From dc5fc5366dfa9a3c69ef078efffed1d4d4e8646f Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Tue, 11 Aug 2020 15:26:06 +0200
Subject: [PATCH] Creation of an archive for each related dump part

---
 .../eu/dnetlib/dhp/oa/graph/dump/MakeTar.java | 114 ++++++++++++++++++
 1 file changed, 114 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java
new file mode 100644
index 000000000..199960104
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java
@@ -0,0 +1,114 @@
+
+package eu.dnetlib.dhp.oa.graph.dump;
+
+import java.io.*;
+
+import org.apache.commons.compress.archivers.ar.ArArchiveEntry;
+import org.apache.commons.compress.archivers.ar.ArArchiveOutputStream;
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+
+public class MakeTar implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(MakeTar.class);
+
+	public static void main(String[] args) throws Exception {
+		String jsonConfiguration = IOUtils
+			.toString(
+				MakeTar.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
+
+		final String outputPath = parser.get("hdfsPath");
+		log.info("hdfsPath: {}", outputPath);
+
+		final String hdfsNameNode = parser.get("nameNode");
+		log.info("nameNode: {}", hdfsNameNode);
+
+		final String inputPath = parser.get("sourcePath");
+		log.info("input path : {}", inputPath);
+
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		makeTArArchive(fileSystem, inputPath, outputPath);
+
+	}
+
+	public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
+
+		RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
+
+		while (dir_iterator.hasNext()) {
+			LocatedFileStatus fileStatus = dir_iterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
+
+			write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
+		}
+
+	}
+
+	private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
+		throws IOException {
+
+		Path hdfsWritePath = new Path(outputPath);
+		FSDataOutputStream fsDataOutputStream = null;
+		if (fileSystem.exists(hdfsWritePath)) {
+			fileSystem.delete(hdfsWritePath, true);
+
+		}
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+
+		TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
+
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			.listFiles(
+				new Path(inputPath), true);
+
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			if (!p_string.endsWith("_SUCCESS")) {
+				String name = p_string.substring(p_string.lastIndexOf("/") + 1);
+				TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
+				entry.setSize(fileStatus.getLen());
+				ar.putArchiveEntry(entry);
+
+				InputStream is = fileSystem.open(fileStatus.getPath());
+
+				BufferedInputStream bis = new BufferedInputStream(is);
+
+				int count;
+				byte data[] = new byte[1024];
+				while ((count = bis.read(data, 0, data.length)) != -1) {
+					ar.write(data, 0, count);
+				}
+				bis.close();
+				ar.closeArchiveEntry();
+
+			}
+
+		}
+
+		ar.close();
+	}
+
+}