/**
* '$RCSfile$'
* Copyright: 2000-2019 Regents of the University of California and the
* National Center for Ecological Analysis and Synthesis
*
* '$Author: $'
* '$Date: $'
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package edu.ucsb.nceas.metacat.doi.datacite;
import java.io.InputStream;
import java.text.SimpleDateFormat;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.xml.xpath.XPathExpressionException;
import org.apache.log4j.Logger;
import org.apache.wicket.protocol.http.mock.MockHttpServletRequest;
import org.dataone.service.exceptions.InvalidRequest;
import org.dataone.service.exceptions.InvalidToken;
import org.dataone.service.exceptions.NotAuthorized;
import org.dataone.service.exceptions.NotFound;
import org.dataone.service.exceptions.NotImplemented;
import org.dataone.service.exceptions.ServiceFailure;
import org.dataone.service.types.v1.Identifier;
import org.dataone.service.types.v1.Session;
import org.dataone.service.types.v1.Subject;
import org.dataone.service.types.v2.Node;
import org.dataone.service.types.v2.SystemMetadata;
import org.ecoinformatics.datamanager.parser.DataPackage;
import org.ecoinformatics.datamanager.parser.Party;
import org.ecoinformatics.datamanager.parser.UserId;
import org.ecoinformatics.datamanager.parser.generic.DataPackageParserInterface;
import org.ecoinformatics.datamanager.parser.generic.Eml200DataPackageParser;
import org.w3c.dom.Document;
import edu.ucsb.nceas.ezid.profile.DataCiteProfileResourceTypeValues;
import edu.ucsb.nceas.metacat.dataone.MNodeService;
/**
* A factory to generate data cite meta data for the scientific meta data standards - eml-2.*
* @author tao
*
*/
public class EML2DataCiteFactory extends DataCiteMetadataFactory {
private static Logger logMetacat = Logger.getLogger(EML2DataCiteFactory.class);
/**
* Determine if the given name space can be handled by this factory
*/
@Override
public boolean canProcess(String namespace) {
boolean can = false;
if(namespace != null && namespace.startsWith("eml://ecoinformatics.org/eml-2")) {
can = true;
}
logMetacat.debug("EML2DataCitFactory.canProcess - If this factory can process the xml with the name space " + namespace + "? " + can);
return can;
}
/**
* Method to generate the data cite xml document
*/
@Override
public String generateMetadata(Identifier identifier, SystemMetadata sysmeta) throws InvalidRequest, ServiceFailure {
if(identifier != null && sysmeta != null) {
try {
DataPackage emlPackage = getEMLPackage(sysmeta);
if (emlPackage != null) {
String language = emlPackage.getLanguage();
Document doc = generateROOTDoc();
//identifier
String scheme = DOI;
String id = removeIdSchemePrefix(identifier.getValue(), scheme);
addIdentifier(doc, id, scheme);
//creator
appendCreators(sysmeta.getRightsHolder(), emlPackage, doc);
//title
String title = emlPackage.getTitle();
if(title == null || title.trim().equals("")) {
throw new InvalidRequest(INVALIDCODE, "The datacite instance must have a title. It can't be null or blank");
}
appendTitle(title, doc, language);
//publisher
String publisher = lookupPublisher(emlPackage);
addPublisher(doc, publisher);
//publication year
String year = lookupPublishingYear(emlPackage, sysmeta);
addPublicationYear(doc, year);
//subjects (keywords)
List<String> subjects = emlPackage.getKeywords();
if(subjects != null) {
for(String subject : subjects) {
appendSubject(subject, doc, language);
}
}
//language
addLanguage(doc, language);
//resource type
//String resourceType = lookupResourceType(sysmeta);
String resourceType = null; //only set the attribute to "dataset"
addResourceType(doc, DataCiteProfileResourceTypeValues.DATASET.toString(), resourceType);
//version
//description (abstract)
String description = emlPackage.getAbstract();
if(description != null) {
appendDescription(description, doc, language, ABSTRACT);
}
//size
// format
String format = lookupFormat(sysmeta);
if(format != null) {
appendFormat(doc, format);
}
return serializeDoc(doc);
} else {
throw new ServiceFailure("1030", "Metacat can't parse the eml object " + identifier.getValue() + " so we can't get the needed information from it.");
}
} catch (InvalidRequest e) {
throw e;
} catch (Exception e) {
e.printStackTrace();
throw new ServiceFailure("1030", e.getMessage());
}
} else {
return null;
}
}
/**
* Get a parsed eml2 data package if it is an eml 2 document
* @param sysMeta
* @return null if it is not an eml document.
