forked from D-Net/dnet-hadoop
updated stuff for zenodo upload
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eeebd5a920
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@ -42,21 +42,32 @@ class QueryTest {
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}
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def extractId(input:String):String = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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(json \ "id").extractOrElse[String](null)
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}
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def myQuery(spark:SparkSession, sc:SparkContext): Unit = {
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implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
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val mapper = new ObjectMapper()
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mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
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val ds:Dataset[Publication] = spark.read.load("/tmp/p").as[Publication]
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val sc = spark.sparkContext
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ds.filter(p =>p.getBestaccessright!= null && p.getBestaccessright.getClassname.nonEmpty).count()
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val typologies =List("dataset","datasource","organization","otherresearchproduct","project","publication","software")
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val basePath ="/tt"
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typologies.map(tp => sc.textFile(s"$basePath/dataset").map(s =>extractId(tp) ).distinct.count()).sum()
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}
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@ -12,6 +12,7 @@ import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.MakeTarArchive;
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public class MakeTar implements Serializable {
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@ -41,71 +42,71 @@ public class MakeTar implements Serializable {
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FileSystem fileSystem = FileSystem.get(conf);
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makeTArArchive(fileSystem, inputPath, outputPath);
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MakeTarArchive.tarMaxSize(fileSystem, inputPath, outputPath, "scholix_dump", 25);
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}
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public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
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RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
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while (dir_iterator.hasNext()) {
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LocatedFileStatus fileStatus = dir_iterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
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write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
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}
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}
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private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
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throws IOException {
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Path hdfsWritePath = new Path(outputPath);
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FSDataOutputStream fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fileSystem.delete(hdfsWritePath, true);
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}
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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new Path(inputPath), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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if (!p_string.endsWith("_SUCCESS")) {
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String name = p_string.substring(p_string.lastIndexOf("/") + 1);
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TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
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entry.setSize(fileStatus.getLen());
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ar.putArchiveEntry(entry);
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InputStream is = fileSystem.open(fileStatus.getPath());
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BufferedInputStream bis = new BufferedInputStream(is);
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int count;
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byte data[] = new byte[1024];
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while ((count = bis.read(data, 0, data.length)) != -1) {
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ar.write(data, 0, count);
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}
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bis.close();
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ar.closeArchiveEntry();
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}
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}
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ar.close();
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}
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// public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException {
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//
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// RemoteIterator<LocatedFileStatus> dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath));
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//
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// while (dir_iterator.hasNext()) {
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// LocatedFileStatus fileStatus = dir_iterator.next();
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//
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// Path p = fileStatus.getPath();
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// String p_string = p.toString();
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// String entity = p_string.substring(p_string.lastIndexOf("/") + 1);
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//
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// write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity);
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// }
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//
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// }
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//
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// private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
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// throws IOException {
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//
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// Path hdfsWritePath = new Path(outputPath);
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// FSDataOutputStream fsDataOutputStream = null;
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// if (fileSystem.exists(hdfsWritePath)) {
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// fileSystem.delete(hdfsWritePath, true);
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//
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// }
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// fsDataOutputStream = fileSystem.create(hdfsWritePath);
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//
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// TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
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//
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// RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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// .listFiles(
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// new Path(inputPath), true);
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//
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// while (fileStatusListIterator.hasNext()) {
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// LocatedFileStatus fileStatus = fileStatusListIterator.next();
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//
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// Path p = fileStatus.getPath();
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// String p_string = p.toString();
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// if (!p_string.endsWith("_SUCCESS")) {
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// String name = p_string.substring(p_string.lastIndexOf("/") + 1);
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// TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz");
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// entry.setSize(fileStatus.getLen());
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// ar.putArchiveEntry(entry);
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//
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// InputStream is = fileSystem.open(fileStatus.getPath());
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//
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// BufferedInputStream bis = new BufferedInputStream(is);
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//
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// int count;
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// byte data[] = new byte[1024];
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// while ((count = bis.read(data, 0, data.length)) != -1) {
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// ar.write(data, 0, count);
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// }
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// bis.close();
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// ar.closeArchiveEntry();
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//
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// }
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//
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// }
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//
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// ar.close();
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// }
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}
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@ -73,7 +73,7 @@ public class SendToZenodoHDFS implements Serializable {
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}
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zenodoApiClient.sendMretadata(metadata);
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zenodoApiClient.publish();
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// zenodoApiClient.publish();
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}
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@ -8,10 +8,10 @@
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<name>targetPath</name>
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<description>the target path</description>
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</property>
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<property>
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<name>metadata</name>
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<description>the metadata</description>
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</property>
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<!-- <property>-->
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<!-- <name>metadata</name>-->
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<!-- <description>the metadata</description>-->
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<!-- </property>-->
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</parameters>
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<start to="send_zenodo"/>
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@ -34,20 +34,20 @@
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</action>
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<action name="send_zenodo">
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<java>
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<main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class>
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<arg>--hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg>
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<arg>--connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg>
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<arg>--metadata</arg><arg>${metadata}</arg>
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<arg>--conceptRecordId</arg><arg>1200252</arg>
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<arg>--newDeposition</arg><arg>false</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<!-- <action name="send_zenodo">-->
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<!-- <java>-->
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<!-- <main-class>eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS</main-class>-->
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<!-- <arg>--hdfsPath</arg><arg>/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar</arg>-->
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<!-- <arg>--nameNode</arg><arg>${nameNode}</arg>-->
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<!-- <arg>--accessToken</arg><arg>b6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv</arg>-->
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<!-- <arg>--connectionUrl</arg><arg>https://zenodo.org/api/deposit/depositions</arg>-->
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<!-- <arg>--metadata</arg><arg>${metadata}</arg>-->
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<!-- <arg>--conceptRecordId</arg><arg>1200252</arg>-->
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<!-- <arg>--newDeposition</arg><arg>false</arg>-->
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<!-- </java>-->
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<!-- <ok to="End"/>-->
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<!-- <error to="Kill"/>-->
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<!-- </action>-->
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<end name="End"/>
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</workflow-app>
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