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parser of orcid summaries from tar gz file on hdfs, that creates a sequence file with authors informations (oid, name, surname, credit name)

This commit is contained in:
Enrico Ottonello 2020-04-17 18:52:39 +02:00
parent a329ea5575
commit 7011d4203e
5 changed files with 400 additions and 0 deletions
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99
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/orciddsmanager/OrcidDSManager.java Normal file
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package orciddsmanager;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.net.URI;
import java.util.Properties;
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.log4j.Logger;
public class OrcidDSManager {
private static final Logger logger = Logger.getLogger(OrcidDSManager.class);
private String hdfsServerUri;
private String hadoopUsername;
private String hdfsOrcidDefaultPath;
private String summariesFileNameTarGz;
private String outputAuthorsPath;
public static void main(String[] args) {
logger.info("OrcidDSManager started");
OrcidDSManager orcidDSManager = new OrcidDSManager();
try {
orcidDSManager.initGARRProperties();
orcidDSManager.generateAuthors();
} catch (Exception e) {
logger.error("Generating authors data: "+e.getMessage());
}
}
public void generateAuthors() throws Exception {
Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf);
String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz);
logger.info("Started parsing "+tarGzUri);
Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsPath).concat(Long.toString(System.currentTimeMillis())).concat("/authors_part"));
SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
}
private Configuration initConfigurationObject() {
// ====== Init HDFS File System Object
Configuration conf = new Configuration();
// Set FileSystem URI
conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath));
// Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
// Set HADOOP user
System.setProperty("HADOOP_USER_NAME", hadoopUsername);
System.setProperty("hadoop.home.dir", "/");
return conf;
}
private FileSystem initFileSystemObject(Configuration conf) {
//Get the filesystem - HDFS
FileSystem fs = null;
try {
fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return fs;
}
private void loadProperties() throws FileNotFoundException, IOException {
Properties appProps = new Properties();
ClassLoader classLoader = ClassLoader.getSystemClassLoader();
appProps.load(classLoader.getResourceAsStream("orciddsmanager/props/app.properties"));
hdfsServerUri = appProps.getProperty("hdfs.server.uri");
hadoopUsername = appProps.getProperty("hdfs.hadoopusername");
hdfsOrcidDefaultPath = appProps.getProperty("hdfs.orcid.defaultpath");
summariesFileNameTarGz = appProps.getProperty("hdfs.orcid.summariesfilename.tar.gz");
outputAuthorsPath = appProps.getProperty("hdfs.orcid.output.authorspath");
}
private void initDefaultProperties() throws FileNotFoundException, IOException {
hdfsServerUri = "hdfs://localhost:9000";
hadoopUsername = "enrico.ottonello";
hdfsOrcidDefaultPath = "/user/enrico.ottonello/orcid/";
summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
outputAuthorsPath = "output/";
}
private void initGARRProperties() throws FileNotFoundException, IOException {
hdfsServerUri = "hdfs://hadoop-rm1.garr-pa1.d4science.org:8020";
hadoopUsername = "root";
hdfsOrcidDefaultPath = "/data/orcid_summaries/";
summariesFileNameTarGz = "ORCID_2019_summaries.tar.gz";
outputAuthorsPath = "output/";
}
}

143
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/orciddsmanager/SummariesDecompressor.java Normal file
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package orciddsmanager;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IOUtils;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.log4j.Logger;
import org.xml.sax.SAXException;
import orciddsmanager.json.JsonWriter;
import orciddsmanager.model.AuthorData;
import orciddsmanager.xml.XMLRecordParser;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URI;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.XPathExpressionException;
public class SummariesDecompressor {
private static final Logger logger = Logger.getLogger(SummariesDecompressor.class);
public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath) throws Exception {
String uri = inputUri;
FileSystem fs = FileSystem.get(URI.create(uri), conf);
Path inputPath = new Path(uri);
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodec(inputPath);
if (codec == null) {
System.err.println("No codec found for " + uri);
System.exit(1);
}
CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
InputStream gzipInputStream = null;
try {
gzipInputStream = codec.createInputStream(fs.open(inputPath));
parseTarSummaries(fs, conf, gzipInputStream, outputPath);
} finally {
logger.debug("Closing gzip stream");
IOUtils.closeStream(gzipInputStream);
}
}
private static void parseTarSummaries(FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
int counter = 0;
int nameFound = 0;
int surnameFound = 0;
int creditNameFound = 0;
int errorFromOrcidFound = 0;
int xmlParserErrorFound = 0;
try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
TarArchiveEntry entry = null;
try (SequenceFile.Writer writer = SequenceFile.createWriter(conf,
SequenceFile.Writer.file(outputPath), SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
while ((entry = tais.getNextTarEntry()) != null) {
String filename = entry.getName();
if (entry.isDirectory()) {
logger.debug("Directory entry name: "+entry.getName());
} else {
logger.debug("XML record entry name: "+entry.getName());
counter++;
BufferedReader br = new BufferedReader(new InputStreamReader(tais)); // Read directly from tarInput
String line;
StringBuffer buffer = new StringBuffer();
while ((line = br.readLine()) != null) {
buffer.append(line);
}
try (ByteArrayInputStream bais = new ByteArrayInputStream(buffer.toString().getBytes())) {
AuthorData authorData = XMLRecordParser.parse(bais);
if (authorData!=null) {
if (authorData.getErrorCode()!=null) {
errorFromOrcidFound+=1;
logger.debug("error from Orcid with code "+authorData.getErrorCode()+" for oid "+entry.getName());
continue;
}
String jsonData = JsonWriter.create(authorData);
logger.debug("oid: "+authorData.getOid() + " data: "+jsonData);
final Text key = new Text(authorData.getOid());
final Text value = new Text(jsonData);
try {
writer.append(key, value);
} catch (IOException e) {
logger.error("Writing to sequence file: "+e.getMessage());
e.printStackTrace();
throw new RuntimeException(e);
}
if (authorData.getName()!=null) {
nameFound+=1;
}
if (authorData.getSurname()!=null) {
surnameFound+=1;
}
if (authorData.getCreditName()!=null) {
creditNameFound+=1;
}
}
else {
logger.error("Data not retrievable ["+entry.getName()+"] "+buffer.toString());
xmlParserErrorFound+=1;
}
} catch (XPathExpressionException | ParserConfigurationException | SAXException e) {
logger.error("Parsing record from tar archive: "+e.getMessage());
e.printStackTrace();
}
}
if ((counter % 1000) == 0) {
logger.info("Current xml records parsed: "+counter);
}
}
}
} catch (IOException e) {
logger.error("Parsing record from gzip archive: "+e.getMessage());
e.printStackTrace();
}
logger.info("Summaries parse completed");
logger.info("Total XML records parsed: "+counter);
logger.info("Name found: "+nameFound);
logger.info("Surname found: "+surnameFound);
logger.info("Credit name found: "+creditNameFound);
logger.info("Error from Orcid found: "+errorFromOrcidFound);
logger.info("Error parsing xml record found: "+xmlParserErrorFound);
}
}

