[ImportOC] fix to move original folder instead of extracted ones

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java

@@ -46,6 +46,9 @@ public class GetOpenCitationsRefs implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
 
+		final String backupPath = parser.get("backupPath");
+		log.info("backupPath {}", backupPath);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
@@ -53,11 +56,11 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
-		ocr.doExtract(inputPath, outputPath, fileSystem);
+		ocr.doExtract(inputPath, outputPath, backupPath, fileSystem);
 
 	}
 
-	private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
+	private void doExtract(String inputPath, String outputPath, String backupPath, FileSystem fileSystem)
 		throws IOException {
 
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
@@ -89,6 +92,7 @@ public class GetOpenCitationsRefs implements Serializable {
 				}
 
 			}
+			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
 		}
 
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java

@@ -49,9 +49,6 @@ public class ReadCOCI implements Serializable {
 		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
-		final String backupPath = parser.get("backupPath");
-		log.info("backupPath {}", backupPath);
-
 		SparkConf sconf = new SparkConf();
 
 		Configuration conf = new Configuration();
@@ -71,14 +68,12 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					fileSystem,
 					outputPath,
-					backupPath,
 					delimiter);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
-		String backupPath,
 		String delimiter) throws IOException {
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
 			.listFiles(
@@ -113,7 +108,7 @@ public class ReadCOCI implements Serializable {
 				.option("compression", "gzip")
 				.json(outputPath);
 
-			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
+			fileSystem.delete(fileStatus.getPath());
 		}
 
 	}

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json

@@ -16,5 +16,11 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  },
+  {
+    "paramName": "bp",
+    "paramLongName": "backupPath",
+    "paramDescription": "the hdfs path to move the OC data after the extraction",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json

@@ -30,12 +30,6 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },
-  {
-    "paramName": "bp",
-    "paramLongName": "backupPath",
-    "paramDescription": "the hdfs path to move the OC data after the extraction",
-    "paramRequired": true
   }
 ]
 

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

@@ -94,17 +94,7 @@
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
             <arg>--inputPath</arg><arg>${inputPath}/Original</arg>
             <arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
-        </java>
+            <arg>--backupPath</arg><arg>${inputPath}/backup</arg>
-        <ok to="read"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="extract_correspondence">
-        <java>
-            <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
-            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
-            <arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -129,7 +119,6 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
             <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
-            <arg>--backupPath</arg><arg>${inputPath}/backup</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
         </spark>