnetlib.dhp.oa.provision.XmlIndexingJob dhp-graph-provision-${projectVersion}.jar - --executor-cores ${sparkExecutorCoresForIndexing} - --executor-memory ${sparkExecutorMemoryForIndexing} + --executor-memory=${sparkExecutorMemoryForIndexing} --driver-memory=${sparkDriverMemoryForIndexing} + --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.maxExecutors=${sparkExecutorCoresForIndexing} - --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener" - --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - -mt yarn - -is ${isLookupUrl} - --sourcePath${outputPath}/xml + --inputPath${workingDir}/xml + --isLookupUrl ${isLookupUrl} --format${format} --batchSize${batchSize} diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 4b5fb4b4f..ce0e28112 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -21,6 +21,7 @@ dhp-graph-provision dhp-dedup-scholexplorer dhp-graph-provision-scholexplorer + dhp-actionmanager @@ -257,7 +258,10 @@ nameNode,jobTracker,queueName,importerQueueName,oozieLauncherQueueName, workingDir,oozieTopWfApplicationPath,oozieServiceLoc, sparkDriverMemory,sparkExecutorMemory,sparkExecutorCores, - oozie.wf.application.path,projectVersion,oozie.use.system.libpath + oozie.wf.application.path,projectVersion,oozie.use.system.libpath, + oozieActionShareLibForSpark1,spark1YarnHistoryServerAddress,spark1EventLogDir, + oozieActionShareLibForSpark2,spark2YarnHistoryServerAddress,spark2EventLogDir + true diff --git a/pom.xml b/pom.xml index ae19ddbe5..1d36d42f9 100644 --- a/pom.xml +++ b/pom.xml @@ -293,6 +293,12 @@ dnet-actionmanager-common 6.0.5 + + eu.dnetlib + dnet-actionmanager-api + [4.0.1,5.0.0) + + eu.dnetlib dnet-openaire-data-protos @@ -346,6 +352,12 @@ mongo-java-driver ${mongodb.driver.version} + + org.postgresql + postgresql + 42.2.10 + + org.antlr stringtemplate