* @throws Exception
*/
private DataPackage getEMLPackage(SystemMetadata sysMeta) throws Exception{
DataPackage dataPackage = null;
if (sysMeta.getFormatId().getValue().startsWith("eml://")) {
DataPackageParserInterface parser = new Eml200DataPackageParser();
// for using the MN API as the MN itself
MockHttpServletRequest request = new MockHttpServletRequest(null, null, null);
Session session = new Session();
Subject subject = MNodeService.getInstance(request).getCapabilities().getSubject(0);
session.setSubject(subject);
InputStream emlStream = MNodeService.getInstance(request).get(session, sysMeta.getIdentifier());
parser.parse(emlStream);
dataPackage = parser.getDataPackage();
}
return dataPackage;
}
/**
* Append the creator information to the datacite document
* According to https://ezid.cdlib.org/doc/apidoc.html#profile-datacite
* Each name may be a corporate, institutional, or personal name. In personal names list family name before given name, as in:
* Shakespeare, William
* @param subject
* @return fullName if found
* @throws ServiceFailure
* @throws NotAuthorized
* @throws NotImplemented
* @throws NotFound
* @throws InvalidToken
* @throws XPathExpressionException
*/
private void appendCreators(Subject subject, DataPackage emlPackage, Document doc) throws InvalidRequest, ServiceFailure, NotAuthorized, NotImplemented, NotFound, InvalidToken, XPathExpressionException {
String nameSep =", ";
List<Party> parties = emlPackage.getCreators();
if (parties == null || parties.isEmpty()) {
throw new InvalidRequest(INVALIDCODE, "The datacite instance must have a creator. It can't be null or blank");
}
boolean found = false;
for(Party party : parties) {
String surName = party.getSurName();
String positionName = party.getPositionName();
String organization = party.getOrganization();
String fullName = null;
if(surName != null && !surName.trim().equals("")) {
//this is a person
List<String> givenNames = party.getGivenNames();
//System.out.println("the surname ============== "+surName);
fullName = surName;
if(givenNames!=null && givenNames.size() > 0 && givenNames.get(0) != null && !givenNames.get(0).trim().equals("")) {
fullName = fullName + nameSep + givenNames.get(0);
}
} else if(positionName != null && !positionName.trim().equals("")) {
//it has a positionName and we will use the positionName as the full name (it doesn't have the individual name)
fullName = positionName;
} else {
//organization name
fullName=organization; //organization is the creator.
organization = null; //affiliation is null
}
String nameIdentifier = null;
String nameIdentifierSchemeURI = null;
String nameIdentifierScheme = null;
List<UserId> userIds = party.getUserIdList();
if(userIds != null && !userIds.isEmpty()) {
UserId userId = userIds.get(0);//nameIdentifier only can happen at most once. So only choose the first one.
if(userId != null) {
String value = userId.getValue();
String directory = userId.getDirectory();
if(directory != null && (directory.startsWith("https://orcid.org") || directory.startsWith("http://orcid.org"))) {
nameIdentifierScheme = "ORCID";
if(!directory.endsWith("/")) {
directory = directory+"/";
}
nameIdentifierSchemeURI = directory;
if(value.indexOf(nameIdentifierSchemeURI) > -1) {
nameIdentifier = value.replaceFirst(nameIdentifierSchemeURI, "");//get rid of nameIdentifierSchemeURI from the id.
