/**
  * Save settings.
  */
 function execute($editArticleId)
 {
     $this->editArticleID = $editArticleId;
     $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
     //add Original Journal to Abstract
     $orig_journal = $this->getData('originalJournal');
     $abstr = $this->getData('abstract');
     foreach (array_keys($abstr) as $abs_key) {
         $abstr[$abs_key] .= '  <p id="originalPub"> ' . $orig_journal . ' </p> ';
         //		$abstr[$abs_key] .=  '  <p id="originalPub"> ' . $orig_journal[$abs_key]. ' </p> ';
         //OriginalJournal in EditPlugin only a string and not an array...
         $this->setData('abstract', $abstr);
     }
     $article->setAbstract($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);
     // As article has an ID already set it
     $article->setId($this->editArticleID);
     $articleId = $this->editArticleID;
     //delete prior Authors to prevent from double saving the same authors
     $authorDao =& DAORegistry::getDAO('AuthorDAO');
     $authorDao->deleteAuthorsByArticle($articleId);
     // 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);
             }
         }
     }
     // Check whether the user gave a handle and create a handleSubmissionFile in case
     $submissionHandle = $this->getData('submissionHandle');
     $handleSubmissionFileId;
     $handleCheck = FALSE;
     //import FileManager before creating files because otherwise naming of the copied files failes
     import('classes.file.ArticleFileManager');
     foreach (array_keys($submissionHandle) as $locale) {
         if (!empty($submissionHandle[$locale])) {
             $this->deleteOldFile("submission/original", $articleId);
             // $this->deleteOldFile("submission/copyedit", $articleId);
             $handleCheck = TRUE;
             $handleSubmissionId = $this->createHandleTXTFile($submissionHandle[$locale], $articleId, 'submission');
             $handleSubmissionPDFId = $this->createHandlePDF($submissionHandle[$locale], $articleId, 'submission');
             //Add the handle submission files as galley
             $this->setGalley($articleId, $handleSubmissionPDFId, $locale, 'application/pdf');
         }
         if ($handleCheck == TRUE) {
             if ($locale == $journal->getPrimaryLocale()) {
                 $article->setSubmissionFileId($handleSubmissionPDFId);
                 $article->SetReviewFileId($handleSubmissionPDFId);
             }
             // Update file search index
             import('classes.search.ArticleSearchIndex');
             if (isset($galley)) {
                 ArticleSearchIndex::updateFileIndex($galley->getArticleId(), ARTICLE_SEARCH_GALLEY_FILE, $galley->getFileId());
             }
         }
     }
     // 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);
     $tempFileCheck = FALSE;
     foreach (array_keys($tempFileIds) as $locale) {
         $temporaryFile = $temporaryFileManager->getFile($tempFileIds[$locale], $user->getId());
         $fileId = null;
         if ($temporaryFile) {
             $this->deleteOldFile("submission/original", $articleId);
             $this->deleteOldFile("submission/copyedit", $articleId);
             $tempFileCheck = TRUE;
             $fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUBMISSION);
             $fileType = $temporaryFile->getFileType();
             $this->setGalley($articleId, $fileId, $locale, $fileType);
             // $galley =& $this->setGalley($articleId, $fileId, $locale, $fileType);
         }
         if ($tempFileCheck == TRUE) {
             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());
             }
         }
     }
     //Check whether the user gave a handle and create handleSupplFile in case
     $supplHandle = $this->getData('supplHandle');
     $handleSuppFileId = null;
     foreach (array_keys($supplHandle) as $locale) {
         if (!empty($supplHandle[$locale])) {
             $this->deleteOldFile("supp", $articleId);
             $handleSuppFileId = $this->createHandleTXTFile($supplHandle[$locale], $articleId, 'supplementary');
             $handleSupplPDFFileID = $this->createHandlePDF($submissionHandle[$locale], $articleId, 'supplementary');
         }
     }
     //Add uploaded Supplementary file
     $tempSupplFileIds = $this->getData('tempSupplFileId');
     foreach (array_keys($tempSupplFileIds) as $locale) {
         $temporaryFile = $temporaryFileManager->getFile($tempSupplFileIds[$locale], $user->getId());
         $fileId = null;
         if ($temporaryFile) {
             $this->deleteOldFile("supp", $articleId);
             $fileId = $articleFileManager->temporaryFileToArticleFile($temporaryFile, ARTICLE_FILE_SUPP);
             $fileType = $temporaryFile->getFileType();
         }
     }
     // Designate this as the review version by default.
     /*$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);
     }
     // As the article already has an issue, just get it from database
     $issueDao =& DAORegistry::getDAO('IssueDAO');
     $issue =& $issueDao->getIssueByArticleId($this->editArticleID);
     $issueId = $issue->getIssueId();
     //$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);
 }