parser of orcid summaries from tar gz file on hdfs, that creates a sequence file with authors informations (oid, name, surname, credit name)
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package orciddsmanager;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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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.log4j.Logger;
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public class OrcidDSManager {
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private static final Logger logger = Logger.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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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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}
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public void generateAuthors() throws Exception {
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Configuration conf = initConfigurationObject();
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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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SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
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}
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private Configuration initConfigurationObject() {
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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// Set FileSystem URI
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conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath));
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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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private FileSystem initFileSystemObject(Configuration conf) {
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//Get the filesystem - HDFS
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FileSystem fs = null;
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try {
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fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf);
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} catch (IOException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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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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}
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}
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package orciddsmanager;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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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.apache.hadoop.io.IOUtils;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.CompressionCodecFactory;
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import org.apache.log4j.Logger;
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import org.xml.sax.SAXException;
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import orciddsmanager.json.JsonWriter;
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import orciddsmanager.model.AuthorData;
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import orciddsmanager.xml.XMLRecordParser;
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import java.io.BufferedReader;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.net.URI;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPathExpressionException;
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public class SummariesDecompressor {
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private static final Logger logger = Logger.getLogger(SummariesDecompressor.class);
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public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath) throws Exception {
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String uri = inputUri;
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FileSystem fs = FileSystem.get(URI.create(uri), conf);
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Path inputPath = new Path(uri);
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CompressionCodecFactory factory = new CompressionCodecFactory(conf);
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CompressionCodec codec = factory.getCodec(inputPath);
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if (codec == null) {
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System.err.println("No codec found for " + uri);
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System.exit(1);
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}
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CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
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InputStream gzipInputStream = null;
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try {
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gzipInputStream = codec.createInputStream(fs.open(inputPath));
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parseTarSummaries(fs, conf, gzipInputStream, outputPath);
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} finally {
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logger.debug("Closing gzip stream");
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IOUtils.closeStream(gzipInputStream);
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}
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}
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private static void parseTarSummaries(FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
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int counter = 0;
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int nameFound = 0;
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int surnameFound = 0;
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int creditNameFound = 0;
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int errorFromOrcidFound = 0;
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int xmlParserErrorFound = 0;
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try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
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TarArchiveEntry entry = null;
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try (SequenceFile.Writer writer = SequenceFile.createWriter(conf,
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SequenceFile.Writer.file(outputPath), SequenceFile.Writer.keyClass(Text.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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while ((entry = tais.getNextTarEntry()) != null) {
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String filename = entry.getName();
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if (entry.isDirectory()) {
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logger.debug("Directory entry name: "+entry.getName());
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} else {
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logger.debug("XML record entry name: "+entry.getName());
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counter++;
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BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput
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String line;
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StringBuffer buffer = new StringBuffer();
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while ((line = br.readLine()) != null) {
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buffer.append(line);
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}
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try (ByteArrayInputStream bais = new ByteArrayInputStream(buffer.toString().getBytes())) {
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AuthorData authorData = XMLRecordParser.parse(bais);
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if (authorData!=null) {
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if (authorData.getErrorCode()!=null) {
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errorFromOrcidFound+=1;
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logger.debug("error from Orcid with code "+authorData.getErrorCode()+" for oid "+entry.getName());
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continue;
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}
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String jsonData = JsonWriter.create(authorData);
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logger.debug("oid: "+authorData.getOid() + " data: "+jsonData);
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final Text key = new Text(authorData.getOid());
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final Text value = new Text(jsonData);
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try {
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writer.append(key, value);
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} catch (IOException e) {
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logger.error("Writing to sequence file: "+e.getMessage());
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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if (authorData.getName()!=null) {
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nameFound+=1;
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}
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if (authorData.getSurname()!=null) {
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surnameFound+=1;
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}
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if (authorData.getCreditName()!=null) {
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creditNameFound+=1;
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}
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}
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else {
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logger.error("Data not retrievable ["+entry.getName()+"] "+buffer.toString());
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xmlParserErrorFound+=1;
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}
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} catch (XPathExpressionException | ParserConfigurationException | SAXException e) {
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logger.error("Parsing record from tar archive: "+e.getMessage());
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e.printStackTrace();
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}
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}
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if ((counter % 1000) == 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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}
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logger.info("Summaries parse completed");
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logger.info("Total XML records parsed: "+counter);
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logger.info("Name found: "+nameFound);
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logger.info("Surname found: "+surnameFound);
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logger.info("Credit name found: "+creditNameFound);
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logger.info("Error from Orcid found: "+errorFromOrcidFound);
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logger.info("Error parsing xml record found: "+xmlParserErrorFound);
