[PKP-LIB][main] pkp#7505 Initial Commit Upload - Delete - Download JA…

…TS File (pkp#9536)

* pkp#7505 Support for JATS files/content added

* pkp#7505 Review Fixes

* pkp#7505 Remove locale keys as vue component props

* pkp#7505 Remove new Jats Component dependency from ListPanel

* pkp#7505 Handle Jats creation Errors

* pkp#7505 Fix UI in error cases

* pkp#7505 Remove JATS Component from PKPWorkflow

* pkp#7505 Review Changes

api/v1/jats/PKPJatsController.php

@@ -0,0 +1,213 @@
+<?php
+
+/**
+ * @file api/v1/jats/PKPJatsController.php
+ *
+ * Copyright (c) 2023 Simon Fraser University
+ * Copyright (c) 2023 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class PKPJatsController
+ *
+ * @ingroup api_v1_jats
+ *
+ * @brief Handle API requests for JATS File operations.
+ *
+ */
+
+namespace PKP\API\v1\jats;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use Illuminate\Http\JsonResponse;
+use Illuminate\Http\Request;
+use Illuminate\Http\Response;
+use Illuminate\Support\Facades\Route;
+use PKP\core\PKPBaseController;
+use PKP\core\PKPRequest;
+use PKP\db\DAORegistry;
+use PKP\security\authorization\ContextAccessPolicy;
+use PKP\security\authorization\internal\SubmissionFileStageAccessPolicy;
+use PKP\security\authorization\PublicationWritePolicy;
+use PKP\security\authorization\SubmissionFileAccessPolicy;
+use PKP\security\authorization\UserRolesRequiredPolicy;
+use PKP\security\Role;
+use PKP\services\PKPSchemaService;
+use PKP\submissionFile\SubmissionFile;
+
+class PKPJatsController extends PKPBaseController
+{
+    /**
+     * @copydoc \PKP\core\PKPBaseController::getHandlerPath()
+     */
+    public function getHandlerPath(): string
+    {
+        return 'submissions/{submissionId}/publications/{publicationId}/jats';
+    }
+
+    /**
+     * @copydoc \PKP\core\PKPBaseController::getRouteGroupMiddleware()
+     */
+    public function getRouteGroupMiddleware(): array
+    {
+        return [
+            'has.user',
+            'has.context',
+        ];
+    }
+
+    public function getGroupRoutes(): void
+    {
+        Route::middleware([
+            self::roleAuthorizer([
+                Role::ROLE_ID_MANAGER,
+                Role::ROLE_ID_SITE_ADMIN,
+                Role::ROLE_ID_SUB_EDITOR,
+                Role::ROLE_ID_ASSISTANT,
+                Role::ROLE_ID_AUTHOR,
+            ]),
+        ])->group(function () {
+
+            Route::get('', $this->get(...))
+                ->name('publication.jats.get');
+
+            Route::post('', $this->add(...))
+                ->name('publication.jats.add');
+
+            Route::delete('', $this->delete(...))
+                ->name('publication.jats.delete');
+
+        })->whereNumber(['submissionId', 'publicationId']);
+    }
+
+    /**
+     * @copydoc \PKP\core\PKPBaseController::authorize()
+     */
+    public function authorize(PKPRequest $request, array &$args, array $roleAssignments): bool
+    {
+        $illuminateRequest = $args[0]; /** @var \Illuminate\Http\Request $illuminateRequest */
+        $actionName = static::getRouteActionName($illuminateRequest);
+
+        $this->addPolicy(new UserRolesRequiredPolicy($request), true);
+
+        $this->addPolicy(new ContextAccessPolicy($request, $roleAssignments));
+
+        $this->addPolicy(new PublicationWritePolicy($request, $args, $roleAssignments));
+
+        if ($actionName === 'add') {
+            $params = $illuminateRequest->input();
+            $fileStage = isset($params['fileStage']) ? (int) $params['fileStage'] : SubmissionFile::SUBMISSION_FILE_JATS;
+            $this->addPolicy(
+                new SubmissionFileStageAccessPolicy(
+                    $fileStage,
+                    SubmissionFileAccessPolicy::SUBMISSION_FILE_ACCESS_MODIFY,
+                    'api.submissionFiles.403.unauthorizedFileStageIdWrite'
+                )
+            );
+        }
+
