Adds new features

HypothesisPlugin.inc.php

@@ -14,14 +14,26 @@
 
 import('lib.pkp.classes.plugins.GenericPlugin');
 
+define('NMI_TYPE_ANNOTATIONS',	'NMI_TYPE_ANNOTATIONS');
+
 class HypothesisPlugin extends GenericPlugin {
 	/**
 	 * @copydoc Plugin::register()
 	 */
 	function register($category, $path, $mainContextId = null) {
 		if (parent::register($category, $path, $mainContextId)) {
-			HookRegistry::register('ArticleHandler::download',array(&$this, 'callback'));
+			HookRegistry::register('ArticleHandler::download', array(&$this, 'callback'));
 			HookRegistry::register('TemplateManager::display', array(&$this, 'callbackTemplateDisplay'));
+			HookRegistry::register('TemplateManager::display', [$this, 'addAnnotationNumberViewers']);
+			HookRegistry::register('LoadHandler', array($this, 'addAnnotationsHandler'));
+			HookRegistry::register('LoadComponentHandler', array($this, 'setupHypothesisHandler'));
+			HookRegistry::register('AcronPlugin::parseCronTab', [$this, 'addTasksToCrontab']);
+
+			HookRegistry::register('NavigationMenus::itemTypes', array($this, 'addNavigationMenuItemType'));
+			HookRegistry::register('NavigationMenus::displaySettings', array($this, 'setNavigationMenuItemUrl'));
+
+			$this->addHandlerURLToJavaScript();
+
 			return true;
 		}
 		return false;
@@ -55,12 +67,13 @@ function callbackTemplateDisplay($hookName, $args) {
 		$templateMgr = $args[0];
 		$template = $args[1];
 		$plugin = 'plugins-generic-pdfJsViewer';
-		$submissiontpl = 'submissionGalley.tpl';
-		$issuetpl = 'issueGalley.tpl';
-		
+		$submissionGalleyTpl = 'submissionGalley.tpl';
+		$issueGalleyTpl = 'issueGalley.tpl';
+
 		// template path contains the plugin path, and ends with the tpl file
-		if ( (strpos($template, $plugin) !== false) && (  (strpos($template, ':'.$submissiontpl,  -1 - strlen($submissiontpl)) !== false)  ||  (strpos($template, ':'.$issuetpl,  -1 - strlen($issuetpl)) !== false))) {
+		if ( (strpos($template, $plugin) !== false) && (  (strpos($template, ':'.$submissionGalleyTpl,  -1 - strlen($submissionGalleyTpl)) !== false)  ||  (strpos($template, ':'.$issueGalleyTpl,  -1 - strlen($issueGalleyTpl)) !== false))) {
 			$templateMgr->registerFilter("output", array($this, 'changePdfjsPath'));
+			$templateMgr->registerFilter("output", array($this, 'addHypothesisConfig'));
 		}
 		return false;
 	}
@@ -76,6 +89,114 @@ function changePdfjsPath($output, $templateMgr) {
 		return $newOutput;
 	}
 
