*4965* Changed DOI storage and expanded capabilities

classes/article/Article.inc.php

@@ -143,6 +143,22 @@ function setSectionId($sectionId) {
 		return $this->setData('sectionId', $sectionId);
 	}
 
+	/**
+	 * Get stored DOI of the submission.
+	 * @return int
+	 */
+	function getStoredDOI() {
+		return $this->getData('doi');
+	}
+
+	/**
+	 * Set the stored DOI of the submission.
+	 * @param $doi string
+	 */
+	function setStoredDOI($doi) {
+		return $this->setData('doi', $doi);
+	}
+
 	/**
 	 * Get title of article's section.
 	 * @return string

classes/article/ArticleDAO.inc.php

@@ -146,6 +146,7 @@ function _articleFromRow(&$article, &$row) {
 		$article->setSectionId($row['section_id']);
 		$article->setSectionTitle($row['section_title']);
 		$article->setSectionAbbrev($row['section_abbrev']);
+		$article->setStoredDOI($row['doi']);
 		$article->setLanguage($row['language']);
 		$article->setCommentsToEditor($row['comments_to_ed']);
 		$article->setCitations($row['citations']);
@@ -180,9 +181,9 @@ function insertArticle(&$article) {
 		$article->stampModified();
 		$this->update(
 			sprintf('INSERT INTO articles
-				(locale, user_id, journal_id, section_id, language, comments_to_ed, citations, date_submitted, date_status_modified, last_modified, status, submission_progress, current_round, submission_file_id, revised_file_id, review_file_id, editor_file_id, pages, fast_tracked, hide_author, comments_status)
+				(locale, user_id, journal_id, section_id, language, comments_to_ed, citations, date_submitted, date_status_modified, last_modified, status, submission_progress, current_round, submission_file_id, revised_file_id, review_file_id, editor_file_id, pages, fast_tracked, hide_author, comments_status, doi)
 				VALUES
-				(?, ?, ?, ?, ?, ?, ?, %s, %s, %s, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
+				(?, ?, ?, ?, ?, ?, ?, %s, %s, %s, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
 				$this->datetimeToDB($article->getDateSubmitted()), $this->datetimeToDB($article->getDateStatusModified()), $this->datetimeToDB($article->getLastModified())),
 			array(
 				$article->getLocale(),
@@ -202,7 +203,8 @@ function insertArticle(&$article) {
 				$article->getPages(),
 				$article->getFastTracked()?1:0,
 				$article->getHideAuthor() === null ? 0 : $article->getHideAuthor(),
-				$article->getCommentsStatus() === null ? 0 : $article->getCommentsStatus()
+				$article->getCommentsStatus() === null ? 0 : $article->getCommentsStatus(),
+				$article->getStoredDOI()
 			)
 		);
 
@@ -246,7 +248,8 @@ function updateArticle(&$article) {
 					pages = ?,
 					fast_tracked = ?,
 					hide_author = ?,
-					comments_status = ?
+					comments_status = ?,
+					doi = ?
 				WHERE article_id = ?',
 				$this->datetimeToDB($article->getDateSubmitted()), $this->datetimeToDB($article->getDateStatusModified()), $this->datetimeToDB($article->getLastModified())),
 			array(
@@ -266,6 +269,7 @@ function updateArticle(&$article) {
 				$article->getFastTracked(),
 				$article->getHideAuthor(),
 				$article->getCommentsStatus(),
+				$article->getStoredDOI(),
 				$article->getId()
 			)
 		);
@@ -383,16 +387,28 @@ function deleteArticleById($articleId) {
 	}
 
 	/**
-	 * Get all articles for a journal.
+	 * Get all articles for a journal (or all articles in the system).
 	 * @param $userId int
 	 * @param $journalId int
 	 * @return DAOResultFactory containing matching Articles
 	 */
-	function &getArticlesByJournalId($journalId) {
+	function &getArticlesByJournalId($journalId = null) {
 		$primaryLocale = Locale::getPrimaryLocale();
 		$locale = Locale::getLocale();
 		$articles = array();
 
