/**
* Save changes to the supplementary file.
* @return int the supplementary file ID
*/
function execute($fileName = null)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->article->getArticleId());
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$fileName = isset($fileName) ? $fileName : 'uploadSuppFile';
if (isset($this->suppFile)) {
parent::execute();
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $this->suppFile->getFileId();
if ($fileId != 0) {
$articleFileManager->uploadSuppFile($fileName, $fileId);
} else {
$fileId = $articleFileManager->uploadSuppFile($fileName);
$this->suppFile->setFileId($fileId);
}
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($this->article->getArticleId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
}
// Index metadata
ArticleSearchIndex::indexSuppFileMetadata($this->suppFile);
// Update existing supplementary file
$this->setSuppFileData($this->suppFile);
$suppFileDao->updateSuppFile($this->suppFile);
} else {
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $articleFileManager->uploadSuppFile($fileName);
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($this->article->getArticleId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
} else {
$fileId = 0;
}
// Insert new supplementary file
$this->suppFile = new SuppFile();
$this->suppFile->setArticleId($this->article->getArticleId());
$this->suppFile->setFileId($fileId);
parent::execute();
$this->setSuppFileData($this->suppFile);
$suppFileDao->insertSuppFile($this->suppFile);
$this->suppFileId = $this->suppFile->getId();
}
return $this->suppFileId;
}
/**
* Save changes to the supplementary file.
* @return int the supplementary file ID
*/
function execute()
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->articleId);
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$fileName = 'uploadSuppFile';
// edit an existing supp file, otherwise create new supp file entry
if (isset($this->suppFile)) {
$suppFile =& $this->suppFile;
// Remove old file and upload new, if file is selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
$suppFileId = $articleFileManager->uploadSuppFile($fileName, $suppFile->getFileId(), true);
$suppFile->setFileId($suppFileId);
}
// Update existing supplementary file
$this->setSuppFileData($suppFile);
$suppFileDao->updateSuppFile($suppFile);
} else {
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $articleFileManager->uploadSuppFile($fileName);
// Insert new supplementary file
$suppFile = new SuppFile();
$suppFile->setArticleId($this->articleId);
$suppFile->setFileId($fileId);
$this->setSuppFileData($suppFile);
$suppFileDao->insertSuppFile($suppFile);
$this->suppFileId = $suppFile->getId();
} else {
$fileId = 0;
}
}
return $this->suppFileId;
}
/**
* Save changes to the supplementary file.
* @return int the supplementary file ID
*/
function execute($fileName = null, $createRemote = false)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->article->getId());
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$fileName = isset($fileName) ? $fileName : 'uploadSuppFile';
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
if (isset($this->suppFile)) {
parent::execute();
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $this->suppFile->getFileId();
if ($fileId != 0) {
$articleFileManager->uploadSuppFile($fileName, $fileId);
} else {
$fileId = $articleFileManager->uploadSuppFile($fileName);
$this->suppFile->setFileId($fileId);
}
$articleSearchIndex->articleFileChanged($this->article->getId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
}
// Update existing supplementary file
$this->setSuppFileData($this->suppFile);
if ($this->getData('remoteURL')) {
$this->suppFile->setRemoteURL($this->getData('remoteURL'));
}
$suppFileDao->updateSuppFile($this->suppFile);
} else {
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $articleFileManager->uploadSuppFile($fileName);
$articleSearchIndex->articleFileChanged($this->article->getId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
} else {
$fileId = 0;
}
// Insert new supplementary file
$this->suppFile = new SuppFile();
$this->suppFile->setArticleId($this->article->getId());
$this->suppFile->setFileId($fileId);
if ($createRemote) {
$this->suppFile->setRemoteURL(__('common.remoteURL'));
}
parent::execute();
$this->setSuppFileData($this->suppFile);
$suppFileDao->insertSuppFile($this->suppFile);
$this->suppFileId = $this->suppFile->getId();
}
// Index updated metadata.
