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used vtd for parsing orcid xml record, set 4g heapspace

This commit is contained in:
Enrico Ottonello 2020-04-22 14:41:19 +02:00
parent 5d46ec7d5f
commit 7d759947ae
8 changed files with 408 additions and 256 deletions
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89
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/OrcidDSManager.java
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@ -1,75 +1,78 @@
package eu.dnetlib.doiboost.orcid; package eu.dnetlib.doiboost.orcid;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.io.IOException; import java.io.IOException;
import java.net.URI; import java.net.URI;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.slf4j.Logger; import org.mortbay.log.Log;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class OrcidDSManager { public class OrcidDSManager {
private static final Logger logger = LoggerFactory.getLogger(OrcidDSManager.class); private String hdfsServerUri;
private String hdfsServerUri;
private String hdfsOrcidDefaultPath; private String hdfsOrcidDefaultPath;
private String summariesFileNameTarGz; private String summariesFileNameTarGz;
private String outputAuthorsPath; private String outputAuthorsPath;
public static void main(String[] args) throws IOException, Exception { public static void main(String[] args) throws IOException, Exception {
logger.info("OrcidDSManager started"); OrcidDSManager orcidDSManager = new OrcidDSManager();
OrcidDSManager orcidDSManager = new OrcidDSManager(); orcidDSManager.loadArgs(args);
orcidDSManager.loadArgs(args); orcidDSManager.generateAuthors();
orcidDSManager.generateAuthors();
} }
public void generateAuthors() throws Exception { public void generateAuthors() throws Exception {
Configuration conf = initConfigurationObject(); Configuration conf = initConfigurationObject();
FileSystem fs = initFileSystemObject(conf); FileSystem fs = initFileSystemObject(conf);
String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz); String tarGzUri = hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(summariesFileNameTarGz);
logger.info("Started parsing "+tarGzUri); Path outputPath =
Path outputPath = new Path(hdfsServerUri.concat(hdfsOrcidDefaultPath).concat(outputAuthorsPath).concat(Long.toString(System.currentTimeMillis())).concat("/authors.seq")); new Path(
SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath); hdfsServerUri
.concat(hdfsOrcidDefaultPath)
.concat(outputAuthorsPath)
.concat("authors.seq"));
SummariesDecompressor.parseGzSummaries(conf, tarGzUri, outputPath);
} }
private Configuration initConfigurationObject() { private Configuration initConfigurationObject() {
// ====== Init HDFS File System Object // ====== Init HDFS File System Object
Configuration conf = new Configuration(); Configuration conf = new Configuration();
// Set FileSystem URI // Set FileSystem URI
conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath)); conf.set("fs.defaultFS", hdfsServerUri.concat(hdfsOrcidDefaultPath));
// Because of Maven // Because of Maven
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName()); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
return conf; return conf;
} }
private FileSystem initFileSystemObject(Configuration conf) { private FileSystem initFileSystemObject(Configuration conf) {
//Get the filesystem - HDFS // Get the filesystem - HDFS
FileSystem fs = null; FileSystem fs = null;
try { try {
fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf); fs = FileSystem.get(URI.create(hdfsServerUri.concat(hdfsOrcidDefaultPath)), conf);
} catch (IOException e) { } catch (IOException e) {
// TODO Auto-generated catch block // TODO Auto-generated catch block
e.printStackTrace(); e.printStackTrace();
} }
return fs; return fs;
} }
private void loadArgs(String[] args) throws IOException, Exception { private void loadArgs(String[] args) throws IOException, Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(OrcidDSManager.class.getResourceAsStream("/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json"))); final ArgumentApplicationParser parser =
new ArgumentApplicationParser(
IOUtils.toString(
OrcidDSManager.class.getResourceAsStream(
"/eu/dnetlib/dhp/doiboost/create_orcid_authors_data.json")));
parser.parseArgument(args); parser.parseArgument(args);
final String hdfsServerUri = parser.get("hdfsServerUri"); hdfsServerUri = parser.get("hdfsServerUri");
logger.info("HDFS URI: "+hdfsServerUri); Log.info("HDFS URI: " + hdfsServerUri);
Path hdfsOrcidDefaultPath = new Path(parser.get("hdfsOrcidDefaultPath")); hdfsOrcidDefaultPath = parser.get("hdfsOrcidDefaultPath");
logger.info("Default Path: "+hdfsOrcidDefaultPath); Log.info("Default Path: " + hdfsOrcidDefaultPath);
final String summariesFileNameTarGz = parser.get("summariesFileNameTarGz"); summariesFileNameTarGz = parser.get("summariesFileNameTarGz");
logger.info("Summaries File Name: "+summariesFileNameTarGz); Log.info("Summaries File Name: " + summariesFileNameTarGz);
final String outputAuthorsPath = parser.get("summariesFileNameTarGz"); outputAuthorsPath = parser.get("outputAuthorsPath");
logger.info("Output Authors Data: "+outputAuthorsPath); Log.info("Output Authors Data: " + outputAuthorsPath);
} }
} }

