/**
* Create deposit package of article metadata.
* @param $article Article
* @return DataversePackager
*/
function createMetadataPackage($article)
{
$journalDao =& DAORegistry::getDAO('JournalDAO');
$journal =& $journalDao->getById($article->getJournalId());
$package = new DataversePackager();
// Add article metadata, in language of article locale
$package->addMetadata('title', $article->getTitle($article->getLocale()));
// If study description not provided, use article abstract
$package->addMetadata('description', $article->getData('studyDescription', $article->getLocale()) ? $article->getData('studyDescription', $article->getLocale()) : String::html2text($article->getAbstract($article->getLocale())));
foreach ($article->getAuthors() as $author) {
$package->addMetadata('creator', $author->getFullName(true), array('affiliation' => $this->_formatAffiliation($author, $article->getLocale())));
}
// Article metadata: fields with multiple values
$pattern = '/\\s*' . DATAVERSE_PLUGIN_SUBJECT_SEPARATOR . '\\s*/';
foreach (String::regexp_split($pattern, $article->getCoverageGeo($article->getLocale())) as $coverage) {
if ($coverage) {
$package->addMetadata('coverage', $coverage);
}
}
// Article metadata: filter subject(s) to prevent repeated values in dataset subject field
$subjects = array();
foreach (String::regexp_split($pattern, $article->getDiscipline($article->getLocale())) as $subject) {
if ($subject) {
$subjects[String::strtolower($subject)] = $subject;
}
}
foreach (String::regexp_split($pattern, $article->getSubjectClass($article->getLocale())) as $subject) {
if ($subject) {
$subjects[String::strtolower($subject)] = $subject;
}
}
foreach (String::regexp_split($pattern, $article->getSubject($article->getLocale())) as $subject) {
if ($subject) {
$subjects[String::strtolower($subject)] = $subject;
}
}
// Article metadata: filter contributors(s) to prevent repeated values in dataset contributor field
$contributors = array();
foreach (String::regexp_split($pattern, $article->getSponsor($article->getLocale())) as $contributor) {
if ($contributor) {
$contributors[String::strtolower($contributor)] = $contributor;
}
}
// Published article metadata
$pubIdAttributes = array();
if ($article->getStatus() == STATUS_PUBLISHED) {
// publication date
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
$publishedArticle =& $publishedArticleDao->getPublishedArticleByArticleId($article->getId(), $article->getJournalId());
$datePublished = $publishedArticle->getDatePublished();
if (!$datePublished) {
// If article has no pub date, use issue pub date
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issue =& $issueDao->getIssueByArticleId($article->getId(), $article->getJournalId());
$datePublished = $issue->getDatePublished();
}
$package->addMetadata('date', strftime('%Y-%m-%d', strtotime($datePublished)));
// isReferencedBy: add persistent URL to citation using specified pubid plugin
$pubIdPlugin =& PluginRegistry::getPlugin('pubIds', $this->getSetting($article->getJournalId(), 'pubIdPlugin'));
if ($pubIdPlugin && $pubIdPlugin->getEnabled()) {
$pubIdAttributes['agency'] = $pubIdPlugin->getDisplayName();
$pubIdAttributes['IDNo'] = $article->getPubId($pubIdPlugin->getPubIdType());
$pubIdAttributes['holdingsURI'] = $pubIdPlugin->getResolvingUrl($article->getJournalId(), $pubIdAttributes['IDNo']);
}
// If no pubIdP plugin selected or enabled, provide OJS URL
if (!array_key_exists('holdingsURI', $pubIdAttributes)) {
$pubIdAttributes['holdingsURI'] = Request::url($journal->getPath(), 'article', 'view', array($article->getId()));
}
// Add copyright notice.
if ($article->getCopyrightYear() && $article->getCopyrightHolder($article->getLocale())) {
AppLocale::requireComponents(LOCALE_COMPONENT_APPLICATION_COMMON);
$package->addMetadata('rights', __('submission.copyrightStatement', array('copyrightYear' => $article->getCopyrightYear(), 'copyrightHolder' => $article->getCopyrightHolder($article->getLocale()))));
}
}
// Journal metadata
$package->addMetadata('publisher', $journal->getSetting('publisherInstitution'));
$package->addMetadata('isReferencedBy', String::html2text($this->getCitation($article)), $pubIdAttributes);
// Suppfile metadata
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$dvFileDao =& DAORegistry::getDAO('DataverseFileDAO');
$dvFiles =& $dvFileDao->getDataverseFilesBySubmissionId($article->getId());
// Filter type field to prevent repeated values in dataset 'Kind of data' field
$suppFileTypes = array();
foreach ($dvFiles as $dvFile) {
$suppFile =& $suppFileDao->getSuppFile($dvFile->getSuppFileId(), $article->getId());
if ($suppFile) {
// Split & filter subjects and/or contributors that may be repeated in article metadata
foreach (String::regexp_split($pattern, $suppFile->getSubject($article->getLocale())) as $subject) {
$subjects[String::strtolower($subject)] = $subject;
}
foreach (String::regexp_split($pattern, $suppFile->getSponsor($article->getLocale())) as $contributor) {
if ($contributor) {
$contributors[String::strtolower($contributor)] = $contributor;
}
}
// File type has single value but possibly repeated across suppfiles
if ($suppFile->getType()) {
$suppFileTypes[String::strtolower($suppFile->getType())] = $suppFile->getType();
}
if ($suppFile->getTypeOther($article->getLocale())) {
$suppFileTypes[String::strtolower($suppFile->getTypeOther($article->getLocale()))] = $suppFile->getTypeOther($article->getLocale());
}
}
}
// Add subjects, contributors & types to entry
foreach (array_values($subjects) as $subject) {
$package->addMetadata('subject', $subject);
}
foreach (array_values($contributors) as $contributor) {
$package->addMetadata('contributor', $contributor, array('type' => 'funder'));
}
foreach (array_values($suppFileTypes) as $type) {
$package->addMetadata('type', $type);
}
// Write metadata as Atom entry
$package->createAtomEntry();
// Return package for deposit
return $package;
}
/**
* Update cataloguing information for an existing study.
