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dnet-hadoop
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merged with master branch

This commit is contained in:
Sandro La Bruzzo 2020-04-17 12:23:54 +02:00
parent 205e9521c6 01ea7721f3
commit a329ea5575
380 changed files with 22489 additions and 3394 deletions
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5
.gitignore vendored
View File

@ -1,9 +1,12 @@
.DS_Store
.idea
*.iws
*.ipr
*.iml
*.ipr
*.iws
*~
.vscode
.classpath
/*/.classpath
/*/*/.classpath
@ -11,7 +14,6 @@
/*/.metadata
/*/*/.metadata
.project
.log
.settings
/*/*/target
/*/target
@ -21,4 +23,5 @@
/build
spark-warehouse
/**/job-override.properties
/**/*.log

2
dhp-build/dhp-build-assembly-resources/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-assembly-resources</artifactId>

4
dhp-build/dhp-build-properties-maven-plugin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-properties-maven-plugin</artifactId>
@ -102,7 +102,7 @@
</goals>
</pluginExecutionFilter>
<action>
<ignore></ignore>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>

13
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java
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@ -1,22 +1,21 @@
package eu.dnetlib.maven.plugin.properties;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_WF_SOURCE_DIR;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNull;
import org.junit.Before;
import org.junit.Test;
import static org.junit.jupiter.api.Assertions.*;
/**
* @author mhorst
* @author mhorst, claudio.atzori
*
*/
public class GenerateOoziePropertiesMojoTest {
private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
@Before
@BeforeEach
public void clearSystemProperties() {
System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);

128
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
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@ -1,51 +1,41 @@
package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.doReturn;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Properties;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject;
import org.junit.Before;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TemporaryFolder;
import org.junit.runner.RunWith;
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.runners.MockitoJUnitRunner;
import org.mockito.MockitoAnnotations;
import org.mockito.junit.jupiter.MockitoExtension;
import java.io.*;
import java.util.Properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.lenient;
/**
* @author mhorst
* @author mhorst, claudio.atzori
*
*/
@RunWith(MockitoJUnitRunner.class)
@ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest {
@Rule
public TemporaryFolder testFolder = new TemporaryFolder();
@Mock
private MavenProject mavenProject;
private WritePredefinedProjectProperties mojo;
@Before
public void init() {
@BeforeEach
public void init(@TempDir File testFolder) {
MockitoAnnotations.initMocks(this);
mojo = new WritePredefinedProjectProperties();
mojo.outputFile = getPropertiesFileLocation();
mojo.outputFile = getPropertiesFileLocation(testFolder);
mojo.project = mavenProject;
doReturn(new Properties()).when(mavenProject).getProperties();
lenient().doReturn(new Properties()).when(mavenProject).getProperties();
}
// ----------------------------------- TESTS ---------------------------------------------
@ -57,7 +47,7 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(0, storedProperties.size());
}
@ -75,28 +65,28 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(mojo.outputFile.getParentFile());
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test(expected=MojoExecutionException.class)
public void testExecuteWithProjectPropertiesAndInvalidOutputFile() throws Exception {
@Test()
public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
Properties projectProperties = new Properties();
projectProperties.setProperty(key, value);
doReturn(projectProperties).when(mavenProject).getProperties();
mojo.outputFile = testFolder.getRoot();
mojo.outputFile = testFolder;
// execute
mojo.execute();
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithProjectPropertiesExclusion() throws Exception {
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -113,14 +103,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithProjectPropertiesInclusion() throws Exception {
public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -137,14 +127,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromFile() throws Exception {
public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -155,7 +145,7 @@ public class WritePredefinedProjectPropertiesTest {
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder.getRoot(), "included.properties");
File includedPropertiesFile = new File(testFolder, "included.properties");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileWriter(includedPropertiesFile), null);
@ -167,14 +157,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test
public void testExecuteIncludingPropertyKeysFromClasspathResource() throws Exception {
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -192,14 +182,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test(expected=MojoExecutionException.class)
public void testExecuteIncludingPropertyKeysFromBlankLocation() throws Exception {
@Test
public void testExecuteIncludingPropertyKeysFromBlankLocation() {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -213,11 +203,11 @@ public class WritePredefinedProjectPropertiesTest {
mojo.setIncludePropertyKeysFromFiles(new String[] {""});
// execute
mojo.execute();
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteIncludingPropertyKeysFromXmlFile() throws Exception {
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -228,7 +218,7 @@ public class WritePredefinedProjectPropertiesTest {
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder.getRoot(), "included.xml");
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null);
@ -240,14 +230,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(1, storedProperties.size());
assertTrue(storedProperties.containsKey(includedKey));
assertEquals(includedValue, storedProperties.getProperty(includedKey));
}
@Test(expected=MojoExecutionException.class)
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile() throws Exception {
@Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -258,7 +248,7 @@ public class WritePredefinedProjectPropertiesTest {
projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties();
File includedPropertiesFile = new File(testFolder.getRoot(), "included.xml");
File includedPropertiesFile = new File(testFolder, "included.xml");
Properties includedProperties = new Properties();
includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileOutputStream(includedPropertiesFile), null);
@ -266,11 +256,11 @@ public class WritePredefinedProjectPropertiesTest {
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()});
// execute
mojo.execute();
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithQuietModeOn() throws Exception {
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
// given
mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
@ -280,21 +270,21 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertEquals(0, storedProperties.size());
}
@Test(expected=MojoExecutionException.class)
public void testExecuteIncludingPropertyKeysFromInvalidFile() throws Exception {
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"});
// execute
mojo.execute();
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
}
@Test
public void testExecuteWithEnvironmentProperties() throws Exception {
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
@ -303,7 +293,7 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
for (Object currentKey : storedProperties.keySet()) {
assertTrue(((String)currentKey).startsWith(PROPERTY_PREFIX_ENV));
@ -311,7 +301,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithSystemProperties() throws Exception {
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
@ -323,14 +313,14 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertTrue(storedProperties.containsKey(key));
assertEquals(value, storedProperties.getProperty(key));
}
@Test
public void testExecuteWithSystemPropertiesAndEscapeChars() throws Exception {
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey ";
String value = "systemPropertyValue";
@ -344,7 +334,7 @@ public class WritePredefinedProjectPropertiesTest {
// assert
assertTrue(mojo.outputFile.exists());
Properties storedProperties = getStoredProperties();
Properties storedProperties = getStoredProperties(testFolder);
assertTrue(storedProperties.size() > 0);
assertFalse(storedProperties.containsKey(key));
assertTrue(storedProperties.containsKey(key.trim()));
@ -353,13 +343,13 @@ public class WritePredefinedProjectPropertiesTest {
// ----------------------------------- PRIVATE -------------------------------------------
private File getPropertiesFileLocation() {
return new File(testFolder.getRoot(), "test.properties");
private File getPropertiesFileLocation(File testFolder) {
return new File(testFolder, "test.properties");
}
private Properties getStoredProperties() throws FileNotFoundException, IOException {
private Properties getStoredProperties(File testFolder) throws FileNotFoundException, IOException {
Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation()));
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties;
}
}

2
dhp-build/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
</parent>
<artifactId>dhp-build</artifactId>
<packaging>pom</packaging>

