/**
* Return string containing the contents of the HTML file.
* This function performs any necessary filtering, like image URL replacement.
* @param $baseImageUrl string base URL for image references
* @return string
*/
function getHTMLContents()
{
import('classes.file.ArticleFileManager');
$fileManager = new ArticleFileManager($this->getArticleId());
$contents = $fileManager->readFile($this->getFileId());
$journal =& Request::getJournal();
// Replace media file references
$images =& $this->getImageFiles();
foreach ($images as $image) {
$imageUrl = Request::url(null, 'article', 'viewFile', array($this->getArticleId(), $this->getBestGalleyId($journal), $image->getFileId()));
$pattern = preg_quote(rawurlencode($image->getOriginalFileName()));
$contents = preg_replace('/([Ss][Rr][Cc]|[Hh][Rr][Ee][Ff]|[Dd][Aa][Tt][Aa])\\s*=\\s*"([^"]*' . $pattern . ')"/', '\\1="' . $imageUrl . '"', $contents);
// Replacement for Flowplayer
$contents = preg_replace('/[Uu][Rr][Ll]\\s*\\:\\s*\'(' . $pattern . ')\'/', 'url:\'' . $imageUrl . '\'', $contents);
// Replacement for other players (ested with odeo; yahoo and google player won't work w/ OJS URLs, might work for others)
$contents = preg_replace('/[Uu][Rr][Ll]=([^"]*' . $pattern . ')/', 'url=' . $imageUrl, $contents);
}
// Perform replacement for ojs://... URLs
$contents = String::regexp_replace_callback('/(<[^<>]*")[Oo][Jj][Ss]:\\/\\/([^"]+)("[^<>]*>)/', array(&$this, '_handleOjsUrl'), $contents);
// Perform variable replacement for journal, issue, site info
$issueDao =& DAORegistry::getDAO('IssueDAO');
$issue =& $issueDao->getIssueByArticleId($this->getArticleId());
$journal =& Request::getJournal();
$site =& Request::getSite();
$paramArray = array('issueTitle' => $issue ? $issue->getIssueIdentification() : Locale::translate('editor.article.scheduleForPublication.toBeAssigned'), 'journalTitle' => $journal->getLocalizedTitle(), 'siteTitle' => $site->getLocalizedTitle(), 'currentUrl' => Request::getRequestUrl());
foreach ($paramArray as $key => $value) {
$contents = str_replace('{$' . $key . '}', $value, $contents);
}
return $contents;
}
public function testNativeDoiImport()
{
$testfile = 'tests/functional/plugins/importexport/native/testissue.xml';
$args = array('import', $testfile, 'test', 'admin');
$result = $this->executeCli('NativeImportExportPlugin', $args);
self::assertRegExp('/##plugins.importexport.native.import.success.description##/', $result);
$daos = array('Issue' => 'IssueDAO', 'PublishedArticle' => 'PublishedArticleDAO', 'Galley' => 'ArticleGalleyDAO', 'SuppFile' => 'SuppFileDAO');
$articelId = null;
foreach ($daos as $objectType => $daoName) {
$dao = DAORegistry::getDAO($daoName);
$pubObject = call_user_func(array($dao, "get{$objectType}ByPubId"), 'doi', $this->expectedDois[$objectType]);
self::assertNotNull($pubObject, "Error while testing {$objectType}: object or DOI has not been imported.");
$pubObjectByURN = call_user_func(array($dao, "get{$objectType}ByPubId"), 'other::urn', $this->expectedURNs[$objectType]);
self::assertNotNull($pubObjectByURN, "Error while testing {$objectType}: object or URN has not been imported.");
if ($objectType == 'PublishedArticle') {
$articelId = $pubObject->getId();
}
}
// Trying to import the same file again should lead to an error.
$args = array('import', $testfile, 'test', 'admin');
$result = $this->executeCli('NativeImportExportPlugin', $args);
self::assertRegExp('/##plugins.importexport.native.import.error.duplicatePubId##/', $result);
// Delete inserted article files from the filesystem.
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($articelId);
$articleFileManager->deleteArticleTree();
}
/**
* Return absolute path to the file on the host filesystem.
* @return string
*/
function getFilePath()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $articleDao->getArticle($this->getArticleId());
$journalId = $article->getJournalId();
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->getArticleId());
return Config::getVar('files', 'files_dir') . '/journals/' . $journalId . '/articles/' . $this->getArticleId() . '/' . $articleFileManager->fileStageToPath($this->getFileStage()) . '/' . $this->getFileName();
}
/**
* Delete a submission.
*/
function deleteSubmission($args)
{
$articleId = isset($args[0]) ? (int) $args[0] : 0;
$this->validate($articleId);
$authorSubmission =& $this->submission;
$this->setupTemplate(true);
// If the submission is incomplete, allow the author to delete it.
if ($authorSubmission->getSubmissionProgress() != 0) {
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($articleId);
$articleFileManager->deleteArticleTree();
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$articleDao->deleteArticleById($args[0]);
}
Request::redirect(null, null, 'index');
}
/**
* Upload the submission file.
* @param $fileName string
* @return boolean
*/
function uploadSubmissionFile($fileName)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->articleId);
$articleDao =& DAORegistry::getDAO('ArticleDAO');
if ($articleFileManager->uploadedFileExists($fileName)) {
// upload new submission file, overwriting previous if necessary
$submissionFileId = $articleFileManager->uploadSubmissionFile($fileName, $this->article->getSubmissionFileId(), true);
}
if (isset($submissionFileId)) {
$this->article->setSubmissionFileId($submissionFileId);
return $articleDao->updateArticle($this->article);
} else {
return false;
}
}
/**
* Add a file to the search index.
* @param $articleId int
* @param $type int
* @param $fileId int
*/
function updateFileIndex($articleId, $type, $fileId)
{
import('classes.file.ArticleFileManager');
$fileMgr = new ArticleFileManager($articleId);
$file =& $fileMgr->getFile($fileId);
if (isset($file)) {
$parser =& SearchFileParser::fromFile($file);
}
if (isset($parser)) {
if ($parser->open()) {
$searchDao =& DAORegistry::getDAO('ArticleSearchDAO');
$objectId = $searchDao->insertObject($articleId, $type, $fileId);
$position = 0;
while (($text = $parser->read()) !== false) {
ArticleSearchIndex::indexObjectKeywords($objectId, $text, $position);
}
$parser->close();
}
}
}
/**
* Delete a submission.
* @param $args array
* @param $request PKPRequest
*/
function deleteSubmission($args, $request)
{
$articleId = (int) array_shift($args);
$this->validate($request, $articleId);
$authorSubmission =& $this->submission;
$this->setupTemplate($request, true);
// If the submission is incomplete, allow the author to delete it.
if ($authorSubmission->getSubmissionProgress() != 0) {
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($articleId);
$articleFileManager->deleteArticleTree();
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$articleDao->deleteArticleById($articleId);
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
$articleSearchIndex->articleDeleted($articleId);
$articleSearchIndex->articleChangesFinished();
}
$request->redirect(null, null, 'index');
}
/**
* Delete submission data and associated files
*/
function execute()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
foreach ($this->parameters as $articleId) {
$article =& $articleDao->getArticle($articleId);
if (isset($article)) {
// remove files first, to prevent orphans
$articleFileManager = new ArticleFileManager($articleId);
if (!file_exists($articleFileManager->filesDir)) {
printf("Warning: no files found for submission {$articleId}.\n");
} else {
if (!is_writable($articleFileManager->filesDir)) {
printf("Error: Skipping submission {$articleId}. Can't delete files in " . $articleFileManager->filesDir . "\n");
continue;
} else {
$articleFileManager->deleteArticleTree();
}
}
$articleDao->deleteArticleById($articleId);
continue;
}
printf("Error: Skipping {$articleId}. Unknown submission.\n");
}
}
/**
* Upload the copyedited version of an article.