+        return parent::authorize($request, $args, $roleAssignments);
+    }
+
+    /**
+     * Get JATS XML Files
+     */
+    public function get(Request $illuminateRequest): JsonResponse
+    {
+        $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
+        $publication = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_PUBLICATION);
+
+        if (!$publication) {
+            return response()->json([
+                'error' => __('api.404.resourceNotFound'),
+            ], Response::HTTP_NOT_FOUND);
+        }
+
+        $context = Application::get()->getRequest()->getContext();
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        $genres = $genreDao->getEnabledByContextId($context->getId());
+
+        $jatsFile = Repo::jats()
+            ->getJatsFile($publication->getId(), $submission->getId(), $genres->toArray());
+
+        $jatsFilesProp = Repo::jats()
+            ->summarize($jatsFile);
+
+        return response()->json($jatsFilesProp, Response::HTTP_OK);
+    }
+
+    /**
+     * Add a JATS XML Submission File to a publication
+     */
+    public function add(Request $illuminateRequest): JsonResponse
+    {
+        $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
+        $publication = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_PUBLICATION);
+
+        if (empty($_FILES)) {
+            return response()->json([
+                'error' => __('api.files.400.noUpload'),
+            ], Response::HTTP_BAD_REQUEST);
+        }
+
+        if ($_FILES['file']['error'] !== UPLOAD_ERR_OK) {
+            return $this->getUploadErrorResponse($_FILES['file']['error']);
+        }
+
+        $params = $this->convertStringsToSchema(PKPSchemaService::SCHEMA_SUBMISSION_FILE, $illuminateRequest->input());
+
+        Repo::jats()
+            ->addJatsFile(
+                $_FILES['file']['tmp_name'],
+                $_FILES['file']['name'],
+                $publication->getId(),
+                $submission->getId(),
+                SubmissionFile::SUBMISSION_FILE_JATS,
+                $params);
+
+        $context = Application::get()->getRequest()->getContext();
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        $genres = $genreDao->getEnabledByContextId($context->getId());
+
+        $jatsFile = Repo::jats()
+            ->getJatsFile($publication->getId(), $submission->getId(), $genres->toArray());
+
+        $jatsFilesProp = Repo::jats()
+            ->summarize($jatsFile);
+
+        return response()->json($jatsFilesProp, Response::HTTP_OK);
+    }
+
+    /**
+     * Delete the publication's JATS Submission file
+     */
+    public function delete(Request $illuminateRequest): JsonResponse
+    {
+        $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
+        $publication = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_PUBLICATION);
+
+        $context = Application::get()->getRequest()->getContext();
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        $genres = $genreDao->getEnabledByContextId($context->getId());
+
+        $jatsFile = Repo::jats()
+            ->getJatsFile($publication->getId(), $submission->getId(), $genres->toArray());
+
+        if (!$jatsFile->submissionFile) {
+            return response()->json([
+                'error' => __('api.404.resourceNotFound'),
+            ], Response::HTTP_NOT_FOUND);
+        }
+
+        Repo::submissionFile()
+            ->delete($jatsFile->submissionFile);
+
+        $jatsFile = Repo::jats()
+            ->getJatsFile($publication->getId(), $submission->getId(), $genres->toArray());
+
+        $jatsFilesProp = Repo::jats()
+            ->summarize($jatsFile);
+
+        return response()->json($jatsFilesProp, Response::HTTP_OK);
+    }
+}

api/v1/submissions/PKPSubmissionController.php

@@ -292,9 +292,6 @@ public function getGroupRoutes(): void
             ]);
     }
 
