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api/v1/_dois/BackendDoiHandler.php

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+<?php
+
+/**
+ * @file api/v1/_dois/BackendDoiHandler.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 BackendDoiHandler
+ *
+ * @ingroup api_v1_backend
+ *
+ * @brief Handle API requests for backend operations.
+ *
+ */
+
+namespace APP\API\v1\_dois;
+
+use APP\facades\Repo;
+use Illuminate\Support\LazyCollection;
+use PKP\core\APIResponse;
+use PKP\db\DAORegistry;
+use PKP\security\Role;
+use Slim\Http\Request as SlimRequest;
+
+class BackendDoiHandler extends \PKP\API\v1\_dois\PKPBackendDoiHandler
+{
+    /**
+     * Constructor
+     */
+    public function __construct()
+    {
+        $this->_handlerPath = '_dois';
+        $this->_endpoints = array_merge_recursive($this->_endpoints, [
+            'PUT' => [
+                [
+                    'pattern' => $this->getEndpointPattern() . "/issues/{issueId:\d+}",
+                    'handler' => [$this, 'editIssue'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . "/galleys/{galleyId:\d+}",
+                    'handler' => [$this, 'editGalley'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ]
+            ]
+        ]);
+        parent::__construct();
+    }
+
+    /**
+     * Edit galley to add DOI
+     *
+     * @throws \Exception
+     */
+    public function editGalley(SlimRequest $slimRequest, APIResponse $response, array $args): \Slim\Http\Response
+    {
+        $request = $this->getRequest();
+        $context = $request->getContext();
+
+        $galley = Repo::galley()->get((int)$args['galleyId']);
+        if (!$galley) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        $publicationId = $galley->getData('publicationId');
+        $publication = Repo::publication()->get((int)$publicationId);
+        $submissionId = $publication->getData('submissionId');
+        $submission = Repo::submission()->get((int) $submissionId);
+
+        if ($submission->getData('contextId') !== $context->getId()) {
+            return $response->withStatus(403)->withJsonError('api.dois.403.editItemOutOfContext');
+        }
+
+        $params = $this->convertStringsToSchema(\PKP\services\PKPSchemaService::SCHEMA_GALLEY, $slimRequest->getParsedBody());
+
+        $doi = Repo::doi()->get((int) $params['doiId']);
+        if (!$doi) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.doiNotFound');
+        }
+
+        Repo::galley()->edit($galley, ['doiId' => $doi->getId()]);
+
+        /** @var \PKP\submission\GenreDAO $genreDao */
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        $genres = $genreDao->getByContextId($context->getId())->toArray();
+        // Re-fetch submission and publication to reflect changes in galley
+        $submission = Repo::submission()->get((int) $submissionId);
+        $publication = Repo::publication()->get((int) $publicationId);
+        $galley = Repo::galley()->get($galley->getId());
+
+        $galleyProps = Repo::galley()->getSchemaMap($submission, $publication, $genres)->map($galley);
+
+        return $response->withJson($galleyProps, 200);
+    }
+
+    /**
+     * Edit issue to add DOI
+     *
+     * @throws \Exception
+     */
+    public function editIssue(SlimRequest $slimRequest, APIResponse $response, array $args): \Slim\Http\Response
+    {
+        $request = $this->getRequest();
+        $context = $request->getContext();
+
+        $issue = Repo::issue()->get($args['issueId']);
+        if (!$issue) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        if ($issue->getData('journalId') !== $context->getId()) {
+            return $response->withStatus(403)->withJsonError('api.dois.403.editItemOutOfContext');
+        }
+
+        $params = $this->convertStringsToSchema(\PKP\services\PKPSchemaService::SCHEMA_ISSUE, $slimRequest->getParsedBody());
+
+        $doi = Repo::doi()->get((int) $params['doiId']);
+        if (!$doi) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.doiNotFound');
+        }
+
+        Repo::issue()->edit($issue, ['doiId' => $doi->getId()]);
+        $issue = Repo::issue()->get($issue->getId());
+
+        return $response->withJson(Repo::issue()->getSchemaMap()->map(
+            $issue,
+            $context,
+            $this->getUserGroups($context->getId()),
+            $this->getGenres($context->getId())
+        ), 200);
+    }
+
+    protected function getUserGroups(int $contextId): LazyCollection
+    {
+        return Repo::userGroup()->getCollector()
+            ->filterByContextIds([$contextId])
+            ->getMany();
+    }
+
+    protected function getGenres(int $contextId): array
+    {
+        /** @var \PKP\submission\GenreDAO $genreDao */
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        return $genreDao->getByContextId($contextId)->toArray();
+    }
+}