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}
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}
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package orciddsmanager.json;
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import com.google.gson.JsonObject;
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import orciddsmanager.model.AuthorData;
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public class JsonWriter {
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public static String create(AuthorData authorData) {
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JsonObject author = new JsonObject();
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author.addProperty("oid", authorData.getOid());
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author.addProperty("name", authorData.getName());
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author.addProperty("surname", authorData.getSurname());
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if (authorData.getCreditName()!=null) {
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author.addProperty("creditname", authorData.getCreditName());
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}
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return author.toString();
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}
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}
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package orciddsmanager.model;
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public class AuthorData {
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private String oid;
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private String name;
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private String surname;
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private String creditName;
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private String errorCode;
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public String getErrorCode() {
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return errorCode;
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}
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public void setErrorCode(String errorCode) {
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this.errorCode = errorCode;
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}
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public String getName() {
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return name;
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}
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public void setName(String name) {
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this.name = name;
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}
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public String getSurname() {
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return surname;
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}
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public void setSurname(String surname) {
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this.surname = surname;
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}
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public String getCreditName() {
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return creditName;
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}
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public void setCreditName(String creditName) {
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this.creditName = creditName;
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}
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public String getOid() {
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return oid;
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}
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public void setOid(String oid) {
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this.oid = oid;
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}
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}
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package orciddsmanager.xml;
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import java.io.ByteArrayInputStream;
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import java.io.IOException;
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import java.util.Iterator;
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import javax.xml.namespace.NamespaceContext;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.xpath.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpressionException;
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import javax.xml.xpath.XPathFactory;
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import org.apache.commons.lang.StringUtils;
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import org.w3c.dom.Document;
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import org.xml.sax.SAXException;
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import orciddsmanager.model.AuthorData;
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public class XMLRecordParser {
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public static AuthorData parse(ByteArrayInputStream bytesStream) throws ParserConfigurationException, SAXException, IOException, XPathExpressionException {
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bytesStream.reset();
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DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
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builderFactory.setNamespaceAware(true);
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DocumentBuilder builder = builderFactory.newDocumentBuilder();
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Document xmlDocument = builder.parse(bytesStream);
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XPath xPath = XPathFactory.newInstance().newXPath();
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xPath.setNamespaceContext(new NamespaceContext() {
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@Override
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public Iterator getPrefixes(String arg0) {
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return null;
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}
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@Override
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public String getPrefix(String arg0) {
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return null;
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}
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@Override
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public String getNamespaceURI(String arg0) {
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if ("common".equals(arg0)) {
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return "http://www.orcid.org/ns/common";
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}
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else if ("person".equals(arg0)) {
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return "http://www.orcid.org/ns/person";
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}
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else if ("personal-details".equals(arg0)) {
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return "http://www.orcid.org/ns/personal-details";
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}
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else if ("other-name".equals(arg0)) {
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return "http://www.orcid.org/ns/other-name";
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}
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else if ("record".equals(arg0)) {
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return "http://www.orcid.org/ns/record";
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}
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else if ("error".equals(arg0)) {
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return "http://www.orcid.org/ns/error";
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}
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return null;
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}
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});
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AuthorData authorData = new AuthorData();
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String errorPath = "//error:response-code";
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String error = (String)xPath.compile(errorPath).evaluate(xmlDocument, XPathConstants.STRING);
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if (!StringUtils.isBlank(error)) {
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authorData.setErrorCode(error);
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return authorData;
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}
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String oidPath = "//record:record/@path";
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String oid = (String)xPath.compile(oidPath).evaluate(xmlDocument, XPathConstants.STRING);
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if (!StringUtils.isBlank(oid)) {
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oid = oid.substring(1);
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authorData.setOid(oid);
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}
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else {
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return null;
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}
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String namePath = "//personal-details:given-names";
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String name = (String)xPath.compile(namePath).evaluate(xmlDocument, XPathConstants.STRING);
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if (!StringUtils.isBlank(name)) {
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authorData.setName(name);
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}
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String surnamePath = "//personal-details:family-name";
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String surname = (String)xPath.compile(surnamePath).evaluate(xmlDocument, XPathConstants.STRING);
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if (!StringUtils.isBlank(surname)) {
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authorData.setSurname(surname);
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}
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String creditnamePath = "//personal-details:credit-name";
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String creditName = (String)xPath.compile(creditnamePath).evaluate(xmlDocument, XPathConstants.STRING);
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if (!StringUtils.isBlank(creditName)) {
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authorData.setCreditName(creditName);
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}
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return authorData;
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}
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}
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