setDoi() public method

Set doi
public setDoi ( string $doi )
$doi string
 /**
  * Imports the given article.
  * @param int $id Article's ID
  * @param int $newJournalId New journal's ID
  * @param array|int $issueIds IDs of issues
  * @param array|int $sectionIds IDs of sections
  * @return Article
  * @throws \Doctrine\DBAL\DBALException
  * @throws \Doctrine\ORM\ORMException
  */
 public function importArticle($id, $newJournalId, $issueIds, $sectionIds)
 {
     /** @var Journal $journal */
     $journal = $this->em->getReference('OjsJournalBundle:Journal', $newJournalId);
     $this->consoleOutput->writeln("Reading article #" . $id . "... ", true);
     $articleSql = "SELECT articles.*, published_articles.issue_id, published_articles.seq, published_articles.date_published FROM articles " . " LEFT JOIN published_articles ON published_articles.article_id = articles.article_id WHERE" . " articles.article_id = :id";
     $articleStatement = $this->dbalConnection->prepare($articleSql);
     $articleStatement->bindValue('id', $id);
     $articleStatement->execute();
     $settingsSql = "SELECT locale, setting_name, setting_value FROM article_settings WHERE article_id = :id";
     $settingsStatement = $this->dbalConnection->prepare($settingsSql);
     $settingsStatement->bindValue('id', $id);
     $settingsStatement->execute();
     $pkpArticle = $articleStatement->fetch();
     $pkpSettings = $settingsStatement->fetchAll();
     $settings = array();
     foreach ($pkpSettings as $setting) {
         $locale = !empty($setting['locale']) ? $setting['locale'] : 'none';
         $name = $setting['setting_name'];
         $value = $setting['setting_value'];
         $settings[$locale][$name] = $value;
     }
     $article = new Article();
     $article->setJournal($journal);
     $article->setCurrentLocale(!empty($pkpArticle['language']) ? $pkpArticle['language'] : 'en');
     $article->setPrimaryLanguage(!empty($pkpArticle['language']) ? mb_substr($pkpArticle['language'], 0, 2, 'UTF-8') : 'en');
     $article->setDoi(!empty($settings['none']['pub-id::doi']) ? $settings['none']['pub-id::doi'] : null);
     foreach ($settings as $fieldLocale => $fields) {
         $subject = !empty($fields['subject']) ? mb_substr($fields['subject'], 0, 254, 'UTF-8') : '-';
         $article->setCurrentLocale(mb_substr($fieldLocale, 0, 2, 'UTF-8'));
         $article->setTitle(!empty($fields['title']) ? $fields['title'] : '-');
         $article->setAbstract(!empty($fields['abstract']) ? $fields['abstract'] : '-');
         $article->setKeywords($subject);
         $article->setTags($subject);
     }
     switch ($pkpArticle['status']) {
         case 0:
             // STATUS_ARCHIVED
             $article->setStatus(ArticleStatuses::STATUS_REJECTED);
             break;
         case 1:
             // STATUS_QUEUED
             $article->setStatus($this->determineStatus($id));
             break;
         case 3:
             // STATUS_PUBLISHED
             $article->setStatus(ArticleStatuses::STATUS_PUBLISHED);
             break;
         case 4:
             // STATUS_DECLINED
             $article->setStatus(ArticleStatuses::STATUS_REJECTED);
             break;
         case 5:
             // STATUS_QUEUED_UNASSIGNED
             $article->setStatus(ArticleStatuses::STATUS_INREVIEW);
             break;
         case 6:
             // STATUS_QUEUED_REVIEW
             $article->setStatus(ArticleStatuses::STATUS_INREVIEW);
             break;
         case 7:
             // STATUS_QUEUED_EDITING
             $article->setStatus(ArticleStatuses::STATUS_PUBLISH_READY);
             break;
         case 8:
             // STATUS_INCOMPLETE
             $article->setStatus(ArticleStatuses::STATUS_NOT_SUBMITTED);
             break;
     }
     if (!empty($issueIds)) {
         if (!is_array($issueIds)) {
             /** @var Issue $issue */
             $issue = $this->em->getReference('OjsJournalBundle:Issue', $issueIds);
             $article->setIssue($issue);
         } else {
             if (!empty($pkpArticle['issue_id']) && isset($issueIds[$pkpArticle['issue_id']])) {
                 /** @var Issue $issue */
                 $issue = $this->em->getReference('OjsJournalBundle:Issue', $issueIds[$pkpArticle['issue_id']]);
                 $article->setIssue($issue);
             }
         }