api/v1/_dois/index.php

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+<?php
+/**
+ * @defgroup api_v1_dois Backend DOI API requests
+ */
+
+/**
+ * @file api/v1/_dois/index.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.
+ *
+ * @ingroup api_v1_dois
+ *
+ * @brief Handle API requests for backend DOI operations.
+ */
+
+return new \APP\API\v1\_dois\BackendDoiHandler();

api/v1/_email/index.php

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+<?php
+
+/**
+ * @defgroup api_v1__email User API requests
+ */
+
+/**
+ * @file api/v1/_email/index.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.
+ *
+ * @ingroup api_v1__email
+ *
+ * @brief Handle requests for user API functions.
+ *
+ */
+
+return new \PKP\API\v1\_email\PKPEmailHandler();

api/v1/_library/index.php

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+<?php
+/**
+ * @defgroup api_v1_library Library files API requests
+ */
+
+/**
+ * @file api/v1/library/index.php
+ *
+ * Copyright (c) 2014-2022 Simon Fraser University
+ * Copyright (c) 2003-2022 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup api_v1_library
+ *
+ * @brief Handle API requests for the publisher and submission library files.
+ */
+
+return new \PKP\API\v1\_library\PKPLibraryHandler();

api/v1/_payments/BackendPaymentsSettingsHandler.php

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+<?php
+/**
+ * @file api/v1/_payments/BackendPaymentsSettingsHandler.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 BackendPaymentsSettingsHandler
+ *
+ * @ingroup api_v1_backend
+ */
+
+namespace APP\API\v1\_payments;
+
+class BackendPaymentsSettingsHandler extends \PKP\API\v1\_payments\PKPBackendPaymentsSettingsHandler
+{
+}

api/v1/_payments/index.php

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+<?php
+
+/**
+ * @defgroup api_v1_backend Backend API requests for payments settings
+ */
+
+/**
+ * @file api/v1/_payments/index.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.
+ *
+ * @ingroup api_v1_backend
+ *
+ * @brief Handle requests for backend API.
+ *
+ */
+
+return new \APP\API\v1\_payments\BackendPaymentsSettingsHandler();

