Add new features for 3.4.0 version

HypothesisPlugin.php

@@ -16,15 +16,31 @@
 
 use PKP\plugins\GenericPlugin;
 use PKP\plugins\Hook;
+use APP\core\Application;
+use PKP\facades\Locale;
+use PKP\db\DAORegistry;
+use APP\template\TemplateManager;
 
 class HypothesisPlugin extends GenericPlugin {
+	private const NMI_TYPE_ANNOTATIONS = 'NMI_TYPE_ANNOTATIONS';
+
 	/**
 	 * @copydoc Plugin::register()
 	 */
 	function register($category, $path, $mainContextId = null) {
 		if (parent::register($category, $path, $mainContextId)) {
-			Hook::add('ArticleHandler::download',array(&$this, 'callback'));
+			Hook::add('ArticleHandler::download', array(&$this, 'callback'));
 			Hook::add('TemplateManager::display', array(&$this, 'callbackTemplateDisplay'));
+			Hook::add('TemplateManager::display', [$this, 'addAnnotationNumberViewers']);
+			Hook::add('LoadHandler', array($this, 'addAnnotationsHandler'));
+			Hook::add('LoadComponentHandler', array($this, 'setupHypothesisHandler'));
+			Hook::add('AcronPlugin::parseCronTab', [$this, 'addTasksToCrontab']);
+
+			Hook::add('NavigationMenus::itemTypes', [$this, 'addNavigationMenuItemType']);
+			Hook::add('NavigationMenus::displaySettings', [$this, 'setNavigationMenuItemUrl']);
+
+			$this->addHandlerURLToJavaScript();
+
 			return true;
 		}
 		return false;
@@ -64,6 +80,7 @@ function callbackTemplateDisplay($hookName, $args) {
 		// template path contains the plugin path, and ends with the tpl file
 		if ( (strpos($template, $plugin) !== false) && (  (strpos($template, ':'.$submissiontpl,  -1 - strlen($submissiontpl)) !== false)  ||  (strpos($template, ':'.$issuetpl,  -1 - strlen($issuetpl)) !== false))) {
 			$templateMgr->registerFilter("output", array($this, 'changePdfjsPath'));
+			$templateMgr->registerFilter("output", array($this, 'addHypothesisConfig'));
 		}
 		return false;
 	}
@@ -79,6 +96,110 @@ 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') {
+            define('HANDLER_CLASS', 'APP\plugins\generic\hypothesis\pages\annotations\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();
+        $templateMgr = TemplateManager::getManager($request);
+        $handlerUrl = $request->getDispatcher()->url($request, Application::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];
+
+		$itemTypes[self::NMI_TYPE_ANNOTATIONS] = [
+			'title' => __('plugins.generic.hypothesis.annotationsMenuItem.title'),
+			'description' => __('plugins.generic.hypothesis.annotationsMenuItem.description')
+		];
+
+		return Hook::CONTINUE;
+	}
+
+	public function setNavigationMenuItemUrl($hookName, $args) {
+		$menuItem = &$args[0];
+
+		if ($menuItem->getType() === self::NMI_TYPE_ANNOTATIONS) {
+			$request = Application::get()->getRequest();
+			$dispatcher = $request->getDispatcher();
+			$menuItem->setUrl($dispatcher->url(
+				$request,
+				ROUTE_PAGE,
+				null,
+				'annotations',
+				null,
+				null
+			));
+		}
+	}
+
 	/**
 	 * Get the display name of this plugin
 	 * @return string
@@ -94,5 +215,23 @@ function getDisplayName() {
 	function getDescription() {
 		return __('plugins.generic.hypothesis.description');
 	}
+
+	public function setEnabled($enabled){
+        parent::setEnabled($enabled);
+
+		$contextId = $this->getCurrentContextId();
+        if ($enabled && $contextId != Application::CONTEXT_SITE) {
+			$navigationMenuItemDao = DAORegistry::getDAO('NavigationMenuItemDAO');
+			$menuItems = $navigationMenuItemDao->getByType(self::NMI_TYPE_ANNOTATIONS, $contextId)->toArray();
+			if(empty($menuItems)) {
+				$locale = Locale::getLocale();
+				$menuItem = $navigationMenuItemDao->newDataObject();
+				$menuItem->setTitle(__('plugins.generic.hypothesis.annotationsMenuItem.title'), $locale);
+				$menuItem->setContextId($contextId);
+				$menuItem->setType(self::NMI_TYPE_ANNOTATIONS);
+				$navigationMenuItemDao->insertObject($menuItem);
+			}
+        }
+    }
 }
 

classes/Annotation.php

@@ -0,0 +1,22 @@
+<?php
+
+namespace APP\plugins\generic\hypothesis\classes;
+
+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.php

@@ -0,0 +1,23 @@
+<?php
+
+namespace APP\plugins\generic\hypothesis\classes;
+
+use PKP\db\DAO;
+use Illuminate\Support\Facades\DB;
+
+class HypothesisDAO extends DAO {
+    public function getDatePublished($submissionId): string {
+        $result = DB::table('submissions')
+            ->where('submission_id', $submissionId)
+            ->select('current_publication_id')
+            ->first();
+        $currentPublicationId = get_object_vars($result)['current_publication_id'];
+
+        $result = DB::table('publications')
+            ->where('publication_id', $currentPublicationId)
+            ->select('date_published')
+            ->first();
+
+        return get_object_vars($result)['date_published'];
+    }
+}

classes/HypothesisHelper.php

@@ -0,0 +1,142 @@
+<?php
+
+namespace APP\plugins\generic\hypothesis\classes;
+
+use APP\facades\Repo;
+use APP\core\Application;
+use APP\submission\Submission;
+use APP\plugins\generic\hypothesis\classes\Annotation;
+use APP\plugins\generic\hypothesis\classes\SubmissionAnnotations;
+
+class HypothesisHelper {
+    public function getSubmissionsAnnotations($contextId) {
+        $submissions = Repo::submission()->getCollector()
+            ->filterByContextIds([$contextId])
+            ->filterByStatus([Submission::STATUS_PUBLISHED])
+            ->getMany();
+
+        $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, $contextId)
+                );
+            }
+        }
+
+        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, $contextId) {
+        $submissionsAnnotations = [];
+
+        foreach ($groupResponse['rows'] as $annotationResponse) {
+            $urlBySlash = explode("/", $annotationResponse['links']['incontext']);
+            $submissionBestId = $urlBySlash[count($urlBySlash) - 3];
+            $submissionId = Repo::submission()->getByBestId($submissionBestId, $contextId)->getId();
+
+            if(!array_key_exists($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();
+        $context = Application::getContextDAO()->getById($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";
+    }
+}

classes/SubmissionAnnotations.php

@@ -0,0 +1,26 @@
+<?php
+
+namespace APP\plugins\generic\hypothesis\classes;
+
+use APP\plugins\generic\hypothesis\classes\Annotation;
+
+class SubmissionAnnotations {
+    public $submissionId;
+    public $submission;
+    public $annotations;
+
+    public function __construct(int $submissionId) {
+        $this->submissionId = $submissionId;
+        $this->annotations = [];
+    }
+
+    public static function __set_state($dump) {
+        $obj = new SubmissionAnnotations($dump['submissionId']);
+        $obj->annotations = $dump['annotations'];
+        return $obj;
+    }
+
+    public function addAnnotation(Annotation $annotation) {
+        $this->annotations[] = $annotation;
+    }
+}