v1

.github/workflows/main.yml

@@ -1,54 +1,20 @@
-on: [push,pull_request]
-name: ops
+on: [push, pull_request]
+name: upgrade
 jobs:
-  validate:
-    name: validate
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        application: ['ojs','omp','ops']
-        php-version: [ '8.1','8.2' ]
-    steps:
-      - uses: withanage/validate-action@v1
-        with:
-          application: '${{matrix.application}}'
-          repository: '${{github.repository_owner}}'
-          branch: '${{ github.head_ref || github.ref_name }}'
-  test:
-    name: test
-    runs-on: ubuntu-latest
-    # needs: validate
-    strategy:
-      fail-fast: false
-      matrix:
-        application: ['ojs','omp','ops']
-        php-version: [ '8.1','8.2' ]
-        database: [ 'pgsql', 'mysql','mariadb']
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: withanage/test-action@v1
-        with:
-          application: '${{matrix.application}}'
-          repository: '${{github.repository_owner}}'
-          branch: '${{ github.head_ref || github.ref_name }}'
   upgrade:
-    name: upgrade
     runs-on: ubuntu-latest
-    # needs: test
     strategy:
       fail-fast: false
       matrix:
-        application: ['ojs','omp','ops']
-        dataset-branch: [ 'stable-3_4_0','stable-3_3_0','stable-3_2_1','stable-3_2_0' ]
-        database: [ 'pgsql','mysql']
-        php-version: [ '8.1' ]
+        application: ['omp','ojs','ops']
+        database: ['pgsql','mysql']
+        php-version: [ '8.1' ,'8.2']
 
+    name: upgrade
     steps:
-      - uses: withanage/upgrade-action@v1
+      - uses: xmlFlow/upgrade-action@v1
         with:
-          application: '${{matrix.application}}'
-          repository: '${{github.repository_owner}}'
-          branch: '${{ github.head_ref || github.ref_name }}'
-
+          application:  ${{matrix.application}}
+          repository: 'pkp'
+          branch: 'main'
+          upgrade: true

api/v1/jats/PKPJatsController.php

@@ -0,0 +1,218 @@
+<?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\PublicationAccessPolicy;
+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, $roleAssignments));
+
+        if ($actionName === 'get') {
+            $this->addPolicy(new PublicationAccessPolicy($request, $args, $roleAssignments));
+        } else {
+            $this->addPolicy(new PublicationWritePolicy($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/author/Author.php

@@ -228,4 +228,32 @@ public function getLocalizedUserGroupName()
         $userGroup = $this->getUserGroup();
         return $userGroup->getLocalizedName();
     }
+
+    /**
+     * Get competing interests.
+     *
+     * @return string|array|null
+     */
+    public function getCompetingInterests(?string $locale)
+    {
+        return $this->getData('competingInterests', $locale);
+    }
+
+    /**
+     * Set competing interests.
+     *
+     * @param $competingInterests string|array|null
+     */
+    public function setCompetingInterests($competingInterests, ?string $locale)
+    {
+        $this->setData('competingInterests', $competingInterests, $locale);
+    }
+
+    /**
+     * Get a localized version competing interest statement
+     */
+    public function getLocalizedCompetingInterests(): ?string
+    {
+        return $this->getLocalizedData('competingInterests');
+    }
 }

classes/cliTool/CommandLineTool.php

@@ -30,7 +30,6 @@
 use PKP\config\Config;
 use PKP\core\Registry;
 use PKP\plugins\PluginRegistry;
-use PKP\security\Role;
 use PKP\session\SessionManager;
 use PKP\user\User;
 
@@ -109,26 +108,18 @@ private function checkArgsForUsername()
 
             unset($this->argv[$usernameKeyPos]);
         }
-
         if ($this->username) {
             $user = Repo::user()->getByUsername($this->username, true);
 
             $this->setUser($user);
         }
 
         if (!$this->user) {
-            $adminGroups = Repo::userGroup()->getArrayIdByRoleId(Role::ROLE_ID_SITE_ADMIN);
-
-            if (count($adminGroups)) {
-                $groupUsers = Repo::user()->getCollector()
-                    ->filterByUserGroupIds([$adminGroups[0]])
-                    ->getMany();
-
-                if ($groupUsers->isNotEmpty()) {
-                    $this->setUser($groupUsers->first());
-                } else {
-                    $this->exitWithUsageMessage();
-                }
+            $adminUsers = Repo::user()->getAdminUsers();
+            if ($adminUsers->isNotEmpty()) {
+                $this->setUser($adminUsers->first());
+            } else {
+                $this->exitWithUsageMessage();
             }
         }
     }