210
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SummariesDecompressor.java
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@ -3,6 +3,11 @@ package eu.dnetlib.doiboost.orcid;
import eu.dnetlib.doiboost.orcid.json.JsonWriter; import eu.dnetlib.doiboost.orcid.json.JsonWriter;
import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser; import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URI;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry; import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
@ -13,23 +18,14 @@ import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.hadoop.io.compress.CompressionCodec; import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory; import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.apache.log4j.Logger; import org.mortbay.log.Log;
import org.xml.sax.SAXException;
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 { public class SummariesDecompressor {
private static final Logger logger = Logger.getLogger(SummariesDecompressor.class); private static final int MAX_XML_RECORDS_PARSED = -1;
public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath) throws Exception { public static void parseGzSummaries(Configuration conf, String inputUri, Path outputPath)
throws Exception {
String uri = inputUri; String uri = inputUri;
FileSystem fs = FileSystem.get(URI.create(uri), conf); FileSystem fs = FileSystem.get(URI.create(uri), conf);
Path inputPath = new Path(uri); Path inputPath = new Path(uri);
@ -42,101 +38,123 @@ public class SummariesDecompressor {
CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension()); CompressionCodecFactory.removeSuffix(uri, codec.getDefaultExtension());
InputStream gzipInputStream = null; InputStream gzipInputStream = null;
try { try {
gzipInputStream = codec.createInputStream(fs.open(inputPath)); gzipInputStream = codec.createInputStream(fs.open(inputPath));
parseTarSummaries(fs, conf, gzipInputStream, outputPath); parseTarSummaries(fs, conf, gzipInputStream, outputPath);
} finally { } finally {
logger.debug("Closing gzip stream"); Log.debug("Closing gzip stream");
IOUtils.closeStream(gzipInputStream); IOUtils.closeStream(gzipInputStream);
} }
} }
private static void parseTarSummaries(FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) { private static void parseTarSummaries(
int counter = 0; FileSystem fs, Configuration conf, InputStream gzipInputStream, Path outputPath) {
int nameFound = 0; int counter = 0;
int surnameFound = 0; int nameFound = 0;
int creditNameFound = 0; int surnameFound = 0;
int errorFromOrcidFound = 0; int creditNameFound = 0;
int xmlParserErrorFound = 0; int errorFromOrcidFound = 0;
try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { int xmlParserErrorFound = 0;
TarArchiveEntry entry = null; try (TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) {
TarArchiveEntry entry = null;
try (SequenceFile.Writer writer = SequenceFile.createWriter(conf, try (SequenceFile.Writer writer =
SequenceFile.Writer.file(outputPath), SequenceFile.Writer.keyClass(Text.class), SequenceFile.createWriter(
SequenceFile.Writer.valueClass(Text.class))) { conf,
SequenceFile.Writer.file(outputPath),
SequenceFile.Writer.keyClass(Text.class),
