/**
* Create a Dataverse study: create deposit package with journal-, article-,
* and suppfile-level metadata, then deposit in Dataverse to create study.
* @param $article Article
* @return DataverseStudy
*/
function createStudy($article)
{
$package = $this->createMetadataPackage($article);
$client = $this->_initSwordClient();
$depositReceipt = $client->depositAtomEntry($this->getSetting($article->getJournalId(), 'dvUri'), $this->getSetting($article->getJournalId(), 'username'), $this->getSetting($article->getJournalId(), 'password'), '', $package->getAtomEntryFilePath());
$study = null;
if ($depositReceipt->sac_status == DATAVERSE_PLUGIN_HTTP_STATUS_CREATED) {
$this->import('classes.DataverseStudy');
$study = new DataverseStudy();
$study->setSubmissionId($article->getId());
$study->setEditUri($depositReceipt->sac_edit_iri);
$study->setEditMediaUri($depositReceipt->sac_edit_media_iri);
$study->setStatementUri($depositReceipt->sac_state_iri_atom);
$study->setDataCitation($depositReceipt->sac_dcterms['bibliographicCitation'][0]);
// Persistent URI may be present, as an altenate
foreach ($depositReceipt->sac_links as $link) {
if ($link->sac_linkrel == 'alternate') {
$study->setPersistentUri($link->sac_linkhref);
break;
}
}
// Insert new Dataverse study for this submission
$dataverseStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$dataverseStudyDao->insertStudy($study);
}
return $study;
}
/**
* Internal function to return DataverseStudy object from a row.
* @param $row array
* @return DataverseStudy
*/
function &_returnStudyFromRow(&$row)
{
$dataversePlugin =& PluginRegistry::getPlugin('generic', $this->_parentPluginName);
$dataversePlugin->import('classes.DataverseStudy');
$study = new DataverseStudy();
$study->setId($row['study_id']);
$study->setSubmissionId($row['submission_id']);
$study->setEditUri($row['edit_uri']);
$study->setEditMediaUri($row['edit_media_uri']);
$study->setStatementUri($row['statement_uri']);
$study->setPersistentUri($row['persistent_uri']);
$study->setDataCitation($row['data_citation']);
return $study;
}
/**
* Create a Dataverse study: create and deposit Atom entry; package and deposit
* files, if files submitted.
* @param $article
* @param $dvFiles array of files to deposit
* @return DataverseStudy
*/
function &createStudy(&$article, $dvFiles = array())
{
$journal =& Request::getJournal();
// Go no further if plugin is not configured.
if (!$this->getSetting($journal->getId(), 'dvUri')) {
return false;
}
$packager = new DataversePackager();
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
// 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);
}
// publisher
$packager->addMetadata('publisher', $journal->getSetting('publisherInstitution'));
// rights
$packager->addMetadata('rights', $journal->getLocalizedSetting('copyrightNotice'));
// isReferencedBy
$packager->addMetadata('isReferencedBy', $this->getCitation($article));
// Include (some) suppfile metadata in study
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 file
$packager->createAtomEntry();
// Create the study in Dataverse
$client = $this->_initSwordClient();
$depositReceipt = $client->depositAtomEntry($this->getSetting($article->getJournalId(), 'dvUri'), $this->getSetting($article->getJournalId(), 'username'), $this->getSetting($article->getJournalId(), 'password'), '', $packager->getAtomEntryFilePath());
// Exit & notify if study failed to be created
if ($depositReceipt->sac_status != DATAVERSE_PLUGIN_HTTP_STATUS_CREATED) {
return false;
}
// Insert new Dataverse study for this submission
$dataverseStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$this->import('classes.DataverseStudy');
$study = new DataverseStudy();
$study->setSubmissionId($article->getId());
$study->setEditUri($depositReceipt->sac_edit_iri);
$study->setEditMediaUri($depositReceipt->sac_edit_media_iri);
$study->setStatementUri($depositReceipt->sac_state_iri_atom);
$study->setDataCitation($depositReceipt->sac_dcterms['bibliographicCitation'][0]);
// Persistent URI may be present, as an altenate
foreach ($depositReceipt->sac_links as $link) {
if ($link->sac_linkrel == 'alternate') {
$study->setPersistentUri($link->sac_linkhref);
break;
}
}
$dataverseStudyDao->insertStudy($study);
// Fine. Now add the files, if any are present.
for ($i = 0; $i < sizeof($dvFiles); $i++) {
$dvFile =& $dvFiles[$i];
$suppFile =& $suppFileDao->getSuppFile($dvFile->getSuppFileId(), $article->getId());
$dvFileIndex[str_replace(' ', '_', $suppFile->getOriginalFileName())] =& $dvFile;
$packager->addFile($suppFile);
}
// Create the deposit package & add package to Dataverse
$packager->createPackage();
$depositReceipt = $client->deposit($study->getEditMediaUri(), $this->getSetting($journal->getId(), 'username'), $this->getSetting($journal->getId(), 'password'), '', $packager->getPackageFilePath(), $packager->getPackaging(), $packager->getContentType(), false);
// in progress? false
if ($depositReceipt->sac_status != DATAVERSE_PLUGIN_HTTP_STATUS_CREATED) {
return false;
}
// Get the study statement & update the local file list
$studyStatement = $client->retrieveAtomStatement($study->getStatementUri(), $this->getSetting($journal->getId(), 'username'), $this->getSetting($journal->getId(), 'password'), '');
if (!isset($studyStatement)) {
return false;
}
// Update each Dataverse file with study id & content source URI
$dvFileDao =& DAORegistry::getDAO('DataverseFileDAO');
foreach ($studyStatement->sac_entries as $entry) {
$dvUriFileName = substr($entry->sac_content_source, strrpos($entry->sac_content_source, '/') + 1);
if (array_key_exists($dvUriFileName, $dvFileIndex)) {
$dvFile =& $dvFileIndex[$dvUriFileName];
$dvFile->setContentSourceUri($entry->sac_content_source);
$dvFile->setStudyId($study->getId());
$dvFileDao->updateDataverseFile($dvFile);
}
}
// Done.
return $study;
}