+		$params = array(
+			'title',
+			$primaryLocale,
+			'title',
+			$locale,
+			'abbrev',
+			$primaryLocale,
+			'abbrev',
+			$locale
+		);
+		if ($journalId !== null) $params[] = (int) $journalId;
+
 		$result =& $this->retrieve(
 			'SELECT	a.*,
 				COALESCE(stl.setting_value, stpl.setting_value) AS section_title,
@@ -403,18 +419,8 @@ function &getArticlesByJournalId($journalId) {
 				LEFT JOIN section_settings stl ON (s.section_id = stl.section_id AND stl.setting_name = ? AND stl.locale = ?)
 				LEFT JOIN section_settings sapl ON (s.section_id = sapl.section_id AND sapl.setting_name = ? AND sapl.locale = ?)
 				LEFT JOIN section_settings sal ON (s.section_id = sal.section_id AND sal.setting_name = ? AND sal.locale = ?)
-			WHERE a.journal_id = ?',
-			array(
-				'title',
-				$primaryLocale,
-				'title',
-				$locale,
-				'abbrev',
-				$primaryLocale,
-				'abbrev',
-				$locale,
-				$journalId
-			)
+			' . ($journalId !== null ? 'WHERE a.journal_id = ?' : ''),
+			$params
 		);
 
 		$returner = new DAOResultFactory($result, $this, '_returnArticleFromRow');
@@ -527,12 +533,45 @@ function incompleteSubmissionExists($articleId, $userId, $journalId) {
 	 */
 	function changeArticleStatus($articleId, $status) {
 		$this->update(
-			'UPDATE articles SET status = ? WHERE article_id = ?', array($status, $articleId)
+			'UPDATE articles SET status = ? WHERE article_id = ?', array((int) $status, (int) $articleId)
+		);
+
+		$this->flushCache();
+	}
+
+	/**
+	 * Change the DOI of an article
+	 * @param $articleId int
+	 * @param $doi string
+	 */
+	function changeDOI($articleId, $doi) {
+		$this->update(
+			'UPDATE articles SET doi = ? WHERE article_id = ?', array($doi, (int) $articleId)
 		);
 
 		$this->flushCache();
 	}
 
+	function assignDOIs($forceReassign = false, $journalId = null) {
+		if ($forceReassign) {
+			$this->update(
+				'UPDATE articles SET doi = null' . ($journalId !== null?' WHERE journal_id = ?':''),
+				$journalId !== null?array((int) $journalId):false
+			);
+			$this->flushCache();
+		}
+
+		$publishedArticleDao =& DAORegistry::getDAO('PublishedArticleDAO');
+		$articles =& $publishedArticleDao->getPublishedArticlesByJournalId($journalId);
+		while ($article =& $articles->next()) {
+			// Cause a DOI to be fetched and stored.
+			$article->getDOI();
+			unset($article);
+		}
+
+		$this->flushCache();
+	}
+
 	/**
 	 * Removes articles from a section by section ID
 	 * @param $sectionId int

classes/article/PublishedArticle.inc.php

@@ -248,6 +248,11 @@ function getBestArticleId($journal = null) {
 	 * Get a DOI for this article.
 	 */
 	function getDOI() {
+		// If we already have an assigned DOI, use it.
+		$storedDOI = $this->getStoredDOI();
+		if ($storedDOI) return $storedDOI;
+
+		// Otherwise, create a new one.
 		$journalId = $this->getJournalId();
 
 		// Get the Journal object (optimized)
@@ -269,7 +274,7 @@ function getDOI() {
 
 		switch ( $doiSuffixSetting ) {
 			case 'customIdentifier':
-				return $doiPrefix . '/' . $this->getBestArticleId();
+				$doi = $doiPrefix . '/' . $this->getBestArticleId();
 				break;
 			case 'pattern':
 				$suffixPattern = $journal->getSetting('doiSuffixPattern');
@@ -283,11 +288,18 @@ function getDOI() {
 				$suffixPattern = String::regexp_replace('/%a/', $this->getArticleId(), $suffixPattern);
 				// %p - page number
 				$suffixPattern = String::regexp_replace('/%p/', $this->getPages(), $suffixPattern);
-				return $doiPrefix . '/' . $suffixPattern;
+				$doi = $doiPrefix . '/' . $suffixPattern;
 				break;
 			default:
-				return $doiPrefix . '/' . String::strtolower($journal->getLocalizedSetting('initials')) . '.v' . $issue->getVolume() . 'i' . $issue->getNumber() . '.' . $this->getArticleId();
+				$doi = $doiPrefix . '/' . String::strtolower($journal->getLocalizedSetting('initials')) . '.v' . $issue->getVolume() . 'i' . $issue->getNumber() . '.' . $this->getArticleId();
 		}
+
+		// Save the generated DOI
+		$this->setStoredDOI($doi);
+		$articleDao =& DAORegistry::getDAO('ArticleDAO');
+		$articleDao->changeDOI($this->getId(), $doi);
+
+		return $doi;
 	}
 }
 