+	/**
+	 * Adds Hypothesis tab configuration so sidebar opens automatically when PDF has annotations
+	 * @param $output string
+	 * @param $templateMgr TemplateManager
+	 * @return $string
+	 */
+	public function addHypothesisConfig($output, $templateMgr) {
+		if (preg_match('/<div[^>]+id="pdfCanvasContainer/', $output, $matches, PREG_OFFSET_CAPTURE)) {
+			$posMatch = $matches[0][1];
+			$config = $templateMgr->fetch($this->getTemplateResource('hypothesisConfig.tpl'));
+
+			$output = substr_replace($output, $config, $posMatch, 0);
+			$templateMgr->unregisterFilter('output', array($this, 'addHypothesisConfig'));
+		}
+		return $output;
+	}
+
+	public function addAnnotationNumberViewers($hookName, $args) {
+		$templateMgr = $args[0];
+		$template = $args[1];
+		$pagesToInsert = [
+			'frontend/pages/indexServer.tpl',
+			'frontend/pages/preprint.tpl',
+			'frontend/pages/preprints.tpl',
+			'frontend/pages/sections.tpl',
+			'frontend/pages/indexJournal.tpl',
+			'frontend/pages/article.tpl',
+			'frontend/pages/issue.tpl'
+		];
+
+		if (in_array($template, $pagesToInsert)) {
+			$request = Application::get()->getRequest();
+
+			$jsUrl = $request->getBaseUrl() . '/' . $this->getPluginPath() . '/js/addAnnotationViewers.js';
+			$styleUrl = $request->getBaseUrl() . '/' . $this->getPluginPath() . '/styles/annotationViewer.css';
+
+			$templateMgr->addJavascript('AddAnnotationViewers', $jsUrl, ['contexts' => 'frontend']);
+			$templateMgr->addStyleSheet('AnnotationViewerStyleSheet', $styleUrl, ['contexts' => 'frontend']);
+		}
+
+		return false;
+	}
+
+	public function addAnnotationsHandler($hookName, $args) {
+		$page = $args[0];
+		if ($page == 'annotations') {
+			$this->import('pages.annotations.AnnotationsHandler');
+			define('HANDLER_CLASS', 'AnnotationsHandler');
+			return true;
+		}
+		return false;
+	}
+
+	public function setupHypothesisHandler($hookName, $args) {
+		$component = &$args[0];
+		if ($component == 'plugins.generic.hypothesis.controllers.HypothesisHandler') {
+			return true;
+		}
+		return false;
+	}
+
+	public function addTasksToCrontab($hookName, $args) {
+		$taskFilesPath = &$args[0];
+		$taskFilesPath[] = $this->getPluginPath() . DIRECTORY_SEPARATOR . 'scheduledTasks.xml';
+		return false;
+	}
+
+	public function addHandlerURLToJavaScript()
+	{
+		$request = Application::get()->getRequest();
+		$context = $request->getContext();
+
+		if ($context) {
+			$templateMgr = TemplateManager::getManager($request);
+			$handlerUrl = $request->getDispatcher()->url($request, ROUTE_COMPONENT, null, 'plugins.generic.hypothesis.controllers.HypothesisHandler');
+			$data = ['hypothesisHandlerUrl' => $handlerUrl];
+
+			$templateMgr->addJavaScript('HypothesisHandler', 'app = ' . json_encode($data) . ';', ['contexts' => 'frontend', 'inline' => true]);
+		}
+	}
+
+	public function addNavigationMenuItemType($hookName, $args) {
+		$itemTypes = &$args[0];
+		$itemTypes[NMI_TYPE_ANNOTATIONS] = [
+			'title' => __('plugins.generic.hypothesis.annotationsMenuItem.title'),
+			'description' => __('plugins.generic.hypothesis.annotationsMenuItem.description'),
+		];
+		return false;
+	}
+
+	public function setNavigationMenuItemUrl($hookName, $args) {
+		$menuItem = &$args[0];
+
+		if ($menuItem->getType() === NMI_TYPE_ANNOTATIONS) {
+			$request = Application::get()->getRequest();
+			$dispatcher = $request->getDispatcher();
+
+			$menuItem->setUrl($dispatcher->url(
+				$request,
+				ROUTE_PAGE,
+				null,
+				'annotations',
+				null,
+				null
+			));
+		}
+	}
+
 	/**
 	 * Get the display name of this plugin
 	 * @return string
@@ -91,5 +212,31 @@ function getDisplayName() {
 	function getDescription() {
 		return __('plugins.generic.hypothesis.description');
 	}
+
+	function getStyleSheet() {
+		return $this->getPluginPath() . '/styles/annotationViewer.css';
+	}
+
+	public function setEnabled($enabled)
+    {
+        parent::setEnabled($enabled);
+
+		$contextId = $this->getCurrentContextId();
+        if ($enabled && $contextId != CONTEXT_SITE) {
+			$navigationMenuItemDao = DAORegistry::getDAO('NavigationMenuItemDAO');
+			$menuItems = $navigationMenuItemDao->getByType(NMI_TYPE_ANNOTATIONS, $contextId)->toArray();
+
+			if(empty($menuItems)) {
+				$locale = AppLocale::getLocale();
+
+				$menuItem = $navigationMenuItemDao->newDataObject();
+				$menuItem->setTitle(__('plugins.generic.hypothesis.annotationsMenuItem.title'), $locale);
+				$menuItem->setContextId($contextId);
+				$menuItem->setType(NMI_TYPE_ANNOTATIONS);
+
+				$navigationMenuItemDao->insertObject($menuItem);
+			}
+        }
+    }
 }
 