* @param $copyeditorSubmission object
* @param $copyeditStage string
* @param $request object
*/
function uploadCopyeditVersion($copyeditorSubmission, $copyeditStage, $request)
{
import('classes.file.ArticleFileManager');
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
$copyeditorSubmissionDao =& DAORegistry::getDAO('CopyeditorSubmissionDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
if ($copyeditStage == 'initial') {
$signoff = $signoffDao->build('SIGNOFF_COPYEDITING_INITIAL', ASSOC_TYPE_ARTICLE, $copyeditorSubmission->getId());
} else {
if ($copyeditStage == 'final') {
$signoff = $signoffDao->build('SIGNOFF_COPYEDITING_FINAL', ASSOC_TYPE_ARTICLE, $copyeditorSubmission->getId());
}
}
// Only allow an upload if they're in the initial or final copyediting
// stages.
if ($copyeditStage == 'initial' && ($signoff->getDateNotified() == null || $signoff->getDateCompleted() != null)) {
return;
} else {
if ($copyeditStage == 'final' && ($signoff->getDateNotified() == null || $signoff->getDateCompleted() != null)) {
return;
} else {
if ($copyeditStage != 'initial' && $copyeditStage != 'final') {
return;
}
}
}
$articleFileManager = new ArticleFileManager($copyeditorSubmission->getId());
$user =& $request->getUser();
$fileName = 'upload';
if ($articleFileManager->uploadedFileExists($fileName)) {
HookRegistry::call('CopyeditorAction::uploadCopyeditVersion', array(&$copyeditorSubmission));
if ($signoff->getFileId() != null) {
$fileId = $articleFileManager->uploadCopyeditFile($fileName, $copyeditorSubmission->getFileBySignoffType('SIGNOFF_COPYEDITING_INITIAL', true));
} else {
$fileId = $articleFileManager->uploadCopyeditFile($fileName);
}
}
if (isset($fileId) && $fileId != 0) {
$signoff->setFileId($fileId);
$signoff->setFileRevision($articleFileDao->getRevisionNumber($fileId));
$signoffDao->updateObject($signoff);
// Add log
import('classes.article.log.ArticleLog');
ArticleLog::logEvent($request, $copyeditorSubmission, ARTICLE_LOG_COPYEDITOR_FILE, 'log.copyedit.copyeditorFile', array('copyeditorName' => $user->getFullName(), 'fileId' => $fileId));
}
}
function &generateArticleDom(&$doc, &$journal, &$issue, &$article, &$galley)
{
$unavailableString = Locale::translate('plugins.importexport.erudit.unavailable');
$root =& XMLCustomWriter::createElement($doc, 'article');
XMLCustomWriter::setAttribute($root, 'idprop', $journal->getId() . '-' . $issue->getId() . '-' . $article->getId() . '-' . $galley->getId(), false);
XMLCustomWriter::setAttribute($root, 'arttype', 'article');
$lang = $article->getLanguage();
XMLCustomWriter::setAttribute($root, 'lang', isset($lang) ? $lang : 'en');
XMLCustomWriter::setAttribute($root, 'processing', 'cart');
/* --- admin --- */
$adminNode =& XMLCustomWriter::createElement($doc, 'admin');
XMLCustomWriter::appendChild($root, $adminNode);
/* --- articleinfo --- */
$articleInfoNode =& XMLCustomWriter::createElement($doc, 'articleinfo');
XMLCustomWriter::appendChild($adminNode, $articleInfoNode);
// The first public ID should be a full URL to the article.
$urlIdNode =& XMLCustomWriter::createChildWithText($doc, $articleInfoNode, 'idpublic', Request::url($journal->getPath(), 'article', 'view', array($article->getId(), $galley->getId())));
XMLCustomWriter::setAttribute($urlIdNode, 'scheme', 'sici');
/* --- journal --- */
$journalNode =& XMLCustomWriter::createElement($doc, 'journal');
XMLCustomWriter::appendChild($adminNode, $journalNode);
XMLCustomWriter::setAttribute($journalNode, 'id', 'ojs-' . $journal->getPath());
XMLCustomWriter::createChildWithText($doc, $journalNode, 'jtitle', $journal->getLocalizedTitle());
XMLCustomWriter::createChildWithText($doc, $journalNode, 'jshorttitle', $journal->getLocalizedSetting('initials'), false);
if (!($printIssn = $journal->getSetting('printIssn'))) {
$printIssn = $unavailableString;
}
XMLCustomWriter::createChildWithText($doc, $journalNode, 'idissn', $printIssn);
if (!($onlineIssn = $journal->getSetting('onlineIssn'))) {
$onlineIssn = $unavailableString;
}
XMLCustomWriter::createChildWithText($doc, $journalNode, 'iddigissn', $onlineIssn);
/* --- issue --- */
$issueNode =& XMLCustomWriter::createElement($doc, 'issue');
XMLCustomWriter::appendChild($adminNode, $issueNode);
XMLCustomWriter::setAttribute($issueNode, 'id', 'ojs-' . $issue->getBestIssueId());
XMLCustomWriter::createChildWithText($doc, $issueNode, 'volume', $issue->getVolume(), false);
XMLCustomWriter::createChildWithText($doc, $issueNode, 'issueno', $issue->getNumber(), false);
$pubNode =& XMLCustomWriter::createElement($doc, 'pub');
XMLCustomWriter::appendChild($issueNode, $pubNode);
XMLCustomWriter::createChildWithText($doc, $pubNode, 'year', $issue->getYear());
$digPubNode =& XMLCustomWriter::createElement($doc, 'digpub');
XMLCustomWriter::appendChild($issueNode, $digPubNode);
if ($issue->getDatePublished()) {
XMLCustomWriter::createChildWithText($doc, $digPubNode, 'date', EruditExportDom::formatDate($issue->getDatePublished()));
}
/* --- Publisher & DTD --- */
$publisherInstitution =& $journal->getSetting('publisherInstitution');
$publisherNode =& XMLCustomWriter::createElement($doc, 'publisher');
XMLCustomWriter::setAttribute($publisherNode, 'id', 'ojs-' . $journal->getId() . '-' . $issue->getId() . '-' . $article->getId());
XMLCustomWriter::appendChild($adminNode, $publisherNode);
$publisherInstitution = $unavailableString;
if (empty($publisherInstitution)) {
$publisherInstitution = $unavailableString;
}
XMLCustomWriter::createChildWithText($doc, $publisherNode, 'orgname', $publisherInstitution);
$digprodNode =& XMLCustomWriter::createElement($doc, 'digprod');
XMLCustomWriter::createChildWithText($doc, $digprodNode, 'orgname', $publisherInstitution);
XMLCustomWriter::setAttribute($digprodNode, 'id', 'ojs-prod-' . $journal->getId() . '-' . $issue->getId() . '-' . $article->getId());
XMLCustomWriter::appendChild($adminNode, $digprodNode);
$digdistNode =& XMLCustomWriter::createElement($doc, 'digdist');
XMLCustomWriter::createChildWithText($doc, $digdistNode, 'orgname', $publisherInstitution);
XMLCustomWriter::setAttribute($digdistNode, 'id', 'ojs-dist-' . $journal->getId() . '-' . $issue->getId() . '-' . $article->getId());
XMLCustomWriter::appendChild($adminNode, $digdistNode);
$dtdNode =& XMLCustomWriter::createElement($doc, 'dtd');
XMLCustomWriter::appendChild($adminNode, $dtdNode);
XMLCustomWriter::setAttribute($dtdNode, 'name', 'Erudit Article');
XMLCustomWriter::setAttribute($dtdNode, 'version', '3.0.0');
/* --- copyright --- */
$copyright = $journal->getLocalizedSetting('copyrightNotice');
XMLCustomWriter::createChildWithText($doc, $adminNode, 'copyright', empty($copyright) ? $unavailableString : $copyright);
/* --- frontmatter --- */
$frontMatterNode =& XMLCustomWriter::createElement($doc, 'frontmatter');
XMLCustomWriter::appendChild($root, $frontMatterNode);
$titleGroupNode =& XMLCustomWriter::createElement($doc, 'titlegr');
XMLCustomWriter::appendChild($frontMatterNode, $titleGroupNode);
XMLCustomWriter::createChildWithText($doc, $titleGroupNode, 'title', strip_tags($article->getLocalizedTitle()));
/* --- authorgr --- */
$authorGroupNode =& XMLCustomWriter::createElement($doc, 'authorgr');
XMLCustomWriter::appendChild($frontMatterNode, $authorGroupNode);
$authorNum = 1;
foreach ($article->getAuthors() as $author) {
$authorNode =& XMLCustomWriter::createElement($doc, 'author');
XMLCustomWriter::appendChild($authorGroupNode, $authorNode);
XMLCustomWriter::setAttribute($authorNode, 'id', 'ojs-' . $journal->getId() . '-' . $issue->getId() . '-' . $article->getId() . '-' . $galley->getId() . '-' . $authorNum);
$persNameNode =& XMLCustomWriter::createElement($doc, 'persname');
XMLCustomWriter::appendChild($authorNode, $persNameNode);
XMLCustomWriter::createChildWithText($doc, $persNameNode, 'firstname', $author->getFirstName());
XMLCustomWriter::createChildWithText($doc, $persNameNode, 'middlename', $author->getMiddleName(), false);
XMLCustomWriter::createChildWithText($doc, $persNameNode, 'familyname', $author->getLastName());
if ($author->getLocalizedAffiliation() != '') {
$affiliationNode =& XMLCustomWriter::createElement($doc, 'affiliation');
XMLCustomWriter::appendChild($authorNode, $affiliationNode);
XMLCustomWriter::createChildWithText($doc, $affiliationNode, 'blocktext', $author->getLocalizedAffiliation(), false);
}
$authorNum++;
}
/* --- abstract and keywords --- */
foreach ((array) $article->getAbstract(null) as $locale => $abstract) {
$abstract = strip_tags($abstract);
$abstractNode =& XMLCustomWriter::createElement($doc, 'abstract');
XMLCustomWriter::setAttribute($abstractNode, 'lang', $locale);
XMLCustomWriter::appendChild($frontMatterNode, $abstractNode);
XMLCustomWriter::createChildWithText($doc, $abstractNode, 'blocktext', $abstract);
unset($abstractNode);
}
if ($keywords = $article->getLocalizedSubject()) {
$keywordGroupNode =& XMLCustomWriter::createElement($doc, 'keywordgr');
XMLCustomWriter::setAttribute($keywordGroupNode, 'lang', ($language = $article->getLanguage()) ? $language : 'en');
foreach (explode(';', $keywords) as $keyword) {
XMLCustomWriter::createChildWithText($doc, $keywordGroupNode, 'keyword', trim($keyword), false);
}
XMLCustomWriter::appendChild($frontMatterNode, $keywordGroupNode);
}
/* --- body --- */
$bodyNode =& XMLCustomWriter::createElement($doc, 'body');
XMLCustomWriter::appendChild($root, $bodyNode);
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($article->getId());
$file =& $articleFileManager->getFile($galley->getFileId());
$parser =& SearchFileParser::fromFile($file);
if (isset($parser)) {
if ($parser->open()) {
// File supports text indexing.