25
dhp-common/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
@ -13,6 +13,20 @@
<packaging>jar</packaging>
<dependencies>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-common</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
@ -58,6 +72,15 @@
<groupId>eu.dnetlib</groupId>
<artifactId>cnr-rmi-api</artifactId>
</dependency>
<dependency>
<groupId>com.ximpleware</groupId>
<artifactId>vtd-xml</artifactId>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
</dependencies>
</project>

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

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

71
dhp-common/src/main/java/eu/dnetlib/dhp/common/SparkSessionSupport.java Normal file
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@ -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<SparkSession, Exception> 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<SparkSession, Exception> 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<SparkConf, SparkSession> sparkSessionBuilder,
SparkConf conf,
Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) {
SparkSession spark = null;
try {
spark = sparkSessionBuilder.apply(conf);
fn.accept(spark);
} catch (Exception e) {
throw new RuntimeException(e);
} finally {
if (Objects.nonNull(spark) && isSparkSessionManaged) {
spark.stop();
}
}
}
}

76
dhp-common/src/main/java/eu/dnetlib/dhp/common/ThrowingSupport.java Normal file
View File

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

12
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdException.java Normal file
View File

@ -0,0 +1,12 @@
package eu.dnetlib.dhp.parser.utility;
public class VtdException extends Exception {
public VtdException(final Exception e) {
super(e);
}
public VtdException(final Throwable e) {
super(e);
}
}

107
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java Normal file
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@ -0,0 +1,107 @@
package eu.dnetlib.dhp.parser.utility;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav;
/**
* Created by sandro on 9/29/16.
*/
public class VtdUtilityParser {
public static List<Node> getTextValuesWithAttributes(final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException {
final List<Node> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
final Node currentNode = new Node();
int t = vn.getText();
if (t >= 0) {
currentNode.setTextValue(vn.toNormalizedString(t));
}
currentNode.setAttributes(getAttributes(vn, attributes));
results.add(currentNode);
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
private static Map<String, String> getAttributes(final VTDNav vn, final List<String> attributes) {
final Map<String, String> currentAttributes = new HashMap<>();
if (attributes != null) {
attributes.forEach(attributeKey -> {
try {
int attr = vn.getAttrVal(attributeKey);
if (attr > -1) {
currentAttributes.put(attributeKey, vn.toNormalizedString(attr));
}
} catch (Throwable e) {
throw new RuntimeException(e);
}
});
}
return currentAttributes;
}
public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath) throws VtdException {
List<String> results = new ArrayList<>();
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t > -1) results.add(vn.toNormalizedString(t));
}
return results;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath) throws VtdException {
try {
ap.selectXPath(xpath);
while (ap.evalXPath() != -1) {
int it = nav.getText();
if (it > -1)
return nav.toNormalizedString(it);
}
return null;
} catch (Exception e) {
throw new VtdException(e);
}
}
public static class Node {
private String textValue;
private Map<String, String> attributes;
public String getTextValue() {
return textValue;
}
public void setTextValue(final String textValue) {
this.textValue = textValue;
}
public Map<String, String> getAttributes() {
return attributes;
}
public void setAttributes(final Map<String, String> attributes) {
this.attributes = attributes;
}
}
}

15
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -1,5 +1,7 @@
package eu.dnetlib.dhp.utils;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
@ -56,4 +58,17 @@ public class DHPUtils {
}
public static String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);
if (o instanceof String)
return (String) o;
if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
return (String) ((JSONArray) o).get(0);
return o.toString();
} catch (Exception e) {
return "";
}
}
}

24
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java Normal file
View File

@ -0,0 +1,24 @@
package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable;
public class RelInfo implements Serializable {
private String original;
private String inverse;
public String getOriginal() {
return original;
}
public void setOriginal(String original) {
this.original = original;
}
public String getInverse() {
return inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
}

19
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.scholexplorer.relation;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.apache.commons.io.IOUtils;
import java.io.Serializable;
import java.util.HashMap;
public class RelationMapper extends HashMap<String,RelInfo > implements Serializable {
public static RelationMapper load() throws Exception {
final String json = IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class);
}
}

158
dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json Normal file
View File

@ -0,0 +1,158 @@
{
"cites":{
"original":"Cites",
"inverse":"IsCitedBy"
},
"compiles":{
"original":"Compiles",
"inverse":"IsCompiledBy"
},
"continues":{
"original":"Continues",
"inverse":"IsContinuedBy"
},
"derives":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"describes":{
"original":"Describes",
"inverse":"IsDescribedBy"
},
"documents":{
"original":"Documents",
"inverse":"IsDocumentedBy"
},
"hasmetadata":{
"original":"HasMetadata",
"inverse":"IsMetadataOf"
},
"hasassociationwith":{
"original":"HasAssociationWith",
"inverse":"HasAssociationWith"
},
"haspart":{
"original":"HasPart",
"inverse":"IsPartOf"
},
"hasversion":{
"original":"HasVersion",
"inverse":"IsVersionOf"
},
"iscitedby":{
"original":"IsCitedBy",
"inverse":"Cites"
},
"iscompiledby":{
"original":"IsCompiledBy",
"inverse":"Compiles"
},
"iscontinuedby":{
"original":"IsContinuedBy",
"inverse":"Continues"
},
"isderivedfrom":{
"original":"IsDerivedFrom",
"inverse":"IsSourceOf"
},
"isdescribedby":{
"original":"IsDescribedBy",
"inverse":"Describes"
},
"isdocumentedby":{
"original":"IsDocumentedBy",
"inverse":"Documents"
},
"isidenticalto":{
"original":"IsIdenticalTo",
"inverse":"IsIdenticalTo"
},
"ismetadatafor":{
"original":"IsMetadataFor",
"inverse":"IsMetadataOf"
},
"ismetadataof":{
"original":"IsMetadataOf",
"inverse":"IsMetadataFor"
},
"isnewversionof":{
"original":"IsNewVersionOf",
"inverse":"IsPreviousVersionOf"
},
"isobsoletedby":{
"original":"IsObsoletedBy",
"inverse":"Obsoletes"
},
"isoriginalformof":{
"original":"IsOriginalFormOf",
"inverse":"IsVariantFormOf"
},
"ispartof":{
"original":"IsPartOf",
"inverse":"HasPart"
},
"ispreviousversionof":{
"original":"IsPreviousVersionOf",
"inverse":"IsNewVersionOf"
},
"isreferencedby":{
"original":"IsReferencedBy",
"inverse":"References"
},
"isrelatedto":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"isrequiredby":{
"original":"IsRequiredBy",
"inverse":"Requires"
},
"isreviewedby":{
"original":"IsReviewedBy",
"inverse":"Reviews"
},
"issourceof":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"issupplementedby":{
"original":"IsSupplementedBy",
"inverse":"IsSupplementTo"
},
"issupplementto":{
"original":"IsSupplementTo",
"inverse":"IsSupplementedBy"
},
"isvariantformof":{
"original":"IsVariantFormOf",
"inverse":"IsOriginalFormOf"
},
"isversionof":{
"original":"IsVersionOf",
"inverse":"HasVersion"
},
"obsoletes":{
"original":"Obsoletes",
"inverse":"IsObsoletedBy"
},
"references":{
"original":"References",
"inverse":"IsReferencedBy"
},
"requires":{
"original":"Requires",
"inverse":"IsRequiredBy"
},
"related":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"reviews":{
"original":"Reviews",
"inverse":"IsReviewedBy"
},
"unknown":{
"original":"Unknown",
"inverse":"Unknown"
}
}

