[personEntity] updated the property file to include also the db parameters. The same for the wf definition. Refactoring for compilation

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java

@@ -61,8 +61,7 @@ public class CoAuthorshipIterator implements Iterator<Relation> {
 	private Relation getRelation(String orcid1, String orcid2) {
 		String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
 		String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
-		Relation relation =
+		Relation relation = OafMapperUtils
-		OafMapperUtils
 			.getRelation(
 				source, target, ModelConstants.PERSON_PERSON_RELTYPE,
 				ModelConstants.PERSON_PERSON_SUBRELTYPE,

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java

@@ -13,9 +13,12 @@ import java.sql.SQLException;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.common.DbClient;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -27,13 +30,13 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.spark_project.jetty.util.StringUtil;
 
-
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.collection.orcid.model.Employment;
 import eu.dnetlib.dhp.collection.orcid.model.Work;
+import eu.dnetlib.dhp.common.DbClient;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -49,11 +52,6 @@ import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
 public class ExtractPerson implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
 	private static final String QUERY = "SELECT * FROM project_person WHERE pid_type = 'ORCID'";
@@ -79,7 +77,6 @@ public class ExtractPerson implements Serializable {
 	public static List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
 		.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
-
 	public static final DataInfo DATAINFO = OafMapperUtils
 		.dataInfo(
 			false,
@@ -136,7 +133,8 @@ public class ExtractPerson implements Serializable {
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
 				extractInfoForActionSetFromORCID(spark, inputPath, workingDir);
-				extractInfoForActionSetFromProjects(spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
+				extractInfoForActionSetFromProjects(
+					spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
 				createActionSet(spark, outputPath, workingDir);
 			});
 
@@ -164,7 +162,8 @@ public class ExtractPerson implements Serializable {
 
 	public static Relation getRelationWithProject(ResultSet rs) {
 		try {
-			return getProjectRelation(rs.getString("project"), rs.getString("pid"),
+			return getProjectRelation(
+				rs.getString("project"), rs.getString("pid"),
 				rs.getString("role"));
 		} catch (final SQLException e) {
 			throw new RuntimeException(e);
@@ -194,12 +193,10 @@ public class ExtractPerson implements Serializable {
 			properties.add(kv);
 		}
 
-
 		if (!properties.isEmpty())
 			relation.setProperties(properties);
 		return relation;
 
-
 	}
 
 	protected static void writeRelation(final Relation relation, BufferedWriter writer) {

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json

@@ -21,5 +21,30 @@
   "paramLongName": "workingDir",
   "paramDescription": "the hdfs name node",
   "paramRequired": false
+},
+  {
+    "paramName": "pu",
+    "paramLongName": "postgresUrl",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+
+  {
+    "paramName": "ps",
+    "paramLongName": "postgresUser",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+  "paramName": "pp",
+  "paramLongName": "postgresPassword",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
+},{
+  "paramName": "nn",
+  "paramLongName": "hdfsNameNode",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
 }
+
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties

@@ -1,2 +1,5 @@
 inputPath=/data/orcid_2023/tables/
 outputPath=/user/miriam.baglioni/peopleAS
+postgresUrl=jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus
+postgresUser=dnet'
+postgresPassword=dnetPwd

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml

@@ -9,6 +9,18 @@
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
         </property>
+        <property>
+            <name>postgresUrl</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>postgresUser</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>postgresPassword</name>
+            <description>the path where to store the actionset</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -102,6 +114,10 @@
             <arg>--inputPath</arg><arg>${inputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--postgresUrl</arg><arg>${postgresUrl}</arg>
+            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
+            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala

@@ -31,6 +31,7 @@ class ORCIDAuthorMatchersTest {
     assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin"))
     // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented
   }
+
   @Test def testDocumentationNames(): Unit = {
     assertTrue(matchOrderedTokenAndAbbreviations("James C. A. Miller-Jones", "James Antony Miller-Jones"))
   }