forked from D-Net/dnet-hadoop
added description, changed parameter name and added method
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dc5fc5366d
commit
cf4d918787
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@ -1,31 +1,28 @@
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/**
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* This class connects with the IS related to the isLookUpUrl got as parameter.
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* It saves the information about the context that will guide the dump of the results.
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* The information saved is a HashMap. The key is the id of a community - research infrastructure/initiative , the
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* value is the label of the research community - research infrastructure/initiative.
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*
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*/
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package eu.dnetlib.dhp.oa.graph.dump.community;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.spark.SparkConf;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextEntities;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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public class SaveCommunityMap implements Serializable {
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@ -74,45 +71,10 @@ public class SaveCommunityMap implements Serializable {
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final String isLookUpUrl = parser.get("isLookUpUrl");
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log.info("isLookUpUrl: {}", isLookUpUrl);
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// Boolean isSparkSessionManaged = Optional
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// .ofNullable(parser.get("isSparkSessionManaged"))
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// .map(Boolean::valueOf)
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// .orElse(Boolean.TRUE);
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// log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl);
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scm.saveCommunityMap();
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// CommunityMap communityMap = queryInformationSystem.getCommunityMap();
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// SparkConf conf = new SparkConf();
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//
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// runWithSparkSession(
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// conf,
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// isSparkSessionManaged,
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// spark -> {
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// Utils.removeOutputDir(spark, outputPath);
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//
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//// execDump(spark, inputPath, outputPath, communityMap, inputClazz, outputClazz, graph);// ,
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// // dumpClazz);
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// });
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// Configuration conf = new Configuration();
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// conf.set("fs.defaultFS", nameNode);
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// FileSystem fileSystem = FileSystem.get(conf);
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// Path hdfsWritePath = new Path(outputPath);
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// FSDataOutputStream fsDataOutputStream = null;
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// if (fileSystem.exists(hdfsWritePath)) {
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// fsDataOutputStream = fileSystem.append(hdfsWritePath);
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// } else {
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// fsDataOutputStream = fileSystem.create(hdfsWritePath);
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// }
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//
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// BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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//
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// writer.write(OBJECT_MAPPER.writeValueAsString(communityMap));
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// writer.close();
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}
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private void saveCommunityMap() throws ISLookUpException, IOException {
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@ -1,25 +1,17 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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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 com.google.gson.Gson;
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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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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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public class SendToZenodoHDFS implements Serializable {
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@ -36,7 +28,7 @@ public class SendToZenodoHDFS implements Serializable {
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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("hdfsNameNode");
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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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@ -51,7 +43,7 @@ public class SendToZenodoHDFS implements Serializable {
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FileSystem fileSystem = FileSystem.get(conf);
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CommunityMap communityMap = readCommunityMap(fileSystem, communityMapPath);
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CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath);
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RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
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.listFiles(
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@ -72,13 +64,15 @@ public class SendToZenodoHDFS implements Serializable {
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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 community = tmp.substring(tmp.lastIndexOf("/") + 1);
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log.info("Sending information for community: " + community);
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String community_name = communityMap.get(community).replace(" ", "_") + ".json.gz";
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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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if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) {
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name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar";
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}
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FSDataInputStream inputStream = fileSystem.open(p);
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zenodoApiClient.uploadIS(inputStream, community_name, fileStatus.getLen());
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zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
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}
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@ -89,20 +83,4 @@ public class SendToZenodoHDFS implements Serializable {
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}
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public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
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BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
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StringBuffer sb = new StringBuffer();
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try {
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String line;
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while ((line = br.readLine()) != null) {
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sb.append(line);
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}
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} finally {
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br.close();
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}
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return new Gson().fromJson(sb.toString(), CommunityMap.class);
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}
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}
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@ -1,6 +1,12 @@
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package eu.dnetlib.dhp.oa.graph.dump;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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@ -48,4 +54,20 @@ public class Utils {
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return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class);
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}
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public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
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BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
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StringBuffer sb = new StringBuffer();
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try {
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String line;
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while ((line = br.readLine()) != null) {
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sb.append(line);
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}
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} finally {
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br.close();
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}
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return new Gson().fromJson(sb.toString(), CommunityMap.class);
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}
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}
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