11
dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java
View File

@ -1,18 +1,13 @@
package eu.dnetlib.dhp.application;
import org.apache.commons.io.IOUtils;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import java.io.ByteArrayOutputStream;
import java.util.Base64;
import java.util.zip.GZIPOutputStream;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
public class ArgumentApplicationParserTest {
@Test
public void testParseParameter() throws Exception {
final String jsonConfiguration = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));

78
dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java Normal file
View File

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

54
dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java Normal file
View File

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

6
dhp-common/src/test/java/eu/dnetlib/dhp/model/mdstore/MetadataRecordTest.java
View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.model.mdstore;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import static org.junit.Assert.assertTrue;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class MetadataRecordTest {
@ -10,6 +10,6 @@ public class MetadataRecordTest {
public void getTimestamp() {
MetadataRecord r = new MetadataRecord();
assertTrue(r.getDateOfCollection() >0);
assertTrue(r.getDateOfCollection() > 0);
}
}

4
dhp-common/src/test/java/eu/dnetlib/message/MessageTest.java
View File

@ -1,12 +1,12 @@
package eu.dnetlib.message;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import static org.junit.Assert.*;
import static org.junit.jupiter.api.Assertions.*;
public class MessageTest {

15
dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java Normal file
View File

@ -0,0 +1,15 @@
package eu.dnetlib.scholexplorer.relation;
import org.junit.jupiter.api.Test;
public class RelationMapperTest {
@Test
public void testLoadRels() throws Exception{
RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println);
}
}

158
dhp-common/src/test/resources/eu/dnetlib/scholexplorer/relation/relations.json Normal file
View File

@ -0,0 +1,158 @@
{
"cites":{
"original":"Cites",
"inverse":"IsCitedBy"
},
"compiles":{
"original":"Compiles",
"inverse":"IsCompiledBy"
},
"continues":{
"original":"Continues",
"inverse":"IsContinuedBy"
},
"derives":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"describes":{
"original":"Describes",
"inverse":"IsDescribedBy"
},
"documents":{
"original":"Documents",
"inverse":"IsDocumentedBy"
},
"hasmetadata":{
"original":"HasMetadata",
"inverse":"IsMetadataOf"
},
"hasassociationwith":{
"original":"HasAssociationWith",
"inverse":"HasAssociationWith"
},
"haspart":{
"original":"HasPart",
"inverse":"IsPartOf"
},
"hasversion":{
"original":"HasVersion",
"inverse":"IsVersionOf"
},
"iscitedby":{
"original":"IsCitedBy",
"inverse":"Cites"
},
"iscompiledby":{
"original":"IsCompiledBy",
"inverse":"Compiles"
},
"iscontinuedby":{
"original":"IsContinuedBy",
"inverse":"Continues"
},
"isderivedfrom":{
"original":"IsDerivedFrom",
"inverse":"IsSourceOf"
},
"isdescribedby":{
"original":"IsDescribedBy",
"inverse":"Describes"
},
"isdocumentedby":{
"original":"IsDocumentedBy",
"inverse":"Documents"
},
"isidenticalto":{
"original":"IsIdenticalTo",
"inverse":"IsIdenticalTo"
},
"ismetadatafor":{
"original":"IsMetadataFor",
"inverse":"IsMetadataOf"
},
"ismetadataof":{
"original":"IsMetadataOf",
"inverse":"IsMetadataFor"
},
"isnewversionof":{
"original":"IsNewVersionOf",
"inverse":"IsPreviousVersionOf"
},
"isobsoletedby":{
"original":"IsObsoletedBy",
"inverse":"Obsoletes"
},
"isoriginalformof":{
"original":"IsOriginalFormOf",
"inverse":"IsVariantFormOf"
},
"ispartof":{
"original":"IsPartOf",
"inverse":"HasPart"
},
"ispreviousversionof":{
"original":"IsPreviousVersionOf",
"inverse":"IsNewVersionOf"
},
"isreferencedby":{
"original":"IsReferencedBy",
"inverse":"References"
},
"isrelatedto":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"isrequiredby":{
"original":"IsRequiredBy",
"inverse":"Requires"
},
"isreviewedby":{
"original":"IsReviewedBy",
"inverse":"Reviews"
},
"issourceof":{
"original":"IsSourceOf",
"inverse":"IsDerivedFrom"
},
"issupplementedby":{
"original":"IsSupplementedBy",
"inverse":"IsSupplementTo"
},
"issupplementto":{
"original":"IsSupplementTo",
"inverse":"IsSupplementedBy"
},
"isvariantformof":{
"original":"IsVariantFormOf",
"inverse":"IsOriginalFormOf"
},
"isversionof":{
"original":"IsVersionOf",
"inverse":"HasVersion"
},
"obsoletes":{
"original":"Obsoletes",
"inverse":"IsObsoletedBy"
},
"references":{
"original":"References",
"inverse":"IsReferencedBy"
},
"requires":{
"original":"Requires",
"inverse":"IsRequiredBy"
},
"related":{
"original":"IsRelatedTo",
"inverse":"IsRelatedTo"
},
"reviews":{
"original":"Reviews",
"inverse":"IsReviewedBy"
},
"unknown":{
"original":"Unknown",
"inverse":"Unknown"
}
}

15
dhp-schemas/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.1.6-SNAPSHOT</version>
<version>1.1.7-SNAPSHOT</version>
<relativePath>../</relativePath>
</parent>
@ -36,19 +36,6 @@
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
</dependency>
</dependencies>

23
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/EntityType.java Normal file
View File

@ -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 <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends OafEntity> EntityType fromClass(Class<T> clazz) {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
}
}

9
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/MainEntityType.java Normal file
View File

@ -0,0 +1,9 @@
package eu.dnetlib.dhp.schema.common;
/**
* Main entity types in the Graph
*/
public enum MainEntityType {
result, datasource, organization, project
}

151
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java Normal file
View File

@ -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<EntityType, MainEntityType> 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<EntityType, Class> entityTypes = Maps.newHashMap();
static {
entityTypes.put(EntityType.datasource, Datasource.class);
entityTypes.put(EntityType.organization, Organization.class);
entityTypes.put(EntityType.project, Project.class);
entityTypes.put(EntityType.dataset, Dataset.class);
entityTypes.put(EntityType.otherresearchproduct, OtherResearchProduct.class);
entityTypes.put(EntityType.software, Software.class);
entityTypes.put(EntityType.publication, Publication.class);
}
public final static Map<String, Class> 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 <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Y superClazzObject) {
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazzObject Subclass object instance
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Class<Y> superClazz) {
return isSubClass(subClazzObject.getClass(), superClazz);
}
/**
* Checks subclass-superclass relationship.
*
* @param subClazz Subclass class
* @param superClazz Superclass class
* @param <X> Subclass type
* @param <Y> Superclass type
* @return True if X is a subclass of Y
*/
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(Class<X> subClazz, Class<Y> superClazz) {
return superClazz.isAssignableFrom(subClazz);
}
/**
* Lists all the OAF model classes
*
* @param <T>
* @return
*/
public static <T extends Oaf> Class<T>[] 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());
}
}

19
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Author.java
View File

@ -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<Field<String>> 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);
}
}

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Country.java
View File

@ -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);
}
}

19
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/DataInfo.java
View File

@ -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);
}
}

26
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Dataset.java
View File

@ -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);
}
}

53
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Datasource.java
View File

@ -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);
}
}

21
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExternalReference.java
View File

@ -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);
}
}

18
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/ExtraInfo.java
View File