api/v1/_submissions/BackendSubmissionsHandler.php

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+<?php
+
+/**
+ * @file api/v1/_submissions/BackendSubmissionsHandler.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 BackendSubmissionsHandler
+ *
+ * @ingroup api_v1_backend
+ *
+ * @brief Handle API requests for backend operations.
+ *
+ */
+
+namespace APP\API\v1\_submissions;
+
+use APP\core\Application;
+use APP\payment\ojs\OJSCompletedPaymentDAO;
+use APP\payment\ojs\OJSPaymentManager;
+use APP\submission\Collector;
+use PKP\core\APIResponse;
+use PKP\db\DAORegistry;
+use PKP\security\authorization\SubmissionAccessPolicy;
+use PKP\security\Role;
+use PKP\stageAssignment\StageAssignmentDAO;
+use Slim\Http\Request;
+
+class BackendSubmissionsHandler extends \PKP\API\v1\_submissions\PKPBackendSubmissionsHandler
+{
+    /**
+     * Constructor
+     */
+    public function __construct()
+    {
+        $this->_endpoints = array_merge_recursive($this->_endpoints, [
+            'PUT' => [
+                [
+                    'pattern' => '/{contextPath}/api/{version}/_submissions/{submissionId:\d+}/payment',
+                    'handler' => [$this, 'payment'],
+                    'roles' => [
+                        Role::ROLE_ID_SUB_EDITOR,
+                        Role::ROLE_ID_MANAGER,
+                        Role::ROLE_ID_SITE_ADMIN,
+                        Role::ROLE_ID_ASSISTANT,
+                    ],
+                ],
+            ],
+        ]);
+
+        parent::__construct();
+    }
+
+    /**
+     * @copydoc PKPHandler::authorize()
+     */
+    public function authorize($request, &$args, $roleAssignments)
+    {
+        $routeName = $this->getSlimRequest()->getAttribute('route')->getName();
+
+        if ($routeName === 'payment') {
+            $this->addPolicy(new SubmissionAccessPolicy($request, $args, $roleAssignments));
+        }
+
+        return parent::authorize($request, $args, $roleAssignments);
+    }
+
+    /**
+     * Change the status of submission payments.
+     *
+     * @param Request $slimRequest Slim request object
+     * @param APIResponse $response object
+     * @param array $args arguments
+     *
+     * @return APIResponse
+     */
+    public function payment($slimRequest, $response, $args)
+    {
+        $request = $this->getRequest();
+        $context = $request->getContext();
+        $submission = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_SUBMISSION);
+
+        if (!$submission || !$context || $context->getId() != $submission->getContextId()) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        $paymentManager = Application::getPaymentManager($context);
+        $publicationFeeEnabled = $paymentManager->publicationEnabled();
+        if (!$publicationFeeEnabled) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        $params = $slimRequest->getParsedBody();
+
+        if (empty($params['publicationFeeStatus'])) {
+            return $response->withJson([
+                'publicationFeeStatus' => [__('validator.required')],
+            ], 400);
+        }
+
+        $completedPaymentDao = DAORegistry::getDAO('OJSCompletedPaymentDAO'); /** @var OJSCompletedPaymentDAO $completedPaymentDao */
+        $publicationFeePayment = $completedPaymentDao->getByAssoc(null, OJSPaymentManager::PAYMENT_TYPE_PUBLICATION, $submission->getId());
+
+        switch ($params['publicationFeeStatus']) {
+            case 'waived':
+                // Check if a waiver already exists; if so, don't do anything.
+                if ($publicationFeePayment && !$publicationFeePayment->getAmount()) {
+                    break;
+                }
+
+                // If a fulfillment (nonzero amount) already exists, remove it.
+                if ($publicationFeePayment) {
+                    $completedPaymentDao->deleteById($publicationFeePayment->getId());
+                }
+
+                // Record a waived payment.
+                $queuedPayment = $paymentManager->createQueuedPayment(
+                    $request,
+                    OJSPaymentManager::PAYMENT_TYPE_PUBLICATION,
+                    $request->getUser()->getId(),
+                    $submission->getId(),
+                    0,
+                    '' // Zero amount, no currency
+                );
+                $paymentManager->queuePayment($queuedPayment);
+                $paymentManager->fulfillQueuedPayment($request, $queuedPayment, 'ManualPayment');
+                break;
+            case 'paid':
+                // Check if a fulfilled payment already exists; if so, don't do anything.
+                if ($publicationFeePayment && $publicationFeePayment->getAmount()) {
+                    break;
+                }
+
+                // If a waiver (0 amount) already exists, remove it.
+                if ($publicationFeePayment) {
+                    $completedPaymentDao->deleteById($publicationFeePayment->getId());
+                }
+
+                // Record a fulfilled payment.
+                $stageAssignmentDao = DAORegistry::getDAO('StageAssignmentDAO'); /** @var StageAssignmentDAO $stageAssignmentDao */
+                $submitterAssignments = $stageAssignmentDao->getBySubmissionAndRoleIds($submission->getId(), [Role::ROLE_ID_AUTHOR]);
+                $submitterAssignment = $submitterAssignments->next();
+                $queuedPayment = $paymentManager->createQueuedPayment(
+                    $request,
+                    OJSPaymentManager::PAYMENT_TYPE_PUBLICATION,
+                    $submitterAssignment->getUserId(),
+                    $submission->getId(),
+                    $context->getSetting('publicationFee'),
+                    $context->getSetting('currency')
+                );
+                $paymentManager->queuePayment($queuedPayment);
+                $paymentManager->fulfillQueuedPayment($request, $queuedPayment, 'Waiver');
+                break;
+            case 'unpaid':
+                if ($publicationFeePayment) {
+                    $completedPaymentDao->deleteById($publicationFeePayment->getId());
+                }
+                break;
+            default:
+                return $response->withJson([
+                    'publicationFeeStatus' => [__('validator.required')],
+                ], 400);
+        }
+
+        return $response->withJson(true);
+    }
+
+    /** @copydoc PKPSubmissionHandler::getSubmissionCollector() */
+    protected function getSubmissionCollector(array $queryParams): Collector
+    {
+        $collector = parent::getSubmissionCollector($queryParams);
+
+        if (isset($queryParams['issueIds'])) {
+            $collector->filterByIssueIds(
+                array_map('intval', $this->paramToArray($queryParams['issueIds']))
+            );
+        }
+
+        if (isset($queryParams['sectionIds'])) {
+            $collector->filterBySectionIds(
+                array_map('intval', $this->paramToArray($queryParams['sectionIds']))
+            );
+        }
+
+        return $collector;
+    }
+}

api/v1/_submissions/index.php

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+<?php
+
+/**
+ * @defgroup api_v1_backend Backend API requests for submissions
+ */
+
+/**
+ * @file api/v1/_submissions/index.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.
+ *
+ * @ingroup api_v1_backend
+ *
+ * @brief Handle requests for backend API.
+ *
+ */
+
+return new \APP\API\v1\_submissions\BackendSubmissionsHandler();

api/v1/_uploadPublicFile/index.php

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+<?php
+/**
+ * @defgroup api_v1_uploadPublicFile Email templates API requests
+ */
+
+/**
+ * @file api/v1/uploadPublicFile/index.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.
+ *
+ * @ingroup api_v1_uploadPublicFile
+ *
+ * @brief Handle API requests for uploadPublicFile.
+ */
+
+return new \PKP\API\v1\_uploadPublicFile\PKPUploadPublicFileHandler();

