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dnet-hadoop
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This commit is contained in:
Miriam Baglioni 2020-06-19 17:39:46 +02:00
parent 44a12d244f
commit 669a509430
4 changed files with 85 additions and 78 deletions
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33
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/APIClient.java
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@ -5,21 +5,12 @@ import java.io.*;
import java.io.IOException; import java.io.IOException;
import java.nio.charset.StandardCharsets; import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.http.HttpEntity; import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse; import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient; import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.HttpPost; import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpPut; import org.apache.http.client.methods.HttpPut;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.InputStreamEntity;
import org.apache.http.entity.StringEntity; import org.apache.http.entity.StringEntity;
import org.apache.http.entity.mime.MultipartEntityBuilder; import org.apache.http.entity.mime.MultipartEntityBuilder;
import org.apache.http.impl.client.DefaultHttpClient; import org.apache.http.impl.client.DefaultHttpClient;
import org.apache.http.util.EntityUtils; import org.apache.http.util.EntityUtils;
@ -28,6 +19,8 @@ import com.google.gson.Gson;
import eu.dnetlib.dhp.oa.graph.dump.zenodo.ZenodoModel; import eu.dnetlib.dhp.oa.graph.dump.zenodo.ZenodoModel;
//import org.apache.http.entity.mime.MultipartEntityBuilder;
public class APIClient implements Serializable { public class APIClient implements Serializable {
String urlString; String urlString;
@ -81,9 +74,26 @@ public class APIClient implements Serializable {
return response.getStatusLine().getStatusCode(); return response.getStatusLine().getStatusCode();
} }
// public int upload(InputStream is, String file_name) throws IOException {
// HttpClient client = new DefaultHttpClient();
//
// HttpPut put = new HttpPut(bucket + "/" + file_name);
// put.setHeader("Authorization", "Bearer " + access_token);
// put.addHeader("Content-Type", "application/zip");
//
// HttpEntity data = MultipartEntityBuilder
// .create()
// // .addPart("file", new ByteArrayInputStream(is));
// .addBinaryBody(file_name, is, ContentType.APPLICATION_OCTET_STREAM, file_name)
// .build();
// put.setEntity(data);
//
// HttpResponse response = client.execute(put);
//
// return response.getStatusLine().getStatusCode();
// }
public int upload(File file, String file_name) throws IOException { public int upload(File file, String file_name) throws IOException {
HttpClient client = new DefaultHttpClient(); HttpClient client = new DefaultHttpClient();
@ -112,12 +122,11 @@ public class APIClient implements Serializable {
HttpResponse response = client.execute(post); HttpResponse response = client.execute(post);
return response.getStatusLine().getStatusCode(); return response.getStatusLine().getStatusCode();
} }
public int publish() throws IOException { public int publish() throws IOException {
HttpClient client = new DefaultHttpClient(); HttpClient client = new DefaultHttpClient();
HttpPost post = new HttpPost(urlString +"/"+ deposition_id +"/actions/publish") ; HttpPost post = new HttpPost(urlString + "/" + deposition_id + "/actions/publish");
post.setHeader("Authorization", "Bearer " + access_token); post.setHeader("Authorization", "Bearer " + access_token);
HttpResponse response = client.execute(post); HttpResponse response = client.execute(post);

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java
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@ -40,7 +40,7 @@ public class QueryInformationSystem {
this.isLookUp = isLookUpService; this.isLookUp = isLookUpService;
} }
public static CommunityMap getMap(List<String> communityMap) { private CommunityMap getMap(List<String> communityMap) {
final CommunityMap map = new CommunityMap(); final CommunityMap map = new CommunityMap();
communityMap.stream().forEach(xml -> { communityMap.stream().forEach(xml -> {

128
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodo.java
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@ -1,14 +1,11 @@
package eu.dnetlib.dhp.oa.graph.dump; package eu.dnetlib.dhp.oa.graph.dump;
import com.fasterxml.jackson.databind.ObjectMapper; import java.io.File;
import com.google.gson.Gson; import java.io.Serializable;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient; import javax.management.Query;
import eu.dnetlib.dhp.oa.graph.dump.zenodo.Creator;
import eu.dnetlib.dhp.oa.graph.dump.zenodo.Metadata;
import eu.dnetlib.dhp.oa.graph.dump.zenodo.ZenodoModel;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
@ -18,72 +15,73 @@ import org.apache.hadoop.fs.LocatedFileStatus;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.RemoteIterator; import org.apache.hadoop.fs.RemoteIterator;
import java.io.BufferedWriter; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.io.File; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import java.io.Serializable;
import java.sql.ResultSet;
import java.util.Arrays;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
public class SendToZenodo implements Serializable { public class SendToZenodo implements Serializable {
private static final Log log = LogFactory.getLog(SendToZenodo.class); private static final Log log = LogFactory.getLog(SendToZenodo.class);
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SendToZenodo.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json")));
public static void main(final String[] args) throws Exception { parser.parseArgument(args);
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SendToZenodo.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json")));
parser.parseArgument(args); final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("hdfsNameNode");
final String access_token = parser.get("accessToken");
final String connection_url = parser.get("connectionUrl");
final String metadata = parser.get("metadata");
final String isLookUpUrl = parser.get("isLookUpUrl");
QueryInformationSystem qis = new QueryInformationSystem();
qis.setIsLookUp(ISLookupClientFactory.getLookUpService(isLookUpUrl));
CommunityMap communityMap = qis.getCommunityMap();
final String hdfsPath = parser.get("hdfsPath"); Configuration conf = new Configuration();
final String hdfsNameNode = parser.get("hdfsNameNode"); conf.set("fs.defaultFS", hdfsNameNode);
final String access_token = parser.get("accessToken");
final String connection_url = parser.get("url");
final String metadata = parser.get("metadata");
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf); FileSystem fileSystem = FileSystem.get(conf);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
new Path(hdfsPath), true);
APIClient apiClient = new APIClient(connection_url, access_token);
apiClient.connect();
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem.listFiles( Path p = fileStatus.getPath();
new Path(hdfsPath), true); String p_string = p.toString();
APIClient apiClient = new APIClient(connection_url, access_token); String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
apiClient.connect(); String community = tmp.substring(tmp.lastIndexOf("/") + 1);
while(fileStatusListIterator.hasNext()){ log.info("Sending information for community: " + community);
LocatedFileStatus fileStatus = fileStatusListIterator.next(); String community_name = communityMap.get(community).replace(" ", "_");
log.info("Copying information for community: " + community);
fileSystem.copyToLocalFile(p, new Path("/tmp/" + community_name));
File f = new File("/tmp/" + community_name);
try {
apiClient.upload(f, community_name);
apiClient.sendMretadata(metadata);
apiClient.publish();
} catch (Exception e) {
if (f.exists()) {
log.info("Deleting information for community: " + community);
f.delete();
}
} finally {
if (f.exists()) {
log.info("Deleting information for community: " + community);
f.delete();
}
}
}
Path p = fileStatus.getPath(); }
String p_string = p.toString();
String tmp = p_string.substring(0, p_string.lastIndexOf("/") );
String community = tmp.substring(tmp.lastIndexOf("/") + 1);
log.info("Sending information for community: " + community);
fileSystem.copyToLocalFile(p, new Path("/tmp/" + community));
}
File f = new File("/tmp/" + community);
apiClient.upload(f, community);
apiClient.sendMretadata(metadata);
apiClient.publish();
if (f.exists()){
f.delete();
}
}
}
}

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json Normal file
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