$articleSearchIndex->suppFileMetadataChanged($this->suppFile);
$articleSearchIndex->articleChangesFinished();
return $this->suppFileId;
}
/**
* Hook callback: handle suppfile form execution for completed submissions
* @see Form::execute()
*/
function suppFileFormExecute($hookName, $args)
{
$form =& $args[0];
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $form->article;
// Notify on successful study updates or errors
import('classes.notification.NotificationManager');
$notificationManager = new NotificationManager();
$user =& Request::getUser();
// Dataset metadata: fields stored with article metadata, but provided in suppfile
// form, at point of data deposit, to support data publishing
$article->setData('studyDescription', $form->getData('studyDescription'), $form->getFormLocale());
$article->setData('externalDataCitation', $form->getData('externalDataCitation'), $form->getFormLocale());
$articleDao->updateArticle($article);
// Form executed for completed submissions. Draft studies are created on
// submission completion. A study may or may not exist for this submission.
switch ($form->getData('publishData')) {
case 'none':
// Supplementary file: do not deposit.
if ($form->suppFile->getId()) {
// Suppfile exists & may previously have been flagged for deposit /
// deposited in Dataverse
$dvFileDao =& DAORegistry::getDAO('DataverseFileDAO');
$dvFile =& $dvFileDao->getDataverseFileBySuppFileId($form->suppFile->getId(), $article->getId());
if (isset($dvFile)) {
// Remove file from pending deposit (if submission is incomplete) or
// dataset previously deposited
$fileDeleted = $this->deleteFile($dvFile);
if ($fileDeleted) {
$dvFileDao->deleteDataverseFile($dvFile);
}
// Deleting a file may affect study cataloguing information
$dvStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$study =& $dvStudyDao->getStudyBySubmissionId($article->getId());
if (isset($study)) {
$this->replaceStudyMetadata($article, $study);
}
// Notify
$notificationManager->createTrivialNotification($user->getId(), $fileDeleted ? NOTIFICATION_TYPE_DATAVERSE_STUDY_UPDATED : NOTIFICATION_TYPE_ERROR);
}
}
break;
case 'dataverse':
// Deposit file. Create a study, if submission doesn't have one already.
$dvStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$study =& $dvStudyDao->getStudyBySubmissionId($article->getId());
if (!$study) {
$study = $this->createStudy($article);
}
if (!$study) {
// If study is not created, warn & exit
$notificationManager->createTrivialNotification($user->getId(), NOTIFICATION_TYPE_ERROR);
return false;
}
if (!$form->suppFile->getId()) {
// Suppfile is new, but inserted in db after hook is called. Handle
// insertion here & prevent duplicates in handleSuppFileInsertion() callback
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$form->setSuppFileData($form->suppFile);
$suppFileDao->insertSuppFile($form->suppFile);
$form->suppFileId = $form->suppFile->getId();
$form->suppFile =& $suppFileDao->getSuppFile($form->suppFileId, $article->getId());
// Add suppfile to study.
$deposited = $this->depositFiles($study, array($form->suppFile));
// File-level metadata may need to be added to study.
$this->replaceStudyMetadata($article, $study);
// & notify:
$notificationManager->createTrivialNotification($user->getId(), $deposited ? NOTIFICATION_TYPE_DATAVERSE_STUDY_UPDATED : NOTIFICATION_TYPE_ERROR);
} else {
// Suppfile exists, and uploaded file may be new or a replacement
// (form validator requires file upload if Dataverse option selected).
// Hook is called before suppfile object is updated with details of
// uploaded file, so refresh suppfile object here.
import('classes.file.ArticleFileManager');
$fileName = 'uploadSuppFile';
$articleFileManager = new ArticleFileManager($article->getId());
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $form->suppFile->getFileId();
if ($fileId != 0) {
$articleFileManager->uploadSuppFile($fileName, $fileId);
} else {
$fileId = $articleFileManager->uploadSuppFile($fileName);
$form->suppFile->setFileId($fileId);
}
}
// Store form metadata. It may be used to update study cataloguing information.
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$form->suppFile =& $suppFileDao->getSuppFile($form->suppFileId, $article->getId());
$form->setSuppFileData($form->suppFile);
$suppFileDao->updateSuppFile($form->suppFile);
// The uploaded file may be new, or it may replace a previously-deposited
// file. If it's a replacement, delete the existing file from Dataverse:
// this prevents orphaned files on the Dataverse side, and filename collisions
// described in https://redmine.hmdc.harvard.edu/issues/3301
$dvFileDao =& DAORegistry::getDAO('DataverseFileDAO');
$dvFile =& $dvFileDao->getDataverseFileBySuppFileId($form->suppFileId, $article->getId());
if (isset($dvFile)) {
$this->deleteFile($dvFile);
$dvFileDao->deleteDataverseFile($dvFile);
}
// Add uploaded suppfile to study.
