Merge remote-tracking branch 'origin/master' into 1861-fix

Puckohue · Jan 12, 2017 · 13e8808 · 13e8808
2 parents 207c8da + 6cf3342
commit 13e8808
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Showing 278 changed files with 2,319 additions and 6,975 deletions.
diff --git a/classes/article/Article.inc.php b/classes/article/Article.inc.php
@@ -297,7 +297,24 @@ function setCoverImageAltText($coverImageAltText, $locale) {
 		$this->setData('coverImageAltText', $coverImageAltText, $locale);
 	}
 
+	/**
+	 * Get a full URL to the localized cover image
+	 *
+	 * @return string
+	 */
+	function getLocalizedCoverImageUrl() {
+		$coverImage = $this->getLocalizedCoverImage();
+		if (!$coverImage) {
+			return '';
+		}
 
+		$request = Application::getRequest();
+
+		import('classes.file.PublicFileManager');
+		$publicFileManager = new PublicFileManager();
+
+		return $request->getBaseUrl() . '/' . $publicFileManager->getJournalFilesPath($this->getContextId()) . '/' . $coverImage;
+	}
 }
 
 ?>
diff --git a/classes/article/ArticleGalley.inc.php b/classes/article/ArticleGalley.inc.php
@@ -36,7 +36,12 @@ function __construct() {
 	 */
 	function getViews() {
 		$application = PKPApplication::getApplication();
-		return $application->getPrimaryMetricByAssoc(ASSOC_TYPE_GALLEY, $this->getId());
+		$fileId = $this->getFileId();
+		if ($fileId) {
+			return $application->getPrimaryMetricByAssoc(ASSOC_TYPE_SUBMISSION_FILE, $fileId);
+		} else {
+			return 0;
+		}
 	}
 
 	/**

diff --git a/classes/core/Application.inc.php b/classes/core/Application.inc.php
@@ -93,7 +93,6 @@ function getDAOMap() {
 			'ArticleGalleyDAO' => 'classes.article.ArticleGalleyDAO',
 			'ArticleSearchDAO' => 'classes.search.ArticleSearchDAO',
 			'AuthorDAO' => 'classes.article.AuthorDAO',
-			'EditorSubmissionDAO' => 'classes.submission.editor.EditorSubmissionDAO',
 			'EmailTemplateDAO' => 'classes.mail.EmailTemplateDAO',
 			'GiftDAO' => 'classes.gift.GiftDAO',
 			'IndividualSubscriptionDAO' => 'classes.subscription.IndividualSubscriptionDAO',

diff --git a/classes/file/IssueFileManager.inc.php b/classes/file/IssueFileManager.inc.php
@@ -35,7 +35,7 @@ class IssueFileManager extends FileManager {
 	function __construct($issueId) {
 		$issueDao = DAORegistry::getDAO('IssueDAO');
 		$issue = $issueDao->getById($issueId);
-		assert($issue);
+		assert(isset($issue));
 
 		$this->setIssueId($issueId);
 		$this->setFilesDir(Config::getVar('files', 'files_dir') . '/journals/' . $issue->getJournalId() . '/issues/' . $issueId . '/');

diff --git a/classes/install/Upgrade.inc.php b/classes/install/Upgrade.inc.php
diff --git a/classes/issue/Issue.inc.php b/classes/issue/Issue.inc.php
@@ -387,6 +387,25 @@ function getCoverImageAltText($locale) {
 		return $this->getData('coverImageAltText', $locale);
 	}
 
+	/**
+	 * Get a full URL to the localized cover image
+	 *
+	 * @return string
+	 */
+	function getLocalizedCoverImageUrl() {
+		$coverImage = $this->getLocalizedCoverImage();
+		if (!$coverImage) {
+			return '';
+		}
+
+		$request = Application::getRequest();
+
+		import('classes.file.PublicFileManager');
+		$publicFileManager = new PublicFileManager();
+
+		return $request->getBaseUrl() . '/' . $publicFileManager->getJournalFilesPath($this->getJournalId()) . '/' . $coverImage;
+	}
+
 	/**
 	 * Set issue cover image alternate text
 	 * @param $coverImageAltText string

diff --git a/classes/journal/Section.inc.php b/classes/journal/Section.inc.php
@@ -194,22 +194,6 @@ function setHideAuthor($hideAuthor) {
 		return $this->setData('hideAuthor', $hideAuthor);
 	}
 