classes/article/PublishedArticleDAO.inc.php

@@ -137,11 +137,23 @@ function getPublishedArticleCountByJournalId($journalId) {
 	 * Retrieve all published articles in a journal.
 	 * @param $journalId int
 	 * @param $rangeInfo object
+	 * @param $reverse boolean Whether to reverse the sort order
 	 * @return object
 	 */
-	function &getPublishedArticlesByJournalId($journalId, $rangeInfo = null, $reverse = false) {
+	function &getPublishedArticlesByJournalId($journalId = null, $rangeInfo = null, $reverse = false) {
 		$primaryLocale = Locale::getPrimaryLocale();
 		$locale = Locale::getLocale();
+		$params = array(
+			'title',
+			$primaryLocale,
+			'title',
+			$locale,
+			'abbrev',
+			$primaryLocale,
+			'abbrev',
+			$locale
+		);
+		if ($journalId !== null) $params[] = (int) $journalId;
 		$result =& $this->retrieveRange(
 			'SELECT	pa.*,
 				a.*,
@@ -155,21 +167,59 @@ function &getPublishedArticlesByJournalId($journalId, $rangeInfo = null, $revers
 				LEFT JOIN section_settings stl ON (s.section_id = stl.section_id AND stl.setting_name = ? AND stl.locale = ?)
 				LEFT JOIN section_settings sapl ON (s.section_id = sapl.section_id AND sapl.setting_name = ? AND sapl.locale = ?)
 				LEFT JOIN section_settings sal ON (s.section_id = sal.section_id AND sal.setting_name = ? AND sal.locale = ?)
-			WHERE a.journal_id = ?
-				AND i.published = 1
+			WHERE 	i.published = 1
+				' . ($journalId !== null?'AND a.journal_id = ?':'') . '
 				AND a.status <> ' . STATUS_ARCHIVED . '
 			ORDER BY date_published '. ($reverse?'DESC':'ASC'),
-			array(
-				'title',
-				$primaryLocale,
-				'title',
-				$locale,
-				'abbrev',
-				$primaryLocale,
-				'abbrev',
-				$locale,
-				$journalId
-			),
+			$params,
+			$rangeInfo
+		);
+
+		$returner = new DAOResultFactory($result, $this, '_returnPublishedArticleFromRow');
+		return $returner;
+	}
+
+	/**
+	 * Retrieve all published articles in a journal by DOI.
+	 * @param $doi string
+	 * @param $journalId int
+	 * @param $rangeInfo object
+	 * @return object
+	 */
+	function &getPublishedArticlesByDOI($doi, $journalId = null, $rangeInfo = null) {
+		$primaryLocale = Locale::getPrimaryLocale();
+		$locale = Locale::getLocale();
+		$params = array(
+			'title',
+			$primaryLocale,
+			'title',
+			$locale,
+			'abbrev',
+			$primaryLocale,
+			'abbrev',
+			$locale,
+			$doi
+		);
+		if ($journalId !== null) $params[] = (int) $journalId;
+		$result =& $this->retrieveRange(
+			'SELECT	pa.*,
+				a.*,
+				COALESCE(stl.setting_value, stpl.setting_value) AS section_title,
+				COALESCE(sal.setting_value, sapl.setting_value) AS section_abbrev
+			FROM	published_articles pa
+				LEFT JOIN articles a ON pa.article_id = a.article_id
+				LEFT JOIN issues i ON pa.issue_id = i.issue_id
+				LEFT JOIN sections s ON s.section_id = a.section_id
+				LEFT JOIN section_settings stpl ON (s.section_id = stpl.section_id AND stpl.setting_name = ? AND stpl.locale = ?)
+				LEFT JOIN section_settings stl ON (s.section_id = stl.section_id AND stl.setting_name = ? AND stl.locale = ?)
+				LEFT JOIN section_settings sapl ON (s.section_id = sapl.section_id AND sapl.setting_name = ? AND sapl.locale = ?)
+				LEFT JOIN section_settings sal ON (s.section_id = sal.section_id AND sal.setting_name = ? AND sal.locale = ?)
+			WHERE 	i.published = 1
+				AND a.doi = ?
+				' . ($journalId !== null?'AND a.journal_id = ?':'') . '
+				AND a.status <> ' . STATUS_ARCHIVED . '
+			ORDER BY date_published '. ($reverse?'DESC':'ASC'),
+			$params,
 			$rangeInfo
 		);
 