SequenceFile.Writer.valueClass(Text.class))) {
while ((entry = tais.getNextTarEntry()) != null) {
String filename = entry.getName();
try {
if (entry.isDirectory()) {
Log.debug("Directory entry name: " + entry.getName());
} else {
Log.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);
}
AuthorData authorData =
XMLRecordParser.VTDParse(buffer.toString().getBytes());
if (authorData != null) {
if (authorData.getErrorCode() != null) {
errorFromOrcidFound += 1;
Log.debug(
"error from Orcid with code "
+ authorData.getErrorCode()
+ " for oid "
+ entry.getName());
continue;
}
String jsonData = JsonWriter.create(authorData);
Log.debug("oid: " + authorData.getOid() + " data: " + jsonData);
while ((entry = tais.getNextTarEntry()) != null) { final Text key = new Text(authorData.getOid());
String filename = entry.getName(); final Text value = new Text(jsonData);
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()); try {
final Text value = new Text(jsonData); writer.append(key, value);
} catch (IOException e) {
Log.debug("Writing to sequence file: " + e.getMessage());
Log.debug(e);
throw new RuntimeException(e);
}
try { if (authorData.getName() != null) {
writer.append(key, value); nameFound += 1;
} catch (IOException e) { }
logger.error("Writing to sequence file: "+e.getMessage()); if (authorData.getSurname() != null) {
e.printStackTrace(); surnameFound += 1;
throw new RuntimeException(e); }
} if (authorData.getCreditName() != null) {
creditNameFound += 1;
}
if (authorData.getName()!=null) { } else {
nameFound+=1; Log.warn(
} "Data not retrievable ["
if (authorData.getSurname()!=null) { + entry.getName()
surnameFound+=1; + "] "
} + buffer.toString());
if (authorData.getCreditName()!=null) { xmlParserErrorFound += 1;
creditNameFound+=1; }
} }
} catch (Exception e) {
Log.warn(
"Parsing record from tar archive and xml record: "
+ filename
+ " "
+ e.getMessage());
Log.warn(e);
}
} if ((counter % 100000) == 0) {
else { Log.info("Current xml records parsed: " + counter);
logger.error("Data not retrievable ["+entry.getName()+"] "+buffer.toString()); }
xmlParserErrorFound+=1;
}
} catch (XPathExpressionException | ParserConfigurationException | SAXException e) { if ((MAX_XML_RECORDS_PARSED > -1) && (counter > MAX_XML_RECORDS_PARSED)) {
logger.error("Parsing record from tar archive: "+e.getMessage()); break;
e.printStackTrace(); }
} }
} }
} catch (IOException e) {
if ((counter % 100000) == 0) { Log.warn("Parsing record from gzip archive: " + e.getMessage());
logger.info("Current xml records parsed: "+counter); Log.warn(e);
} throw new RuntimeException(e);
} }
} Log.info("Summaries parse completed");
} catch (IOException e) { Log.info("Total XML records parsed: " + counter);
logger.error("Parsing record from gzip archive: "+e.getMessage()); Log.info("Name found: " + nameFound);
throw new RuntimeException(e); Log.info("Surname found: " + surnameFound);
} Log.info("Credit name found: " + creditNameFound);
logger.info("Summaries parse completed"); Log.info("Error from Orcid found: " + errorFromOrcidFound);
logger.info("Total XML records parsed: "+counter); Log.info("Error parsing xml record found: " + xmlParserErrorFound);
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);
} }
} }