* @param Article $article
* @param DataverseStudy $study
* @return DataverseStudy
*/
function &updateStudy(&$article, &$study)
{
$journal =& Request::getJournal();
$packager = new DataversePackager();
// Add article metadata
$packager->addMetadata('title', $article->getLocalizedTitle());
$packager->addMetadata('description', $article->getLocalizedAbstract());
foreach ($article->getAuthors() as $author) {
$packager->addMetadata('creator', $author->getFullName(true));
}
// subject: academic disciplines
$split = '/\\s*' . DATAVERSE_PLUGIN_SUBJECT_SEPARATOR . '\\s*/';
foreach (preg_split($split, $article->getLocalizedDiscipline(), NULL, PREG_SPLIT_NO_EMPTY) as $subject) {
$packager->addMetadata('subject', $subject);
}
// subject: subject classifications
foreach (preg_split($split, $article->getLocalizedSubjectClass(), NULL, PREG_SPLIT_NO_EMPTY) as $subject) {
$packager->addMetadata('subject', $subject);
}
// subject: keywords
foreach (preg_split($split, $article->getLocalizedSubject(), NULL, PREG_SPLIT_NO_EMPTY) as $subject) {
$packager->addMetadata('subject', $subject);
}
// geographic coverage
foreach (preg_split($split, $article->getLocalizedCoverageGeo(), NULL, PREG_SPLIT_NO_EMPTY) as $coverage) {
$packager->addMetadata('coverage', $coverage);
}
// rights
$packager->addMetadata('rights', $journal->getLocalizedSetting('copyrightNotice'));
// publisher
$packager->addMetadata('publisher', $journal->getSetting('publisherInstitution'));
// metadata for published articles: public IDs, publication dates
$pubIdAttributes = array();
if ($article->getStatus() == STATUS_PUBLISHED) {
// publication date
$publishedArticleDao = DAORegistry::getDAO('PublishedArticleDAO');
$publishedArticle =& $publishedArticleDao->getPublishedArticleByArticleId($article->getId(), $article->getJournalId());
$datePublished = $publishedArticle->getDatePublished();
if (!$datePublished) {
// If article has no pub date, use issue pub date
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issue =& $issueDao->getIssueByArticleId($article->getId(), $article->getJournalId());
$datePublished = $issue->getDatePublished();
}
$packager->addMetadata('date', strftime('%Y-%m-%d', strtotime($datePublished)));
// isReferencedBy: If article is published, add a persistent URL to citation using specified pubid plugin
$pubIdPlugin =& PluginRegistry::getPlugin('pubIds', $this->getSetting($article->getJournalId(), 'pubIdPlugin'));
if ($pubIdPlugin && $pubIdPlugin->getEnabled()) {
$pubIdAttributes['agency'] = $pubIdPlugin->getDisplayName();
$pubIdAttributes['IDNo'] = $article->getPubId($pubIdPlugin->getPubIdType());
$pubIdAttributes['holdingsURI'] = $pubIdPlugin->getResolvingUrl($article->getJournalId(), $pubIdAttributes['IDNo']);
} else {
// If no pub id plugin selected, use OJS URL
$pubIdAttributes['holdingsURI'] = Request::url($journal->getPath(), 'article', 'view', array($article->getId()));
}
}
// isReferencedBy
$packager->addMetadata('isReferencedBy', $this->getCitation($article), $pubIdAttributes);
// Include (some) suppfile metadata in study
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$dataverseFileDao =& DAORegistry::getDAO('DataverseFileDAO');
$dvFiles =& $dataverseFileDao->getDataverseFilesByStudyId($study->getId());
foreach ($dvFiles as $dvFile) {
$suppFile =& $suppFileDao->getSuppFile($dvFile->getSuppFileId(), $article->getId());
if (isset($suppFile)) {
// subject
foreach (preg_split($split, $suppFile->getSuppFileSubject(), NULL, PREG_SPLIT_NO_EMPTY) as $subject) {
$packager->addMetadata('subject', $subject);
}
// Type of file
if ($suppFile->getType()) {
$packager->addMetadata('type', $suppFile->getType());
}
// Type of file, user-defined:
if ($suppFile->getSuppFileTypeOther()) {
$packager->addMetadata('type', $suppFile->getSuppFileTypeOther());
}
}
}
// Write atom entry to file
$packager->createAtomEntry();
// Update the study in Dataverse
$client = $this->_initSwordClient();
$depositReceipt = $client->replaceMetadata($study->getEditUri(), $this->getSetting($article->getJournalId(), 'username'), $this->getSetting($article->getJournalId(), 'password'), '', $packager->getAtomEntryFilePath());
if ($depositReceipt->sac_status != DATAVERSE_PLUGIN_HTTP_STATUS_OK) {
return false;
}
// Updating the metadata may have updated the data citation
$study->setDataCitation($depositReceipt->sac_dcterms['bibliographicCitation'][0]);
$dataverseStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$dataverseStudyDao->updateStudy($study);
return $study;
}