-	/**
-	 * Return boolean indicating if title should be hidden in About.
-	 * @return boolean
-	 */
-	function getHideAbout() {
-		return $this->getData('hideAbout');
-	}
-
-	/**
-	 * Set if title should be hidden in About.
-	 * @param $hideAbout boolean
-	 */
-	function setHideAbout($hideAbout) {
-		return $this->setData('hideAbout', $hideAbout);
-	}
-
 	/**
 	 * Get localized section policy.
 	 * @return string

diff --git a/classes/journal/SectionDAO.inc.php b/classes/journal/SectionDAO.inc.php
@@ -155,7 +155,6 @@ function _fromRow($row) {
 		$section->setAbstractsNotRequired($row['abstracts_not_required']);
 		$section->setHideTitle($row['hide_title']);
 		$section->setHideAuthor($row['hide_author']);
-		$section->setHideAbout($row['hide_about']);
 		$section->setAbstractWordCount($row['abstract_word_count']);
 
 		$this->getDataObjectSettings('section_settings', 'section_id', $row['section_id'], $section);
@@ -193,9 +192,9 @@ function updateLocaleFields($section) {
 	function insertObject($section) {
 		$this->update(
 			'INSERT INTO sections
-				(journal_id, review_form_id, seq, meta_indexed, meta_reviewed, abstracts_not_required, editor_restricted, hide_title, hide_author, hide_about, abstract_word_count)
+				(journal_id, review_form_id, seq, meta_indexed, meta_reviewed, abstracts_not_required, editor_restricted, hide_title, hide_author, abstract_word_count)
 				VALUES
-				(?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
+				(?, ?, ?, ?, ?, ?, ?, ?, ?, ?)',
 			array(
 				(int)$section->getJournalId(),
 				(int)$section->getReviewFormId(),
@@ -206,7 +205,6 @@ function insertObject($section) {
 				$section->getEditorRestricted() ? 1 : 0,
 				$section->getHideTitle() ? 1 : 0,
 				$section->getHideAuthor() ? 1 : 0,
-				$section->getHideAbout() ? 1 : 0,
 				(int) $section->getAbstractWordCount()
 			)
 		);
@@ -232,7 +230,6 @@ function updateObject($section) {
 					editor_restricted = ?,
 					hide_title = ?,
 					hide_author = ?,
-					hide_about = ?,
 					abstract_word_count = ?
 				WHERE section_id = ?',
 			array(
@@ -244,7 +241,6 @@ function updateObject($section) {
 				(int)$section->getEditorRestricted(),
 				(int)$section->getHideTitle(),
 				(int)$section->getHideAuthor(),
-				(int)$section->getHideAbout(),
 				$this->nullOrInt($section->getAbstractWordCount()),
 				(int)$section->getId()
 			)
@@ -394,20 +390,13 @@ function getEmptyByJournalId($journalId) {
 	 * Retrieve the IDs and titles of the sections for a journal in an associative array.
 	 * @return array
 	 */
-	function &getSectionTitles($journalId, $submittableOnly = false) {
+	function getTitles($journalId, $submittableOnly = false) {
 		$sections = array();
-
 		$sectionsIterator = $this->getByJournalId($journalId);
 		while ($section = $sectionsIterator->next()) {
-			if ($submittableOnly) {
-				if (!$section->getEditorRestricted()) {
-					$sections[$section->getId()] = $section->getLocalizedTitle();
-				}
-			} else {
-				$sections[$section->getId()] = $section->getLocalizedTitle();
-			}
+			if ($submittableOnly && $section->getEditorRestricted()) continue;
+			$sections[$section->getId()] = $section->getLocalizedTitle();
 		}
-
 		return $sections;
 	}
 

diff --git a/classes/plugins/CitationPlugin.inc.php b/classes/plugins/CitationPlugin.inc.php
@@ -61,10 +61,12 @@ function loadJavaScript($hookName, $args) {
 	 */
 	function fetchCitation($article, $issue, $journal) {
 		$templateMgr = TemplateManager::getManager($this->getRequest());
-		$templateMgr->assign('citationPlugin', $this);
-		$templateMgr->assign('article', $article);
-		$templateMgr->assign('issue', $issue);
-		$templateMgr->assign('journal', $journal);
+		$templateMgr->assign(array(
+			'citationPlugin' => $this,
+			'article' => $article,
+			'issue' => $issue,
+			'journal' => $journal,
+		));
 		return $templateMgr->fetch($this->getTemplatePath() . '/citation.tpl');
 	}
 

