lsmyrnaios
/
dnet-hadoop
forked from D-Net/dnet-hadoop
1
0
Fork 0
Code Pull Requests Activity

disabled test. The testing functionalities for hte upload in Zenode are moved to common

This commit is contained in:
Miriam Baglioni 2020-08-10 12:41:11 +02:00
parent 63ad0ed209
commit c378c38546
1 changed files with 49 additions and 36 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

85
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java
View File

@ -2,16 +2,21 @@
package eu.dnetlib.dhp.oa.graph.dump; package eu.dnetlib.dhp.oa.graph.dump;
import java.io.*; import java.io.*;
import java.io.File;
import java.nio.file.Files; import java.nio.file.Files;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*; import org.apache.hadoop.fs.*;
import org.junit.jupiter.api.BeforeAll; import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import com.google.gson.Gson;
import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
@Disabled
public class ZenodoUploadTest { public class ZenodoUploadTest {
private static String workingDir; private static String workingDir;
@ -27,7 +32,7 @@ public class ZenodoUploadTest {
} }
@Test @Test
public void HDFSConnection() throws IOException { public void testNewDeposition() throws IOException {
CommunityMap communityMap = new CommunityMap(); CommunityMap communityMap = new CommunityMap();
communityMap.put("ni", "Neuroinformatics"); communityMap.put("ni", "Neuroinformatics");
communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage");
@ -46,9 +51,9 @@ public class ZenodoUploadTest {
.getPath()), .getPath()),
new Path(workingDir + "/zenodo/dh-ch/dh-ch")); new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
APIClient client = new APIClient(URL_STRING, ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN); ACCESS_TOKEN);
client.connect(); client.newDeposition();
// the second boolean parameter here sets the recursion to true // the second boolean parameter here sets the recursion to true
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
@ -63,15 +68,12 @@ public class ZenodoUploadTest {
String community = p_string.substring(0, index); String community = p_string.substring(0, index);
community = community.substring(community.lastIndexOf("/") + 1); community = community.substring(community.lastIndexOf("/") + 1);
String community_name = communityMap.get(community).replace(" ", "_"); String community_name = communityMap.get(community).replace(" ", "_");
fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name));
System.out.println(community); System.out.println(community);
File f = new File("/tmp/" + community_name); // File f = new File("/tmp/" + community_name);
System.out.println(client.upload(f, community_name)); FSDataInputStream inputStream = fs.open(fileStatus.getPath());
System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen()));
if (f.exists()) {
f.delete();
}
} }
@ -84,33 +86,34 @@ public class ZenodoUploadTest {
} }
@Test @Test
public void sendAsInputStream() throws IOException { public void testNewVersion() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
client.newVersion("656628");
CommunityMap communityMap = new CommunityMap(); CommunityMap communityMap = new CommunityMap();
communityMap.put("ni", "Neuroinformatics"); communityMap.put("ni", "Neuroinformatics");
communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage");
LocalFileSystem fs = FileSystem.getLocal(new Configuration()); LocalFileSystem fs = FileSystem.getLocal(new Configuration());
fs fs
.copyFromLocalFile( .copyFromLocalFile(
false, new Path(getClass() false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
.getPath()), .getPath()),
new Path(workingDir + "/zenodo/ni/ni")); new Path(workingDir + "/zenodo/ni/ni"));
fs fs
.copyFromLocalFile( .copyFromLocalFile(
false, new Path(getClass() false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
.getPath()), .getPath()),
new Path(workingDir + "/zenodo/dh-ch/dh-ch")); new Path(workingDir + "/zenodo/dh-ch/dh-ch"));
APIClient client = new APIClient(URL_STRING,
ACCESS_TOKEN);
client.connect();
// the second boolean parameter here sets the recursion to true
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs RemoteIterator<LocatedFileStatus> fileStatusListIterator = fs
.listFiles( .listFiles(
new Path(workingDir + "/zenodo"), true); new Path(workingDir + "/zenodo"), true);
while (fileStatusListIterator.hasNext()) { while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next(); LocatedFileStatus fileStatus = fileStatusListIterator.next();
@ -120,21 +123,31 @@ public class ZenodoUploadTest {
String community = p_string.substring(0, index); String community = p_string.substring(0, index);
community = community.substring(community.lastIndexOf("/") + 1); community = community.substring(community.lastIndexOf("/") + 1);
String community_name = communityMap.get(community).replace(" ", "_"); String community_name = communityMap.get(community).replace(" ", "_");
//fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name));
System.out.println(community); System.out.println(community);
//File f = new File("/tmp/" + community_name); // File f = new File("/tmp/" + community_name);
FSDataInputStream inputStream = fs.open(fileStatus.getPath()); FSDataInputStream inputStream = fs.open(fileStatus.getPath());
System.out.println(client.uploadIS(inputStream, community_name)); System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen()));
} }
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\"}}";
System.out.println(client.sendMretadata(metadata));
System.out.println(client.publish()); System.out.println(client.publish());
} }
@Test
public void readCommunityMap() throws IOException {
LocalFileSystem fs = FileSystem.getLocal(new Configuration());
System.out
.println(
new Gson()
.toJson(
SendToZenodoHDFS
.readCommunityMap(
fs, getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath())));
}
} }