api/v1/announcements/index.php

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+<?php
+/**
+ * @defgroup api_v1_announcements Email templates API requests
+ */
+
+/**
+ * @file api/v1/announcements/index.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.
+ *
+ * @ingroup api_v1_announcements
+ *
+ * @brief Handle API requests for announcements.
+ */
+
+return new \PKP\API\v1\announcements\PKPAnnouncementHandler();

api/v1/contexts/ContextHandler.php

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+<?php
+/**
+ * @file api/v1/contexts/ContextHandler.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 ContextHandler
+ *
+ * @ingroup api_v1_contexts
+ *
+ * @brief Handle API requests for contexts (journals/presses).
+ */
+
+namespace APP\API\v1\contexts;
+
+class ContextHandler extends \PKP\API\v1\contexts\PKPContextHandler
+{
+}

api/v1/contexts/index.php

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+<?php
+/**
+ * @defgroup api_v1_contexts Context API requests
+ */
+
+/**
+ * @file api/v1/contexts/index.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.
+ *
+ * @ingroup api_v1_contexts
+ *
+ * @brief Handle API requests for contexts (journals/presses).
+ */
+
+return new \APP\API\v1\contexts\ContextHandler();

api/v1/dois/DoiHandler.php

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+<?php
+
+/**
+ * @file api/v1/dois/DoiHandler.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 DoiHandler
+ *
+ * @ingroup api_v1_dois
+ *
+ * @brief Handle API requests for DOI operations.
+ *
+ */
+
+namespace APP\API\v1\dois;
+
+use APP\facades\Repo;
+use APP\issue\Issue;
+use APP\jobs\doi\DepositIssue;
+use PKP\context\Context;
+use PKP\core\APIResponse;
+use PKP\doi\Doi;
+use PKP\doi\exceptions\DoiException;
+use PKP\security\Role;
+use Slim\Http\Request as SlimRequest;
+use Slim\Http\Response;
+
+class DoiHandler extends \PKP\API\v1\dois\PKPDoiHandler
+{
+    /**
+     * Constructor
+     */
+    public function __construct()
+    {
+        $this->_handlerPath = 'dois';
+        $this->_endpoints = array_merge_recursive($this->_endpoints, [
+            'POST' => [
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/assignDois',
+                    'handler' => [$this, 'assignIssueDois'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN]
+                ]
+            ],
+            'PUT' => [
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/export',
+                    'handler' => [$this, 'exportIssues'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/deposit',
+                    'handler' => [$this, 'depositIssues'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/markRegistered',
+                    'handler' => [$this, 'markIssuesRegistered'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/markUnregistered',
+                    'handler' => [$this, 'markIssuesUnregistered'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/issues/markStale',
+                    'handler' => [$this, 'markIssuesStale'],
+                    'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
+                ],
+            ],
+        ]);
+        parent::__construct();
+    }
+
+    /**
+     * Export XML for configured DOI registration agency
+     */
+    public function exportIssues(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve and validate issues
+        $requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($requestIds)) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
+        }
+
+        $context = $this->getRequest()->getContext();
+
+        $validIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([$context->getId()])
+            ->filterByPublished(true)
+            ->getIds()
+            ->toArray();
+
+        $invalidIds = array_diff($requestIds, $validIds);
+        if (count($invalidIds)) {
+            return $response->withStatus(400)->withJsonError('api.dois.400.invalidPubObjectIncluded');
+        }
+
+        /** @var Issue[] $issues */
+        $issues = [];
+        foreach ($requestIds as $id) {
+            $issues[] = Repo::issue()->get($id);
+        }
+
+        if (empty($issues[0])) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.doiNotFound');
+        }
+
+        $agency = $context->getConfiguredDoiAgency();
+        if ($agency === null) {
+            return $response->withStatus(400)->withJsonError('api.dois.400.noRegistrationAgencyConfigured');
+        }
+
+        // Invoke IDoiRegistrationAgency::exportIssues
+        $responseData = $agency->exportIssues($issues, $context);
+        if (!empty($responseData['xmlErrors'])) {
+            return $response->withStatus(400)->withJsonError('api.dois.400.xmlExportFailed');
+        }
+        return $response->withJson(['temporaryFileId' => $responseData['temporaryFileId']], 200);
+    }
+
+    /**
+     * Deposit XML for configured DOI registration agency
+     */
+    public function depositIssues(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve and validate issues
+        $requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($requestIds)) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
+        }
+
+        $context = $this->getRequest()->getContext();
+
+        $validIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([$context->getId()])
+            ->filterByPublished(true)
+            ->getIds()
+            ->toArray();
+
+        $invalidIds = array_diff($requestIds, $validIds);
+        if (count($invalidIds)) {
+            return $response->withStatus(400)->withJsonError('api.dois.400.invalidPubObjectIncluded');
+        }
+
+        $agency = $context->getConfiguredDoiAgency();
+        if ($agency === null) {
+            return $response->withStatus(400)->withJsonError('api.dois.400.noRegistrationAgencyConfigured');
+        }
+
+        $doisToUpdate = [];
+        foreach ($requestIds as $issueId) {
+            dispatch(new DepositIssue($issueId, $context, $agency));
+            array_merge($doisToUpdate, Repo::doi()->getDoisForIssue($issueId));
+        }
+        Repo::doi()->markSubmitted($doisToUpdate);
+
+        return $response->withStatus(200);
+    }
+
+    /**
+     * Mark submission DOIs as registered with a DOI registration agency.
+     */
+    public function markIssuesRegistered(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve issues
+        $requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($requestIds)) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
+        }
+
+        $context = $this->getRequest()->getContext();
+
+        $validIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([$context->getId()])