diff --git a/classes/plugins/PubObjectsExportPlugin.inc.php b/classes/plugins/PubObjectsExportPlugin.inc.php
@@ -275,38 +275,18 @@ function exportXML($objects, $filter, $context) {
 		libxml_use_internal_errors(true);
 		$exportXml = $exportFilter->execute($objects, true);
 		$xml = $exportXml->saveXml();
-		$errors = array_filter(libxml_get_errors(), create_function('$a', 'return $a->level == LIBXML_ERR_ERROR ||  $a->level == LIBXML_ERR_FATAL;'));
+		$errors = array_filter(libxml_get_errors(), create_function('$a', 'return $a->level == LIBXML_ERR_ERROR || $a->level == LIBXML_ERR_FATAL;'));
 		if (!empty($errors)) {
 			$charset = Config::getVar('i18n', 'client_charset');
 			header('Content-type: text/html; charset=' . $charset);
 			echo '<html><body>';
 			$this->displayXMLValidationErrors($errors, $xml);
-			fatalError(__('plugins.importexport.common.error.validation'));
 			echo '</body></html>';
+			fatalError(__('plugins.importexport.common.error.validation'));
 		}
 		return $xml;
 	}
 
-	/**
-	 * Display XML validation errors.
-	 * @param $errors array
-	 * @param $xml string
-	 */
-	function displayXMLValidationErrors($errors, $xml) {
-		echo '<h2>' . __('plugins.importexport.common.validationErrors') .'</h2>';
-
-		foreach ($errors as $error) {
-			switch ($error->level) {
-				case LIBXML_ERR_ERROR:
-				case LIBXML_ERR_FATAL:
-					echo '<p>' .trim($error->message) .'</p>';
-			}
-		}
-		libxml_clear_errors();
-		echo '<h3>' . __('plugins.importexport.common.invalidXML') .'</h3>';
-		echo '<p><pre>' .htmlspecialchars($xml) .'</pre></p>';
-	}
-
 	/**
 	 * Mark selected submissions or issues as registered.
 	 * @param $context Context

diff --git a/classes/search/ArticleSearchIndex.inc.php b/classes/search/ArticleSearchIndex.inc.php
@@ -143,9 +143,10 @@ static function submissionFilesChanged($article) {
 		// default database search implementation.
 		if ($hookResult === false || is_null($hookResult)) {
 			$fileDao = DAORegistry::getDAO('SubmissionFileDAO');
+			import('lib.pkp.classes.submission.SubmissionFile'); // Constants
 			// Index galley files
 			$files = $fileDao->getLatestRevisions(
-				$article->getId(), WORKFLOW_STAGE_ID_PRODUCTION
+				$article->getId(), SUBMISSION_FILE_PROOF
 			);
 			foreach ($files as $file) {
 				if ($file->getFileId()) {

diff --git a/classes/security/RoleDAO.inc.php b/classes/security/RoleDAO.inc.php
@@ -20,7 +20,6 @@
 /** ID codes for all user roles */
 define('ROLE_ID_SECTION_EDITOR',	0x00000011);
 define('ROLE_ID_SUBSCRIPTION_MANAGER',	0x00200000);
-define('ROLE_ID_GUEST_EDITOR',		0x00000201);
 
 /** Fill in the blanks for roles used in PKP lib */
 define('ROLE_ID_SUB_EDITOR',		ROLE_ID_SECTION_EDITOR);
@@ -44,7 +43,6 @@ static function getRoleNames($contextOnly = false, $roleIds = null) {
 