161
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParser.java
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@ -1,98 +1,81 @@
package eu.dnetlib.doiboost.orcid.xml; package eu.dnetlib.doiboost.orcid.xml;
import java.io.ByteArrayInputStream; import com.ximpleware.AutoPilot;
import java.io.IOException; import com.ximpleware.EOFException;
import java.util.Iterator; import com.ximpleware.EncodingException;
import com.ximpleware.EntityException;
import javax.xml.namespace.NamespaceContext; import com.ximpleware.ParseException;
import javax.xml.parsers.DocumentBuilder; import com.ximpleware.VTDGen;
import javax.xml.parsers.DocumentBuilderFactory; import com.ximpleware.VTDNav;
import javax.xml.parsers.ParserConfigurationException; import eu.dnetlib.dhp.parser.utility.VtdException;
import javax.xml.xpath.XPath; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import eu.dnetlib.doiboost.orcid.model.AuthorData; import eu.dnetlib.doiboost.orcid.model.AuthorData;
import org.apache.commons.lang.StringUtils; import java.util.Arrays;
import org.w3c.dom.Document; import java.util.List;
import org.xml.sax.SAXException;
public class XMLRecordParser { public class XMLRecordParser {
public static AuthorData parse(ByteArrayInputStream bytesStream) throws ParserConfigurationException, SAXException, IOException, XPathExpressionException { private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common";
bytesStream.reset(); private static final String NS_COMMON = "common";
DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance(); private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person";
builderFactory.setNamespaceAware(true); private static final String NS_PERSON = "person";
DocumentBuilder builder = builderFactory.newDocumentBuilder(); private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details";
private static final String NS_DETAILS = "personal-details";
private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name";
private static final String NS_OTHER = "other-name";
private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record";
private static final String NS_RECORD = "record";
private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error";
private static final String NS_ERROR = "error";
Document xmlDocument = builder.parse(bytesStream); public static AuthorData VTDParse(byte[] bytes)
XPath xPath = XPathFactory.newInstance().newXPath(); throws VtdException, EncodingException, EOFException, EntityException, ParseException {
xPath.setNamespaceContext(new NamespaceContext() { final VTDGen vg = new VTDGen();
@Override vg.setDoc(bytes);
public Iterator getPrefixes(String arg0) { vg.parse(true);
return null; final VTDNav vn = vg.getNav();
} final AutoPilot ap = new AutoPilot(vn);
@Override ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
public String getPrefix(String arg0) { ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL);
return null; ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL);
} ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL);
@Override ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL);
public String getNamespaceURI(String arg0) { ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
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(); AuthorData authorData = new AuthorData();
String errorPath = "//error:response-code"; final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
String error = (String)xPath.compile(errorPath).evaluate(xmlDocument, XPathConstants.STRING); if (!errors.isEmpty()) {
if (!StringUtils.isBlank(error)) { authorData.setErrorCode(errors.get(0));
authorData.setErrorCode(error); return authorData;
return authorData; }
}
String oidPath = "//record:record/@path"; List<VtdUtilityParser.Node> recordNodes =
String oid = (String)xPath.compile(oidPath).evaluate(xmlDocument, XPathConstants.STRING); VtdUtilityParser.getTextValuesWithAttributes(
if (!StringUtils.isBlank(oid)) { ap, vn, "//record:record", Arrays.asList("path"));
oid = oid.substring(1); if (!recordNodes.isEmpty()) {
authorData.setOid(oid); final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
} authorData.setOid(oid);
else { } else {
return null; return null;
} }
String namePath = "//personal-details:given-names";
String name = (String)xPath.compile(namePath).evaluate(xmlDocument, XPathConstants.STRING); final List<String> names =
if (!StringUtils.isBlank(name)) { VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names");
authorData.setName(name); if (!names.isEmpty()) {
} authorData.setName(names.get(0));
String surnamePath = "//personal-details:family-name"; }
String surname = (String)xPath.compile(surnamePath).evaluate(xmlDocument, XPathConstants.STRING);
if (!StringUtils.isBlank(surname)) { final List<String> surnames =
authorData.setSurname(surname); VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name");
} if (!surnames.isEmpty()) {
String creditnamePath = "//personal-details:credit-name"; authorData.setSurname(surnames.get(0));
String creditName = (String)xPath.compile(creditnamePath).evaluate(xmlDocument, XPathConstants.STRING); }
if (!StringUtils.isBlank(creditName)) {
authorData.setCreditName(creditName); final List<String> creditNames =
} VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name");
return authorData; if (!creditNames.isEmpty()) {
} authorData.setCreditName(creditNames.get(0));
}
return authorData;
}
} }

