forked from D-Net/dnet-hadoop
Merge branch 'doiboost' of code-repo.d4science.org:D-Net/dnet-hadoop into doiboost
This commit is contained in:
commit
7029942e06
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@ -1,35 +1,30 @@
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package eu.dnetlib.doiboost.orcid;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.net.URI;
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import java.util.Properties;
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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.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class OrcidDSManager {
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private static final Logger logger = LoggerFactory.getLogger(OrcidDSManager.class);
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private String hdfsServerUri;
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private String hadoopUsername;
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private String hdfsOrcidDefaultPath;
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private String summariesFileNameTarGz;
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private String outputAuthorsPath;
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public static void main(String[] args) {
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public static void main(String[] args) throws IOException, Exception {
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logger.info("OrcidDSManager started");
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OrcidDSManager orcidDSManager = new OrcidDSManager();
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try {
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orcidDSManager.initGARRProperties();
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orcidDSManager.generateAuthors();
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} catch (Exception e) {
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logger.error("Generating authors data: "+e.getMessage());
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}
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orcidDSManager.loadArgs(args);
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orcidDSManager.generateAuthors();
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}
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public void generateAuthors() throws Exception {
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@ -37,7 +32,7 @@ public class OrcidDSManager {
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FileSystem fs = initFileSystemObject(conf);
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String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz);
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logger.info("Started parsing "+tarGzUri);
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Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsPath).concat(Long.toString(System.currentTimeMillis())).concat("/authors_part"));
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Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsPath).concat(Long.toString(System.currentTimeMillis())).concat("/authors.seq"));
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SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
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}
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@ -49,9 +44,6 @@ public class OrcidDSManager {
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// Because of Maven
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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// Set HADOOP user
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System.setProperty("HADOOP_USER_NAME", hadoopUsername);
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System.setProperty("hadoop.home.dir", "/");
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return conf;
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}
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@ -66,34 +58,18 @@ public class OrcidDSManager {
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}
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return fs;
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}
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private void loadProperties() throws FileNotFoundException, IOException {
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Properties appProps = new Properties();
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ClassLoader classLoader = ClassLoader.getSystemClassLoader();
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appProps.load(classLoader.getResourceAsStream("orciddsmanager/props/app.properties"));
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hdfsServerUri = appProps.getProperty("hdfs.server.uri");
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hadoopUsername = appProps.getProperty("hdfs.hadoopusername");
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hdfsOrcidDefaultPath = appProps.getProperty("hdfs.orcid.defaultpath");
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summariesFileNameTarGz = appProps.getProperty("hdfs.orcid.summariesfilename.tar.gz");
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outputAuthorsPath = appProps.getProperty("hdfs.orcid.output.authorspath");
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}
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private void initDefaultProperties() throws FileNotFoundException, IOException {
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hdfsServerUri = "hdfs://localhost:9000";
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hadoopUsername = "enrico.ottonello";
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hdfsOrcidDefaultPath = "/user/enrico.ottonello/orcid/";
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summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
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outputAuthorsPath = "output/";
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}
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private void initGARRProperties() throws FileNotFoundException, IOException {
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hdfsServerUri = "hdfs://hadoop-rm1.garr-pa1.d4science.org:8020";
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hadoopUsername = "root";
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hdfsOrcidDefaultPath = "/data/orcid_summaries/";
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summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
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outputAuthorsPath = "output/";
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private void loadArgs(String[] args) throws IOException, Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(OrcidDSManager.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json")));
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parser.parseArgument(args);
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final String hdfsServerUri = parser.get("hdfsServerUri");
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logger.info("HDFS URI: "+hdfsServerUri);
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Path hdfsOrcidDefaultPath = new Path(parser.get("hdfsOrcidDefaultPath"));
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logger.info("Default Path: "+hdfsOrcidDefaultPath);
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final String summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
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logger.info("Summaries File Name: "+summariesFileNameTarGz);
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final String outputAuthorsPath = parser.get("summariesFileNameTarGz");
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logger.info("Output Authors Data: "+outputAuthorsPath);
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}
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}
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@ -122,14 +122,14 @@ public class SummariesDecompressor {
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}
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}
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if ((counter % 1000) == 0) {
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if ((counter % 100000) == 0) {
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logger.info("Current xml records parsed: "+counter);
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}
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}
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}
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} catch (IOException e) {
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logger.error("Parsing record from gzip archive: "+e.getMessage());
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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logger.info("Summaries parse completed");
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logger.info("Total XML records parsed: "+counter);
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@ -0,0 +1,6 @@
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[
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{"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true},
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{"paramName":"d", "paramLongName":"hdfsOrcidDefaultPath", "paramDescription": "the default work path", "paramRequired": true},
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{"paramName":"f", "paramLongName":"summariesFileNameTarGz", "paramDescription": "the name of the summaries orcid file", "paramRequired": true},
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{"paramName":"o", "paramLongName":"outputAuthorsPath", "paramDescription": "the relative folder of the sequencial file to write", "paramRequired": true}
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]
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@ -29,10 +29,10 @@
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
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<!-- ENRICO FILL THE RIGHT ARG SECTION -->
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<arg>-t</arg><arg>${workingPath}/input/crossref/index_dump</arg>
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<arg>-d</arg><arg>${workingPath}/</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
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<arg>-o</arg><arg>output/</arg>
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</java>
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<ok to="End"/>
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<error to="Kill"/>
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