19
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/orciddsmanager/json/JsonWriter.java Normal file
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package orciddsmanager.json;
import com.google.gson.JsonObject;
import orciddsmanager.model.AuthorData;
public class JsonWriter {
public static String create(AuthorData authorData) {
JsonObject author = new JsonObject();
author.addProperty("oid", authorData.getOid());
author.addProperty("name", authorData.getName());
author.addProperty("surname", authorData.getSurname());
if (authorData.getCreditName()!=null) {
author.addProperty("creditname", authorData.getCreditName());
}
return author.toString();
}
}

41
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/orciddsmanager/model/AuthorData.java Normal file
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package orciddsmanager.model;
public class AuthorData {
private String oid;
private String name;
private String surname;
private String creditName;
private String errorCode;
public String getErrorCode() {
return errorCode;
}
public void setErrorCode(String errorCode) {
this.errorCode = errorCode;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getSurname() {
return surname;
}
public void setSurname(String surname) {
this.surname = surname;
}
public String getCreditName() {
return creditName;
}
public void setCreditName(String creditName) {
this.creditName = creditName;
}
public String getOid() {
return oid;
}
public void setOid(String oid) {
this.oid = oid;
}
}

98
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/orciddsmanager/xml/XMLRecordParser.java Normal file
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package orciddsmanager.xml;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.Iterator;
import javax.xml.namespace.NamespaceContext;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.apache.commons.lang.StringUtils;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;
import orciddsmanager.model.AuthorData;
public class XMLRecordParser {
public static AuthorData parse(ByteArrayInputStream bytesStream) throws ParserConfigurationException, SAXException, IOException, XPathExpressionException {
bytesStream.reset();
DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance();
builderFactory.setNamespaceAware(true);
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document xmlDocument = builder.parse(bytesStream);
XPath xPath = XPathFactory.newInstance().newXPath();
xPath.setNamespaceContext(new NamespaceContext() {
@Override
public Iterator getPrefixes(String arg0) {
return null;
}
@Override
public String getPrefix(String arg0) {
return null;
}
@Override
public String getNamespaceURI(String arg0) {
if ("common".equals(arg0)) {
return "http://www.orcid.org/ns/common";
}
else if ("person".equals(arg0)) {
return "http://www.orcid.org/ns/person";
}
else if ("personal-details".equals(arg0)) {
return "http://www.orcid.org/ns/personal-details";
}
else if ("other-name".equals(arg0)) {
return "http://www.orcid.org/ns/other-name";
}
else if ("record".equals(arg0)) {
return "http://www.orcid.org/ns/record";
}
else if ("error".equals(arg0)) {
return "http://www.orcid.org/ns/error";
}
return null;
}
});
AuthorData authorData = new AuthorData();
String errorPath = "//error:response-code";
String error = (String)xPath.compile(errorPath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(error)) {
authorData.setErrorCode(error);
return authorData;
}
String oidPath = "//record:record/@path";
String oid = (String)xPath.compile(oidPath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(oid)) {
oid = oid.substring(1);
authorData.setOid(oid);
}
else {
return null;
}
String namePath = "//personal-details:given-names";
String name = (String)xPath.compile(namePath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(name)) {
authorData.setName(name);
}
String surnamePath = "//personal-details:family-name";
String surname = (String)xPath.compile(surnamePath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(surname)) {
authorData.setSurname(surname);
}
String creditnamePath = "//personal-details:credit-name";
String creditName = (String)xPath.compile(creditnamePath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(creditName)) {
authorData.setCreditName(creditName);
}
return authorData;
}
}