+            ->filterByPublished(true)
+            ->getIds()
+            ->toArray();
+
+        $invalidIds = array_diff($requestIds, $validIds);
+        if (count($invalidIds)) {
+            $failedDoiActions = array_map(function (int $id) {
+                $issueTitle = Repo::issue()->get($id)?->getIssueIdentification() ?? 'Issue not found';
+                return new DoiException(DoiException::ISSUE_NOT_PUBLISHED, $issueTitle, $issueTitle);
+            }, $invalidIds);
+
+            return $response->withJson(
+                [
+                    'failedDoiActions' => array_map(
+                        function (DoiException $item) {
+                            return $item->getMessage();
+                        },
+                        $failedDoiActions
+                    )
+                ],
+                400
+            );
+        }
+
+        foreach ($requestIds as $id) {
+            $doiIds = Repo::doi()->getDoisForIssue($id);
+            foreach ($doiIds as $doiId) {
+                Repo::doi()->markRegistered($doiId);
+            }
+        }
+
+        return $response->withStatus(200);
+    }
+
+    /**
+     * Mark issues DOIs as no longer registered with a DOI registration agency.
+     */
+    public function markIssuesUnregistered(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve issues
+        $requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($requestIds)) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
+        }
+
+        $context = $this->getRequest()->getContext();
+
+        $validIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([$context->getId()])
+            ->getIds()
+            ->toArray();
+
+        $invalidIds = array_diff($requestIds, $validIds);
+        if (count($invalidIds)) {
+            $failedDoiActions = array_map(function (int $id) {
+                $issueTitle = Repo::issue()->get($id)?->getIssueIdentification() ?? 'Issue not found';
+                return new DoiException(DoiException::INCORRECT_ISSUE_CONTEXT, $issueTitle, $issueTitle);
+            }, $invalidIds);
+
+            return $response->withJson(
+                [
+                    'failedDoiActions' => array_map(
+                        function (DoiException $item) {
+                            return $item->getMessage();
+                        },
+                        $failedDoiActions
+                    )
+                ],
+                400
+            );
+        }
+
+        foreach ($requestIds as $id) {
+            $doiIds = Repo::doi()->getDoisForIssue($id);
+            foreach ($doiIds as $doiId) {
+                Repo::doi()->markUnregistered($doiId);
+            }
+        }
+
+        return $response->withStatus(200);
+    }
+
+    /**
+     * Mark submission DOIs as stale, indicating a need to be resubmitted to registration agency with updated metadata.
+     */
+    public function markIssuesStale(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve issues
+        $requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($requestIds)) {
+            return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
+        }
+
+        $context = $this->getRequest()->getContext();
+
+        $validIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([$context->getId()])
+            ->filterByPublished(true)
+            // Items can only be considered stale if they have been deposited/queued for deposit in the first place
+            ->filterByDoiStatuses([Doi::STATUS_SUBMITTED, Doi::STATUS_REGISTERED])
+            ->getIds()
+            ->toArray();
+
+        $invalidIds = array_diff($requestIds, $validIds);
+        if (count($invalidIds)) {
+            $failedDoiActions = array_map(function (int $id) {
+                $issueTitle = Repo::issue()->get($id)?->getIssueIdentification() ?? 'Issue not found';
+                return new DoiException(DoiException::INCORRECT_STALE_STATUS, $issueTitle, $issueTitle);
+            }, $invalidIds);
+
+            return $response->withJson(
+                [
+                    'failedDoiActions' => array_map(
+                        function (DoiException $item) {
+                            return $item->getMessage();
+                        },
+                        $failedDoiActions
+                    )
+                ],
+                400
+            );
+        }
+
+        foreach ($requestIds as $id) {
+            $doiIds = Repo::doi()->getDoisForIssue($id);
+            Repo::doi()->markStale($doiIds);
+        }
+
+        return $response->withStatus(200);
+    }
+
+    /**
+     * Assign DOIs to issue
+     */
+    public function assignIssueDois(SlimRequest $slimRequest, APIResponse $response, array $args): Response
+    {
+        // Retrieve issues
+        $ids = $slimRequest->getParsedBody()['ids'] ?? [];
+        if (!count($ids)) {
+            return $response->withStatus(404)->withJsonError('api.issue.404.issuesNotFound');
+        }
+
+        $context = $this->getRequest()->getContext();
+        $doiPrefix = $context->getData(Context::SETTING_DOI_PREFIX);
+        if (empty($doiPrefix)) {
+            return $response->withStatus(403)->withJsonError('api.dois.403.prefixRequired');
+        }
+
+        $failedDoiActions = [];
+
+        // Assign DOIs
+        foreach ($ids as $id) {
+            $issue = Repo::issue()->get($id);
+            if ($issue !== null) {
+                $creationFailureResults = Repo::issue()->createDoi($issue);
+                $failedDoiActions = array_merge($failedDoiActions, $creationFailureResults);
+            }
+        }
+
+        if (!empty($failedDoiActions)) {
+            return $response->withJson(
+                [
+                    'failedDoiActions' => array_map(
+                        function (DoiException $item) {
+                            return $item->getMessage();
+                        },
+                        $failedDoiActions
+                    )
+                ],
+                400
+            );
+        }
+
+        return $response->withJson(['failedDoiActions' => $failedDoiActions], 200);
+    }
+
+    /**
+     * @copydoc PKPDoiHandler::getPubObjectHandler()
+     */
+    protected function getPubObjectHandler(string $type): mixed
+    {
+        $handler = parent::getPubObjectHandler($type);
+        if ($handler !== null) {
+            return $handler;
+        }
+
+        return match ($type) {
+            Repo::doi()::TYPE_ISSUE => Repo::issue(),
+            default => null,
+        };
+    }
+}