classes/Annotation.inc.php

@@ -0,0 +1,20 @@
+<?php
+
+class Annotation {
+	public $user;
+	public $dateCreated;
+	public $target;
+	public $content;
+
+	public function __construct(string $user, string $dateCreated, string $target, string $content) {
+		$this->user = $user;
+		$this->dateCreated = $dateCreated;
+		$this->target = $target;
+		$this->content = $content;
+	}
+
+	public static function __set_state($dump) {
+		$obj = new Annotation($dump['user'], $dump['dateCreated'], $dump['target'], $dump['content']);
+		return $obj;
+	}
+}

classes/HypothesisDAO.inc.php

@@ -0,0 +1,36 @@
+<?php
+
+import('lib.pkp.classes.db.DAO');
+
+use Illuminate\Database\Capsule\Manager as Capsule;
+use Illuminate\Support\Collection;
+
+class HypothesisDAO extends DAO {
+	public function getDatePublished($submissionId): string {
+		$result = Capsule::table('submissions')
+			->where('submission_id', $submissionId)
+			->select('current_publication_id')
+			->first();
+		$currentPublicationId = get_object_vars($result)['current_publication_id'];
+
+		$result = Capsule::table('publications')
+			->where('publication_id', $currentPublicationId)
+			->select('date_published')
+			->first();
+
+		return get_object_vars($result)['date_published'];
+	}
+
+	public function getSubmissionIdByBestId($submissionBestId): int {
+		$result = Capsule::table('publications')
+			->where('url_path', $submissionBestId)
+			->select('submission_id')
+			->first();
+
+		if (!is_null($result)) {
+			return (int) get_object_vars($result)['submission_id'];
+		}
+
+		return (int) $submissionBestId;
+	}
+}