$textNode =& XMLCustomWriter::createElement($doc, 'text');
XMLCustomWriter::appendChild($bodyNode, $textNode);
while (($line = $parser->read()) !== false) {
$line = trim($line);
if ($line != '') {
XMLCustomWriter::createChildWithText($doc, $textNode, 'blocktext', $line, false);
}
}
$parser->close();
}
}
return $root;
}
/**
* Save the email in the article email log.
*/
function log()
{
import('classes.article.log.ArticleEmailLogEntry');
import('classes.article.log.ArticleLog');
$entry = new ArticleEmailLogEntry();
$article =& $this->article;
// Log data
$entry->setEventType($this->eventType);
$entry->setAssocType($this->assocType);
$entry->setAssocId($this->assocId);
// Email data
$entry->setSubject($this->getSubject());
$entry->setBody($this->getBody());
$entry->setFrom($this->getFromString(false));
$entry->setRecipients($this->getRecipientString());
$entry->setCcs($this->getCcString());
$entry->setBccs($this->getBccString());
// Add log entry
$logEntryId = ArticleLog::logEmailEntry($article->getId(), $entry);
// Add attachments
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($article->getId());
foreach ($this->getAttachmentFiles() as $attachment) {
$articleFileManager->temporaryFileToArticleFile($attachment, ARTICLE_FILE_ATTACHMENT, $logEntryId);
}
}
/**
* Upload a review on behalf of its reviewer.
* @param $reviewId int
*/
function uploadReviewForReviewer($reviewId, $article, $request)
{
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
$userDao =& DAORegistry::getDAO('UserDAO');
$user =& $request->getUser();
$reviewAssignment =& $reviewAssignmentDao->getById($reviewId);
$reviewer =& $userDao->getUser($reviewAssignment->getReviewerId(), true);
if (HookRegistry::call('SectionEditorAction::uploadReviewForReviewer', array(&$reviewAssignment, &$reviewer))) {
return;
}
// Upload the review file.
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($reviewAssignment->getSubmissionId());
// Only upload the file if the reviewer has yet to submit a recommendation
if (($reviewAssignment->getRecommendation() === null || $reviewAssignment->getRecommendation() === '') && !$reviewAssignment->getCancelled()) {
$fileName = 'upload';
if ($articleFileManager->uploadedFileExists($fileName)) {
if ($reviewAssignment->getReviewerFileId() != null) {
$fileId = $articleFileManager->uploadReviewFile($fileName, $reviewAssignment->getReviewerFileId());
} else {
$fileId = $articleFileManager->uploadReviewFile($fileName);
}
}
}
if (isset($fileId) && $fileId != 0) {
// Only confirm the review for the reviewer if
// he has not previously done so.
if ($reviewAssignment->getDateConfirmed() == null) {
$reviewAssignment->setDeclined(0);
$reviewAssignment->setDateConfirmed(Core::getCurrentDate());
}
$reviewAssignment->setReviewerFileId($fileId);
$reviewAssignment->stampModified();
$reviewAssignmentDao->updateReviewAssignment($reviewAssignment);
// Add log
import('classes.article.log.ArticleLog');
ArticleLog::logEvent($request, $article, ARTICLE_LOG_REVIEW_FILE_BY_PROXY, 'log.review.reviewFileByProxy', array('reviewerName' => $reviewer->getFullName(), 'round' => $reviewAssignment->getRound(), 'userName' => $user->getFullName(), 'reviewId' => $reviewAssignment->getId()));
}
}
/**
* Save changes to the report file.
* @return int the report file ID
*/
function execute($fileName = null)
{
$sectionDecisionDao =& DAORegistry::getDAO('SectionDecisionDAO');
$articleDao =& DAORegistry::getDAO('ArticleDAO');
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($this->article->getArticleId());
$fileName = isset($fileName) ? $fileName : 'uploadReportFile';
$lastDecision = $this->article->getLastSectionDecision();
$lastDecisionDecision = $lastDecision->getDecision();
$lastDecisionType = $lastDecision->getReviewType();
// Ensure to start a new round of review when needed, and if the file to upload is correct
if (($lastDecisionDecision == SUBMISSION_SECTION_DECISION_APPROVED || $lastDecisionDecision == SUBMISSION_SECTION_DECISION_EXEMPTED || $lastDecisionType == REVIEW_TYPE_SAE && ($lastDecisionDecision == SUBMISSION_SECTION_DECISION_INCOMPLETE || $lastDecisionDecision == SUBMISSION_SECTION_DECISION_RESUBMIT)) && $articleFileManager->uploadedFileExists($fileName)) {
$this->fileId = $articleFileManager->uploadSAEFile($fileName);
} else {
$this->fileId = 0;
}
if ($this->fileId && $this->fileId > 0) {
$sectionDecision =& new SectionDecision();
$sectionDecision->setSectionId($lastDecision->getSectionId());
$sectionDecision->setDecision(0);
$sectionDecision->setDateDecided(date(Core::getCurrentDate()));
$sectionDecision->setArticleId($this->article->getArticleId());
$sectionDecision->setReviewType(REVIEW_TYPE_SAE);
if ($lastDecisionType == $sectionDecision->getReviewType()) {
$lastRound = (int) $lastDecision->getRound();
$sectionDecision->setRound($lastRound + 1);
} else {
$sectionDecision->setRound(1);
}
$sectionDecisionDao->insertSectionDecision($sectionDecision);
$articleDao->changeArticleStatus($this->article->getArticleId(), STATUS_QUEUED);
}
// 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(), $lastDecision->getSectionId());
foreach ($sectionEditors as $sectionEditor) {
$notificationSectionEditors[] = array('id' => $sectionEditor->getId());
}
foreach ($notificationSectionEditors as $userRole) {
$notificationManager->createNotification($userRole['id'], 'notification.type.sae', $this->article->getProposalId(), $url, 1, NOTIFICATION_TYPE_METADATA_MODIFIED);
}
return $this->fileId;
}
/**
* Delete a supplementary file.
* @param $args array, the first parameter is the supplementary file to delete
* @param $request PKPRequest
*/
function deleteSubmitSuppFile($args, $request)
{
import('classes.file.ArticleFileManager');
$articleId = (int) $request->getUserVar('articleId');
$suppFileId = (int) array_shift($args);
$this->validate($request, $articleId, 4);
$article =& $this->article;
$this->setupTemplate($request, true);
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
$suppFile = $suppFileDao->getSuppFile($suppFileId, $articleId);
$suppFileDao->deleteSuppFileById($suppFileId, $articleId);
if ($suppFile->getFileId()) {
$articleFileManager = new ArticleFileManager($articleId);
$articleFileManager->deleteFile($suppFile->getFileId());
}
$request->redirect(null, null, 'submit', '4', array('articleId' => $articleId));
}
/**
* Retrieve all article files for a type and assoc ID.
* @param $assocId int
* @param $type int
* @return array ArticleFiles
*/
function &getArticleFilesByAssocId($assocId, $type)
{
import('file.ArticleFileManager');
$articleFiles = array();
$result =& $this->retrieve('SELECT * FROM article_files WHERE assoc_id = ? AND type = ?', array($assocId, ArticleFileManager::typeToPath($type)));
while (!$result->EOF) {
$articleFiles[] =& $this->_returnArticleFileFromRow($result->GetRowAssoc(false));
$result->moveNext();
}
$result->Close();
unset($result);
return $articleFiles;
}
/**
* Delete a submission.