api/v1/dois/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_dois DOI API requests
+ */
+
+/**
+ * @file api/v1/dois/index.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.
+ *
+ * @ingroup api_v1_dois
+ *
+ * @brief Handle API requests for DOI operations.
+ */
+
+return new \APP\API\v1\dois\DoiHandler();

api/v1/emailTemplates/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_emailTemplates Email templates API requests
+ */
+
+/**
+ * @file api/v1/emailTemplates/index.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.
+ *
+ * @ingroup api_v1_emailTemplates
+ *
+ * @brief Handle API requests for emailTemplates.
+ */
+
+return new \PKP\API\v1\emailTemplates\PKPEmailTemplateHandler();

api/v1/highlights/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_highlights Highlights API requests
+ */
+
+/**
+ * @file api/v1/highlights/index.php
+ *
+ * Copyright (c) 2014-2023 Simon Fraser University
+ * Copyright (c) 2003-2023 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup api_v1_highlights
+ *
+ * @brief Handle API requests for highlights.
+ */
+
+return new \PKP\API\v1\highlights\HighlightsHandler();

api/v1/institutions/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_institutions Institution API requests
+ */
+
+/**
+ * @file api/v1/institutions/index.php
+ *
+ * Copyright (c) 2022 Simon Fraser University
+ * Copyright (c) 2022 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup api_v1_institutions
+ *
+ * @brief Handle API requests for institutions.
+ */
+
+return new \PKP\API\v1\institutions\PKPInstitutionHandler();