     }
     if (!empty($sectionIds)) {
         if (!is_array($sectionIds)) {
             /** @var Section $section */
             $section = $this->em->getReference('OjsJournalBundle:Section', $sectionIds);
             $article->setSection($section);
         } else {
             if (!empty($pkpArticle['section_id']) && isset($sectionIds[$pkpArticle['section_id']])) {
                 /** @var Section $section */
                 $section = $this->em->getReference('OjsJournalBundle:Section', $sectionIds[$pkpArticle['section_id']]);
                 $article->setSection($section);
             }
         }
     }
     $article->setSubmissionDate(!empty($pkpArticle['date_submitted']) ? DateTime::createFromFormat('Y-m-d H:i:s', $pkpArticle['date_submitted']) : new DateTime());
     $article->setPubdate(!empty($pkpArticle['date_published']) ? DateTime::createFromFormat('Y-m-d H:i:s', $pkpArticle['date_published']) : null);
     if (isset($pkpArticle['pages'])) {
         $pages = explode('-', $pkpArticle['pages']);
         isset($pages[0]) && $article->setFirstPage((int) $pages[0] == 0 && !empty($pages[0]) ? (int) StringHelper::roman2int($pages[0]) : (int) $pages[0]);
         isset($pages[1]) && $article->setLastPage((int) $pages[1] == 0 && !empty($pages[1]) ? (int) StringHelper::roman2int($pages[1]) : (int) $pages[1]);
     }
     if (!empty($pkpArticle['seq'])) {
         $article->setOrderNum(intval($pkpArticle['seq']));
     }
     $this->em->persist($article);
     $this->importCitations($id, $article);
     $this->importAuthors($id, $article);
     $articleFileImporter = new ArticleFileImporter($this->dbalConnection, $this->em, $this->logger, $this->consoleOutput);
     $articleFileImporter->importArticleFiles($article, $id, $journal->getSlug());
     $supFileImporter = new SupFileImporter($this->dbalConnection, $this->em, $this->logger, $this->consoleOutput);
     $supFileImporter->importSupFiles($article, $id, $journal->getSlug());
     $pendingStatImport = new PendingStatisticImport($article, $id);
     $pendingSubmitterImport = new PendingSubmitterImport($article, $pkpArticle['user_id']);
     $this->em->persist($pendingStatImport);
     $this->em->persist($pendingSubmitterImport);
     return $article;
 }
Example #2
0
 protected function execute(InputInterface $input, OutputInterface $output)
 {
     $output->writeln('Creating sample data...');
     $em = $this->getContainer()->get('doctrine')->getManager();
     $manipulator = $this->getContainer()->get('fos_user.util.user_manipulator');
     $manipulator->create('sample_author', 'author', '*****@*****.**', false, false);
     $user = $em->getRepository('OjsUserBundle:User')->findOneBy(['username' => 'sample_author']);
     $announcement = new AdminAnnouncement();
     $announcement->setTitle('We are online!');
     $announcement->setContent('We are now online and accepting submissions!');
     $em->persist($announcement);
     $em->flush();
     $post = new AdminPost();
     $post->setCurrentLocale('en');
     $post->setTitle('Welcome to OJS!');
     $post->setSlug('Welcome to OJS!');
     $post->setContent('Hello! We are now online and waiting for your submissions. ' . 'Our readers will be able to follow you and read your work ' . 'right after it gets published!');
     $em->persist($post);
     $em->flush();
     $publisherTypes = ['University', 'Government', 'Association', 'Foundation', 'Hospital', 'Chamber', 'Private'];
     foreach ($publisherTypes as $typeName) {
         $publisherType = new PublisherTypes();
         $publisherType->setCurrentLocale('en');
         $publisherType->setName($typeName);
         $em->persist($publisherType);
     }
     $em->flush();
     $slug = $this->getContainer()->getParameter('defaultPublisherSlug');
     $publisherType = $em->getRepository('OjsJournalBundle:PublisherTypes')->find(1);
     $publisher = new Publisher();
     $publisher->setCurrentLocale('en');
     $publisher->setName('OJS');
     $publisher->setSlug($slug);
     $publisher->setEmail('*****@*****.**');
     $publisher->setAddress('First Avenue, Exampletown');
     $publisher->setPhone('+908501234567');
     $publisher->setVerified(1);
     $publisher->setStatus(PublisherStatuses::STATUS_COMPLETE);
     $publisher->setPublisherType($publisherType);
     $em->persist($publisher);
     $em->flush();