*/
function deleteSubmission($args, $request)
{
$articleId = (int) array_shift($args);
$this->validate($articleId);
parent::setupTemplate(true);
$journal =& $request->getJournal();
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $articleDao->getArticle($articleId);
$status = $article->getStatus();
if ($article->getJournalId() == $journal->getId() && ($status == STATUS_DECLINED || $status == STATUS_ARCHIVED)) {
// Delete article files
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($articleId);
$articleFileManager->deleteArticleTree();
// Delete article database entries
$articleDao->deleteArticleById($articleId);
}
$request->redirect(null, null, 'submissions', 'submissionsArchives');
}
/**
* Upload the revised version of a copyedit file.
* @param $authorSubmission object
* @param $copyeditStage string
*/
function uploadCopyeditVersion($authorSubmission, $copyeditStage)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($authorSubmission->getId());
$authorSubmissionDao =& DAORegistry::getDAO('AuthorSubmissionDAO');
$articleFileDao =& DAORegistry::getDAO('ArticleFileDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
// Authors cannot upload if the assignment is not active, i.e.
// they haven't been notified or the assignment is already complete.
$authorSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_AUTHOR', ASSOC_TYPE_ARTICLE, $authorSubmission->getId());
if (!$authorSignoff->getDateNotified() || $authorSignoff->getDateCompleted()) {
return;
}
$fileName = 'upload';
if ($articleFileManager->uploadedFileExists($fileName)) {
HookRegistry::call('AuthorAction::uploadCopyeditVersion', array(&$authorSubmission, &$copyeditStage));
if ($authorSignoff->getFileId() != null) {
$fileId = $articleFileManager->uploadCopyeditFile($fileName, $authorSignoff->getFileId());
} else {
$fileId = $articleFileManager->uploadCopyeditFile($fileName);
}
}
$authorSignoff->setFileId($fileId);
if ($copyeditStage == 'author') {
$authorSignoff->setFileRevision($articleFileDao->getRevisionNumber($fileId));
}
$signoffDao->updateObject($authorSignoff);
}
/**
* 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 $this->suppFileId;
}
function importArticles()
{
assert($this->xml->name == 'articles');
$articleDAO =& DAORegistry::getDAO('ArticleDAO');
$articles = $articleDAO->getArticlesByJournalId($this->journal->getId());
$journalFileManager = new JournalFileManager($this->journal);
$publicFileManager =& new PublicFileManager();
$this->nextElement();
while ($this->xml->name == 'article') {
$articleXML = $this->getCurrentElementAsDom();
$article = new Article();
$article->setJournalId($this->journal->getId());
$article->setUserId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $articleXML->userId));
$article->setSectionId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_SECTION, (int) $articleXML->sectionId));
$article->setLocale((string) $articleXML->locale);
$article->setLanguage((string) $articleXML->language);
$article->setCommentsToEditor((string) $articleXML->commentsToEditor);
$article->setCitations((string) $articleXML->citations);
$article->setDateSubmitted((string) $articleXML->dateSubmitted);
$article->setDateStatusModified((string) $articleXML->dateStatusModified);
$article->setLastModified((string) $articleXML->lastModified);
$article->setStatus((int) $articleXML->status);
$article->setSubmissionProgress((int) $articleXML->submissionProgress);
$article->setCurrentRound((int) $articleXML->currentRound);
$article->setPages((string) $articleXML->pages);
$article->setFastTracked((int) $articleXML->fastTracked);
$article->setHideAuthor((int) $articleXML->hideAuthor);
$article->setCommentsStatus((int) $articleXML->commentsStatus);
$articleDAO->insertArticle($article);
$oldArticleId = (int) $articleXML->oldId;
$this->restoreDataObjectSettings($articleDAO, $articleXML->settings, 'article_settings', 'article_id', $article->getId());
$article =& $articleDAO->getArticle($article->getId());
// Reload article with restored settings
$covers = $article->getFileName(null);
if ($covers) {
foreach ($covers as $locale => $oldCoverFileName) {
$sourceFile = $this->publicFolderPath . '/' . $oldCoverFileName;
$extension = $publicFileManager->getExtension($oldCoverFileName);
$destFile = 'cover_issue_' . $article->getId() . "_{$locale}.{$extension}";
$publicFileManager->copyJournalFile($this->journal->getId(), $sourceFile, $destFile);
unlink($sourceFile);
$article->setFileName($destFile, $locale);
$articleDAO->updateArticle($article);
}
}
$articleFileManager = new ArticleFileManager($article->getId());
$authorDAO =& DAORegistry::getDAO('AuthorDAO');
foreach ($articleXML->author as $authorXML) {
$author = new Author();
$author->setArticleId($article->getId());
$author->setFirstName((string) $authorXML->firstName);
$author->setMiddleName((string) $authorXML->middleName);
$author->setLastName((string) $authorXML->lastName);
$author->setSuffix((string) $authorXML->suffix);
$author->setCountry((string) $authorXML->country);
$author->setEmail((string) $authorXML->email);
$author->setUrl((string) $authorXML->url);
$author->setUserGroupId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_GROUP, (int) $authorXML->userGroupId));
$author->setPrimaryContact((int) $authorXML->primaryContact);
$author->setSequence((int) $authorXML->sequence);
$authorDAO->insertAuthor($author);
$this->restoreDataObjectSettings($authorDAO, $authorXML->settings, 'author_settings', 'author_id', $author->getId());
unset($author);
}
$articleEmailLogDAO =& DAORegistry::getDAO('ArticleEmailLogDAO');
$emailLogsXML = array();
foreach ($articleXML->emailLogs->emailLog as $emailLogXML) {
array_unshift($emailLogsXML, $emailLogXML);
}
foreach ($emailLogsXML as $emailLogXML) {
$emailLog = new ArticleEmailLogEntry();
$emailLog->setAssocType(ASSOC_TYPE_ARTICLE);
$emailLog->setAssocId($article->getId());
$emailLog->setSenderId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $emailLogXML->senderId));
$emailLog->setDateSent((string) $emailLogXML->dateSent);
$emailLog->setIPAddress((string) $emailLogXML->IPAddress);
$emailLog->setEventType((int) $emailLogXML->eventType);
$emailLog->setFrom((string) $emailLogXML->from);
$emailLog->setRecipients((string) $emailLogXML->recipients);
$emailLog->setCcs((string) $emailLogXML->ccs);
$emailLog->setBccs((string) $emailLogXML->bccs);
$emailLog->setSubject((string) $emailLogXML->subject);
$emailLog->setBody((string) $emailLogXML->body);
$articleEmailLogDAO->insertObject($emailLog);
$this->idTranslationTable->register(INTERNAL_TRANSFER_OBJECT_ARTICLE_EMAIL_LOG, (int) $emailLogXML->oldId, $emailLog->getId());
}
$articleFileDAO =& DAORegistry::getDAO('ArticleFileDAO');
foreach ($articleXML->articleFile as $articleFileXML) {
try {
$articleFile = new ArticleFile();
$articleFile->setArticleId($article->getId());
$articleFile->setSourceFileId((int) $articleFileXML->sourceFileId);
$articleFile->setSourceRevision((int) $articleFileXML->sourceRevision);
$articleFile->setRevision((int) $articleFileXML->revision);
$articleFile->setFileName((string) $articleFileXML->fileName);
$articleFile->setFileType((string) $articleFileXML->fileType);
$articleFile->setFileSize((string) $articleFileXML->fileSize);
$articleFile->setOriginalFileName((string) $articleFileXML->originalFileName);
$articleFile->setFileStage((int) $articleFileXML->fileStage);
$articleFile->setAssocId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_EMAIL_LOG, (int) $articleFileXML->assocId));
$articleFile->setDateUploaded((string) $articleFileXML->dateUploaded);
$articleFile->setDateModified((string) $articleFileXML->dateModified);
$articleFile->setRound((int) $articleFileXML->round);
$articleFile->setViewable((int) $articleFileXML->viewable);
$articleFileDAO->insertArticleFile($articleFile);
$oldArticleFileId = (int) $articleFileXML->oldId;
$oldFileName = $articleFile->getFileName();
$stagePath = $articleFileManager->fileStageToPath($articleFile->getFileStage());