@ -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);
}
}

25
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Journal.java
View File

@ -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);
}
}

14
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAIProvenance.java
View File

@ -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);
}
}

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Oaf.java
View File

@ -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);
}
}

19
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java
View File

@ -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);
}
}

35
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Organization.java
View File

@ -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);
}
}

19
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OriginDescription.java
View File

@ -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);
}
}

21
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OtherResearchProduct.java
View File

@ -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);
}
}

45
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Project.java
View File

@ -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);
}
}

17
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Publication.java
View File

@ -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);
}
}

12
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Relation.java
View File

@ -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;
@ -78,7 +76,10 @@ 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())
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()));
}
@ -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

38
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -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);
}
}

23
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Software.java
View File

@ -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);
}
}

80
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIDataset.java Normal file
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@ -0,0 +1,80 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import org.apache.commons.lang3.StringUtils;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class DLIDataset extends Dataset {
private String originalObjIdentifier;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus;
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIDataset p = (DLIDataset) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
}

77
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIPublication.java Normal file
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@ -0,0 +1,77 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
import java.util.*;
public class DLIPublication extends Publication implements Serializable {
private String originalObjIdentifier;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus;
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getOriginalObjIdentifier() {
return originalObjIdentifier;
}
public void setOriginalObjIdentifier(String originalObjIdentifier) {
this.originalObjIdentifier = originalObjIdentifier;
}
@Override
public void mergeFrom(OafEntity e) {
super.mergeFrom(e);
DLIPublication p = (DLIPublication) e;
if (StringUtils.isBlank(completionStatus) && StringUtils.isNotBlank(p.completionStatus))
completionStatus = p.completionStatus;
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
}

15
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java Normal file
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@ -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;
}
}

108
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java Normal file
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@ -0,0 +1,108 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class DLIUnknown extends Oaf implements Serializable {
private String id;
private List<StructuredProperty> pid;
private String dateofcollection;
private String dateoftransformation;
private List<ProvenaceInfo> dlicollectedfrom;
private String completionStatus = "incomplete";
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public List<ProvenaceInfo> getDlicollectedfrom() {
return dlicollectedfrom;
}
public void setDlicollectedfrom(List<ProvenaceInfo> dlicollectedfrom) {
this.dlicollectedfrom = dlicollectedfrom;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<StructuredProperty> getPid() {
return pid;
}
public void setPid(List<StructuredProperty> pid) {
this.pid = pid;
}
public String getDateofcollection() {
return dateofcollection;
}
public void setDateofcollection(String dateofcollection) {
this.dateofcollection = dateofcollection;
}
public String getDateoftransformation() {
return dateoftransformation;
}
public void setDateoftransformation(String dateoftransformation) {
this.dateoftransformation = dateoftransformation;
}
public void mergeFrom(DLIUnknown p) {
if ("complete".equalsIgnoreCase(p.completionStatus))
completionStatus = "complete";
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
}
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null)
a.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
if (b != null)
b.forEach(p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p);
}
} else if (p != null && p.getId() != null && !result.containsKey(p.getId()))
result.put(p.getId(), p);
});
return new ArrayList<>(result.values());
}
}

46
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/ProvenaceInfo.java Normal file
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@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.Serializable;
public class ProvenaceInfo implements Serializable {
private String id;
private String name;
private String completionStatus;
private String collectionMode ="collected";
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getCompletionStatus() {
return completionStatus;
}
public void setCompletionStatus(String completionStatus) {
this.completionStatus = completionStatus;
}
public String getCollectionMode() {
return collectionMode;
}
public void setCollectionMode(String collectionMode) {
this.collectionMode = collectionMode;
}
}

15
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/action/AtomicActionTest.java
View File

@ -3,11 +3,16 @@ package eu.dnetlib.dhp.schema.action;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.lang3.StringUtils;
import org.junit.Assert;
import org.junit.Test;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.*;
/**
* @author claudio.atzori
*/
public class AtomicActionTest {
@Test
@ -25,12 +30,12 @@ public class AtomicActionTest {
final ObjectMapper mapper = new ObjectMapper();
String json = mapper.writeValueAsString(aa1);
Assert.assertTrue(StringUtils.isNotBlank(json));
assertTrue(StringUtils.isNotBlank(json));
AtomicAction aa2 = mapper.readValue(json, AtomicAction.class);
Assert.assertEquals(aa1.getClazz(), aa2.getClazz());
Assert.assertEquals(aa1.getPayload(), aa2.getPayload());
assertEquals(aa1.getClazz(), aa2.getClazz());
assertEquals(aa1.getPayload(), aa2.getPayload());
}

35
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/common/ModelSupportTest.java Normal file
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@ -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);
}
}
}

18
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java
View File

@ -1,11 +1,9 @@
package eu.dnetlib.dhp.schema.oaf;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@ -13,7 +11,7 @@ public class MergeTest {
OafEntity oaf;
@Before
@BeforeEach
public void setUp() {
oaf = new Publication();
}
@ -44,8 +42,8 @@ public class MergeTest {
a.mergeFrom(b);
Assert.assertNotNull(a.getCollectedfrom());
Assert.assertEquals(3, a.getCollectedfrom().size());
assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size());
}
@ -60,8 +58,8 @@ public class MergeTest {
a.mergeFrom(b);
Assert.assertNotNull(a.getSubject());
Assert.assertEquals(3, a.getSubject().size());
assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size());
}

