changes in the blacklist and workflow definition

dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java

@@ -1,13 +1,5 @@
-package eu.dnetlib.dhp.blacklist;
 
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+package eu.dnetlib.dhp.blacklist;
-import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.common.RelationInverse;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 
 import java.io.BufferedWriter;
 import java.io.Closeable;
@@ -19,12 +11,22 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.function.Consumer;
 import java.util.function.Function;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
-import com.fasterxml.jackson.databind.ObjectMapper;
 import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.raw.common.DbClient;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.common.RelationInverse;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class ReadBlacklistFromDB implements Closeable {
 
@@ -38,10 +40,11 @@ public class ReadBlacklistFromDB implements Closeable {
 		"relationship FROM blacklist WHERE status = 'ACCEPTED'";
 
 	public static void main(final String[] args) throws Exception {
-        final ArgumentApplicationParser parser =
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-                new ArgumentApplicationParser(
+			IOUtils
-                        IOUtils.toString(
+				.toString(
-                                ReadBlacklistFromDB.class.getResourceAsStream(
+					ReadBlacklistFromDB.class
+						.getResourceAsStream(
 							"/eu/dnetlib/dhp/blacklist/blacklist_parameters.json")));
 
 		parser.parseArgument(args);
@@ -52,10 +55,8 @@ public class ReadBlacklistFromDB implements Closeable {
 		final String hdfsPath = parser.get("hdfsPath");
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 
-
+		try (final ReadBlacklistFromDB rbl = new ReadBlacklistFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
-
+			dbPassword)) {
-        try (final ReadBlacklistFromDB rbl =
-                     new ReadBlacklistFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser, dbPassword)) {
 
 			log.info("Processing blacklist...");
 			rbl.execute(query, rbl::processBlacklistEntry);
@@ -63,7 +64,6 @@ public class ReadBlacklistFromDB implements Closeable {
 		}
 	}
 
-
 	public void execute(final String sql, final Function<ResultSet, List<Relation>> producer)
 		throws Exception {
 
@@ -72,7 +72,7 @@ public class ReadBlacklistFromDB implements Closeable {
 		dbClient.processResults(sql, consumer);
 	}
 
-    public List<Relation> processBlacklistEntry(ResultSet rs){
+	public List<Relation> processBlacklistEntry(ResultSet rs) {
 		try {
 			Relation direct = new Relation();
 			Relation inverse = new Relation();
@@ -132,7 +132,4 @@ public class ReadBlacklistFromDB implements Closeable {
 		}
 	}
 
-
-
-
 }

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

@@ -1,5 +1,18 @@
-<workflow-app name="blacklsting" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="blacklisting" xmlns="uri:oozie:workflow:0.5">
-
+<parameters>
+    <property>
+        <name>postgresURL</name>
+        <description>the url of the postgress server to query</description>
+    </property>
+    <property>
+        <name>postgresUser</name>
+        <description>the username to access the postgres db</description>
+    </property>
+    <property>
+        <name>postgresPassword</name>
+        <description>the postgres password</description>
+    </property>
+</parameters>
 <start to="reset-outputpath"/>
 
 <kill name="Kill">
@@ -8,7 +21,7 @@
 
     <action name="reset-outputpath">
         <fs>
-            <delete path='${hdfsPath}'/>
+            <delete path='${workingDir}/blacklist'/>
         </fs>
         <ok to="read_blacklist"/>
         <error to="Kill"/>
@@ -21,7 +34,7 @@
             <main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
             <arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--postgresUrl</arg><arg>${postgresUrl}</arg>
+            <arg>--postgresUrl</arg><arg>${postgresURL}</arg>
             <arg>--postgresUser</arg><arg>${postgresUser}</arg>
             <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
         </java>