classes/plugins/GatewayPlugin.inc.php

@@ -109,8 +109,10 @@ function manage($verb, $args) {
 
 	/**
 	 * Handle fetch requests for this plugin.
+	 * @param $args array
+	 * @param $request object
 	 */
-	function fetch($args) {
+	function fetch($args, $request) {
 		// Subclasses should override this function.
 		return false;
 	}

dbscripts/xml/ojs_schema.xml

@@ -456,6 +456,7 @@
 		<field name="review_file_id" type="I8"/>
 		<field name="editor_file_id" type="I8"/>
 		<field name="pages" type="C2" size="255"/>
+		<field name="doi" type="C2" size="255"/>
 		<field name="fast_tracked" type="I1">
 			<NOTNULL/>
 			<DEFAULT VALUE="0"/>

locale/en_US/manager.xml

@@ -247,6 +247,8 @@
 	<message key="manager.setup.doiSuffixPattern.example">For example, vol%viss%ipp%p could create a DOI such as 10.1234/vol3iss2pp230</message>
 	<message key="manager.setup.doiSuffixDescription">A DOI suffix can take any form, but must be unique for each published item.</message>
 	<message key="manager.setup.doiSuffixCustomIdentifier">Use the "Custom Identifier" for published items as the DOI suffix (must be enabled in Step 4).</message>
+	<message key="manager.setup.doiReassign">Reassign DOIs</message>
+	<message key="manager.setup.doiReassign.description">If you change your DOI configuration, DOIs that have already been assigned will not be affected. Once the DOI configuration is saved, use this button to clear all existing DOIs so that the new settings will take effect with existing articles.</message>
 	<message key="manager.setup.editorDecision">Editor Decision</message>
 	<message key="manager.setup.editorialMembers">Go to Board Members and add Editorial Board and/or Review Board members. This can be done at any point in operating the journal.</message>
 	<message key="manager.setup.editorialProcess1">One or more editors handle the basic steps without designated roles.</message>

pages/gateway/GatewayHandler.inc.php

@@ -25,23 +25,23 @@ function GatewayHandler() {
 		parent::Handler();
 	}
 
-	function index() {
-		Request::redirect(null, 'index');
+	function index($args, $request) {
+		$request->redirect(null, 'index');
 	}
 
-	function lockss() {
+	function lockss($args, $request) {
 		$this->validate();
 		$this->setupTemplate();
 
-		$journal =& Request::getJournal();
+		$journal =& $request->getJournal();
 		$templateMgr =& TemplateManager::getManager();
 
 		if ($journal != null) {
 			if (!$journal->getSetting('enableLockss')) {
-				Request::redirect(null, 'index');
+				$request->redirect(null, 'index');
 			}
 
-			$year = Request::getUserVar('year');
+			$year = $request->getUserVar('year');
 
 			$issueDao =& DAORegistry::getDAO('IssueDAO');
 
@@ -117,18 +117,19 @@ function lockss() {
 	/**
 	 * Handle requests for gateway plugins.
 	 */
-	function plugin($args) {
+	function plugin($args, $request) {
 		$this->validate();
 		$pluginName = array_shift($args);
 
 		$plugins =& PluginRegistry::loadCategory('gateways');
 		if (isset($pluginName) && isset($plugins[$pluginName])) {
 			$plugin =& $plugins[$pluginName];
-			if (!$plugin->fetch($args)) {
-				Request::redirect(null, 'index');
+			if (!$plugin->fetch($args, $request)) {
+				$request->redirect(null, 'index');
 			}
+		} else {
+			$request->redirect(null, 'index');
 		}
-		else Request::redirect(null, 'index');
 	}
 }