-
-
-
     /**
      * @copydoc \PKP\core\PKPBaseController::authorize()
      */
@@ -838,6 +835,7 @@ public function getParticipants(Request $illuminateRequest): JsonResponse
         $request = Application::get()->getRequest();
         $context = $request->getContext();
         $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
+        $args = $illuminateRequest->input();
         $stageId = $args['stageId'] ?? null;
 
         if (!$submission || $submission->getData('contextId') !== $context->getId()) {
@@ -1591,8 +1589,11 @@ public function saveContributorsOrder(Request $illuminateRequest): JsonResponse
             ->filterByPublicationIds([$publication->getId()])
             ->getMany();
 
+        $authorsArray = Repo::author()->getSchemaMap()->summarizeMany($authors)->toArray();
+        $indexedArray = array_values($authorsArray);
+
         return response()->json(
-            Repo::author()->getSchemaMap()->summarizeMany($authors),
+            $indexedArray,
             Response::HTTP_OK
         );
     }

classes/components/PublicationSectionJats.php

@@ -0,0 +1,74 @@
+<?php
+/**
+ * @file classes/components/PublicationSectionJats.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 PublicationSectionJats
+ *
+ * @ingroup classes_components
+ *
+ * @brief A Panel component for viewing and managing publication's JATS Files
+ */
+
+namespace PKP\components;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use APP\publication\Publication;
+use APP\submission\Submission;
+use PKP\context\Context;
+use PKP\submissionFile\SubmissionFile;
+
+class PublicationSectionJats
+{
+    public function __construct(
+        public string $id,
+        public string $title,
+        public Submission $submission,
+        public Context $context,
+        public bool $canEditPublication = false,
+        public Publication $publication
+    ) {
+    }
+
+    /**
+     * @copydoc ListPanel::getConfig()
+     */
+    public function getConfig()
+    {
+        $config = [];
+
+        $config = array_merge(
+            $config,
+            [
+                'title' => $this->title,
+                'id' => $this->id,
+                'canEditPublication' => $this->canEditPublication,
+                'publicationApiUrlFormat' => $this->getPublicationUrlFormat(),
+                'fileStage' => SubmissionFile::SUBMISSION_FILE_JATS,
+                'downloadDefaultJatsFileName' => Repo::jats()->getDefaultJatsFileName($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/jats/JatsFile.php

@@ -0,0 +1,53 @@
+<?php
+
+/**
+ * @file classes/jats/JatsFile.php
+ *
+ * Copyright (c) 2014-2021 Simon Fraser University
+ * Copyright (c) 2003-2021 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class JatsFile
+ *
+ * @ingroup jats
+ *
+ * @brief JatsFile file class.
+ */
+
+namespace PKP\jats;
+
+use APP\facades\Repo;
+use PKP\jats\exceptions\UnableToCreateJATSContentException;
+use PKP\submissionFile\exceptions\UnableToCreateFileContentException;
+use PKP\submissionFile\SubmissionFile;
+
+class JatsFile
+{
+    public ?string $loadingContentError = null;
+    public ?string $jatsContent = null;
+    public bool $isDefaultContent = true;
+    public array $props = [];
+
+    public function __construct(
+        public int $publicationId,
+        public ?int $submissionId = null, 
+        public ?SubmissionFile $submissionFile = null, 
+        public array $genres = []
+    ) 
+    {
+        try {
+            if ($submissionFile) {
+                $this->isDefaultContent = false;
+
+                $this->jatsContent = Repo::submissionFile()
+                    ->getSubmissionFileContent($submissionFile);
+            } else {
+                $this->jatsContent = Repo::jats()
+                    ->createDefaultJatsContent($publicationId, $submissionId);
+            }
+        } catch (UnableToCreateFileContentException | UnableToCreateJATSContentException $e) {
+            $this->loadingContentError = $e->getMessage();
+        }
+
+    }
+}