changed to mirror the new Zenodo API interaction
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parent
ec1dac5847
commit
a25e8071c5
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@ -66,7 +66,7 @@ public class MakeTar implements Serializable {
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String pathString = p.toString();
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String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
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MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
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MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit, true);
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}
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}
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@ -83,7 +83,7 @@ public class SendToZenodoHDFS implements Serializable {
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String name = pString.substring(pString.lastIndexOf("/") + 1);
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FSDataInputStream inputStream = fileSystem.open(p);
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zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
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zenodoApiClient.uploadIS(inputStream, name);
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}
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@ -1,154 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.IOException;
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import java.nio.file.Files;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.*;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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import com.google.gson.Gson;
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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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import eu.dnetlib.dhp.oa.graph.dump.eosc.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.eosc.Utils;
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@Disabled
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public class ZenodoUploadTest {
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private static String workingDir;
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private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
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private final String ACCESS_TOKEN = "";
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(UpdateProjectInfoTest.class.getSimpleName())
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.toString();
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}
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@Test
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void testNewDeposition() throws IOException {
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CommunityMap communityMap = new CommunityMap();
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communityMap.put("ni", "Neuroinformatics");
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communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage");
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LocalFileSystem fs = FileSystem.getLocal(new Configuration());
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
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.getPath()),
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new Path(workingDir + "/zenodo/ni/ni"));
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
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.getPath()),
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new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
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ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
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ACCESS_TOKEN);
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client.newDeposition();
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// the second boolean parameter here sets the recursion to true
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
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.listFiles(
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new Path(workingDir + "/zenodo"), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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String p_string = fileStatus.getPath().toString();
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int index = p_string.lastIndexOf("/");
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String community = p_string.substring(0, index);
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community = community.substring(community.lastIndexOf("/") + 1);
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String community_name = communityMap.get(community).replace(" ", "_");
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// fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name));
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System.out.println(community);
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// File f = new File("/tmp/" + community_name);
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FSDataInputStream inputStream = fs.open(fileStatus.getPath());
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System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen()));
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}
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String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}";
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System.out.println(client.sendMretadata(metadata));
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System.out.println(client.publish());
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}
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@Test
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void testNewVersion() throws IOException, MissingConceptDoiException {
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ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
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ACCESS_TOKEN);
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client.newVersion("656628");
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CommunityMap communityMap = new CommunityMap();
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communityMap.put("ni", "Neuroinformatics");
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communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage");
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LocalFileSystem fs = FileSystem.getLocal(new Configuration());
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
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.getPath()),
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new Path(workingDir + "/zenodo/ni/ni"));
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fs
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.copyFromLocalFile(
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false, new Path(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
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.getPath()),
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new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
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.listFiles(
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new Path(workingDir + "/zenodo"), true);
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while (fileStatusListIterator.hasNext()) {
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LocatedFileStatus fileStatus = fileStatusListIterator.next();
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String p_string = fileStatus.getPath().toString();
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int index = p_string.lastIndexOf("/");
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String community = p_string.substring(0, index);
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community = community.substring(community.lastIndexOf("/") + 1);
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String community_name = communityMap.get(community).replace(" ", "_");
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// fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name));
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System.out.println(community);
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// File f = new File("/tmp/" + community_name);
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FSDataInputStream inputStream = fs.open(fileStatus.getPath());
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System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen()));
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}
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System.out.println(client.publish());
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}
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@Test
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void readCommunityMap() throws IOException {
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LocalFileSystem fs = FileSystem.getLocal(new Configuration());
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System.out
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.println(
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new Gson()
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.toJson(
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Utils
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.readCommunityMap(
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fs, getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
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.getPath())));
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}
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}
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