4
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/config-default.xml
View File

@ -15,4 +15,8 @@
<name>oozie.launcher.mapreduce.user.classpath.first</name> <name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value> <value>true</value>
</property> </property>
<property>
<name>oozie.launcher.mapreduce.map.java.opts</name>
<value>-Xmx4g</value>
</property>
</configuration> </configuration>

6
dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/orcid/oozie_app/workflow.xml
View File

@ -1,4 +1,4 @@
<workflow-app name="import Crossref from index into HDFS" xmlns="uri:oozie:workflow:0.5"> <workflow-app name="import Orcid" xmlns="uri:oozie:workflow:0.5">
<parameters> <parameters>
<property> <property>
<name>workingPath</name> <name>workingPath</name>
@ -31,8 +31,8 @@
<main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class> <main-class>eu.dnetlib.doiboost.orcid.OrcidDSManager</main-class>
<arg>-d</arg><arg>${workingPath}/</arg> <arg>-d</arg><arg>${workingPath}/</arg>
<arg>-n</arg><arg>${nameNode}</arg> <arg>-n</arg><arg>${nameNode}</arg>
<arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg> <arg>-f</arg><arg>ORCID_2019_summaries.tar.gz</arg>
<arg>-o</arg><arg>output/</arg> <arg>-o</arg><arg>output/</arg>
</java> </java>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>

40
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/xml/XMLRecordParserTest.java Normal file
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@ -0,0 +1,40 @@
package eu.dnetlib.doiboost.orcid.xml;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
public class XMLRecordParserTest {
@Test
public void testOrcidXMLRecordParser() throws Exception {
String xml =
IOUtils.toString(
this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
XMLRecordParser p = new XMLRecordParser();
AuthorData authorData = p.VTDParse(xml.getBytes());
assertNotNull(authorData);
assertNotNull(authorData.getName());
System.out.println("name: " + authorData.getName());
assertNotNull(authorData.getSurname());
System.out.println("surname: " + authorData.getSurname());
}
@Test
public void testOrcidXMLErrorRecordParser() throws Exception {
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_error.xml"));
XMLRecordParser p = new XMLRecordParser();
AuthorData authorData = p.VTDParse(xml.getBytes());
assertNotNull(authorData);
assertNotNull(authorData.getErrorCode());
System.out.println("error: " + authorData.getErrorCode());
}
}

71
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/orcid/xml/summary_0000-0001-6828-479X.xml Normal file
View File