$fileInTransferPackage = $this->journalFolderPath . "/articles/{$oldArticleId}/{$stagePath}/{$oldFileName}";
$newFileName = $articleFileManager->generateFilename($articleFile, $articleFile->getFileStage(), $articleFile->getOriginalFileName());
$newFilePath = "/articles/" . $article->getId() . "/{$stagePath}/{$newFileName}";
$journalFileManager->copyFile($fileInTransferPackage, $journalFileManager->filesDir . $newFilePath);
unlink($fileInTransferPackage);
$articleFileDAO->updateArticleFile($articleFile);
$this->idTranslationTable->register(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, $oldArticleFileId, $articleFile->getFileId());
} catch (Exception $e) {
}
}
$articleFiles = $articleFileDAO->getArticleFilesByArticle($article->getId());
foreach ($articleFiles as $articleFile) {
try {
$articleFile->setSourceFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, $articleFile->getSourceFileId()));
$articleFileDAO->updateArticleFile($articleFile);
} catch (Exception $e) {
}
}
$suppFileDAO =& DAORegistry::getDAO('SuppFileDAO');
foreach ($articleXML->suppFile as $suppFileXML) {
$suppFile =& new SuppFile();
$suppFile->setArticleId($article->getId());
$suppFile->setRemoteURL((string) $suppFileXML->remoteURL);
$suppFile->setFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $suppFileXML->fileId));
$suppFile->setType((string) $suppFileXML->type);
$suppFile->setDateCreated((string) $suppFileXML->dateCreated);
$suppFile->setLanguage((string) $suppFileXML->language);
$suppFile->setShowReviewers((int) $suppFileXML->showReviewers);
$suppFile->setDateSubmitted((string) $suppFileXML->dateSubmitted);
$suppFile->setSequence((int) $suppFileXML->sequence);
$suppFileDAO->insertSuppFile($suppFile);
$this->restoreDataObjectSettings($suppFileDAO, $suppFileXML->settings, 'article_supp_file_settings', 'supp_id', $suppFile->getId());
}
$articleCommentDAO =& DAORegistry::getDAO('ArticleCommentDAO');
foreach ($articleXML->articleComment as $articleCommentXML) {
$articleComment = new ArticleComment();
$articleComment->setArticleId($article->getId());
$articleComment->setAssocId($article->getId());
$articleComment->setCommentType((int) $articleCommentXML->commentType);
$articleComment->setRoleId((int) $articleCommentXML->roleId);
$articleComment->setAuthorId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $articleCommentXML->authorId));
$articleComment->setCommentTitle((string) $articleCommentXML->commentTitle);
$articleComment->setComments((string) $articleCommentXML->comments);
$articleComment->setDatePosted((string) $articleCommentXML->datePosted);
$articleComment->setDateModified((string) $articleCommentXML->dateModified);
$articleComment->setViewable((int) $articleCommentXML->viewable);
$articleCommentDAO->insertArticleComment($articleComment);
}
$articleGalleyDAO =& DAORegistry::getDAO('ArticleGalleyDAO');
foreach ($articleXML->articleGalley as $articleGalleyXML) {
$articleGalley = null;
if ($articleGalleyXML->htmlGalley == "1") {
$articleGalley = new ArticleHTMLGalley();
} else {
$articleGalley = new ArticleGalley();
}
$articleGalley->setArticleId($article->getId());
$articleGalley->setLocale((string) $articleGalleyXML->locale);
$articleGalley->setFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleGalleyXML->fileId));
$articleGalley->setLabel((string) $articleGalleyXML->label);
$articleGalley->setSequence((int) $articleGalleyXML->sequence);
$articleGalley->setRemoteURL((string) $articleGalleyXML->remoteURL);
if ($articleGalley instanceof ArticleHTMLGalley) {
$articleGalley->setStyleFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleGalleyXML->styleFileId));
}
$articleGalleyDAO->insertGalley($articleGalley);
if ($articleGalley instanceof ArticleHTMLGalley) {
foreach ($articleGalleyXML->htmlGalleyImage as $articleGalleyImageXML) {
$imageId = $this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleGalleyImageXML);
$articleGalleyDAO->insertGalleyImage($articleGalley->getId(), $imageId);
}
}
$this->restoreDataObjectSettings($articleGalleyDAO, $articleGalleyXML->settings, 'article_galley_settings', 'galley_id', $articleGalley->getId());
}
$noteDAO =& DAORegistry::getDAO('NoteDAO');
foreach ($articleXML->articleNote as $articleNoteXML) {
$articleNote = new Note();
$articleNote->setUserId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $articleNoteXML->userId));
$articleNote->setFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleNoteXML->fileId));
$articleNote->setAssocType(ASSOC_TYPE_ARTICLE);
$articleNote->setAssocId($article->getId());
$articleNote->setDateCreated((string) $articleNoteXML->dateCreated);
$articleNote->setDateModified((string) $articleNoteXML->dateModified);
$articleNote->setContents((string) $articleNoteXML->contents);
$articleNote->setTitle((string) $articleNoteXML->title);
$noteDAO->insertObject($articleNote);
}
$editAssignmentDAO =& DAORegistry::getDAO('EditAssignmentDAO');
foreach ($articleXML->editAssignment as $editAssignmentXML) {
$editAssignment = new EditAssignment();
$editAssignment->setArticleId($article->getId());
$editAssignment->setEditorId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $editAssignmentXML->editorId));
$editAssignment->setCanReview((int) $editAssignmentXML->canReview);
$editAssignment->setCanEdit((int) $editAssignmentXML->canEdit);
$editAssignment->setDateUnderway((string) $editAssignmentXML->dateUnderway);
$editAssignment->setDateNotified((string) $editAssignmentXML->dateNotified);
$editAssignmentDAO->insertEditAssignment($editAssignment);
}
$reviewAssignmentDAO =& DAORegistry::getDAO('ReviewAssignmentDAO');
$reviewFormResponseDAO =& DAORegistry::getDAO('ReviewFormResponseDAO');
foreach ($articleXML->reviewAssignment as $reviewAssignmentXML) {
$reviewAssignment = new ReviewAssignment();
$reviewAssignment->setSubmissionId($article->getId());
$reviewAssignment->setReviewerId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $reviewAssignmentXML->reviewerId));
try {
$reviewAssignment->setReviewerFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $reviewAssignmentXML->reviewerFileId));
} catch (Exception $e) {
$this->logger->log("Arquivo do artigo {$oldArticleId} não encontrado. ID: " . (int) $reviewAssignmentXML->reviewerFileId . "\n");
}
$reviewAssignment->setReviewFormId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_REVIEW_FORM, (int) $reviewAssignmentXML->reviewFormId));
$reviewAssignment->setReviewRoundId((int) $reviewAssignmentXML->reviewRoundId);
$reviewAssignment->setStageId((int) $reviewAssignmentXML->stageId);
$reviewAssignment->setReviewerFullName((string) $reviewAssignmentXML->reviewerFullName);
$reviewAssignment->setCompetingInterests((string) $reviewAssignmentXML->competingInterests);
$reviewAssignment->setRegretMessage((string) $reviewAssignmentXML->regretMessage);
$reviewAssignment->setRecommendation((string) $reviewAssignmentXML->recommendation);
$reviewAssignment->setDateAssigned((string) $reviewAssignmentXML->dateAssigned);
$reviewAssignment->setDateNotified((string) $reviewAssignmentXML->dateNotified);
$reviewAssignment->setDateConfirmed((string) $reviewAssignmentXML->dateConfirmed);
$reviewAssignment->setDateCompleted((string) $reviewAssignmentXML->dateCompleted);
$reviewAssignment->setDateAcknowledged((string) $reviewAssignmentXML->dateAcknowledged);
$reviewAssignment->setDateDue((string) $reviewAssignmentXML->dateDue);
$reviewAssignment->setDateResponseDue((string) $reviewAssignmentXML->dateResponseDue);
$reviewAssignment->setLastModified((string) $reviewAssignmentXML->lastModified);
$reviewAssignment->setDeclined((int) $reviewAssignmentXML->declined);
$reviewAssignment->setReplaced((int) $reviewAssignmentXML->replaced);
$reviewAssignment->setCancelled((int) $reviewAssignmentXML->cancelled);
$reviewAssignment->setQuality((int) $reviewAssignmentXML->quality);
$reviewAssignment->setDateRated((string) $reviewAssignmentXML->dateRated);
$reviewAssignment->setDateReminded((string) $reviewAssignmentXML->dateReminded);