classes/HypothesisHelper.inc.php

@@ -0,0 +1,140 @@
+<?php
+
+import('classes.submission.Submission');
+import('plugins.generic.hypothesis.classes.SubmissionAnnotations');
+import('plugins.generic.hypothesis.classes.HypothesisDAO');
+
+class HypothesisHelper {
+	public function getSubmissionsAnnotations($contextId) {
+		$submissions = Services::get('submission')->getMany([
+			'contextId' => $contextId,
+			'status' => STATUS_PUBLISHED
+		]);
+
+		$groupsRequests = $this->getSubmissionsGroupsRequests($submissions, $contextId);
+		$submissionsAnnotations = [];
+		foreach ($groupsRequests as $groupRequest) {
+			$groupResponse = $this->getRequestAnnotations($groupRequest);
+			if (!is_null($groupResponse) && $groupResponse['total'] > 0) {
+				$submissionsAnnotations = array_merge(
+					$submissionsAnnotations,
+					$this->groupSubmissionsAnnotations($groupResponse)
+				);
+			}
+		}
+
+		return $submissionsAnnotations;
+	}
+
+	private function getSubmissionsGroupsRequests($submissions, $contextId) {
+		$requests = [];
+		$requestPrefix = $currentRequest = "https://hypothes.is/api/search?limit=200&group=__world__";
+		$maxRequestLength = 4094;
+
+		foreach ($submissions as $submission) {
+			$submissionRequestParams = $this->getSubmissionRequestParams($submission, $contextId);
+
+			if(!is_null($submissionRequestParams)) {
+				if(strlen($currentRequest.$submissionRequestParams) < $maxRequestLength) {
+					$currentRequest .= $submissionRequestParams;
+				}
+				else {
+					$requests[] = $currentRequest;
+					$currentRequest = $requestPrefix . $submissionRequestParams; 
+				}
+			}
+		}
+
+		if ($currentRequest != $requestPrefix) {
+			$requests[] = $currentRequest;
+		}
+
+		return $requests;
+	}
+
+	private function getSubmissionRequestParams($submission, $contextId) {
+		$submissionRequestParams = "";
+		$publication = $submission->getCurrentPublication();
+
+		if(is_null($publication))
+			return null;
+
+		$galleys = $publication->getData('galleys');
+		foreach ($galleys as $galley) {
+			if ($galley->getFileType() == 'application/pdf') {
+				$galleyDownloadURL = $this->getGalleyDownloadURL($contextId, $submission, $galley);
+
+				if(!is_null($galleyDownloadURL)) {
+					$submissionRequestParams .= "&uri={$galleyDownloadURL}";
+				}
+			}
+		}
+
+		return $submissionRequestParams;
+	}
+
+	private function getRequestAnnotations($requestURL) {
+		$ch = curl_init($requestURL);
+		curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
+		$output = curl_exec($ch);
+		if(!$output || substr($output, 1, 8) != '"total":') return null;
+
+		return json_decode($output, true);
+	}
+
+	private function groupSubmissionsAnnotations($groupResponse) {
+		$submissionsAnnotations = [];
+		$hypothesisDao = new HypothesisDAO();
+
+		foreach ($groupResponse['rows'] as $annotationResponse) {
+			$urlBySlash = explode("/", $annotationResponse['links']['incontext']);
+			$submissionBestId = $urlBySlash[count($urlBySlash) - 3];
+			$submissionId = $hypothesisDao->getSubmissionIdByBestId($submissionBestId);
+
+			if(!array_key_exists($submissionId, $submissionsAnnotations)) {
+				$submissionsAnnotations[$submissionId] = new SubmissionAnnotations($submissionId);
+			}
+
+			$annotation = $this->getAnnotation($annotationResponse);
+			$submissionsAnnotations[$submissionId]->addAnnotation($annotation);
+		}
+
+		return $submissionsAnnotations;
+	}
+
+	private function getAnnotation($annotationResponse): Annotation {
+		$user = substr($annotationResponse['user'], 5, strlen($annotationResponse['user']) - 17);
+		$dateCreated = $annotationResponse['created'];
+		$content = $annotationResponse['text'];
+
+		$target = "";
+		if(isset($annotationResponse['target'][0]['selector'])) {
+			foreach ($annotationResponse['target'][0]['selector'] as $selector) {
+				if($selector['type'] == 'TextQuoteSelector') {
+					$target = $selector['exact'];
+					break;
+				}
+			}
+		}
+
+		return new Annotation($user, $dateCreated, $target, $content);
+	}
+
+	public function getGalleyDownloadURL($contextId, $submission, $galley) {
+		$request = Application::get()->getRequest();
+		$indexUrl = $request->getIndexUrl();
+		$context = Services::get('context')->get($contextId);
+		$contextPath = $context->getPath();
+		$submissionType = (Application::getName() == 'ojs2' ? 'article' : 'preprint');
+
+		$submissionFile = $galley->getFile();
+		if(is_null($submissionFile))
+			return null;
+
+		$submissionBestId = $submission->getBestId();
+		$galleyBestId = $galley->getBestGalleyId();
+		$fileId = $submissionFile->getId();
+
+		return $indexUrl . "/$contextPath/$submissionType/download/$submissionBestId/$galleyBestId/$fileId";
+	}
+}