@ -0,0 +1,71 @@
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<record:record xmlns:address="http://www.orcid.org/ns/address"
xmlns:email="http://www.orcid.org/ns/email
" xmlns:history="http://www.orcid.org/ns/history"
xmlns:employment="http://www.orcid.org/ns/employment"
xmlns:education="http://www.orcid.org/ns/education"
xmlns:other-name="http://www.orcid.org/ns/other-name"
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
xmlns:funding="http://www.orcid.org/ns/funding"
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
xmlns:service="http://www.orcid.org/ns/service"
xmlns:researcher-url="http://www.orcid.org/ns/researcher-url"
xmlns:distinction="http://www.orcid.org/ns/distinction"
xmlns:internal="http://www.orcid.org/ns/internal"
xmlns:membership="http://www.orcid.org/ns/membership"
xmlns:person="http://www.orcid.org/ns/person"
xmlns:personal-details="http://www.orcid.org/ns/personal-details"
xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common"
xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword"
xmlns:activities="http://www.orcid.org/ns/activities"
xmlns:qualification="http://www.orcid.org/ns/qualification"
xmlns:external-identifier="http://www.orcid.org/ns/external-identifier"
xmlns:error="http://www.orcid.org/ns/error"
xmlns:preferences="http://www.orcid.org/ns/preferences"
xmlns:invited-position="http://www.orcid.org/ns/invited-position"
xmlns:work="http://www.orcid.org/ns/work"
xmlns:peer-review="http://www.orcid.org/ns/peer-review" path="/0000-0001-6828-479X">
<common:orcid-identifier>
<common:uri>https://orcid.org/0000-0001-6828-479X</common:uri>
<common:path>0000-0001-6828-479X</common:path>
<common:host>orcid.org</common:host>
</common:orcid-identifier>
<preferences:preferences>
<preferences:locale>en</preferences:locale>
</preferences:preferences>
<history:history>
<history:creation-method>Member-referred</history:creation-method>
<history:submission-date>2017-02-17T06:16:06.428Z</history:submission-date>
<common:last-modified-date>2017-10-04T04:38:43.529Z</common:last-modified-date>
<history:claimed>true</history:claimed>
<history:verified-email>true</history:verified-email>
<history:verified-primary-email>true</history:verified-primary-email>
</history:history>
<person:person path="/0000-0001-6828-479X/person">
<person:name visibility="public" path="0000-0001-6828-479X">
<common:created-date>2017-02-17T06:16:06.428Z</common:created-date>
<common:last-modified-date>2017-02-17T06:16:06.652Z</common:last-modified-date>
<personal-details:given-names>Masahide</personal-details:given-names>
<personal-details:family-name>Terazima</personal-details:family-name>
</person:name>
<other-name:other-names path="/0000-0001-6828-479X/other-names"/>
<researcher-url:researcher-urls path="/0000-0001-6828-479X/researcher-urls"/>
<email:emails path="/0000-0001-6828-479X/email"/>
<address:addresses path="/0000-0001-6828-479X/address"/>
<keyword:keywords path="/0000-0001-6828-479X/keywords"/>
<external-identifier:external-identifiers path="/0000-0001-6828-479X/external-identifiers"/>
</person:person>
<activities:activities-summary path="/0000-0001-6828-479X/activities">
<activities:distinctions path="/0000-0001-6828-479X/distinctions"/>
<activities:educations path="/0000-0001-6828-479X/educations"/>
<activities:employments path="/0000-0001-6828-479X/employments"/>
<activities:fundings path="/0000-0001-6828-479X/fundings"/>
<activities:invited-positions path="/0000-0001-6828-479X/invited-positions"/>
<activities:memberships path="/0000-0001-6828-479X/memberships"/>
<activities:peer-reviews path="/0000-0001-6828-479X/peer-reviews"/>
<activities:qualifications path="/0000-0001-6828-479X/qualifications"/>
<activities:research-resources path="/0000-0001-6828-479X/research-resources"/>
<activities:services path="/0000-0001-6828-479X/services"/>
<activities:works path="/0000-0001-6828-479X/works"/>
</activities:activities-summary>
</record:record>

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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<error:error xmlns:address="http://www.orcid.org/ns/address"
xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history"
xmlns:employment="http://www.orcid.org/ns/employment"
xmlns:education="http://www.orcid.org/ns/education"
xmlns:other-name="http://www.orcid.org/ns/other-name"
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
xmlns:funding="http://www.orcid.org/ns/funding"
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
xmlns:service="http://www.orcid.org/ns/service"
xmlns:researcher-url="http://www.orcid.org/ns/researcher-url"
xmlns:distinction="http://www.orcid.org/ns/distinction"
xmlns:internal="http://www.orcid.org/ns/internal"
xmlns:membership="http://www.orcid.org/ns/membership"
xmlns:person="http://www.orcid.org/ns/person"
xmlns:personal-details="http://www.orcid.org/ns/personal-details"
xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:common="http://www.orcid.org/ns/common"
xmlns:record="http://www.orcid.org/ns/record" xmlns:keyword="http://www.orcid.org/ns/keyword"
xmlns:activities="http://www.orcid.org/ns/activities"
xmlns:qualification="http://www.orcid.org/ns/qualification"
xmlns:external-identifier="http://www.orcid.org/ns/external-identifier"
xmlns:error="http://www.orcid.org/ns/error"
xmlns:preferences="http://www.orcid.org/ns/preferences"
xmlns:invited-position="http://www.orcid.org/ns/invited-position"
xmlns:work="http://www.orcid.org/ns/work"
xmlns:peer-review="http://www.orcid.org/ns/peer-review">
<error:response-code>409</error:response-code>
<error:developer-message>409 Conflict: The ORCID record is locked and cannot be edited. ORCID
https://orcid.org/0000-0002-9716-679X</error:developer-message>
<error:user-message>The ORCID record is locked.</error:user-message>
<error:error-code>9018</error:error-code>
<error:more-info>https://members.orcid.org/api/resources/troubleshooting</error:more-info>
</error:error>