 		$journalRoleNames = array(
 			ROLE_ID_MANAGER => 'user.role.manager',
-			ROLE_ID_GUEST_EDITOR => 'user.role.guestEditor',
 			ROLE_ID_ASSISTANT => 'user.role.journalAssistant',
 			ROLE_ID_SECTION_EDITOR => 'user.role.sectionEditor',
 			ROLE_ID_SUBSCRIPTION_MANAGER => 'user.role.subscriptionManager',

diff --git a/classes/submission/form/SubmissionSubmitStep1Form.inc.php b/classes/submission/form/SubmissionSubmitStep1Form.inc.php
@@ -28,11 +28,15 @@ function __construct($context, $submission = null) {
 	 * Fetch the form.
 	 */
 	function fetch($request) {
-		$templateMgr = TemplateManager::getManager($request);
+		$roleDao = DAORegistry::getDAO('RoleDAO');
+		$user = $request->getUser();
+		$canSubmitAll = $roleDao->userHasRole($this->context->getId(), $user->getId(), ROLE_ID_MANAGER) ||
+			$roleDao->userHasRole($this->context->getId(), $user->getId(), ROLE_ID_SUB_EDITOR);
 
-		// Get section for this context
+		// Get section options for this context
 		$sectionDao = DAORegistry::getDAO('SectionDAO');
-		$sectionOptions = array('0' => '') + $sectionDao->getSectionTitles($this->context->getId());
+		$sectionOptions = array('0' => '') + $sectionDao->getTitles($this->context->getId(), !$canSubmitAll);
+		$templateMgr = TemplateManager::getManager($request);
 		$templateMgr->assign('sectionOptions', $sectionOptions);
 
 		return parent::fetch($request);

diff --git a/classes/tasks/OpenAccessNotification.inc.php b/classes/tasks/OpenAccessNotification.inc.php
@@ -53,11 +53,13 @@ function sendNotification ($users, $journal, $issue) {
 			$mimeBoundary = '==boundary_' . md5(microtime());
 
 			$templateMgr = TemplateManager::getManager();
-			$templateMgr->assign('body', $email->getBody($journal->getPrimaryLocale()));
-			$templateMgr->assign('templateSignature', $journal->getSetting('emailSignature'));
-			$templateMgr->assign('mimeBoundary', $mimeBoundary);
-			$templateMgr->assign('issue', $issue);
-			$templateMgr->assign('publishedArticles', $publishedArticles);
+			$templateMgr->assign(array(
+				'body' => $email->getBody($journal->getPrimaryLocale()),
+				'templateSignature' => $journal->getSetting('emailSignature'),
+				'mimeBoundary' => $mimeBoundary,
+				'issue' => $issue,
+				'publishedArticles' => $publishedArticles,
+			));
 
 			$email->addHeader('MIME-Version', '1.0');
 			$email->setContentType('multipart/alternative; boundary="'.$mimeBoundary.'"');

diff --git a/classes/template/TemplateManager.inc.php b/classes/template/TemplateManager.inc.php
@@ -70,22 +70,21 @@ function __construct($request) {
 			}
 			if (isset($context)) {
 
-				$this->assign('currentJournal', $context);
-				$this->assign('siteTitle', $context->getLocalizedName());
-				$this->assign('publicFilesDir', $request->getBaseUrl() . '/' . $publicFileManager->getJournalFilesPath($context->getId()));
-
-				$this->assign('primaryLocale', $context->getPrimaryLocale());
-				$this->assign('supportedLocales', $context->getSupportedLocaleNames());
-
-				// Assign page header
-				$this->assign('displayPageHeaderTitle', $context->getLocalizedPageHeaderTitle());
-				$this->assign('displayPageHeaderLogo', $context->getLocalizedPageHeaderLogo());
-				$this->assign('displayPageHeaderLogoAltText', $context->getLocalizedSetting('pageHeaderLogoImageAltText'));
-				$this->assign('numPageLinks', $context->getSetting('numPageLinks'));
-				$this->assign('itemsPerPage', $context->getSetting('itemsPerPage'));
-				$this->assign('enableAnnouncements', $context->getSetting('enableAnnouncements'));
-				$this->assign('contextSettings', $context->getSettingsDAO()->getSettings($context->getId()));
-				$this->assign('disableUserReg', $context->getSetting('disableUserReg'));
+				$this->assign(array(
+					'currentJournal' => $context,
+					'siteTitle' => $context->getLocalizedName(),
+					'publicFilesDir' => $request->getBaseUrl() . '/' . $publicFileManager->getJournalFilesPath($context->getId()),
+					'primaryLocale' => $context->getPrimaryLocale(),
+					'supportedLocales' => $context->getSupportedLocaleNames(),
+					'displayPageHeaderTitle' => $context->getLocalizedPageHeaderTitle(),
+					'displayPageHeaderLogo' => $context->getLocalizedPageHeaderLogo(),
+					'displayPageHeaderLogoAltText' => $context->getLocalizedSetting('pageHeaderLogoImageAltText'),
+					'numPageLinks' => $context->getSetting('numPageLinks'),
+					'itemsPerPage' => $context->getSetting('itemsPerPage'),
+					'enableAnnouncements' => $context->getSetting('enableAnnouncements'),
+					'contextSettings' => $context->getSettingsDAO()->getSettings($context->getId()),
+					'disableUserReg' => $context->getSetting('disableUserReg'),
+				));
 