$reviewAssignment->setReminderWasAutomatic((int) $reviewAssignmentXML->reminderWasAutomatic);
$reviewAssignment->setRound((int) $reviewAssignmentXML->round);
$reviewAssignment->setReviewRevision((int) $reviewAssignmentXML->reviewRevision);
$reviewAssignment->setReviewMethod((int) $reviewAssignmentXML->reviewMethod);
$reviewAssignment->setUnconsidered((int) $reviewAssignmentXML->unconsidered);
$reviewAssignmentDAO->insertObject($reviewAssignment);
foreach ($reviewAssignmentXML->formResponses->formResponse as $formResponseXML) {
$reviewFormResponseDAO->update('INSERT INTO review_form_responses
(review_form_element_id, review_id, response_type, response_value)
VALUES
(?, ?, ?, ?)', array($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_REVIEW_FORM_ELEMENT, (int) $formResponseXML->reviewFormElementId), $reviewAssignment->getId(), (string) $formResponseXML->responseType, (string) $formResponseXML->responseValue));
}
}
$signoffDAO =& DAORegistry::getDAO('SignoffDAO');
foreach ($articleXML->signoff as $signoffXML) {
$signoff = new Signoff();
$signoff->setAssocType(ASSOC_TYPE_ARTICLE);
$signoff->setAssocId($article->getId());
$signoff->setUserId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $signoffXML->userId));
$signoff->setFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $signoffXML->fileId));
$signoff->setUserGroupId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_GROUP, (int) $signoffXML->userGroupId));
$signoff->setSymbolic((string) $signoffXML->symbolic);
$signoff->setFileRevision((int) $signoffXML->fileRevision);
$signoff->setDateUnderway((string) $signoffXML->dateUnderway);
$signoff->setDateNotified((string) $signoffXML->dateNotified);
$signoff->setDateCompleted((string) $signoffXML->dateCompleted);
$signoff->setDateAcknowledged((string) $signoffXML->dateAcknowledged);
$signoffDAO->insertObject($signoff);
}
$editorSubmissionDAO =& DAORegistry::getDAO('EditorSubmissionDAO');
foreach ($articleXML->editDecisions as $editDecisionXML) {
$editDecisions =& $editorSubmissionDAO->update('INSERT INTO edit_decisions (article_id, round, editor_id, decision, date_decided) values (?, ?, ?, ?, ?)', array($article->getId(), (string) $editDecisionXML->round, $this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $editDecisionXML->editorId), (string) $editDecisionXML->decision, (string) $editDecisionXML->dateDecided));
}
$publishedArticleDAO =& DAORegistry::getDAO('PublishedArticleDAO');
if (isset($articleXML->publishedArticle)) {
$publishedArticleXML = $articleXML->publishedArticle;
$publishedArticle = new PublishedArticle();
$publishedArticle->setId($article->getId());
$publishedArticle->setIssueId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ISSUE, (int) $publishedArticleXML->issueId));
$publishedArticle->setDatePublished((string) $publishedArticleXML->datePublished);
$publishedArticle->setSeq((int) $publishedArticleXML->seq);
$publishedArticle->setAccessStatus((int) $publishedArticleXML->accessStatus);
$publishedArticleDAO->insertPublishedArticle($publishedArticle);
}
$articleEventLogDAO =& DAORegistry::getDAO('ArticleEventLogDAO');
$eventLogsXML =& iterator_to_array($articleXML->eventLogs->eventLog);
$eventLogsXML = array();
foreach ($articleXML->eventLogs->eventLog as $eventLogXML) {
array_unshift($eventLogsXML, $eventLogXML);
}
foreach ($eventLogsXML as $eventLogXML) {
$eventLog = new ArticleEventLogEntry();
$eventLog->setAssocType(ASSOC_TYPE_ARTICLE);
$eventLog->setAssocId($article->getId());
$eventLog->setUserId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_USER, (int) $eventLogXML->userId));
$eventLog->setDateLogged((string) $eventLogXML->dateLogged);
$eventLog->setIPAddress((string) $eventLogXML->IPAddress);
$eventLog->setEventType((int) $eventLogXML->eventType);
$eventLog->setMessage((string) $eventLogXML->message);
$eventLog->setIsTranslated((int) $eventLogXML->isTranslated);
$articleEventLogDAO->insertObject($eventLog);
$this->restoreDataObjectSettings($articleEventLogDAO, $eventLogXML->settings, 'event_log_settings', 'log_id', $eventLog->getId());
}
try {
$article->setSubmissionFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleXML->submissionFileId));
} catch (Exception $e) {
}
try {
$article->setRevisedFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleXML->revisedFileId));
} catch (Exception $e) {
}
try {
$article->setReviewFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleXML->reviewFileId));
} catch (Exception $e) {
}
try {
$article->setEditorFileId($this->idTranslationTable->resolve(INTERNAL_TRANSFER_OBJECT_ARTICLE_FILE, (int) $articleXML->editorFileId));
} catch (Exception $e) {
}
$articleDAO->updateArticle($article);
$this->nextElement();
}
}
/**
* Rush a new submission into the end of the editing queue.
* @param $article object
*/
function expediteSubmission($article, $request)
{
$user =& $request->getUser();
import('classes.submission.editor.EditorAction');
import('classes.submission.sectionEditor.SectionEditorAction');
import('classes.submission.proofreader.ProofreaderAction');
$sectionEditorSubmissionDao =& DAORegistry::getDAO('SectionEditorSubmissionDAO');
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($article->getId());
$submissionFile = $sectionEditorSubmission->getSubmissionFile();
// Add a log entry before doing anything.
import('classes.article.log.ArticleLog');
import('classes.article.log.ArticleEventLogEntry');
ArticleLog::logEvent($request, $article, ARTICLE_LOG_EDITOR_EXPEDITE, 'log.editor.submissionExpedited', array('editorName' => $user->getFullName()));
// 1. Ensure that an editor is assigned.
$editAssignments =& $sectionEditorSubmission->getEditAssignments();
if (empty($editAssignments)) {
// No editors are currently assigned; assign self.
EditorAction::assignEditor($article->getId(), $user->getId(), true, false, $request);
}
// 2. Accept the submission and send to copyediting.
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($article->getId());
if (!$sectionEditorSubmission->getFileBySignoffType('SIGNOFF_COPYEDITING_INITIAL', true)) {
SectionEditorAction::recordDecision($sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT, $request);
$reviewFile = $sectionEditorSubmission->getReviewFile();
SectionEditorAction::setCopyeditFile($sectionEditorSubmission, $reviewFile->getFileId(), $reviewFile->getRevision(), $request);
}
// 3. Add a galley.
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($article->getId());
$galleys =& $sectionEditorSubmission->getGalleys();
if (empty($galleys)) {
// No galley present -- use copyediting file.
import('classes.file.ArticleFileManager');
$copyeditFile =& $sectionEditorSubmission->getFileBySignoffType('SIGNOFF_COPYEDITING_INITIAL');
$fileType = $copyeditFile->getFileType();
$articleFileManager = new ArticleFileManager($article->getId());
$fileId = $articleFileManager->copyPublicFile($copyeditFile->getFilePath(), $fileType);
if (strstr($fileType, 'html')) {
$galley = new ArticleHTMLGalley();
} else {
$galley = new ArticleGalley();
}
$galley->setArticleId($article->getId());
$galley->setFileId($fileId);
$galley->setLocale(AppLocale::getLocale());
if ($galley->isHTMLGalley()) {
$galley->setLabel('HTML');
} else {
if (strstr($fileType, 'pdf')) {
$galley->setLabel('PDF');
} else {
if (strstr($fileType, 'postscript')) {
$galley->setLabel('Postscript');
} else {
if (strstr($fileType, 'xml')) {
$galley->setLabel('XML');
} else {
$galley->setLabel(__('common.untitled'));
}
}
}
}
$galleyDao =& DAORegistry::getDAO('ArticleGalleyDAO');
$galleyDao->insertGalley($galley);
// Update file search index
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::updateFileIndex($article->getId(), ARTICLE_SEARCH_GALLEY_FILE, $fileId);
}
$sectionEditorSubmission->setStatus(STATUS_QUEUED);
$sectionEditorSubmissionDao->updateSectionEditorSubmission($sectionEditorSubmission);
}
/**
* 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 settings.