} else {
nameIdentifier = value;
}
} else {
nameIdentifierScheme = directory;
nameIdentifier = value;
}
}
}
appendCreator(fullName, doc, organization, nameIdentifier, nameIdentifierSchemeURI, nameIdentifierScheme);
found = true;
}
if(!found) {
throw new InvalidRequest(INVALIDCODE, "The datacite instance must have a creator. It can't be null or blank");
}
}
/**
* Format the publishing year. First, it will look the pubDate of the eml package.
* If the format of the pubDate is yyyy or yyyy-mm-dd, it will get the yyyy from the pubDate.
* If it can't get the value from pubDate, it falls back to get from the upload date from the system metadata.
* If it still can't get anything, an exception will be thrown.
* @param emlPackage
* @param sysMeta
* @return the publishing year of this package
* @throws InvalidRequest
*/
String lookupPublishingYear(DataPackage emlPackage, SystemMetadata sysMeta) throws InvalidRequest {
String publishYear = null;
String pubDate = emlPackage.getPubDate();
if(pubDate != null && !pubDate.trim().equals("")) {
String regex = "^\\d{4}";
Pattern pattern = Pattern.compile(regex);
Matcher matcher = pattern.matcher(pubDate);
if (matcher.matches()) {
publishYear = pubDate;
return publishYear;
} else {
regex = "^\\d{4}-\\d{2}-\\d{2}";
pattern = Pattern.compile(regex);
matcher = pattern.matcher(pubDate);
if (matcher.matches()) {
publishYear = pubDate.substring(0, 4);
return publishYear;
}
}
}
if(publishYear == null) {
//fall back to use system meta data
SimpleDateFormat sdf = new SimpleDateFormat("yyyy");
publishYear = sdf.format(sysMeta.getDateUploaded());
}
if(publishYear == null || publishYear.trim().equals("")) {
throw new InvalidRequest(INVALIDCODE, "The datacite instance must have the publishing year. Metacat looked the eml object and the system meta data. But they are blank.");
}
return publishYear;
}
/**
* Format a publisher. First, it looks at the eml package's publisher element.
* If it can't find anything, it falls back to look the name of the member node.
* If it still can't find anything, an exception will be thrown.
* @param emlPackage
* @return the publisher of the package
* @throws ServiceFailure
* @throws InvalidRequest
*/
String lookupPublisher(DataPackage emlPackage) throws ServiceFailure, InvalidRequest {
String publisherStr = "";
Party publisher = emlPackage.getPublisher();
if(publisher != null) {
String givenNameDelimiter = ", ";
String delimiter = ". ";
String surName = publisher.getSurName();
List<String> givenNames = publisher.getGivenNames();
String positionName = publisher.getPositionName();
String organizationName = publisher.getOrganization();
if(surName != null && !surName.trim().equals("")) {
publisherStr = publisherStr + surName;
}
if(givenNames != null && givenNames.get(0) != null && !givenNames.get(0).trim().equals("")) {
publisherStr = publisherStr + givenNameDelimiter + givenNames.get(0);
}
if(positionName != null && !positionName.trim().equals("")) {
if(!publisherStr.trim().equals("")) {
//already has the individual name, so we need to add the delimiter.
publisherStr = publisherStr + delimiter;
}
publisherStr = publisherStr + positionName;
}
if(organizationName != null && !organizationName.trim().equals("")) {
if(!publisherStr.trim().equals("")) {
//already has something, so we need to add the delimiter.
publisherStr = publisherStr + delimiter;
}
publisherStr = publisherStr + organizationName;
}
}
if(publisherStr == null || publisherStr.trim().equals("")) {
//fall back to use the name of the member node
Node node = MNodeService.getInstance(null).getCapabilities();
publisherStr = node.getName();
}
if(publisherStr == null || publisherStr.trim().equals("")) {
throw new InvalidRequest(INVALIDCODE, "The datacite instance must have a publisher. Metacat looked the eml object and member node name. But they are blank.");
}
return publisherStr;
}
}