[MakeTar] added second step of tar creation to include all the funders with fundRef identifier as id to be in the same folder (Zenodo allows maximum 100 files per deposition)

dump/src/main/java/eu/dnetlib/dhp/oa/common/MakeTarArchive.java

@@ -51,7 +51,7 @@ public class MakeTarArchive implements Serializable {
 		final boolean rename = Optional
 			.ofNullable(parser.get("rename"))
 			.map(Boolean::valueOf)
-			.orElse(Boolean.FALSE);
+			.orElse(Boolean.TRUE);
 
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);

dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java

@@ -5,12 +5,14 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.util.Optional;
 
+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.FileSystem;
 import org.apache.hadoop.fs.LocatedFileStatus;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.fs.RemoteIterator;
+import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -45,18 +47,50 @@ public class MakeTar implements Serializable {
 			.map(Integer::valueOf)
 			.orElse(10);
 
+		final boolean secondTar = Optional
+			.ofNullable(parser.get("secondTar"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.FALSE);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
 		FileSystem fileSystem = FileSystem.get(conf);
 
-		makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit);
+		makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit, secondTar);
 
 	}
 
-	public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
+	public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit,
+		boolean secondTar)
 		throws IOException {
 
+		if (secondTar) {
+			Path movePath = new Path("/tmp/temp_tar/fundRef");
+			fileSystem.mkdirs(movePath);
+
+			RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+				.listFiles(
+					new Path(outputPath), true);
+
+			while (fileStatusListIterator.hasNext()) {
+				Path p = fileStatusListIterator.next().getPath();
+				String pString = p.toString();
+				if (!pString.endsWith("_SUCCESS")) {
+					String name = pString.substring(pString.lastIndexOf("/") + 1);
+					if (name.startsWith("10") || name.startsWith("50")) {
+						fileSystem.rename(p, new Path("/tmp/temp_tar/fundRef/" + name));
+					}
+				}
+			}
+			execOnDir(fileSystem, "/tmp/temp_tar", outputPath, gBperSplit);
+		} else
+			execOnDir(fileSystem, inputPath, outputPath, gBperSplit);
+
+	}
+
+	private static void execOnDir(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
+		throws IOException {
 		RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
 
 		while (dirIterator.hasNext()) {
@@ -68,7 +102,6 @@ public class MakeTar implements Serializable {
 
 			MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit, true);
 		}
-
 	}
 
 }

dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java

@@ -76,11 +76,13 @@ public class ProjectsSubsetSparkJob implements Serializable {
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.json(outputPath);
+		projectList.write().mode(SaveMode.Overwrite).option("compression", "gzip").text("/workingDir/temp");
 		Utils
 			.readPath(spark, outputPath, Project.class)
-			.map((MapFunction<Project, String>) p -> p.getId(), Encoders.STRING())
+			.map((MapFunction<Project, String>) eu.dnetlib.dhp.oa.model.Project::getId, Encoders.STRING())
+			.union(spark.read().textFile("/workingDir/temp"))
 			.write()
-			.mode(SaveMode.Append)
+			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.text(projectListPath);
 	}

dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json

@@ -23,6 +23,12 @@
 		"paramLongName":"splitSize",
 		"paramDescription": "the maximum size of the archive",
 		"paramRequired": false
+	},
+	{
+		"paramName":"st",
+		"paramLongName":"secondTar",
+		"paramDescription": "the maximum size of the archive",
+		"paramRequired": false
 	}
 ]
 

dump/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml

@@ -305,6 +305,25 @@
             <arg>--nameNode</arg><arg>${nameNode}</arg>
             <arg>--sourcePath</arg><arg>${outputPath}/dump</arg>
         </java>
+        <ok to="second_archive"/>
+        <error to="Kill"/>
+    </action>
+
+    <decision name="second_archive">
+        <switch>
+            <case to="make_second_tar">${wf:conf('dumpType') eq "funder"}</case>
+            <default to="should_upload"/>
+        </switch>
+    </decision>
+
+    <action name="make_second_tar">
+        <java>
+            <main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
+            <arg>--hdfsPath</arg><arg>${outputPath}/tar</arg>
+            <arg>--nameNode</arg><arg>${nameNode}</arg>
+            <arg>--sourcePath</arg><arg>${outputPath}/dump</arg>
+            <arg>--secondTar</arg><arg>true</arg>
+        </java>
         <ok to="should_upload"/>
         <error to="Kill"/>
     </action>

dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java

@@ -56,7 +56,7 @@ public class MakeTarTest {
 
 		String inputPath = workingDir + "/zenodo/";
 
-		MakeTar.makeTArArchive(fs, inputPath, "/tmp/out", 0);
+		MakeTar.makeTArArchive(fs, inputPath, "/tmp/out", 0, false);
 
 	}
 }

dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateEntityTest.java

@@ -73,8 +73,11 @@ public class CreateEntityTest {
 					Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("fish"));
 					Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("aqua"));
 					Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("sea"));
-                    Assertions.assertEquals(c
+					Assertions
-                            .getId(), String
+						.assertEquals(
+							c
+								.getId(),
+							String
 								.format(
 									"%s::%s", Constants.CONTEXT_NS_PREFIX,
 									DHPUtils.md5(c.getAcronym())));
@@ -82,9 +85,13 @@ public class CreateEntityTest {
 					Assertions.assertEquals("mes", c.getAcronym());
 					break;
 				case "clarin":
-                    Assertions.assertEquals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE, c.getType());
+					Assertions
-                    Assertions.assertEquals(c
+						.assertEquals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE, c.getType());
-                            .getId(), String
+					Assertions
+						.assertEquals(
+							c
+								.getId(),
+							String
 								.format(
 									"%s::%s", Constants.CONTEXT_NS_PREFIX,
 									DHPUtils.md5(c.getAcronym())));