fix problem in parameters
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5868ff8a86
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e0a777028a
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@ -1,66 +0,0 @@
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package eu.dnetlib.dhp.graph;
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import eu.dnetlib.dhp.graph.model.EntityRelEntity;
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import eu.dnetlib.dhp.graph.model.RelatedEntity;
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import eu.dnetlib.dhp.graph.utils.GraphMappingUtils;
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import org.codehaus.jackson.map.ObjectMapper;
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import org.junit.Before;
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import org.junit.Test;
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import java.io.IOException;
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import java.io.InputStreamReader;
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public class MappingUtilsTest {
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private GraphMappingUtils utils;
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@Before
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public void setUp() {
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utils = new GraphMappingUtils();
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}
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@Test
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public void testOafMappingDatasource() throws IOException {
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final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("datasource.json"));
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final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
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e.getSource().setType("datasource");
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final EntityRelEntity out = utils.asRelatedEntity(e);
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System.out.println(out);
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}
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//@Test
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public void testOafMappingResult() throws IOException {
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final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("result.json"));
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final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
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final EntityRelEntity out = utils.asRelatedEntity(e);
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System.out.println(out);
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}
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@Test
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public void testOafMappingSoftware() throws IOException {
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final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("software.json"));
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final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
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final EntityRelEntity out = utils.asRelatedEntity(e);
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System.out.println(out);
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}
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@Test
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public void testParseRelatedEntity() throws IOException {
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final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json"));
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final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class);
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System.out.println(e);
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}
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}
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@ -1,55 +0,0 @@
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package eu.dnetlib.dhp.graph;
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import eu.dnetlib.dhp.graph.utils.ContextMapper;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.spark.sql.SparkSession;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Test;
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import java.io.File;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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public class XmlRecordFactoryTest {
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private static final Log log = LogFactory.getLog(XmlRecordFactoryTest.class);
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private Path testDir;
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@Before
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public void setup() throws IOException {
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testDir = Files.createTempDirectory(getClass().getSimpleName());
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log.info("created test directory " + testDir.toString());
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}
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@After
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public void tearDown() throws IOException {
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FileUtils.deleteDirectory(testDir.toFile());
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log.info("deleted test directory " + testDir.toString());
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}
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@Test
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public void testXmlSerialization() throws Exception {
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkXmlRecordBuilderJob.class.getSimpleName())
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.master("local[*]")
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.getOrCreate();
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final String inputDir = testDir.toString() + "/3_joined_entities";
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FileUtils.forceMkdir(new File(inputDir));
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FileUtils.copyFile(new File("/Users/claudio/Downloads/joined_entities-part-00000"), new File(inputDir + "/joined_entities-part-00000"));
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final ContextMapper ctx = ContextMapper.fromIS("https://dev-openaire.d4science.org:443/is/services/isLookUp");
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final GraphJoiner g = new GraphJoiner(spark, ctx, inputDir, testDir.toString());
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g.asXML();
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}
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}
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@ -0,0 +1,4 @@
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package eu.dnetlib.dhp;
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public class PropagationConstant {
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}
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@ -3,13 +3,13 @@
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true,
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true,
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"paramRequired": true
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},
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{
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"paramName":"wl",
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@ -49,7 +49,7 @@
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</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--withelist</arg><arg>${whitelist}</arg>
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<arg>--whitelist</arg><arg>${whitelist}</arg>
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<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
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</spark>
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<ok to="End"/>
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@ -0,0 +1,26 @@
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[
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{
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"wl",
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"paramLongName":"whitelist",
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"paramDescription": "datasource id that will be considered even if not in the allowed typology list. Split by ;",
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"paramRequired": true
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},
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{
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"paramName":"at",
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"paramLongName":"allowedtypes",
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"paramDescription": "the types of the allowed datasources. Split by ;",
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"paramRequired": true
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}
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]
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@ -0,0 +1,18 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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@ -0,0 +1,60 @@
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<workflow-app name="country_propagation" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>whitelist</name>
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<description>the white list</description>
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</property>
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<property>
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<name>allowedtypes</name>
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<description>the allowed types</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="CountryPropagation"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="CountryPropagation">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>CountryPropagation</name>
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<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
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--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
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</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--whitelist</arg><arg>${whitelist}</arg>
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<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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