     $subject1 = new Subject();
     $subject1->setCurrentLocale('en');
     $subject1->setSubject('Computer Science');
     $subject1->setTags('computer, science');
     $subject2 = new Subject();
     $subject2->setCurrentLocale('en');
     $subject2->setSubject('Journalism');
     $subject2->setTags('journalism');
     $em->persist($subject1);
     $em->persist($subject2);
     $em->flush();
     $language1 = new Lang();
     $language1->setCurrentLocale('en');
     $language1->setName('English');
     $language1->setCode('en');
     $language1->setRtl(false);
     $language2 = new Lang();
     $language2->setCurrentLocale('tr');
     $language2->setName('Türkçe');
     $language2->setCode('tr');
     $language2->setRtl(false);
     $em->persist($language1);
     $em->persist($language2);
     $em->flush();
     $articleTypes = [['Case Report', 'Olgu Sunumu'], ['Research papers', 'Araştırma Makalesi'], ['Translation', 'Çeviri'], ['Note', 'Not'], ['Letter', 'Editöre Mektup'], ['Review Articles', 'Derleme'], ['Book review', 'Kitap İncelemesi'], ['Correction', 'Düzeltme'], ['Editorial', 'Editoryal'], ['Short Communication', 'Kısa Bildiri'], ['Meeting abstract', 'Toplantı Özetleri'], ['Conference Paper', 'Konferans Bildirisi'], ['Biography', 'Biyografi'], ['Bibliography', 'Bibliyografi'], ['News', 'Haber'], ['Report', 'Rapor'], ['Legislation Review', 'Yasa İncelemesi'], ['Decision Review', 'Karar İncelemesi'], ['Art and Literature', 'Sanat ve Edebiyat'], ['Other', 'Diğer']];
     foreach ($articleTypes as $typeNames) {
         $type = new ArticleTypes();
         $type->setCurrentLocale('en');
         $type->setName($typeNames[0]);
         $type->setCurrentLocale('tr');
         $type->setName($typeNames[1]);
         $em->persist($type);
     }
     $em->flush();
     $contactTypes = ['Journal Contact', 'Primary Contact', 'Technical Contact', 'Author Support', 'Subscription Support', 'Publisher Support', 'Submission Support', 'Advertising', 'Media', 'Editor', 'Co-Editor'];
     foreach ($contactTypes as $typeName) {
         $type = new ContactTypes();
         $type->setCurrentLocale('en');
         $type->setName($typeName);
         $em->persist($type);
     }
     $em->flush();
     $journal = new Journal();
     $journal->setCurrentLocale('en');
     $journal->setPublisher($publisher);
     $journal->setTitle('Introduction to OJS');
     $journal->setSubtitle('How to use OJS');
     $journal->setDescription('A journal about OJS');
     $journal->setTitleAbbr('INTROJS');
     $journal->setUrl('http://ojs.io');
     $journal->setSlug('intro');
     $journal->addSubject($subject1);
     $journal->addSubject($subject2);
     $journal->addLanguage($language1);
     $journal->addLanguage($language2);
     $journal->setMandatoryLang($language2);
     $journal->setFounded(new \DateTime('now'));
     $journal->setIssn('1234-5679');
     $journal->setEissn('1234-5679');
     $journal->setStatus(JournalStatuses::STATUS_PUBLISHED);
     $journal->setPublished(1);
     $em->persist($journal);
     $em->flush();
     $this->createDemoFiles();
     $issueFile = new IssueFile();
     $issueFile->setCurrentLocale('en');
     $issueFile->setTitle('Demo File');
     $issueFile->setDescription('A file');
     $issueFile->setFile('issue.txt');
     $issueFile->setLangCode('en');
     $issueFile->setType(0);
     $issueFile->setVersion(0);
     $issueFile->setUpdatedBy($user->getUsername());
     $issueFileHistory = new FileHistory();
     $issueFileHistory->setFileName('issue.txt');
     $issueFileHistory->setOriginalName('issue.txt');
     $issueFileHistory->setType('issuefiles');
     $em->persist($issueFile);
     $em->persist($issueFileHistory);
     $em->flush();
     $issue = new Issue();
     $issue->setCurrentLocale('en');
     $issue->setJournal($journal);
     $issue->setTitle('First Issue: Hello OJS!');
     $issue->setDescription('First issue of the journal');
     $issue->setNumber(1);
     $issue->setVolume(1);
     $issue->setYear(2015);
     $issue->setSpecial(1);
     $issue->setDatePublished(new \DateTime('now'));
     $issue->setTags('first, guide, tutorial');
     $issue->setDatePublished(new \DateTime('now'));
     $issue->addIssueFile($issueFile);
     $em->persist($issue);
     $em->flush();
     $section = new Section();
     $section->setCurrentLocale('en');