81
dhp-schemas/src/test/java/eu/dnetlib/dhp/schema/scholexplorer/DLItest.java Normal file
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@ -0,0 +1,81 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
public class DLItest {
@Test
public void testMergePublication() throws JsonProcessingException {
DLIPublication a1 = new DLIPublication();
a1.setPid(Arrays.asList( createSP("123456","pdb","dnet:pid_types")));
a1.setTitle(Collections.singletonList(createSP("Un Titolo", "title", "dnetTitle")));
a1.setDlicollectedfrom(Arrays.asList(createCollectedFrom("znd","Zenodo","complete")));
a1.setCompletionStatus("complete");
DLIPublication a = new DLIPublication();
a.setPid(Arrays.asList(createSP("10.11","doi","dnet:pid_types"), createSP("123456","pdb","dnet:pid_types")));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a.setDlicollectedfrom(Arrays.asList(createCollectedFrom("dct","datacite","complete"),createCollectedFrom("dct","datacite","incomplete")));
a.setCompletionStatus("incomplete");
a.mergeFrom(a1);
ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(a));
}
@Test
public void testDeserialization() throws IOException {
final String json ="{\"dataInfo\":{\"invisible\":false,\"inferred\":null,\"deletedbyinference\":false,\"trust\":\"0.9\",\"inferenceprovenance\":null,\"provenanceaction\":null},\"lastupdatetimestamp\":null,\"id\":\"60|bd9352547098929a394655ad1a44a479\",\"originalId\":[\"bd9352547098929a394655ad1a44a479\"],\"collectedfrom\":[{\"key\":\"dli_________::datacite\",\"value\":\"Datasets in Datacite\",\"dataInfo\":null,\"blank\":false}],\"pid\":[{\"value\":\"10.7925/DRS1.DUCHAS_5078760\",\"qualifier\":{\"classid\":\"doi\",\"classname\":\"doi\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\",\"blank\":false},\"dataInfo\":null}],\"dateofcollection\":\"2020-01-09T08:29:31.885Z\",\"dateoftransformation\":null,\"extraInfo\":null,\"oaiprovenance\":null,\"author\":[{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Ireland. Department of Arts, Culture, and the Gaeltacht\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"University College Dublin\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"National Folklore Foundation\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Cathail, S. Ó\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null},{\"fullname\":\"Donnell, Breda Mc\",\"name\":null,\"surname\":null,\"rank\":null,\"pid\":null,\"affiliation\":null}],\"resulttype\":null,\"language\":null,\"country\":null,\"subject\":[{\"value\":\"Recreation\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Entertainments and recreational activities\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null},{\"value\":\"Siamsaíocht agus caitheamh aimsire\",\"qualifier\":{\"classid\":\"dnet:subject\",\"classname\":\"dnet:subject\",\"schemeid\":\"unknown\",\"schemename\":\"unknown\",\"blank\":false},\"dataInfo\":null}],\"title\":[{\"value\":\"Games We Play\",\"qualifier\":null,\"dataInfo\":null}],\"relevantdate\":[{\"value\":\"1938-09-28\",\"qualifier\":{\"classid\":\"date\",\"classname\":\"date\",\"schemeid\":\"dnet::date\",\"schemename\":\"dnet::date\",\"blank\":false},\"dataInfo\":null}],\"description\":[{\"value\":\"Story collected by Breda Mc Donnell, a student at Tenure school (Tinure, Co. Louth) (no informant identified).\",\"dataInfo\":null}],\"dateofacceptance\":null,\"publisher\":{\"value\":\"University College Dublin\",\"dataInfo\":null},\"embargoenddate\":null,\"source\":null,\"fulltext\":null,\"format\":null,\"contributor\":null,\"resourcetype\":null,\"coverage\":null,\"refereed\":null,\"context\":null,\"processingchargeamount\":null,\"processingchargecurrency\":null,\"externalReference\":null,\"instance\":[],\"storagedate\":null,\"device\":null,\"size\":null,\"version\":null,\"lastmetadataupdate\":null,\"metadataversionnumber\":null,\"geolocation\":null,\"dlicollectedfrom\":[{\"id\":\"dli_________::datacite\",\"name\":\"Datasets in Datacite\",\"completionStatus\":\"complete\",\"collectionMode\":\"resolved\"}],\"completionStatus\":\"complete\"}";
ObjectMapper mapper = new ObjectMapper();
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
DLIDataset dliDataset = mapper.readValue(json, DLIDataset.class);
mapper.enable(SerializationFeature.INDENT_OUTPUT);
System.out.println(mapper.writeValueAsString(dliDataset));
}
private ProvenaceInfo createCollectedFrom(final String id, final String name, final String completionStatus) {
ProvenaceInfo p = new ProvenaceInfo();
p.setId(id);
p.setName(name);
p.setCompletionStatus(completionStatus);
return p;
}
private StructuredProperty createSP(final String value, final String className, final String schemeName) {
StructuredProperty p = new StructuredProperty();
p.setValue(value);
Qualifier schema = new Qualifier();
schema.setClassname(className);
schema.setClassid(className);
schema.setSchemename(schemeName);
schema.setSchemeid(schemeName);
p.setQualifier(schema);
return p;
}
}

62
dhp-workflows/dhp-actionmanager/pom.xml Normal file
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@ -0,0 +1,62 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
<version>1.1.7-SNAPSHOT</version>
</parent>
<artifactId>dhp-actionmanager</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-common</artifactId>
<version>${project.version}</version>
<exclusions>
<exclusion>
<groupId>net.sf.saxon</groupId>
<artifactId>Saxon-HE</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>dom4j</groupId>
<artifactId>dom4j</artifactId>
</dependency>
<dependency>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
</dependency>
<dependency>
<groupId>jaxen</groupId>
<artifactId>jaxen</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-api</artifactId>
</dependency>
</dependencies>
</project>

126
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java Normal file
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@ -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<String> getLatestRawsetPaths(String setIds) {
List<String> 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<String> 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);
}
}
}

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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<String> 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<String> inputActionSetPaths,
String outputPath) {
inputActionSetPaths
.forEach(inputActionSetPath -> {
Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
saveActions(actionDS, outputPath);
});
}
private static Dataset<Row> readActionSetFromPath(SparkSession spark,
String path) {
logger.info("Reading actions from path: {}", path);
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Row> 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<Row> 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;
}
}

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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.
* <p>
* 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 <G> Graph table type
* @param <A> Action payload type
* @return BiFunction to be used to merge OAF objects
*/
public static <G extends Oaf, A extends Oaf> SerializableSupplier<BiFunction<G, A, G>> 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 extends Oaf, A extends Oaf> 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 extends Oaf, A extends Oaf> 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()));
}
}

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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<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) 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<? extends Oaf> rowClazz,
Class<? extends Oaf> 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 <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(SparkSession spark,
String inputGraphTablePath,
String inputActionPayloadPath,
String outputGraphTablePath,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
Dataset<G> result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
saveGraphTable(result, outputGraphTablePath);
}
private static <G extends Oaf> Dataset<G> readGraphTable(SparkSession spark,
String path,
Class<G> rowClazz) {
logger.info("Reading graph table from path: {}", path);
return spark.read()
.textFile(path)
.map((MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz), Encoders.bean(rowClazz));
/*
return spark
.read()
.parquet(path)
.as(Encoders.bean(rowClazz));
*/
}
private static <A extends Oaf> Dataset<A> readActionPayload(SparkSession spark,
String path,
Class<A> actionPayloadClazz) {
logger.info("Reading action payload from path: {}", path);
return spark
.read()
.parquet(path)
.map((MapFunction<Row, A>) value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"),
actionPayloadClazz), Encoders.bean(actionPayloadClazz));
}
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
MergeAndGet.Strategy strategy,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName());
SerializableSupplier<Function<G, String>> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn;
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
SerializableSupplier<Function<G, Boolean>> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSource;
Dataset<G> joinedAndMerged = PromoteActionPayloadFunctions
.joinGraphTableWithActionPayloadAndMerge(
rowDS,
actionPayloadDS,
rowIdFn,
actionPayloadIdFn,
mergeRowWithActionPayloadAndGetFn,
rowClazz,
actionPayloadClazz);
return PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge(
joinedAndMerged,
rowIdFn,
mergeRowsAndGetFn,
zeroFn,
isNotZeroFn,
rowClazz);
}
private static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> 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 <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> 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 <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSource() {
return t -> {
if (isSubClass(t, Relation.class)) {
return Objects.nonNull(((Relation) t).getSource());
}
return Objects.nonNull(((OafEntity) t).getId());
};
}
private static <G extends Oaf> void saveGraphTable(Dataset<G> result,
String path) {
logger.info("Saving graph table to path: {}", path);
result
.toJSON()
.write()
.option("compression", "gzip")
.text(path);
}
}

