GetCSV refactoring - moving classes to dhp-common that have dependency with GetCSV class (that was located in graph-mapper)

dhp-common/src/main/java/eu/dnetlib/dhp/common/aggregation/AggregatorReport.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.aggregation.common;
+package eu.dnetlib.dhp.common.aggregation;
 
 import java.io.Closeable;
 import java.io.IOException;

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/CollectorException.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 public class CollectorException extends Exception {
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/GetCSV.java

@@ -0,0 +1,65 @@
+
+package eu.dnetlib.dhp.common.collection;
+
+import java.io.*;
+import java.net.URL;
+import java.net.URLConnection;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+import java.util.Optional;
+
+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 org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.opencsv.bean.CsvToBeanBuilder;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
+public class GetCSV {
+
+	public static void getCsv(FileSystem fileSystem, BufferedReader reader, String hdfsPath,
+							  String modelClass) throws IOException, ClassNotFoundException {
+		getCsv(fileSystem, reader, hdfsPath, modelClass, ',');
+
+	}
+
+	public static void getCsv(FileSystem fileSystem, BufferedReader reader, String hdfsPath,
+		String modelClass, char delimiter) throws IOException, ClassNotFoundException {
+
+		Path hdfsWritePath = new Path(hdfsPath);
+		FSDataOutputStream fsDataOutputStream = null;
+		if (fileSystem.exists(hdfsWritePath)) {
+			fileSystem.delete(hdfsWritePath, false);
+		}
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+
+		try(BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8))){
+
+			ObjectMapper mapper = new ObjectMapper();
+
+			 new CsvToBeanBuilder(reader)
+					.withType(Class.forName(modelClass))
+					.withSeparator(delimiter)
+					.build()
+					.parse()
+					.forEach(line -> {
+						try {
+							writer.write(mapper.writeValueAsString(line));
+							writer.newLine();
+						} catch (IOException e) {
+							throw new RuntimeException(e);
+						}
+					});
+		}
+
+
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpClientParams.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 /**
  * Bundles the http connection parameters driving the client behaviour.

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 import static eu.dnetlib.dhp.utils.DHPUtils.*;
 
@@ -15,7 +15,7 @@ import org.apache.http.HttpHeaders;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 
 /**
  * Migrated from https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-modular-collector-service/trunk/src/main/java/eu/dnetlib/data/collector/plugins/HttpConnector.java