     $section->setJournal($journal);
     $section->setTitle('Tutorials');
     $section->setHideTitle(0);
     $section->setAllowIndex(1);
     $em->persist($section);
     $em->flush();
     $citation1 = new Citation();
     $citation1->setCurrentLocale('en');
     $citation1->setRaw('The Matrix [Motion picture]. (2001). Warner Bros. Pictures.');
     $citation1->setOrderNum(0);
     $em->persist($citation1);
     $em->flush();
     $articleFile = new ArticleFile();
     $articleFile->setCurrentLocale('en');
     $articleFile->setTitle('Demo File');
     $articleFile->setDescription('A file');
     $articleFile->setFile('article.txt');
     $articleFile->setLangCode('en');
     $articleFile->setType(0);
     $articleFile->setVersion(0);
     $articleFile->setUpdatedBy($user->getUsername());
     $articleFileHistory = new FileHistory();
     $articleFileHistory->setFileName('article.txt');
     $articleFileHistory->setOriginalName('article.txt');
     $articleFileHistory->setType('articlefiles');
     $em->persist($articleFile);
     $em->persist($articleFileHistory);
     $em->flush();
     $author = new Author();
     $author->setCurrentLocale('en');
     $author->setTitle('Dr.');
     $author->setFirstName('John');
     $author->setLastName('Doe');
     $author->setEmail('*****@*****.**');
     $em->persist($author);
     $em->flush();
     $article1 = new Article();
     $article1->setCurrentLocale('en');
     $article1->setJournal($journal);
     $article1->setSection($section);
     $article1->setIssue($issue);
     $article1->setTitle('Getting Started with OJS');
     $article1->setAbstract('A tutorial about using OJS');
     $article1->setSubjects('OJS');
     $article1->setKeywords('ojs, intro, starting');
     $article1->setDoi('10.5281/zenodo.14791');
     $article1->setSubmissionDate(new \DateTime('now'));
     $article1->setPubdate(new \DateTime('now'));
     $article1->setAnonymous(0);
     $article1->setFirstPage(1);
     $article1->setLastPage(5);
     $article1->setStatus(ArticleStatuses::STATUS_PUBLISHED);
     $article1->addCitation($citation1);
     $article1->addArticleFile($articleFile);
     $em->persist($article1);
     $em->flush();
     $articleAuthor = new ArticleAuthor();
     $articleAuthor->setAuthor($author);
     $articleAuthor->setArticle($article1);
     $articleAuthor->setAuthorOrder(0);
     $em->persist($articleAuthor);
     $em->flush();
     $checklistItems = [['The title page should include necessary information.', "<ul>\n                    <li>The name(s) of the author(s)</li>\n                     <li>A concise and informative title</li>\n                     <li>The affiliation(s) of the author(s)</li>\n                     <li>The e-mail address, telephone number of the corresponding author </li>\n                 </ul>"], ['Manuscript must be approved.', 'All authors must have read and approved the most recent version of the manuscript.'], ['Manuscript must be <i>spell checked</i>.', 'The most recent version of the manuscript must be spell checked.']];
     foreach ($checklistItems as $checklistItem) {
         $label = $checklistItem[0];
         $detail = $checklistItem[1];
         $item = new SubmissionChecklist();
         $item->setLabel($label);
         $item->setDetail($detail);
         $item->setLocale('en');
         $item->setJournal($journal);
         $em->persist($item);
     }
     $em->flush();
     $periods = ['Monthly', 'Bimonthly', 'Quarterly', 'Triquarterly', 'Biannually', 'Annually', 'Spring', 'Summer', 'Fall', 'Winter'];
     foreach ($periods as $period) {
         $journalPeriod = new Period();
         $journalPeriod->setCurrentLocale('en');
         $journalPeriod->setPeriod($period);
         $em->persist($journalPeriod);
     }
     $em->flush();
 }
Example #3
0
 protected function execute(InputInterface $input, OutputInterface $output)
 {
     $output->writeln('Creating sample data...');
     $em = $this->getContainer()->get('doctrine')->getManager();
     $manipulator = $this->getContainer()->get('fos_user.util.user_manipulator');
     $manipulator->create('sample_author', 'author', '*****@*****.**', false, false);
     $announcement = new AdminAnnouncement();
     $announcement->setTitle('We are online!');
     $announcement->setContent('We are now online and accepting submissions!');
     $em->persist($announcement);
