From e737a47270a8e4aa48e4e1764743f8357777b263 Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Wed, 5 Aug 2020 14:17:40 +0200
Subject: [PATCH] added classes to try to send input stream to zenodo for the
 upload

---
 .../oa/graph/dump/InputStreamRequestBody.java | 53 ++++++++++++
 .../dhp/oa/graph/dump/SendToZenodoHDFS.java   | 80 +++++++++++++++++++
 2 files changed, 133 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/InputStreamRequestBody.java
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/InputStreamRequestBody.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/InputStreamRequestBody.java
new file mode 100644
index 000000000..9ab4773be
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/InputStreamRequestBody.java
@@ -0,0 +1,53 @@
+package eu.dnetlib.dhp.oa.graph.dump;
+
+import okhttp3.MediaType;
+import okhttp3.RequestBody;
+import okhttp3.internal.Util;
+import okio.BufferedSink;
+import okio.Okio;
+import okio.Source;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+public class InputStreamRequestBody extends RequestBody {
+
+    private InputStream inputStream;
+    private MediaType mediaType;
+
+    public static RequestBody create(final MediaType mediaType, final InputStream inputStream) {
+
+
+        return new InputStreamRequestBody(inputStream, mediaType);
+    }
+
+    private InputStreamRequestBody(InputStream inputStream, MediaType mediaType) {
+        this.inputStream = inputStream;
+        this.mediaType = mediaType;
+    }
+
+    @Override
+    public MediaType contentType() {
+        return mediaType;
+    }
+
+    @Override
+    public long contentLength() {
+        try {
+            return inputStream.available();
+        } catch (IOException e) {
+            return 0;
+        }
+    }
+
+    @Override
+    public void writeTo(BufferedSink sink) throws IOException {
+        Source source = null;
+        try {
+            source = Okio.source(inputStream);
+            sink.writeAll(source);
+        } finally {
+            Util.closeQuietly(source);
+        }
+    }
+}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java
new file mode 100644
index 000000000..38a6516bc
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java
@@ -0,0 +1,80 @@
+
+package eu.dnetlib.dhp.oa.graph.dump;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+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.*;
+
+import java.io.File;
+import java.io.Serializable;
+
+public class SendToZenodoHDFS implements Serializable {
+
+	private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class);
+
+	public static void main(final String[] args) throws Exception {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SendToZenodoHDFS.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json")));
+
+		parser.parseArgument(args);
+
+		final String hdfsPath = parser.get("hdfsPath");
+		final String hdfsNameNode = parser.get("hdfsNameNode");
+		final String access_token = parser.get("accessToken");
+		final String connection_url = parser.get("connectionUrl");
+		final String metadata = parser.get("metadata");
+		final String isLookUpUrl = parser.get("isLookUpUrl");
+
+		QueryInformationSystem qis = new QueryInformationSystem();
+		qis.setIsLookUp(ISLookupClientFactory.getLookUpService(isLookUpUrl));
+		CommunityMap communityMap = qis.getCommunityMap();
+
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
+
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			.listFiles(
+				new Path(hdfsPath), true);
+		APIClient apiClient = new APIClient(connection_url, access_token);
+		apiClient.connect();
+		while (fileStatusListIterator.hasNext()) {
+			LocatedFileStatus fileStatus = fileStatusListIterator.next();
+
+			Path p = fileStatus.getPath();
+			String p_string = p.toString();
+			if (!p_string.endsWith("_SUCCESS")) {
+				String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
+				String community = tmp.substring(tmp.lastIndexOf("/") + 1);
+				log.info("Sending information for community: " + community);
+				String community_name = communityMap.get(community).replace(" ", "_") + ".json.gz";
+				//log.info("Copying information for community: " + community);
+				//fileSystem.copyToLocalFile(p, new Path("/tmp/" + community_name));
+				//File f = new File("/tmp/" + community_name);
+				try {
+					FSDataInputStream inputStream = fileSystem.open(p);
+					apiClient.uploadIS(inputStream, community_name);
+
+				} catch(Exception e){
+
+				}
+			}
+
+		}
+
+		apiClient.sendMretadata(metadata);
+		apiClient.publish();
+
+	}
+
+}