pkp#7505 Initial Commit Upload - Delete - Download JATS File

classes/components/listPanels/JatsListPanel.php

@@ -0,0 +1,97 @@
+<?php
+/**
+ * @file classes/components/listPanels/JatsListPanel.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2000-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class JatsListPanel
+ *
+ * @ingroup classes_components_list
+ *
+ * @brief A Panel component for viewing and managing publication's JATS Files
+ */
+
+namespace PKP\components\listPanels;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use APP\publication\Publication;
+use APP\submission\Submission;
+use PKP\components\forms\publication\ContributorForm;
+use PKP\context\Context;
+use PKP\submissionFile\SubmissionFile;
+
+class JatsListPanel extends ListPanel
+{
+    public Submission $submission;
+    public Publication $publication;
+    public Context $context;
+    public array $locales;
+
+    /** Whether the user can edit the current publication */
+    public bool $canEditPublication;
+
+    public function __construct(
+        string $id,
+        string $title,
+        Submission $submission,
+        Context $context,
+        array $locales,
+        bool $canEditPublication = false,
+        Publication $publication
+    ) {
+        parent::__construct($id, $title);
+        $this->submission = $submission;
+        $this->context = $context;
+        $this->locales = $locales;
+        $this->canEditPublication = $canEditPublication;
+        $this->publication = $publication;
+    }
+
+    /**
+     * @copydoc ListPanel::getConfig()
+     */
+    public function getConfig()
+    {
+        $config = parent::getConfig();
+
+        // Remove some props not used in this list panel
+        unset($config['description']);
+        unset($config['expanded']);
+        unset($config['headingLevel']);
+
+        $config = array_merge(
+            $config,
+            [
+                'canEditPublication' => $this->canEditPublication,
+                'publicationApiUrlFormat' => $this->getPublicationUrlFormat(),
+                'uploadProgressLabel' => __('submission.upload.percentComplete'),
+                'fileStage' => SubmissionFile::SUBMISSION_FILE_JATS,
+                'i18nConfirmDeleteFileTitle' => __('publication.jats.confirmDeleteFileTitle'),
+                'i18nDeleteFileMessage' => __('publication.jats.confirmDeleteFileMessage'),
+                'i18nConfirmDeleteFileButton' => __('publication.jats.confirmDeleteFileButton'),
+                'downloadDefaultJatsFileName' => Repo::submissionFile()->getDefaultJatsFileName($this->submission->getId(), $this->publication->getId()),
+            ]
+        );
+
+        return $config;
+    }
+
+    /**
+     * Get an example of the url to a publication's API endpoint,
+     * with a placeholder instead of the publication id, eg:
+     *
+     * http://example.org/api/v1/submissions/1/publications/__publicationId__
+     */
+    protected function getPublicationUrlFormat(): string
+    {
+        return Application::get()->getRequest()->getDispatcher()->url(
+            Application::get()->getRequest(),
+            Application::ROUTE_API,
+            $this->context->getPath(),
+            'submissions/' . $this->submission->getId() . '/publications/__publicationId__/jats'
+        );
+    }
+}

classes/db/DAOResultFactory.php

@@ -259,6 +259,22 @@ public function toAssociativeArray($idField = 'id')
         }
         return $returner;
     }
+
+    /**
+     * Convert this iterator to a collection.
+     *
+     * @return Collection<T>
+     */
+    public function toCollection(): Collection
+    {
+        $retCollection = collect();
+
+        while ($object = $this->next()) {
+            $retCollection->push($object);
+        }
+
+        return $retCollection;
+    }
 }
 
