added upload to zenodo node
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parent
271b4db450
commit
346ed65e2c
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@ -62,6 +62,10 @@
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<artifactId>dhp-schemas</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpmime</artifactId>
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</dependency>
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<dependency>
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<groupId>org.elasticsearch</groupId>
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@ -0,0 +1,80 @@
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package eu.dnetlib.dhp.export.zenodo;
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import java.io.Serializable;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.*;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
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import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
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public class SendToZenodoHDFS implements Serializable {
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private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class);
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public static void main(final String[] args) throws Exception, MissingConceptDoiException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SendToZenodoHDFS.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/export/upload_zenodo.json")));
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parser.parseArgument(args);
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final String hdfsPath = parser.get("hdfsPath");
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final String hdfsNameNode = parser.get("nameNode");
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final String access_token = parser.get("accessToken");
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final String connection_url = parser.get("connectionUrl");
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final String metadata = parser.get("metadata");
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final Boolean newDeposition = Boolean.valueOf(parser.get("newDeposition"));
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final String concept_rec_id = Optional
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.ofNullable(parser.get("conceptRecordId"))
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.orElse(null);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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new Path(hdfsPath), true);
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ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token);
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if (newDeposition) {
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zenodoApiClient.newDeposition();
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} else {
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if (concept_rec_id == null) {
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throw new MissingConceptDoiException("No concept record id has been provided");
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}
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zenodoApiClient.newVersion(concept_rec_id);
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}
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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 tmp = p_string.substring(0, p_string.lastIndexOf("/"));
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String name = p_string.substring(p_string.lastIndexOf("/") + 1);
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log.info("Sending information for community: " + name);
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FSDataInputStream inputStream = fileSystem.open(p);
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zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
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}
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}
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zenodoApiClient.sendMretadata(metadata);
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zenodoApiClient.publish();
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}
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}
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@ -0,0 +1,45 @@
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[
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{
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"paramName":"nd",
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"paramLongName":"newDeposition",
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"paramDescription": "if it is a new deposition (true) or a new version (false)",
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"paramRequired": true
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},
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{
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"paramName":"cri",
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"paramLongName":"conceptRecordId",
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"paramDescription": "The id of the concept record for a new version",
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"paramRequired": false
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},
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{
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"paramName":"hdfsp",
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"paramLongName":"hdfsPath",
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"paramDescription": "the path of the folder tofind files to send to Zenodo",
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"paramRequired": true
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},
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{
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"paramName": "nn",
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"paramLongName": "nameNode",
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"paramDescription": "the name node",
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"paramRequired": true
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},
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{
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"paramName": "at",
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"paramLongName": "accessToken",
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"paramDescription": "the access token for the deposition",
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"paramRequired": false
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},
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{
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"paramName":"cu",
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"paramLongName":"connectionUrl",
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"paramDescription": "the url to connect to deposit",
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"paramRequired": false
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},
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{
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"paramName":"m",
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"paramLongName":"metadata",
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"paramDescription": "metadata associated to the deposition",
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"paramRequired": false
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}
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]
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@ -39,4 +39,10 @@
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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@ -8,9 +8,13 @@
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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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</parameters>
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<start to="MakeTar"/>
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<start to="send_zenodo"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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@ -29,5 +33,21 @@
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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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