fix problem in parameters

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java

@@ -1,66 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import eu.dnetlib.dhp.graph.model.EntityRelEntity;
-import eu.dnetlib.dhp.graph.model.RelatedEntity;
-import eu.dnetlib.dhp.graph.utils.GraphMappingUtils;
-import org.codehaus.jackson.map.ObjectMapper;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.io.IOException;
-import java.io.InputStreamReader;
-
-public class MappingUtilsTest {
-
-    private GraphMappingUtils utils;
-
-    @Before
-    public void setUp() {
-        utils = new GraphMappingUtils();
-    }
-
-    @Test
-    public void testOafMappingDatasource() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("datasource.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-        e.getSource().setType("datasource");
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-    //@Test
-    public void testOafMappingResult() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("result.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-    @Test
-    public void testOafMappingSoftware() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("software.json"));
-        final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class);
-
-        final EntityRelEntity out = utils.asRelatedEntity(e);
-        System.out.println(out);
-
-    }
-
-
-    @Test
-    public void testParseRelatedEntity() throws IOException {
-
-        final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json"));
-        final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class);
-
-        System.out.println(e);
-
-    }
-}

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java

@@ -1,55 +0,0 @@
-package eu.dnetlib.dhp.graph;
-
-import eu.dnetlib.dhp.graph.utils.ContextMapper;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.apache.spark.sql.SparkSession;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import java.io.File;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-
-public class XmlRecordFactoryTest {
-
-    private static final Log log = LogFactory.getLog(XmlRecordFactoryTest.class);
-
-    private Path testDir;
-
-    @Before
-    public void setup() throws IOException {
-        testDir = Files.createTempDirectory(getClass().getSimpleName());
-        log.info("created test directory " + testDir.toString());
-    }
-
-    @After
-    public void tearDown() throws IOException {
-        FileUtils.deleteDirectory(testDir.toFile());
-        log.info("deleted test directory " + testDir.toString());
-    }
-
-    @Test
-    public void  testXmlSerialization() throws Exception {
-
-        final SparkSession spark = SparkSession
-                .builder()
-                .appName(SparkXmlRecordBuilderJob.class.getSimpleName())
-                .master("local[*]")
-                .getOrCreate();
-
-        final String inputDir = testDir.toString() + "/3_joined_entities";
-        FileUtils.forceMkdir(new File(inputDir));
-        FileUtils.copyFile(new File("/Users/claudio/Downloads/joined_entities-part-00000"), new File(inputDir + "/joined_entities-part-00000"));
-
-        final ContextMapper ctx = ContextMapper.fromIS("https://dev-openaire.d4science.org:443/is/services/isLookUp");
-
-        final GraphJoiner g = new GraphJoiner(spark, ctx, inputDir, testDir.toString());
-
-        g.asXML();
-    }
-
-}

dhp-workflows/dhp-propagation/src/main/java/eu/dnetlib/dhp/PropagationConstant.java

@@ -0,0 +1,4 @@
+package eu.dnetlib.dhp;
+
+public class PropagationConstant {
+}

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json

@@ -3,13 +3,13 @@
     "paramName":"mt",
     "paramLongName":"master",
     "paramDescription": "should be local or yarn",
-    "paramRequired": true,
+    "paramRequired": true
   },
   {
     "paramName":"s",
     "paramLongName":"sourcePath",
     "paramDescription": "the path of the sequencial file to read",
-    "paramRequired": true,
+    "paramRequired": true
   },
   {
     "paramName":"wl",

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml

@@ -49,7 +49,7 @@
             </spark-opts>
             <arg>-mt</arg> <arg>yarn-cluster</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
-            <arg>--withelist</arg><arg>${whitelist}</arg>
+            <arg>--whitelist</arg><arg>${whitelist}</arg>
             <arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName":"mt",
+    "paramLongName":"master",
+    "paramDescription": "should be local or yarn",
+    "paramRequired": true
+  },
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName":"wl",
+    "paramLongName":"whitelist",
+    "paramDescription": "datasource id that will be considered even if not in the allowed typology list. Split by ;",
+    "paramRequired": true
+  },
+  {
+    "paramName":"at",
+    "paramLongName":"allowedtypes",
+    "paramDescription": "the types of the allowed datasources. Split by ;",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/config-default.xml

@@ -0,0 +1,18 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+</configuration>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml

@@ -0,0 +1,60 @@
+<workflow-app name="country_propagation" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the source path</description>
+        </property>
+        <property>
+            <name>whitelist</name>
+            <description>the white list</description>
+        </property>
+        <property>
+            <name>allowedtypes</name>
+            <description>the allowed types</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>
+    </parameters>
+
+    <start to="CountryPropagation"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="CountryPropagation">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>CountryPropagation</name>
+            <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>--executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
+                --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
+            </spark-opts>
+            <arg>-mt</arg> <arg>yarn-cluster</arg>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--whitelist</arg><arg>${whitelist}</arg>
+            <arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>