$deposited = $this->depositFiles($study, array($form->suppFile));
// File-level metadata may need to be added to study.
$this->replaceStudyMetadata($article, $study);
// & notify:
$notificationManager->createTrivialNotification($user->getId(), $deposited ? NOTIFICATION_TYPE_DATAVERSE_STUDY_UPDATED : NOTIFICATION_TYPE_ERROR);
}
break;
default:
// Unknown option
assert(false);
}
return false;
}
/**
* Hook callback: handle suppfile form execution for completed submissions
* @see Form::execute()
*/
function suppFileFormExecute($hookName, $args)
{
$form =& $args[0];
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $form->article;
// External data citation: field is article metadata, but provided in
// suppfile form as well, at point of data file deposit, to help support
// data publishing decisions
$article->setData('externalDataCitation', $form->getData('externalDataCitation'), $form->getFormLocale());
$articleDao->updateArticle($article);
// Form executed for completed submissions. Draft studies are created on
// submission completion. A study may or may not exist for this submission.
$dvStudyDao =& DAORegistry::getDAO('DataverseStudyDAO');
$dvFileDao =& DAORegistry::getDAO('DataverseFileDAO');
switch ($form->getData('publishData')) {
case 'none':
// Supplementary file: do not deposit.
if (!$form->suppFile->getId()) {
return false;
}
// New suppfile: not in Dataverse
$dvFile =& $dvFileDao->getDataverseFileBySuppFileId($form->suppFile->getId(), $article->getId());
if (!isset($dvFile)) {
return false;
}
// Edited suppfile, but not in Dataverse
// Remove the file from Dataverse
$this->deleteFile($dvFile);
// Deleting a file may affect study cataloguing information
$study =& $dvStudyDao->getStudyBySubmissionId($article->getId());
$this->updateStudy($article, $study);
break;
case 'dataverse':
// Deposit file. If needed, insert/update suppfile on behalf of form
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
if (!$form->suppFile->getId()) {
// Suppfile is new, but inserted in db after hook is called. Handle
// insertion here & prevent duplicates in handleSuppFileInsertion() callback
$form->setSuppFileData($form->suppFile);
$suppFileDao->insertSuppFile($form->suppFile);
$form->suppFileId = $form->suppFile->getId();
$form->suppFile =& $suppFileDao->getSuppFile($form->suppFileId, $article->getId());
} else {
// Suppfile exists, but uploaded file may be new, replaced, or non-existent.
// Hook called before suppfile object updated with details of uploaded file,
// so refresh suppfile object here.
import('classes.file.ArticleFileManager');
$fileName = 'uploadSuppFile';
$articleFileManager = new ArticleFileManager($article->getId());
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $form->suppFile->getFileId();
if ($fileId != 0) {
$articleFileManager->uploadSuppFile($fileName, $fileId);
} else {
$fileId = $articleFileManager->uploadSuppFile($fileName);
$form->suppFile->setFileId($fileId);
}
}
// Store form metadata. It may be used to update study cataloguing information.
$form->suppFile =& $suppFileDao->getSuppFile($form->suppFileId, $article->getId());
$form->setSuppFileData($form->suppFile);
$suppFileDao->updateSuppFile($form->suppFile);
}
// If, at this point, there is no file id, there is nothing to deposit
if (!$form->suppFile->getFileId()) {
return false;
}
$user =& Request::getUser();
import('classes.notification.NotificationManager');
$notificationManager = new NotificationManager();
// Study may not exist, if this is the first file deposited
$study =& $dvStudyDao->getStudyBySubmissionId($article->getId());
if (!isset($study)) {
$study =& $this->createStudy($article);
$notificationManager->createTrivialNotification($user->getId(), isset($study) ? NOTIFICATION_TYPE_DATAVERSE_STUDY_CREATED : NOTIFICATION_TYPE_ERROR);
}
if (!isset($study)) {
return false;
}
// File already in Dataverse?
$dvFile =& $dvFileDao->getDataverseFileBySuppFileId($form->suppFile->getId(), $article->getId());
if (isset($dvFile)) {
// File is already in Dataverse. Update study with suppfile metadata.