*/
function execute()
{
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$signoffDao =& DAORegistry::getDAO('SignoffDAO');
$sectionEditorSubmissionDao =& DAORegistry::getDAO('SectionEditorSubmissionDAO');
$application =& PKPApplication::getApplication();
$request =& $application->getRequest();
$user =& $request->getUser();
$router =& $request->getRouter();
$journal =& $router->getContext($request);
$article = new Article();
$article->setLocale($journal->getPrimaryLocale());
// FIXME in bug #5543
$article->setUserId($user->getId());
$article->setJournalId($journal->getId());
$article->setSectionId($this->getData('sectionId'));
$article->setLanguage(String::substr($journal->getPrimaryLocale(), 0, 2));
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
$article->setPages($this->getData('pages'));
// Set some default values so the ArticleDAO doesn't complain when adding this article
$article->setDateSubmitted(Core::getCurrentDate());
$article->setStatus(STATUS_PUBLISHED);
$article->setSubmissionProgress(0);
$article->stampStatusModified();
$article->setCurrentRound(1);
$article->setFastTracked(1);
$article->setHideAuthor(0);
$article->setCommentsStatus(0);
// Insert the article to get it's ID
$articleDao->insertArticle($article);
$articleId = $article->getId();
// Add authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $article->getAuthor($authors[$i]['authorId']);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($articleId);
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
if (array_key_exists('affiliation', $authors[$i])) {
$author->setAffiliation($authors[$i]['affiliation'], null);
}
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$article->addAuthor($author);
}
}
}
// Add the submission files as galleys
import('classes.file.TemporaryFileManager');
import('classes.file.ArticleFileManager');
$tempFileIds = $this->getData('tempFileId');
$temporaryFileManager = new TemporaryFileManager();
$articleFileManager = new ArticleFileManager($articleId);
foreach (array_keys($tempFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUBMISSION);
$fileType = $temporaryFile->getFileType();
if (strstr($fileType, 'html')) {
import('classes.article.ArticleHTMLGalley');
$galley = new ArticleHTMLGalley();
} else {
import('classes.article.ArticleGalley');
$galley = new ArticleGalley();
}
$galley->setArticleId($articleId);
$galley->setFileId($fileId);
$galley->setLocale($locale);
if ($galley->isHTMLGalley()) {
$galley->setLabel('HTML');
} else {
if (strstr($fileType, 'pdf')) {
$galley->setLabel('PDF');
} else {
if (strstr($fileType, 'postscript')) {
$galley->setLabel('Postscript');
} else {
if (strstr($fileType, 'xml')) {
$galley->setLabel('XML');
} else {
$galley->setLabel(__('common.untitled'));
}
}
}
}
$galleyDao =& DAORegistry::getDAO('ArticleGalleyDAO');
$galleyDao->insertGalley($galley);
}
if ($locale == $journal->getPrimaryLocale()) {
$article->setSubmissionFileId($fileId);
$article->SetReviewFileId($fileId);
}
// Update file search index
import('classes.search.ArticleSearchIndex');
if (isset($galley)) {
ArticleSearchIndex::updateFileIndex($galley->getArticleId(), ARTICLE_SEARCH_GALLEY_FILE, $galley->getFileId());
}
}
// Designate this as the review version by default.
$authorSubmissionDao =& DAORegistry::getDAO('AuthorSubmissionDAO');
$authorSubmission =& $authorSubmissionDao->getAuthorSubmission($articleId);
import('classes.submission.author.AuthorAction');
AuthorAction::designateReviewVersion($authorSubmission, true);
// Accept the submission
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($articleId);
$articleFileManager = new ArticleFileManager($articleId);
$sectionEditorSubmission->setReviewFile($articleFileManager->getFile($article->getSubmissionFileId()));
import('classes.submission.sectionEditor.SectionEditorAction');
SectionEditorAction::recordDecision($sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT);
// Create signoff infrastructure
$copyeditInitialSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_INITIAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditAuthorSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditFinalSignoff = $signoffDao->build('SIGNOFF_COPYEDITING_FINAL', ASSOC_TYPE_ARTICLE, $articleId);
$copyeditInitialSignoff->setUserId(0);
$copyeditAuthorSignoff->setUserId($user->getId());
$copyeditFinalSignoff->setUserId(0);
$signoffDao->updateObject($copyeditInitialSignoff);
$signoffDao->updateObject($copyeditAuthorSignoff);
$signoffDao->updateObject($copyeditFinalSignoff);
$layoutSignoff = $signoffDao->build('SIGNOFF_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$layoutSignoff->setUserId(0);
$signoffDao->updateObject($layoutSignoff);
$proofAuthorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_AUTHOR', ASSOC_TYPE_ARTICLE, $articleId);
$proofProofreaderSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_PROOFREADER', ASSOC_TYPE_ARTICLE, $articleId);
$proofLayoutEditorSignoff = $signoffDao->build('SIGNOFF_PROOFREADING_LAYOUT', ASSOC_TYPE_ARTICLE, $articleId);
$proofAuthorSignoff->setUserId($user->getId());
$proofProofreaderSignoff->setUserId(0);
$proofLayoutEditorSignoff->setUserId(0);
$signoffDao->updateObject($proofAuthorSignoff);
$signoffDao->updateObject($proofProofreaderSignoff);
$signoffDao->updateObject($proofLayoutEditorSignoff);
import('classes.author.form.submit.AuthorSubmitForm');
AuthorSubmitForm::assignEditors($article);
$articleDao->updateArticle($article);
// Add to end of editing queue
import('classes.submission.editor.EditorAction');
if (isset($galley)) {
EditorAction::expediteSubmission($article);
}
if ($this->getData('destination') == "issue") {
// Add to an existing issue
$issueId = $this->getData('issueId');
$this->scheduleForPublication($articleId, $issueId);
}
// Index article.
import('classes.search.ArticleSearchIndex');
ArticleSearchIndex::indexArticleMetadata($article);
// Import the references list.
$citationDao =& DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $articleId, $rawCitationList);
}
/**
* Download published final report
* @param $args ($articleId, fileId)
*/
function downloadFinalReport($args)
{
$articleId = isset($args[0]) ? $args[0] : 0;
$fileId = isset($args[1]) ? $args[1] : 0;
import("classes.file.ArticleFileManager");
$articleFileManager = new ArticleFileManager($articleId);
return $articleFileManager->downloadFile($fileId);
}
/**
* Delete an image from an HTML galley.
* @param $imageId int the file ID of the image
*/
function deleteImage($imageId)
{
import('classes.file.ArticleFileManager');
$fileManager = new ArticleFileManager($this->articleId);
$galleyDao =& DAORegistry::getDAO('ArticleGalleyDAO');
if (isset($this->galley)) {
$images =& $this->galley->getImageFiles();
if (isset($images)) {
for ($i = 0, $count = count($images); $i < $count; $i++) {
if ($images[$i]->getFileId() == $imageId) {
$fileManager->deleteFile($images[$i]->getFileId());
$galleyDao->deleteGalleyImage($this->galleyId, $imageId);
unset($images[$i]);
break;
}
}
}
}
}
/**
* Download a file.
* @param $args array ($articleId, $fileId, [$revision])
*/
function downloadFile($args)
{
$articleId = isset($args[0]) ? $args[0] : 0;
$fileId = isset($args[1]) ? $args[1] : 0;
$revision = isset($args[2]) ? $args[2] : null;
$articleIdRepo = isset($args[3]) ? $args[3] : null;
//TODO: validation
//%CBP% is we have passed a PID and namespace, download the file from the repository
import('classes.file.ArticleFileManager');
// FIXME
if (intval($articleId) == false && intval($fileId) == false) {
return ArticleFileManager::downloadFile($articleId, $fileId, false, false, false, $articleIdRepo);
} else {
$articleFileManager = new ArticleFileManager($articleId);
return $articleFileManager->downloadFile($fileId, $revision);
}
}
/**
* Signal to the indexing back-end that an article file changed.
*
* @see ArticleSearchIndex::articleMetadataChanged() above for more
* comments.
*
* @param $articleId int
* @param $type int
* @param $fileId int
*/
function articleFileChanged($articleId, $type, $fileId)
{
// Check whether a search plug-in jumps in.
$hookResult =& HookRegistry::call('ArticleSearchIndex::articleFileChanged', array($articleId, $type, $fileId));
// If no search plug-in is activated then fall back to the
// default database search implementation.
if ($hookResult === false || is_null($hookResult)) {
import('classes.file.ArticleFileManager');
$fileManager = new ArticleFileManager($articleId);
$file =& $fileManager->getFile($fileId);
if (isset($file)) {
$parser =& SearchFileParser::fromFile($file);
}
if (isset($parser)) {
if ($parser->open()) {
$searchDao =& DAORegistry::getDAO('ArticleSearchDAO');
$objectId = $searchDao->insertObject($articleId, $type, $fileId);
$position = 0;
while (($text = $parser->read()) !== false) {
$this->_indexObjectKeywords($objectId, $text, $position);
}
$parser->close();
}
}
}
}
/**
* View file.
* @param $articleId int
* @param $fileId int
* @param $revision int
*/
function viewFile($articleId, $fileId, $revision = null)
{
import('classes.file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($articleId);
return $articleFileManager->downloadFile($fileId, $revision, true);
}
/**
* Download a supplementary file
* @param $args array
* @param $request Request
*/
function downloadSuppFile($args, &$request)
{
$articleId = isset($args[0]) ? $args[0] : 0;
$suppId = isset($args[1]) ? $args[1] : 0;
$this->validate($request, $articleId);
$journal =& $this->journal;
$issue =& $this->issue;
$article =& $this->article;
$suppFileDao =& DAORegistry::getDAO('SuppFileDAO');
if ($journal->getSetting('enablePublicSuppFileId')) {
$suppFile =& $suppFileDao->getSuppFileByBestSuppFileId($article->getId(), $suppId);
} else {
$suppFile =& $suppFileDao->getSuppFile((int) $suppId, $article->getId());
}
if ($article && $suppFile) {
import('file.ArticleFileManager');
$articleFileManager = new ArticleFileManager($article->getId());
if ($suppFile->isInlineable()) {
$articleFileManager->viewFile($suppFile->getFileId());
} else {
$articleFileManager->downloadFile($suppFile->getFileId());
}
}
}
/**
* Save settings.