     $em->flush();
     $post = new AdminPost();
     $post->setCurrentLocale('en');
     $post->setTitle('Welcome to OJS!');
     $post->setSlug('Welcome to OJS!');
     $post->setContent('Hello! We are now online and waiting for your submissions. ' . 'Our readers will be able to follow you and read your work ' . 'right after it gets published!');
     $em->persist($post);
     $em->flush();
     $slug = $this->getContainer()->getParameter('defaultPublisherSlug');
     $publisher = new Publisher();
     $publisher->setCurrentLocale('en');
     $publisher->setName('OJS');
     $publisher->setSlug($slug);
     $publisher->setVerified(1);
     $publisher->setStatus(1);
     $em->persist($publisher);
     $em->flush();
     $subject1 = new Subject();
     $subject1->setCurrentLocale('en');
     $subject1->setSubject('Computer Science');
     $subject2 = new Subject();
     $subject2->setCurrentLocale('en');
     $subject2->setSubject('Journalism');
     $em->persist($subject1);
     $em->persist($subject2);
     $em->flush();
     $language1 = new Lang();
     $language1->setCurrentLocale('en');
     $language1->setName('English');
     $language1->setCode('en');
     $language1->setRtl(0);
     $language2 = new Lang();
     $language2->setCurrentLocale('tr');
     $language2->setName('Türkçe');
     $language2->setCode('tr');
     $language2->setRtl(0);
     $em->persist($language1);
     $em->persist($language2);
     $em->flush();
     $articleTypes = ['Research', 'Analysis', 'Clinical Review', 'Practice', 'Research Methods and Reporting', 'Christmas Issue', 'Editorials', 'Blogs', 'Case Reports', 'Letters (rapid responses)', 'Obituaries', 'Personal Views', 'Fillers', 'Minerva Pictures', 'Endgames', 'What Your Patient is Thinking'];
     foreach ($articleTypes as $typeName) {
         $type = new ArticleTypes();
         $type->setCurrentLocale('en');
         $type->setName($typeName);
         $em->persist($type);
     }
     $em->flush();
     $contactTypes = ['Journal Contact', 'Primary Contact', 'Technical Contact', 'Author Support', 'Subscription Support', 'Publisher Support', 'Submission Support', 'Advertising', 'Media'];
     foreach ($contactTypes as $typeName) {
         $type = new ContactTypes();
         $type->setCurrentLocale('en');
         $type->setName($typeName);
         $em->persist($type);
     }
     $em->flush();
     $journal = new Journal();
     $journal->setCurrentLocale('en');
     $journal->setPublisher($publisher);
     $journal->setTitle('Introduction to OJS');
     $journal->setSubtitle('How to use OJS');
     $journal->setTitleAbbr('INTROJS');
     $journal->setUrl('http://ojs.io');
     $journal->setSlug('intro');
     $journal->addSubject($subject1);
     $journal->addSubject($subject2);
     $journal->setMandatoryLang($language2);
     $em->persist($journal);
     $em->flush();
     $issue = new Issue();
     $issue->setCurrentLocale('en');
     $issue->setJournal($journal);
     $issue->setTitle('First Issue: Hello OJS!');
     $issue->setNumber(1);
     $issue->setVolume(1);
     $issue->setYear(2015);
     $issue->setSpecial(1);
     $issue->setTags('fisrt, guide, tutorial');
     $issue->setDatePublished(new \DateTime('now'));
     $em->persist($issue);
     $em->flush();
     $section = new Section();
     $section->setCurrentLocale('en');
     $section->setJournal($journal);
     $section->setTitle('Tutorials');
     $section->setHideTitle(0);
     $section->setAllowIndex(1);
     $em->persist($section);
     $em->flush();
     $citation1 = new Citation();
     $citation1->setCurrentLocale('en');
     $citation1->setRaw('The Matrix [Motion picture]. (2001). Warner Bros. Pictures.');
     $em->persist($citation1);
     $em->flush();
     $article1 = new Article();
     $article1->setCurrentLocale('en');
     $article1->setJournal($journal);
     $article1->setSection($section);
     $article1->setIssue($issue);
     $article1->setTitle('Getting Started with OJS');
     $article1->setKeywords('ojs, intro, starting');
     $article1->setDoi('10.5281/zenodo.14791');
     $article1->setPubdate(new \DateTime('now'));
     $article1->setIsAnonymous(0);
     $article1->setFirstPage(1);
     $article1->setLastPage(5);
     $article1->setStatus(3);
     $article1->addCitation($citation1);
     $em->persist($article1);
     $em->flush();
 }