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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 <G> Type of graph table row
* @param <A> Type of action payload instance
* @return Dataset of merged graph table rows and action payload instances
*/
public static <G extends Oaf, A extends Oaf> Dataset<G> joinGraphTableWithActionPayloadAndMerge(Dataset<G> rowDS,
Dataset<A> actionPayloadDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<Function<A, String>> actionPayloadIdFn,
SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
Class<G> rowClazz,
Class<A> 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<Tuple2<String, G>> rowWithIdDS = mapToTupleWithId(rowDS, rowIdFn, rowClazz);
Dataset<Tuple2<String, A>> actionPayloadWithIdDS = mapToTupleWithId(actionPayloadDS, actionPayloadIdFn, actionPayloadClazz);
return rowWithIdDS
.joinWith(actionPayloadWithIdDS, rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")), "full_outer")
.map((MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>) value -> {
Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);
Optional<A> 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<G>) Objects::nonNull);
}
private static <T extends Oaf> Dataset<Tuple2<String, T>> mapToTupleWithId(Dataset<T> ds,
SerializableSupplier<Function<T, String>> idFn,
Class<T> clazz) {
return ds
.map((MapFunction<T, Tuple2<String, T>>) 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 <G> Type of graph table row
* @return Dataset of aggregated graph table rows
*/
public static <G extends Oaf> Dataset<G> groupGraphTableByIdAndMerge(Dataset<G> rowDS,
SerializableSupplier<Function<G, String>> rowIdFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<G> zeroFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> rowClazz) {
TypedColumn<G, G> aggregator = new TableAggregator<>(zeroFn, mergeAndGetFn, isNotZeroFn, rowClazz).toColumn();
return rowDS
.groupByKey((MapFunction<G, String>) x -> rowIdFn.get().apply(x), Encoders.STRING())
.agg(aggregator)
.map((MapFunction<Tuple2<String, G>, G>) Tuple2::_2, Encoders.kryo(rowClazz));
}
/**
* Aggregator to be used for aggregating graph table rows during grouping.
*
* @param <G> Type of graph table row
*/
public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
private SerializableSupplier<G> zeroFn;
private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
private Class<G> rowClazz;
public TableAggregator(SerializableSupplier<G> zeroFn,
SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn,
SerializableSupplier<Function<G, Boolean>> isNotZeroFn,
Class<G> 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<G, Boolean> 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<G> bufferEncoder() {
return Encoders.kryo(rowClazz);
}
@Override
public Encoder<G> outputEncoder() {
return Encoders.kryo(rowClazz);
}
}
}

26
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json Normal file
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[
{
"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
}
]

44
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json Normal file
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[
{
"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
}
]

184
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml Normal file
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<workflow-app name="promote_action_payload_for_dataset_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteDatasetActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Dataset payload</description>
</property>
<property>
<name>activePromoteResultActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteDatasetActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteDatasetActionPayload">
<switch>
<case to="PromoteDatasetActionPayloadForDatasetTable">
${(activePromoteDatasetActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'dataset')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Dataset')) eq "true")}
</case>
<default to="SkipPromoteDatasetActionPayloadForDatasetTable"/>
</switch>
</decision>
<action name="PromoteDatasetActionPayloadForDatasetTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteDatasetActionPayloadForDatasetTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/dataset</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/dataset</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForDatasetTable"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteDatasetActionPayloadForDatasetTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/dataset"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/dataset</arg>
<arg>${workingDir}/dataset</arg>
</distcp>
<ok to="DecisionPromoteResultActionPayloadForDatasetTable"/>
<error to="Kill"/>
</action>
<decision name="DecisionPromoteResultActionPayloadForDatasetTable">
<switch>
<case to="PromoteResultActionPayloadForDatasetTable">
${(activePromoteResultActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")}
</case>
<default to="SkipPromoteResultActionPayloadForDatasetTable"/>
</switch>
</decision>
<action name="PromoteResultActionPayloadForDatasetTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteResultActionPayloadForDatasetTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/dataset</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/dataset</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteResultActionPayloadForDatasetTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/dataset"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/dataset</arg>
<arg>${outputGraphRootPath}/dataset</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

128
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml Normal file
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<workflow-app name="promote_action_payload_for_datasource_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteDatasourceActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Datasource payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteDatasourceActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteDatasourceActionPayload">
<switch>
<case to="PromoteDatasourceActionPayloadForDatasourceTable">
${(activePromoteDatasourceActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'datasource')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Datasource')) eq "true")}
</case>
<default to="SkipPromoteDatasourceActionPayloadForDatasourceTable"/>
</switch>
</decision>
<action name="PromoteDatasourceActionPayloadForDatasourceTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteDatasourceActionPayloadForDatasourceTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/datasource</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/datasource</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteDatasourceActionPayloadForDatasourceTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/datasource"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/datasource</arg>
<arg>${outputGraphRootPath}/datasource</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

9
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt Normal file
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## 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