api/v1/issues/IssueHandler.php

@@ -0,0 +1,282 @@
+<?php
+
+/**
+ * @file api/v1/issues/IssueHandler.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 IssueHandler
+ *
+ * @ingroup api_v1_issues
+ *
+ * @brief Handle API requests for issues operations.
+ *
+ */
+
+namespace APP\API\v1\issues;
+
+use APP\core\Application;
+use APP\facades\Repo;
+use APP\issue\Collector;
+use APP\security\authorization\OjsIssueRequiredPolicy;
+use APP\security\authorization\OjsJournalMustPublishPolicy;
+use Illuminate\Support\LazyCollection;
+use PKP\core\APIResponse;
+use PKP\db\DAORegistry;
+use PKP\handler\APIHandler;
+use PKP\plugins\Hook;
+use PKP\security\authorization\ContextAccessPolicy;
+use PKP\security\authorization\ContextRequiredPolicy;
+use PKP\security\authorization\UserRolesRequiredPolicy;
+use PKP\security\Role;
+use PKP\submission\GenreDAO;
+use Slim\Http\Request;
+
+class IssueHandler extends APIHandler
+{
+    /** @var int The default number of issues to return in one request */
+    public const DEFAULT_COUNT = 20;
+
+    /** @var int The maximum number of issues to return in one request */
+    public const MAX_COUNT = 100;
+
+    /**
+     * Constructor
+     */
+    public function __construct()
+    {
+        $this->_handlerPath = 'issues';
+        $roles = [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SUB_EDITOR, Role::ROLE_ID_ASSISTANT, Role::ROLE_ID_REVIEWER, Role::ROLE_ID_AUTHOR];
+        $this->_endpoints = [
+            'GET' => [
+                [
+                    'pattern' => $this->getEndpointPattern(),
+                    'handler' => [$this, 'getMany'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/current',
+                    'handler' => [$this, 'getCurrent'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/{issueId:\d+}',
+                    'handler' => [$this, 'get'],
+                    'roles' => $roles
+                ],
+            ]
+        ];
+        parent::__construct();
+    }
+
+    //
+    // Implement methods from PKPHandler
+    //
+    public function authorize($request, &$args, $roleAssignments)
+    {
+        $routeName = null;
+        $slimRequest = $this->getSlimRequest();
+
+        if (!is_null($slimRequest) && ($route = $slimRequest->getAttribute('route'))) {
+            $routeName = $route->getName();
+        }
+
+        $this->addPolicy(new UserRolesRequiredPolicy($request), true);
+        $this->addPolicy(new ContextRequiredPolicy($request));
+        $this->addPolicy(new ContextAccessPolicy($request, $roleAssignments));
+        $this->addPolicy(new OjsJournalMustPublishPolicy($request));
+
+        if ($routeName === 'get') {
+            $this->addPolicy(new OjsIssueRequiredPolicy($request, $args));
+        }
+
+        return parent::authorize($request, $args, $roleAssignments);
+    }
+
+    //
+    // Public handler methods
+    //
+    /**
+     * Get a collection of issues
+     *
+     * @param Request $slimRequest Slim request object
+     * @param APIResponse $response object
+     * @param array $args arguments
+     *
+     * @return APIResponse
+     */
+    public function getMany($slimRequest, $response, $args)
+    {
+        $collector = Repo::issue()->getCollector()
+            ->limit(self::DEFAULT_COUNT)
+            ->offset(0);
+
+        $request = $this->getRequest();
+        $currentUser = $request->getUser();
+        $context = $request->getContext();
+
+        if (!$context) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        // Process query params to format incoming data as needed
+        foreach ($slimRequest->getQueryParams() as $param => $val) {
+            switch ($param) {
+                case 'orderBy':
+                    if (in_array($val, [Collector::ORDERBY_DATE_PUBLISHED, Collector::ORDERBY_LAST_MODIFIED, Collector::ORDERBY_SEQUENCE])) {
+                        $collector->orderBy($val);
+                    }
+                    break;
+
+                    // Enforce a maximum count to prevent the API from crippling the
+                    // server
+                case 'count':
+                    $collector->limit(min((int) $val, self::MAX_COUNT));
+                    break;
+
+                case 'offset':
+                    $collector->offset((int) $val);
+                    break;
+
+                    // Always convert volume, number and year values to array
+                case 'volumes':
+                case 'volume':
+                case 'numbers':
+                case 'number':
+                case 'years':
+                case 'year':
+
+                    // Support deprecated `year`, `number` and `volume` params
+                    if (substr($param, -1) !== 's') {
+                        $param .= 's';
+                    }
+
+                    if (is_string($val)) {
+                        $val = explode(',', $val);
+                    } elseif (!is_array($val)) {
+                        $val = [$val];
+                    }
+                    $values = array_map('intval', $val);
+                    switch ($param) {
+                        case 'volumes':
+                            $collector->filterByVolumes($values);
+                            break;
+                        case 'numbers':
+                            $collector->filterByNumbers($values);
+                            break;
+                        case 'years':
+                            $collector->filterByYears($values);
+                            break;
+                    }
+
+                    break;
+
+                case 'isPublished':
+                    $collector->filterByPublished((bool) $val);
+                    break;
+
+                case 'searchPhrase':
+                    $collector->searchPhrase($val);
+                    break;
+                case 'doiStatus':
+                    $collector->filterByDoiStatuses(array_map('intval', $this->paramToArray($val)));
+                    break;
+                case 'hasDois':
+                    $collector->filterByHasDois((bool) $val, $context->getEnabledDoiTypes());
+            }
+        }
+
+        $collector->filterByContextIds([$context->getId()]);
+
+        Hook::call('API::issues::params', [&$collector, $slimRequest]);
+
+        // You must be a manager or site admin to access unpublished Issues
+        $isAdmin = $currentUser->hasRole([Role::ROLE_ID_MANAGER], $context->getId()) || $currentUser->hasRole([Role::ROLE_ID_SITE_ADMIN], \PKP\core\PKPApplication::CONTEXT_SITE);
+        if (isset($collector->isPublished) && !$collector->isPublished && !$isAdmin) {
+            return $response->withStatus(403)->withJsonError('api.submissions.403.unpublishedIssues');
+        } elseif (!$isAdmin) {
+            $collector->filterByPublished(true);
+        }
+
+        $issues = $collector->getMany();
+
+        return $response->withJson([
+            'items' => Repo::issue()->getSchemaMap()->summarizeMany($issues, $context)->values(),
+            'itemsMax' => $collector->limit(null)->offset(null)->getCount(),
+        ], 200);
+    }
+
+    /**
+     * Get the current issue
+     *
+     * @param Request $slimRequest Slim request object
+     * @param APIResponse $response object
+     * @param array $args arguments
+     *
+     * @return APIResponse
+     */
+    public function getCurrent($slimRequest, $response, $args)
+    {
+        $context = $this->getRequest()->getContext();
+
+        $issue = Repo::issue()->getCurrent($context->getId());
+
+        if (!$issue) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        $data = Repo::issue()->getSchemaMap()->map(
+            $issue,
+            $context,
+            $this->getUserGroups($context->getId()),
+            $this->getGenres($context->getId())
+        );
+
+        return $response->withJson($data, 200);
+    }
+
+    /**
+     * Get a single issue
+     *
+     * @param Request $slimRequest Slim request object
+     * @param APIResponse $response object
+     * @param array $args arguments
+     *
+     * @return APIResponse
+     */
+    public function get($slimRequest, $response, $args)
+    {
+        $context = $this->getRequest()->getContext();
+
+        $issue = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_ISSUE);
+
+        if (!$issue) {
+            return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
+        }
+
+        $data = Repo::issue()->getSchemaMap()->map(
+            $issue,
+            $context,
+            $this->getUserGroups($context->getId()),
+            $this->getGenres($context->getId())
+        );
+
+        return $response->withJson($data, 200);
+    }
+
+    protected function getUserGroups(int $contextId): LazyCollection
+    {
+        return Repo::userGroup()->getCollector()
+            ->filterByContextIds([$contextId])
+            ->getMany();
+    }
+
+    protected function getGenres(int $contextId): array
+    {
+        /** @var GenreDAO $genreDao */
+        $genreDao = DAORegistry::getDAO('GenreDAO');
+        return $genreDao->getByContextId($contextId)->toArray();
+    }
+}

