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added description, changed parameter name and added method

This commit is contained in:
Miriam Baglioni 2020-08-11 15:27:31 +02:00
parent dc5fc5366d
commit cf4d918787
3 changed files with 39 additions and 77 deletions
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54
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SaveCommunityMap.java → dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java
View File

@ -1,31 +1,28 @@
/**
* This class connects with the IS related to the isLookUpUrl got as parameter.
* It saves the information about the context that will guide the dump of the results.
* The information saved is a HashMap. The key is the id of a community - research infrastructure/initiative , the
* value is the label of the research community - research infrastructure/initiative.
*
*/
package eu.dnetlib.dhp.oa.graph.dump.community;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.SparkConf;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextEntities;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
public class SaveCommunityMap implements Serializable {
@ -74,45 +71,10 @@ public class SaveCommunityMap implements Serializable {
final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl);
// Boolean isSparkSessionManaged = Optional
// .ofNullable(parser.get("isSparkSessionManaged"))
// .map(Boolean::valueOf)
// .orElse(Boolean.TRUE);
// log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl);
scm.saveCommunityMap();
// CommunityMap communityMap = queryInformationSystem.getCommunityMap();
// SparkConf conf = new SparkConf();
//
// runWithSparkSession(
// conf,
// isSparkSessionManaged,
// spark -> {
// Utils.removeOutputDir(spark, outputPath);
//
//// execDump(spark, inputPath, outputPath, communityMap, inputClazz, outputClazz, graph);// ,
// // dumpClazz);
// });
// Configuration conf = new Configuration();
// conf.set("fs.defaultFS", nameNode);
// FileSystem fileSystem = FileSystem.get(conf);
// Path hdfsWritePath = new Path(outputPath);
// FSDataOutputStream fsDataOutputStream = null;
// if (fileSystem.exists(hdfsWritePath)) {
// fsDataOutputStream = fileSystem.append(hdfsWritePath);
// } else {
// fsDataOutputStream = fileSystem.create(hdfsWritePath);
// }
//
// BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
//
// writer.write(OBJECT_MAPPER.writeValueAsString(communityMap));
// writer.close();
}
private void saveCommunityMap() throws ISLookUpException, IOException {

40
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java
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@ -1,25 +1,17 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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.utils.ISLookupClientFactory;
public class SendToZenodoHDFS implements Serializable {
@ -36,7 +28,7 @@ public class SendToZenodoHDFS implements Serializable {
parser.parseArgument(args);
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("hdfsNameNode");
final String hdfsNameNode = parser.get("nameNode");
final String access_token = parser.get("accessToken");
final String connection_url = parser.get("connectionUrl");
final String metadata = parser.get("metadata");
@ -51,7 +43,7 @@ public class SendToZenodoHDFS implements Serializable {
FileSystem fileSystem = FileSystem.get(conf);
CommunityMap communityMap = readCommunityMap(fileSystem, communityMapPath);
CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
@ -72,13 +64,15 @@ public class SendToZenodoHDFS implements Serializable {
Path p = fileStatus.getPath();
String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) {
String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
String community = tmp.substring(tmp.lastIndexOf("/") + 1);
log.info("Sending information for community: " + community);
String community_name = communityMap.get(community).replace(" ", "_") + ".json.gz";
// String tmp = p_string.substring(0, p_string.lastIndexOf("/"));
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
log.info("Sending information for community: " + name);
if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) {
name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar";
}
FSDataInputStream inputStream = fileSystem.open(p);
zenodoApiClient.uploadIS(inputStream, community_name, fileStatus.getLen());
zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
}
@ -89,20 +83,4 @@ public class SendToZenodoHDFS implements Serializable {
}
public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
StringBuffer sb = new StringBuffer();
try {
String line;
while ((line = br.readLine()) != null) {
sb.append(line);
}
} finally {
br.close();
}
return new Gson().fromJson(sb.toString(), CommunityMap.class);
}
}

22
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java
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@ -1,6 +1,12 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
@ -48,4 +54,20 @@ public class Utils {
return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class);
}
public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
StringBuffer sb = new StringBuffer();
try {
String line;
while ((line = br.readLine()) != null) {
sb.append(line);
}
} finally {
br.close();
}
return new Gson().fromJson(sb.toString(), CommunityMap.class);
}
}