270
dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml Normal file
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<workflow-app name="promote_actionsets_for_graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteDatasetActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Dataset payload</description>
</property>
<property>
<name>activePromoteDatasourceActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Datasource payload</description>
</property>
<property>
<name>activePromoteOrganizationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Organization payload</description>
</property>
<property>
<name>activePromoteOtherResearchProductActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload</description>
</property>
<property>
<name>activePromoteProjectActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Project payload</description>
</property>
<property>
<name>activePromotePublicationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Publication payload</description>
</property>
<property>
<name>activePromoteRelationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Relation payload</description>
</property>
<property>
<name>activePromoteResultActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload</description>
</property>
<property>
<name>activePromoteSoftwareActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Software payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>isLookupUrl</name>
<description>URL of the ISLookupService</description>
</property>
<property>
<name>inputActionSetIds</name>
<description>comma separated list of action set ids to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="PartitionActionSetsByPayloadType"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="PartitionActionSetsByPayloadType">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PartitionActionSetsByPayloadType</name>
<class>eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${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}${spark2EventLogDir}
</spark-opts>
<arg>--inputActionSetIds</arg><arg>${inputActionSetIds}</arg>
<arg>--outputPath</arg><arg>${workingDir}/action_payload_by_type</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark>
<ok to="ForkPromote"/>
<error to="Kill"/>
</action>
<fork name="ForkPromote">
<path start="PromoteActionPayloadForDatasetTable"/>
<path start="PromoteActionPayloadForDatasourceTable"/>
<path start="PromoteActionPayloadForOrganizationTable"/>
<path start="PromoteActionPayloadForOtherResearchProductTable"/>
<path start="PromoteActionPayloadForProjectTable"/>
<path start="PromoteActionPayloadForPublicationTable"/>
<path start="PromoteActionPayloadForRelationTable"/>
<path start="PromoteActionPayloadForSoftwareTable"/>
</fork>
<action name="PromoteActionPayloadForDatasetTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_dataset_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForDatasourceTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_datasource_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForOrganizationTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_organization_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForOtherResearchProductTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_otherresearchproduct_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForProjectTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_project_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForPublicationTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_publication_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForRelationTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_relation_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<action name="PromoteActionPayloadForSoftwareTable">
<sub-workflow>
<app-path>${wf:appPath()}/promote_action_payload_for_software_table</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>inputActionPayloadRootPath</name>
<value>${workingDir}/action_payload_by_type</value>
</property>
</configuration>
</sub-workflow>
<ok to="JoinPromote"/>
<error to="Kill"/>
</action>
<join name="JoinPromote" to="End"/>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_organization_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteOrganizationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Organization payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteOrganizationActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteOrganizationActionPayload">
<switch>
<case to="PromoteOrganizationActionPayloadForOrganizationTable">
${(activePromoteOrganizationActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'organization')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Organization')) eq "true")}
</case>
<default to="SkipPromoteOrganizationActionPayloadForOrganizationTable"/>
</switch>
</decision>
<action name="PromoteOrganizationActionPayloadForOrganizationTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteOrganizationActionPayloadForOrganizationTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/organization</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/organization</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteOrganizationActionPayloadForOrganizationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/organization"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/organization</arg>
<arg>${outputGraphRootPath}/organization</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_otherresearchproduct_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteOtherResearchProductActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload</description>
</property>
<property>
<name>activePromoteResultActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteOtherResearchProductActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteOtherResearchProductActionPayload">
<switch>
<case to="PromoteOtherResearchProductActionPayloadForOtherResearchProductTable">
${(activePromoteOtherResearchProductActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'otherresearchproduct')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.OtherResearchProduct')) eq "true")}
</case>
<default to="SkipPromoteOtherResearchProductActionPayloadForOtherResearchProductTable"/>
</switch>
</decision>
<action name="PromoteOtherResearchProductActionPayloadForOtherResearchProductTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteOtherResearchProductActionPayloadForOtherResearchProductTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForOtherResearchProductTable"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteOtherResearchProductActionPayloadForOtherResearchProductTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/otherresearchproduct"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/otherresearchproduct</arg>
<arg>${workingDir}/otherresearchproduct</arg>
</distcp>
<ok to="DecisionPromoteResultActionPayloadForOtherResearchProductTable"/>
<error to="Kill"/>
</action>
<decision name="DecisionPromoteResultActionPayloadForOtherResearchProductTable">
<switch>
<case to="PromoteResultActionPayloadForOtherResearchProductTable">
${(activePromoteResultActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")}
</case>
<default to="SkipPromoteResultActionPayloadForOtherResearchProductTable"/>
</switch>
</decision>
<action name="PromoteResultActionPayloadForOtherResearchProductTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteResultActionPayloadForOtherResearchProductTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/otherresearchproduct</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteResultActionPayloadForOtherResearchProductTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/otherresearchproduct"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/otherresearchproduct</arg>
<arg>${outputGraphRootPath}/otherresearchproduct</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_project_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteProjectActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.OtherResearchProduct payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteProjectActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteProjectActionPayload">
<switch>
<case to="PromoteProjectActionPayloadForProjectTable">
${(activePromoteProjectActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'project')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Project')) eq "true")}
</case>
<default to="SkipPromoteProjectActionPayloadForProjectTable"/>
</switch>
</decision>
<action name="PromoteProjectActionPayloadForProjectTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteProjectActionPayloadForProjectTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/project</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/project</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteProjectActionPayloadForProjectTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/project"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/project</arg>
<arg>${outputGraphRootPath}/project</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_publication_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromotePublicationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Publication payload</description>
</property>
<property>
<name>activePromoteResultActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromotePublicationActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromotePublicationActionPayload">
<switch>
<case to="PromotePublicationActionPayloadForPublicationTable">
${(activePromotePublicationActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'publication')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Publication')) eq "true")}
</case>
<default to="SkipPromotePublicationActionPayloadForPublicationTable"/>
</switch>
</decision>
<action name="PromotePublicationActionPayloadForPublicationTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromotePublicationActionPayloadForPublicationTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/publication</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForPublicationTable"/>
<error to="Kill"/>
</action>
<action name="SkipPromotePublicationActionPayloadForPublicationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/publication"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/publication</arg>
<arg>${workingDir}/publication</arg>
</distcp>
<ok to="DecisionPromoteResultActionPayloadForPublicationTable"/>
<error to="Kill"/>
</action>
<decision name="DecisionPromoteResultActionPayloadForPublicationTable">
<switch>
<case to="PromoteResultActionPayloadForPublicationTable">
${(activePromoteResultActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")}
</case>
<default to="SkipPromoteResultActionPayloadForPublicationTable"/>
</switch>
</decision>
<action name="PromoteResultActionPayloadForPublicationTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteResultActionPayloadForPublicationTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/publication</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteResultActionPayloadForPublicationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/publication"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/publication</arg>
<arg>${outputGraphRootPath}/publication</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_relation_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteRelationActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Relation payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteRelationActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteRelationActionPayload">
<switch>
<case to="PromoteRelationActionPayloadForRelationTable">
${(activePromoteRelationActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'relation')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Relation')) eq "true")}
</case>
<default to="SkipPromoteRelationActionPayloadForRelationTable"/>
</switch>
</decision>
<action name="PromoteRelationActionPayloadForRelationTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteRelationActionPayloadForRelationTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Relation</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/relation</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteRelationActionPayloadForRelationTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/relation"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/relation</arg>
<arg>${outputGraphRootPath}/relation</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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<workflow-app name="promote_action_payload_for_software_table" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>activePromoteSoftwareActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Software payload</description>
</property>
<property>
<name>activePromoteResultActionPayload</name>
<description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Result payload</description>
</property>
<property>
<name>inputGraphRootPath</name>
<description>root location of input materialized graph</description>
</property>
<property>
<name>inputActionPayloadRootPath</name>
<description>root location of action payloads to promote</description>
</property>
<property>
<name>outputGraphRootPath</name>
<description>root location for output materialized graph</description>
</property>
<property>
<name>mergeAndGetStrategy</name>
<description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="DecisionPromoteSoftfwareActionPayload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="DecisionPromoteSoftfwareActionPayload">
<switch>
<case to="PromoteSoftwareActionPayloadForSoftwareTable">
${(activePromoteSoftwareActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'software')) eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Software')) eq "true")}
</case>
<default to="SkipPromoteSoftwareActionPayloadForSoftwareTable"/>
</switch>
</decision>
<action name="PromoteSoftwareActionPayloadForSoftwareTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteSoftwareActionPayloadForSoftwareTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputGraphTablePath</arg><arg>${workingDir}/software</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="DecisionPromoteResultActionPayloadForSoftwareTable"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteSoftwareActionPayloadForSoftwareTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${workingDir}/software"/>
</prepare>
<arg>-pb</arg>
<arg>${inputGraphRootPath}/software</arg>
<arg>${workingDir}/software</arg>
</distcp>
<ok to="DecisionPromoteResultActionPayloadForSoftwareTable"/>
<error to="Kill"/>
</action>
<decision name="DecisionPromoteResultActionPayloadForSoftwareTable">
<switch>
<case to="PromoteResultActionPayloadForSoftwareTable">
${(activePromoteResultActionPayload eq "true") and
(fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Result')) eq "true")}
</case>
<default to="SkipPromoteResultActionPayloadForSoftwareTable"/>
</switch>
</decision>
<action name="PromoteResultActionPayloadForSoftwareTable">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>PromoteResultActionPayloadForSoftwareTable</name>
<class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
<jar>dhp-actionmanager-${projectVersion}.jar</jar>
<spark-opts>
--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
</spark-opts>
<arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
<arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/software</arg>
<arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="SkipPromoteResultActionPayloadForSoftwareTable">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<prepare>
<delete path="${outputGraphRootPath}/software"/>
</prepare>
<arg>-pb</arg>
<arg>${workingDir}/software</arg>
<arg>${outputGraphRootPath}/software</arg>
</distcp>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