 				// Assign meta tags
 				$favicon = $context->getLocalizedFavicon();
@@ -118,15 +117,6 @@ function __construct($request) {
 				$this->assign('journalPaymentsEnabled', $paymentManager->isConfigured());
 				$this->assign('pageFooter', $context->getLocalizedSetting('pageFooter'));
 			} else {
-				// Add the site-wide logo, if set for this locale or the primary locale
-				$this->assign('displayPageHeaderTitle', $site->getLocalizedPageHeaderTitle());
-				$this->assign('displayPageHeaderLogo', $site->getLocalizedSetting('pageHeaderTitleImage'));
-
-				$this->assign('siteTitle', $site->getLocalizedTitle());
-				$this->assign('primaryLocale', $site->getPrimaryLocale());
-				$this->assign('supportedLocales', $site->getSupportedLocaleNames());
-				$this->assign('pageFooter', $site->getLocalizedSetting('pageFooter'));
-
 				// Check if registration is open for any contexts
 				$contextDao = Application::getContextDAO();
 				$contexts = $contextDao->getAll(true)->toArray();
@@ -136,8 +126,18 @@ function __construct($request) {
 						$contextsForRegistration[] = $context;
 					}
 				}
-				$this->assign('contexts', $contextsForRegistration);
-				$this->assign('disableUserReg', empty($contextsForRegistration));
+
+				$this->assign(array(
+					'contexts' => $contextsForRegistration,
+					'disableUserReg' => empty($contextsForRegistration),
+					'displayPageHeaderTitle' => $site->getLocalizedPageHeaderTitle(),
+					'displayPageHeaderLogo' => $site->getLocalizedSetting('pageHeaderTitleImage'),
+					'siteTitle' => $site->getLocalizedTitle(),
+					'primaryLocale' => $site->getPrimaryLocale(),
+					'supportedLocales' => $site->getSupportedLocaleNames(),
+					'pageFooter' => $site->getLocalizedSetting('pageFooter'),
+				));
+
 			}
 		}
 	}

diff --git a/controllers/grid/settings/sections/form/SectionForm.inc.php b/controllers/grid/settings/sections/form/SectionForm.inc.php
@@ -62,7 +62,6 @@ function initData($args, $request) {
 				'editorRestriction' => $section->getEditorRestricted(),
 				'hideTitle' => $section->getHideTitle(),
 				'hideAuthor' => $section->getHideAuthor(),
-				'hideAbout' => $section->getHideAbout(),
 				'policy' => $section->getPolicy(null), // Localized
 				'wordCount' => $section->getAbstractWordCount()
 			);
@@ -99,7 +98,7 @@ function fetch($request) {
 	 */
 	function readInputData() {
 		parent::readInputData();
-		$this->readUserVars(array('abbrev', 'policy', 'reviewFormId', 'identifyType', 'metaIndexed', 'metaReviewed', 'abstractsNotRequired', 'editorRestriction', 'hideTitle', 'hideAuthor', 'hideAbout', 'wordCount'));
+		$this->readUserVars(array('abbrev', 'policy', 'reviewFormId', 'identifyType', 'metaIndexed', 'metaReviewed', 'abstractsNotRequired', 'editorRestriction', 'hideTitle', 'hideAuthor', 'wordCount'));
 	}
 
 	/**
@@ -142,7 +141,6 @@ function execute($args, $request) {
 		$section->setEditorRestricted($this->getData('editorRestriction') ? 1 : 0);
 		$section->setHideTitle($this->getData('hideTitle') ? 1 : 0);
 		$section->setHideAuthor($this->getData('hideAuthor') ? 1 : 0);
-		$section->setHideAbout($this->getData('hideAbout') ? 1 : 0);
 		$section->setPolicy($this->getData('policy'), null); // Localized
 		$section->setAbstractWordCount($this->getData('wordCount'));