/**
* =============================================================================
*
* ORCID (R) Open Source
* http://orcid.org
*
* Copyright (c) 2012-2014 ORCID, Inc.
* Licensed under an MIT-Style License (MIT)
* http://orcid.org/open-source-license
*
* This copyright and license information (including a link to the full license)
* shall be included in its entirety in all copies or substantial portion of
* the software.
*
* =============================================================================
*/
package org.orcid.core.cli;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DurationFormatUtils;
import org.kohsuke.args4j.CmdLineException;
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
import org.orcid.core.manager.OrcidProfileManager;
import org.orcid.jaxb.model.message.Contributor;
import org.orcid.jaxb.model.message.ContributorOrcid;
import org.orcid.jaxb.model.message.OrcidProfile;
import org.orcid.jaxb.model.message.OrcidWork;
import org.orcid.jaxb.model.message.OrcidWorks;
import org.orcid.jaxb.model.message.Visibility;
import org.orcid.jaxb.model.message.WorkContributors;
import org.orcid.persistence.dao.ProfileDao;
import org.orcid.persistence.jpa.entities.ProfileEntity;
import org.orcid.utils.NullUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
/**
*
* @author Will Simpson
*
*/
public class CheckAndFixContributorNameVisibility {
private static Logger LOG = LoggerFactory.getLogger(CheckAndFixContributorNameVisibility.class);
private OrcidProfileManager orcidProfileManager;
private ProfileDao profileDao;
private TransactionTemplate transactionTemplate;
@Option(name = "-f", usage = "Path to file containing ORCIDs to resave")
private File fileToLoad;
@Option(name = "-o", usage = "ORCID to resave")
private String orcid;
public static void main(String[] args) throws IOException {
CheckAndFixContributorNameVisibility fixer = new CheckAndFixContributorNameVisibility();
CmdLineParser parser = new CmdLineParser(fixer);
try {
parser.parseArgument(args);
fixer.validateArgs(parser);
fixer.init();
fixer.execute();
} catch (CmdLineException e) {
System.err.println(e.getMessage());
parser.printUsage(System.err);
}
}
private void validateArgs(CmdLineParser parser) throws CmdLineException {
if (NullUtils.allNull(fileToLoad, orcid)) {
throw new CmdLineException(parser, "At least one of -f | -o must be specificed");
}
}
public void execute() throws IOException {
if (fileToLoad != null) {
processFile();
}
if (orcid != null) {
processOrcid(orcid);
}
}
private void processFile() throws IOException {
long startTime = System.currentTimeMillis();
int doneCount = 0;
try (BufferedReader br = new BufferedReader(new FileReader(fileToLoad))) {
String line = null;
while ((line = br.readLine()) != null) {
if (StringUtils.isNotBlank(line)) {
processOrcid(line.trim());
doneCount++;
}
}
long endTime = System.currentTimeMillis();
String timeTaken = DurationFormatUtils.formatDurationHMS(endTime - startTime);
LOG.info("Finished checking and fixing profiles: doneCount={}, timeTaken={} (H:m:s.S)", doneCount, timeTaken);
}
}
private void processOrcid(final String orcid) {
LOG.info("Checking and fixing profile: {}", orcid);
transactionTemplate.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus status) {
OrcidProfile orcidProfile = orcidProfileManager.retrieveOrcidProfile(orcid);
OrcidWorks orcidWorks = orcidProfile.retrieveOrcidWorks();
if (orcidWorks != null) {
for (OrcidWork orcidWork : orcidWorks.getOrcidWork()) {
WorkContributors workContributors = orcidWork.getWorkContributors();
if (workContributors != null) {
for (Contributor contributor : workContributors.getContributor()) {
ContributorOrcid contributorOrcid = contributor.getContributorOrcid();
if (contributorOrcid != null) {
String orcid = contributorOrcid.getPath();
ProfileEntity contributorProfile = profileDao.find(orcid);
if(contributorProfile.getRecordNameEntity() != null && contributorProfile.getRecordNameEntity().getVisibility() != null) {
if (!Visibility.PUBLIC.value().equals(contributorProfile.getRecordNameEntity().getVisibility().value())) {
contributor.setCreditName(null);
}
}
}
}
}
}
}
orcidProfileManager.updateOrcidProfile(orcidProfile);
}
});
}
@SuppressWarnings("resource")
private void init() {
ApplicationContext context = new ClassPathXmlApplicationContext("orcid-core-context.xml");
orcidProfileManager = (OrcidProfileManager) context.getBean("orcidProfileManager");
profileDao = (ProfileDao) context.getBean("profileDao");
transactionTemplate = (TransactionTemplate) context.getBean("transactionTemplate");
}
}