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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<String, List<String>> oafsByClassName = createActionSets(inputActionSetsBaseDir);
List<String> 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<String> 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<String, List<String>> createActionSets(Path inputActionSetsDir) throws IOException {
Path inputActionSetJsonDumpsDir = getInputActionSetJsonDumpsDir();
Map<String, List<String>> oafsByType = new HashMap<>();
Files
.list(inputActionSetJsonDumpsDir)
.forEach(inputActionSetJsonDumpFile -> {
String inputActionSetId = inputActionSetJsonDumpFile.getFileName().toString();
Path inputActionSetDir = inputActionSetsDir.resolve(inputActionSetId);
Dataset<String> actionDS = readActionsFromJsonDump(inputActionSetJsonDumpFile.toString())
.cache();
writeActionsAsJobInput(actionDS, inputActionSetId, inputActionSetDir.toString());
Map<String, List<String>> 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.<String>getAs("clazz"),
mutableSeqAsJavaList(row.<Seq<String>>getAs("payload_list"))))
.collect(Collectors.toMap(AbstractMap.SimpleEntry::getKey, AbstractMap.SimpleEntry::getValue));
actionSetOafsByType.keySet()
.forEach(x -> {
if (oafsByType.containsKey(x)) {
List<String> 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<String> readActionsFromJsonDump(String path) {
return spark
.read()
.textFile(path);
}
private static void writeActionsAsJobInput(Dataset<String> 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 <T extends Oaf> void assertForOafType(Path outputDir, Map<String, List<String>> oafsByClassName, Class<T> clazz) {
Path outputDatasetDir = outputDir.resolve(String.format("clazz=%s", clazz.getCanonicalName()));
Files.exists(outputDatasetDir);
List<T> actuals = readActionPayloadFromJobOutput(outputDatasetDir.toString(), clazz).collectAsList();
actuals.sort(Comparator.comparingInt(Object::hashCode));
List<T> expecteds = oafsByClassName.get(clazz.getCanonicalName()).stream()
.map(json -> mapToOaf(json, clazz))
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
assertIterableEquals(expecteds, actuals);
}
private static <T extends Oaf> Dataset<T> readActionPayloadFromJobOutput(String path,
Class<T> clazz) {
return spark
.read()
.parquet(path)
.map((MapFunction<Row, T>) value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"), clazz),
Encoders.bean(clazz));
}
private static <T extends Oaf> T mapToOaf(String json, Class<T> clazz) {
return rethrowAsRuntimeException(
() -> OBJECT_MAPPER.readValue(json, clazz),
String.format("failed to map json to class: json=%s, class=%s", json, clazz.getCanonicalName())
);
}
}

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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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> 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<BiFunction<Oaf, Oaf, Oaf>> fn =
functionFor(Strategy.SELECT_NEWER_AND_GET);
// then
Oaf x = fn.get().apply(a, b);
assertTrue(OafEntity.class.isAssignableFrom(x.getClass()));
assertEquals(a, x);
}
}
}

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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<Relation> rowClazz = Relation.class;
Class<OafEntity> 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<? extends Oaf> rowClazz,
Class<? extends Oaf> 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<? extends Oaf> 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<? extends Oaf> expectedOutputRows = readGraphTableFromJsonDump(expectedOutputGraphTableJsonDumpFile.toString(), rowClazz)
.collectAsList()
.stream()
.sorted(Comparator.comparingInt(Object::hashCode))
.collect(Collectors.toList());
assertIterableEquals(expectedOutputRows, actualOutputRows);
}
}
public static Stream<Arguments> 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 <G extends Oaf> Path createGraphTable(Path inputGraphRootDir,
Class<G> rowClazz) {
String inputGraphTableJsonDumpPath = inputGraphTableJsonDumpLocation(rowClazz);
Path inputGraphTableJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(inputGraphTableJsonDumpPath)).getFile());
Dataset<G> 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<? extends Oaf> rowClazz) {
return String.format(
"%s/%s.json", "eu/dnetlib/dhp/actionmanager/promote/input/graph", rowClazz.getSimpleName().toLowerCase());
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJsonDump(String path,
Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map((MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz));
}
private static <G extends Oaf> void writeGraphTableAaJobInput(Dataset<G> rowDS,
String path) {
rowDS
.write()
.option("compression", "gzip")
.json(path);
}
private static <G extends Oaf, A extends Oaf> Path createActionPayload(Path inputActionPayloadRootDir,
Class<G> rowClazz,
Class<A> actionPayloadClazz) {
String inputActionPayloadJsonDumpPath = inputActionPayloadJsonDumpLocation(rowClazz, actionPayloadClazz);
Path inputActionPayloadJsonDumpFile = Paths
.get(Objects.requireNonNull(cl.getResource(inputActionPayloadJsonDumpPath)).getFile());
Dataset<String> actionPayloadDS = readActionPayloadFromJsonDump(inputActionPayloadJsonDumpFile.toString());
Path inputActionPayloadDir = inputActionPayloadRootDir.resolve(actionPayloadClazz.getSimpleName().toLowerCase());
writeActionPayloadAsJobInput(actionPayloadDS, inputActionPayloadDir.toString());
return inputActionPayloadDir;
}
private static String inputActionPayloadJsonDumpLocation(Class<? extends Oaf> rowClazz,
Class<? extends Oaf> 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<String> readActionPayloadFromJsonDump(String path) {
return spark
.read()
.textFile(path);
}
private static void writeActionPayloadAsJobInput(Dataset<String> actionPayloadDS,
String path) {
actionPayloadDS
.withColumnRenamed("value", "payload")
.write()
.parquet(path);
}
private static <G extends Oaf> Dataset<G> readGraphTableFromJobOutput(String path,
Class<G> rowClazz) {
return spark
.read()
.textFile(path)
.map((MapFunction<String, G>) json -> OBJECT_MAPPER.readValue(json, rowClazz), Encoders.bean(rowClazz));
}
private static String resultFileLocation(MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> 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());
}
}

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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<OafImplSubSub> rowData = Arrays.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3)
);
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
List<OafImplSubSub> actionPayloadData = Arrays.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2), createOafImplSubSub(id2),
createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3),
createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4), createOafImplSubSub(id4)
);
Dataset<OafImplSubSub> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSubSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSubSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
x.merge(y);
return x;
};
// when
List<OafImplSubSub> 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<OafImplSubSub> rowData = Arrays.asList(
createOafImplSubSub(id0),
createOafImplSubSub(id1),
createOafImplSubSub(id2),
createOafImplSubSub(id3)
);
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
List<OafImplSub> actionPayloadData = Arrays.asList(
createOafImplSub(id1),
createOafImplSub(id2), createOafImplSub(id2),
createOafImplSub(id3), createOafImplSub(id3), createOafImplSub(id3),
createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4), createOafImplSub(id4)
);
Dataset<OafImplSub> actionPayloadDS = spark.createDataset(actionPayloadData, Encoders.bean(OafImplSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<Function<OafImplSub, String>> actionPayloadIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
x.merge(y);
return x;
};
// when
List<OafImplSubSub> 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<OafImplSubSub> rowData = Arrays.asList(
createOafImplSubSub(id1),
createOafImplSubSub(id2), createOafImplSubSub(id2),
createOafImplSubSub(id3), createOafImplSubSub(id3), createOafImplSubSub(id3)
);
Dataset<OafImplSubSub> rowDS = spark.createDataset(rowData, Encoders.bean(OafImplSubSub.class));
SerializableSupplier<Function<OafImplSubSub, String>> rowIdFn = () -> OafImplRoot::getId;
SerializableSupplier<BiFunction<OafImplSubSub, OafImplSubSub, OafImplSubSub>> mergeAndGetFn = () -> (x, y) -> {
x.merge(y);
return x;
};
SerializableSupplier<OafImplSubSub> zeroFn = OafImplSubSub::new;
SerializableSupplier<Function<OafImplSubSub, Boolean>> isNotZeroFn = () -> x -> Objects.nonNull(x.getId());
// when
List<OafImplSubSub> 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;
}
}

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