 if (!PKP_STRICT_MODE) {

classes/submissionFile/Repository.php

@@ -19,19 +19,31 @@
 use APP\facades\Repo;
 use APP\notification\Notification;
 use APP\notification\NotificationManager;
+use APP\plugins\generic\jatsTemplate\classes\Article;
+use APP\plugins\generic\jatsTemplate\classes\ArticleBack;
+use APP\plugins\generic\jatsTemplate\classes\ArticleBody;
+use APP\plugins\generic\jatsTemplate\classes\ArticleFront;
+use APP\publication\Publication;
+use APP\submission\Submission;
+use DOMDocument;
 use Exception;
 use Illuminate\Support\Collection;
 use Illuminate\Support\Facades\DB;
 use Illuminate\Support\Facades\Mail;
+use Illuminate\Support\LazyCollection;
+use PKP\config\Config;
 use PKP\core\Core;
 use PKP\core\PKPApplication;
 use PKP\db\DAORegistry;
+use PKP\file\FileManager;
+use PKP\file\TemporaryFileManager;
 use PKP\log\event\SubmissionFileEventLogEntry;
 use PKP\log\SubmissionEmailLogDAO;
 use PKP\log\SubmissionEmailLogEntry;
 use PKP\mail\mailables\RevisedVersionNotify;
 use PKP\note\NoteDAO;
 use PKP\notification\PKPNotification;
+use PKP\oai\OAIRecord;
 use PKP\plugins\Hook;
 use PKP\query\QueryDAO;
 use PKP\security\authorization\SubmissionFileAccessPolicy;
@@ -54,6 +66,9 @@ abstract class Repository
     /** @var array<int> $reviewFileStages The file stages that are part of a review workflow stage */
     public array $reviewFileStages = [];
 
+    public ?Submission $submission = null;
+    public ?Publication $publication = null;
+
     public function __construct(DAO $dao, Request $request, PKPSchemaService $schemaService)
     {
         $this->schemaService = $schemaService;
@@ -662,7 +677,8 @@ public function getWorkflowStageId(SubmissionFile $submissionFile): ?int
 