$studyUpdated = $this->updateStudy($article, $study);
$notificationManager->createTrivialNotification($user->getId(), $studyUpdated ? NOTIFICATION_TYPE_DATAVERSE_STUDY_UPDATED : NOTIFICATION_TYPE_ERROR);
} else {
// Add file to study
$fileAdded = $this->addFileToStudy($study, $form->suppFile);
$notificationManager->createTrivialNotification($user->getId(), $fileAdded ? NOTIFICATION_TYPE_DATAVERSE_FILE_ADDED : NOTIFICATION_TYPE_ERROR);
}
break;
}
return false;
}
/**
* Save changes to the supplementary file.
* @return int the supplementary file ID
*/
function execute($fileName = null)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->article->getArticleId());
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$fileName = isset($fileName) ? $fileName : 'uploadSuppFile';
if (isset($this->suppFile)) {
$suppFile =& $this->suppFile;
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$articleFileManager->uploadSuppFile($fileName, $suppFile->getFileId());
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($this->article->getArticleId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $suppFile->getFileId());
}
// Index metadata
ArticleSearchIndex::indexSuppFileMetadata($suppFile);
// Update existing supplementary file
$this->setSuppFileData($suppFile);
$suppFileDao->updateSuppFile($suppFile);
} else {
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $articleFileManager->uploadSuppFile($fileName);
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($this->article->getArticleId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
// Insert new supplementary file
$suppFile = new SuppFile();
$suppFile->setArticleId($this->article->getArticleId());
$suppFile->setFileId($fileId);
$this->setSuppFileData($suppFile);
$suppFileDao->insertSuppFile($suppFile);
$this->suppFileId = $suppFile->getId();
} else {
$fileId = 0;
}
}
// Notifications
import('lib.pkp.classes.notification.NotificationManager');
$notificationManager = new NotificationManager();
$journal =& Request::getJournal();
$url = Request::url($journal->getPath(), 'sectionEditor', 'submission', array($this->article->getArticleId(), 'submissionReview'));
$sectionEditorsDao =& DAORegistry::getDAO('SectionEditorsDAO');
$sectionEditors =& $sectionEditorsDao->getEditorsBySectionId($journal->getId(), $this->article->getSectionId());
foreach ($sectionEditors as $sectionEditor) {
$notificationSectionEditors[] = array('id' => $sectionEditor->getId());
}
if ($suppFile->getData('type') == 'Raw Data File') {
$message = 'notification.type.rawDataSubmitted';
}
if ($suppFile->getData('type') == 'Other Supplementary Research Output') {
$message = 'notification.type.otherSuppResearchOutput';
}
if ($suppFile->getData('type') == 'Progress Report') {
$message = 'notification.type.progressReport';
}
if ($suppFile->getData('type') == 'Completion Report') {
$message = 'notification.type.completionReport';
}
if ($suppFile->getData('type') == 'Extension Request') {
$message = 'notification.type.extensionRequest';
}
if ($this->getData('type') == "Supp File") {
$message = 'notification.type.suppFile';
}
if (isset($message)) {
foreach ($notificationSectionEditors as $userRole) {
$notificationManager->createNotification($userRole['id'], $message, $this->article->getLocalizedTitle(), $url, 1, NOTIFICATION_TYPE_SUPP_FILE_MODIFIED);
}
}
return $this->suppFileId;
}
/**
* Save changes to the supplementary file.
* @return int the supplementary file ID
*/
function execute($fileName = null)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->article->getArticleId());
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$fileName = 'uploadSuppFile';
// Upload file, if file selected.
if ($articleFileManager->uploadedFileExists($fileName)) {
$fileId = $articleFileManager->uploadSuppFile($fileName);
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($this->article->getArticleId(), ARTICLE_SEARCH_SUPPLEMENTARY_FILE, $fileId);
// Insert new supplementary file
$suppFile = new SuppFile();
$suppFile->setArticleId($this->article->getArticleId());
$suppFile->setFileId($fileId);
$this->setSuppFileData($suppFile);
$suppFileDao->insertSuppFile($suppFile);
$this->suppFileId = $suppFile->getId();
} else {
$fileId = 0;
}
// Save article settings (withdrawReason and withdrawComments)
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $this->article;
$article->setWithdrawReason($this->getData('withdrawReason'), null);
if ($article->getWithdrawReason('en_US') == "2") {
$article->setWithdrawReason($this->getData('otherReason'), null);
}
$article->setWithdrawComments($this->getData('withdrawComments'), null);
// Save the article
$articleDao->updateArticle($article);
return $this->suppFileId;
}