*/
function execute()
{
$articleDao = DAORegistry::getDAO('ArticleDAO');
$signoffDao = DAORegistry::getDAO('SignoffDAO');
$sectionEditorSubmissionDao = DAORegistry::getDAO('SectionEditorSubmissionDAO');
$application = PKPApplication::getApplication();
$request = $this->request;
$user = $request->getUser();
$router = $request->getRouter();
$journal = $router->getContext($request);
$article = $articleDao->newDataObject();
$article->setLocale($journal->getPrimaryLocale());
// FIXME in bug #5543
$article->setUserId($user->getId());
$article->setJournalId($journal->getId());
$article->setSectionId($this->getData('sectionId'));
$article->setLanguage($this->getData('language'));
$article->setTitle($this->getData('title'), null);
// Localized
$article->setAbstract($this->getData('abstract'), null);
// Localized
$article->setDiscipline($this->getData('discipline'), null);
// Localized
$article->setSubjectClass($this->getData('subjectClass'), null);
// Localized
$article->setSubject($this->getData('subject'), null);
// Localized
$article->setCoverageGeo($this->getData('coverageGeo'), null);
// Localized
$article->setCoverageChron($this->getData('coverageChron'), null);
// Localized
$article->setCoverageSample($this->getData('coverageSample'), null);
// Localized
$article->setType($this->getData('type'), null);
// Localized
$article->setSponsor($this->getData('sponsor'), null);
// Localized
$article->setCitations($this->getData('citations'));
$article->setPages($this->getData('pages'));
// Set some default values so the ArticleDAO doesn't complain when adding this article
$article->setDateSubmitted(Core::getCurrentDate());
$article->setStatus(STATUS_PUBLISHED);
$article->setSubmissionProgress(0);
$article->stampStatusModified();
$article->setCurrentRound(1);
$article->setFastTracked(1);
$article->setHideAuthor(0);
$article->setCommentsStatus(0);
// Insert the article to get it's ID
$articleDao->insertObject($article);
$articleId = $article->getId();
// Add authors
$authors = $this->getData('authors');
for ($i = 0, $count = count($authors); $i < $count; $i++) {
if ($authors[$i]['authorId'] > 0) {
// Update an existing author
$author =& $authorDao->getAuthor($authors[$i]['authorId'], $articleId);
$isExistingAuthor = true;
} else {
// Create a new author
$author = new Author();
$isExistingAuthor = false;
}
if ($author != null) {
$author->setSubmissionId($articleId);
$author->setFirstName($authors[$i]['firstName']);
$author->setMiddleName($authors[$i]['middleName']);
$author->setLastName($authors[$i]['lastName']);
if (array_key_exists('affiliation', $authors[$i])) {
$author->setAffiliation($authors[$i]['affiliation'], null);
}
$author->setCountry($authors[$i]['country']);
$author->setEmail($authors[$i]['email']);
$author->setUrl($authors[$i]['url']);
if (array_key_exists('competingInterests', $authors[$i])) {
$author->setCompetingInterests($authors[$i]['competingInterests'], null);
}
$author->setBiography($authors[$i]['biography'], null);
$author->setPrimaryContact($this->getData('primaryContact') == $i ? 1 : 0);
$author->setSequence($authors[$i]['seq']);
if ($isExistingAuthor == false) {
$authorDao = DAORegistry::getDAO('AuthorDAO');
/* @var $authorDao AuthorDAO */
$authorDao->insertObject($author);
}
}
}
// Add the submission files as galleys
import('lib.pkp.classes.file.TemporaryFileManager');
import('classes.file.ArticleFileManager');
$tempFileIds = $this->getData('tempFileId');
$temporaryFileManager = new TemporaryFileManager();
$articleFileManager = new ArticleFileManager($articleId);
$designatedPrimary = false;
foreach (array_keys($tempFileIds) as $locale) {
$temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
$fileId = null;
if ($temporaryFile) {
$fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, SUBMISSION_FILE_SUBMISSION);
$fileType = $temporaryFile->getFileType();
if (strstr($fileType, 'html')) {
import('classes.article.ArticleHTMLGalley');
$galley = new ArticleHTMLGalley();
} else {
import('classes.article.ArticleGalley');
$galley = new ArticleGalley();
}
$galley->setArticleId($articleId);
$galley->setFileId($fileId);
$galley->setLocale($locale);
if ($galley->isHTMLGalley()) {
$galley->setLabel('HTML');
} else {
if (strstr($fileType, 'pdf')) {
$galley->setLabel('PDF');
} else {
if (strstr($fileType, 'postscript')) {
$galley->setLabel('Postscript');
} else {
if (strstr($fileType, 'xml')) {
$galley->setLabel('XML');
} else {
$galley->setLabel(__('common.untitled'));
}
}
}
}
$galleyDao = DAORegistry::getDAO('ArticleGalleyDAO');
$galleyDao->insertGalley($galley);
if (!$designatedPrimary) {
$article->setSubmissionFileId($fileId);
if ($locale == $journal->getPrimaryLocale()) {
// Used to make sure that *some* file
// is designated Review Version, but
// preferrably the primary locale.
$designatedPrimary = true;
}
}
}
// Update file search index
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
if (isset($galley)) {
$articleSearchIndex->articleFileChanged($galley->getArticleId(), SUBMISSION_SEARCH_GALLEY_FILE, $galley->getFileId());
}
$articleSearchIndex->articleChangesFinished();
}
// Designate this as the review version by default.
$authorSubmissionDao = DAORegistry::getDAO('AuthorSubmissionDAO');
$authorSubmission =& $authorSubmissionDao->getAuthorSubmission($articleId);
import('classes.submission.author.AuthorAction');
AuthorAction::designateReviewVersion($authorSubmission, true);
// Accept the submission
$sectionEditorSubmission =& $sectionEditorSubmissionDao->getSectionEditorSubmission($articleId);
$articleFileManager = new ArticleFileManager($articleId);
import('classes.submission.sectionEditor.SectionEditorAction');
assert(false);
// FIXME: $decisionLabels missing from call below.
SectionEditorAction::recordDecision($this->request, $sectionEditorSubmission, SUBMISSION_EDITOR_DECISION_ACCEPT);
import('classes.author.form.submit.AuthorSubmitForm');
AuthorSubmitForm::assignEditors($article);
$articleDao->updateObject($article);
// Add to end of editing queue
import('classes.submission.editor.EditorAction');
if (isset($galley)) {
EditorAction::expediteSubmission($article, $this->request);
}
if ($this->getData('destination') == "issue") {
// Add to an existing issue
$issueId = $this->getData('issueId');
$this->scheduleForPublication($articleId, $issueId);
}
// Import the references list.
$citationDao = DAORegistry::getDAO('CitationDAO');
$rawCitationList = $article->getCitations();
$citationDao->importCitations($request, ASSOC_TYPE_ARTICLE, $articleId, $rawCitationList);
// Index article.
import('classes.search.ArticleSearchIndex');
$articleSearchIndex = new ArticleSearchIndex();
$articleSearchIndex->articleMetadataChanged($article);
$articleSearchIndex->articleChangesFinished();
}
/**
* Delete an annotated version of an article.
* @param $reviewId int
* @param $fileId int
*/
function deleteReviewerVersion($reviewId, $fileId, $articleId)
{
import('classes.file.ArticleFileManager');
$reviewAssignmentDao =& DAORegistry::getDAO('ReviewAssignmentDAO');
$reviewAssignment =& $reviewAssignmentDao->getById($reviewId);
if (!HookRegistry::call('ReviewerAction::deleteReviewerVersion', array(&$reviewAssignment, &$fileId))) {
$articleFileManager = new ArticleFileManager($articleId);
$articleFileManager->deleteFile($fileId);
//Send a notification to section editors
import('lib.pkp.classes.notification.NotificationManager');
$articleDao =& DAORegistry::getDAO('ArticleDAO');
$article =& $articleDao->getArticle($articleId);
$notificationManager = new NotificationManager();
$notificationUsers = $article->getAssociatedUserIds(false, false);
$user =& Request::getUser();
$message = $article->getProposalId() . ':<br/>' . $user->getUsername();
foreach ($notificationUsers as $userRole) {
$url = Request::url(null, $userRole['role'], 'submission', array($article->getId(), 'submissionReview'), null, 'peerReview');
$notificationManager->createNotification($userRole['id'], 'notification.type.reviewerFileDeleted', $message, $url, 1, NOTIFICATION_TYPE_REVIEWER_COMMENT);
}
}
}