         if (
             $fileStage === SubmissionFile::SUBMISSION_FILE_PROOF ||
-            $fileStage === SubmissionFile::SUBMISSION_FILE_PRODUCTION_READY
+            $fileStage === SubmissionFile::SUBMISSION_FILE_PRODUCTION_READY ||
+            $fileStage === SubmissionFile::SUBMISSION_FILE_JATS
         ) {
             return WORKFLOW_STAGE_ID_PRODUCTION;
         }
@@ -843,4 +859,220 @@ protected function getSubmissionFileLogData(SubmissionFile $submissionFile): arr
             'username' => $user?->getUsername(),
         ];
     }
+
+    /**
+     * Add jatsContent for Submission files that correspont to 
+     */
+    public function getJatsFileProps(SubmissionFile $submissionFile, array $genres): array
+    {
+        $fileProps = $this->getSchemaMap()->summarize($submissionFile, $genres);
+        $jatsFileName = Config::getVar('files', 'files_dir') . '/' . $fileProps['path'] .'';
+        $xmlString = file_get_contents($jatsFileName);
+
+        if ($xmlString) {
+            $fileProps['jatsContent'] = $xmlString;
+        }
+
+        return $fileProps;
+    }
+
+    /**
+     * Returns the SubmissionFile, if any, that corresponds to the JATS contents of the given submission/publication
+     */
+    public function getJatsFiles(int $submissionId, int $publicationId): ?SubmissionFile
+    {
+        $this->validateSubmissionAndPublication($submissionId, $publicationId);
+
+        $submissionFile = Repo::submissionFile()
+            ->getCollector()
+            ->filterBySubmissionIds([$this->submission->getId()])
+            ->filterByFileStages([SubmissionFile::SUBMISSION_FILE_JATS])
+            ->filterByAssoc(Application::ASSOC_TYPE_PUBLICATION, [$this->publication->getId()])
+            ->getMany()
+            ->first();
+
+        return $submissionFile;
+    }
+
+    /**
+     * Returns the name of the file that will contain the default JATS content 
+     */
+    public function getDefaultJatsFileName(int $submissionId, int $publicationId): string
+    {
+        return 'jats-' . $submissionId . '-' . $publicationId . '-' . (string) mt_rand(100000, 999999) . '.xml';
+    }
+
+    /**
+     * Creates the default JATS XML Content from the given submission/publication metadata
+     */
+    public function createDefaultContentJatsFile(int $submissionId, int $publicationId): string
+    {
+        $submission = Repo::submission()->get($submissionId);
+        $context = Services::get('context')->get($submission->getData('contextId'));
+        $publication = Repo::publication()->get($publicationId);
+        $section = Repo::section()->get($submission->getSectionId());
+
+        $issue = null;
+        if ($publication->getData('issueId')) {
+            $issue = Repo::issue()->get($publication->getData('issueId'));
+        }
+
+        $exportXml = $this->convertSubmissionToJatsXml($submission, $context, $section, $issue, $publication, Application::get()->getRequest());
+
+        return $exportXml;
+    }
+
+    /**
+     * Base function that will add a new JATS file
+     */
+    public function addJatsFile(
+        string $fileTmpName,
+        string $fileName,
+        int $submissionId, 
+        ?int $publicationId = null, 
+        int $type = SubmissionFile::SUBMISSION_FILE_JATS,
+        array $params = []
+    ): SubmissionFile
+    {
+        $this->validateSubmissionAndPublication($submissionId, $publicationId);
+
+        $context = $this->request->getContext();
+        $user = $this->request->getUser();
+
+        $existingJatsFile = $this->getJatsFiles($this->submission->getId(), $this->publication->getId());
+        if ($existingJatsFile) {
+            throw new Exception('A JATS file already exists');
+        }
+
+        $fileManager = new FileManager();
+        $extension = $fileManager->parseFileExtension($fileName);
+
+        $submissionDir = Repo::submissionFile()
+            ->getSubmissionDir(
+                $this->submission->getData('contextId'),
+                $this->submission->getId()
+            );
+
+        $fileId = Services::get('file')->add(
+            $fileTmpName,
+            $submissionDir . '/' . uniqid() . '.' . $extension
+        );
+
+        $params['fileId'] = $fileId;
+        $params['submissionId'] = $this->submission->getId();
+        $params['uploaderUserId'] = $user->getId();
+        $params['fileStage'] = $type;
+
+        $primaryLocale = $context->getPrimaryLocale();
+        $allowedLocales = $context->getData('supportedSubmissionLocales');
+
+        $params['name'] = null;
+        $params['name'][$primaryLocale] = $fileName;
+
+        // If no genre has been set and there is only one genre possible, set it automatically
+        /** @var GenreDAO */
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        $genres = $genreDao->getEnabledByContextId($context->getId());
+
+        if (empty($params['genreId'])) {
+
+            [$firstGenre, $secondGenre] = [$genres->next(), $genres->next()];
+            if ($firstGenre && !$secondGenre) {
+                $params['genreId'] = $firstGenre->getId();
+            }
+        }
+
+        $params['assocType'] = Application::ASSOC_TYPE_PUBLICATION;
+        $params['assocId'] = $this->publication->getId();
+
+        $errors = Repo::submissionFile()
+            ->validate(
+                null,
+                $params,
+                $allowedLocales,
+                $primaryLocale
+            );
+
+        if (!empty($errors)) {
+            Services::get('file')->delete($fileId);
+            throw new Exception(''. implode(', ', $errors));
+        }
+
+        $submissionFile = Repo::submissionFile()
+            ->newDataObject($params);
+
+        $submissionFileId = Repo::submissionFile()
+            ->add($submissionFile);
+
+        $submissionFile = Repo::submissionFile()
+            ->get($submissionFileId);
+
+        return $submissionFile;
+    }
+
+    /**
+     * Function to get the Context's genres
+     */
+    public function getGenres(int $contextId) : Collection 
+    {
+        /** @var \PKP\submission\GenreDAO $genreDao */
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        return $genreDao->getByContextId($contextId)
+            ->toCollection();
+    }
+
+    /**
+     * Given a submissionId and a publicationId this function returns true if the given publicationId 
+     * corresponds to the given submission. If no publicationId given, the current publication will be
+     * used
+     */
+    protected function validateSubmissionAndPublication(int $submissionId, ?int $publicationId) : bool
+    {
+        if (isset($this->submission) && isset($this->publication)) {
+            return true;
+        }
+
+        $this->submission = Repo::submission()
+            ->get($submissionId);
+
+        if (!$this->submission) {
+            throw new Exception('The given submission can not be found');
+        }
+
+        $this->publication = $this->submission->getCurrentPublication();
+
+        if ($publicationId) {
+            $this->publication = Repo::publication()
+                ->get($publicationId);
+
+            if (!$this->publication) {
+                throw new Exception('The given publication can not be found');
+            }
+
+            if ($this->publication->getData('submissionId') != $submissionId) {
+                throw new Exception('The given publication is not part of the given submission');
+            }
+        }
+
+        return true;
+    }
+
+    /**
+     * Given a submission and a publication this function returns the JATS XML contents provided by the 
+     * submission/publication metadata
+     */
+    protected function convertSubmissionToJatsXml($submission, $journal, $section, $issue, $publication, $request): string
+    {
+        $articleJats = new Article();
+
+        $articleJats->preserveWhiteSpace = false;
+        $articleJats->formatOutput = true;
+
+        $jatsXML = $articleJats->convertSubmission($submission, $journal, $section, $issue, $publication, $request);
+
+        $articleJats->loadXML($jatsXML);
+        $formattedXml = $articleJats->saveXML();
+
+        return $formattedXml;
+    }
 }