api/v1/issues/index.php

@@ -0,0 +1,20 @@
+<?php
+
+/**
+ * @defgroup api_v1_issues Issues API requests
+ */
+
+/**
+ * @file api/v1/issues/index.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.
+ *
+ * @ingroup api_v1_issues
+ *
+ * @brief Handle requests for issues API functions.
+ *
+ */
+
+return new \APP\API\v1\issues\IssueHandler();

api/v1/jobs/index.php

@@ -0,0 +1,20 @@
+<?php
+
+/**
+ * @defgroup api_v1_jobs Queue Jobs API requests
+ */
+
+/**
+ * @file api/v1/jobs/index.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.
+ *
+ * @ingroup api_v1_users
+ *
+ * @brief Handle requests for Queue Jobs API functions.
+ *
+ */
+
+return new \PKP\API\v1\jobs\PKPJobHandler();

api/v1/mailables/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_mailables Email templates API requests
+ */
+
+/**
+ * @file api/v1/mailables/index.php
+ *
+ * Copyright (c) 2014-2022 Simon Fraser University
+ * Copyright (c) 2003-2022 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @ingroup api_v1_mailables
+ *
+ * @brief Handle API requests for mailables.
+ */
+
+return new \PKP\API\v1\mailables\MailableHandler();

api/v1/site/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_site Site API requests
+ */
+
+/**
+ * @file api/v1/site/index.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.
+ *
+ * @ingroup api_v1_site
+ *
+ * @brief Handle API requests for the site object.
+ */
+
+return new \PKP\API\v1\site\PKPSiteHandler();

api/v1/stats/editorial/StatsEditorialHandler.php

@@ -0,0 +1,29 @@
+<?php
+
+/**
+ * @file api/v1/stats/StatsEditorialHandler.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 StatsEditorialHandler
+ *
+ * @ingroup api_v1_stats
+ *
+ * @brief Handle API requests for editorial statistics.
+ *
+ */
+
+namespace APP\API\v1\stats\editorial;
+
+class StatsEditorialHandler extends \PKP\API\v1\stats\editorial\PKPStatsEditorialHandler
+{
+    /** @var string The name of the section ids query param for this application */
+    public $sectionIdsQueryParam = 'sectionIds';
+
+    public function getSectionIdsQueryParam()
+    {
+        return $this->sectionIdsQueryParam;
+    }
+}

api/v1/stats/index.php

@@ -0,0 +1,43 @@
+<?php
+
+/**
+ * @defgroup api_v1_stats Publication statistics API requests
+ */
+
+/**
+ * @file api/v1/stats/index.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.
+ *
+ * @ingroup api_v1_stats
+ *
+ * @brief Handle API requests for publication statistics
+ *
+ */
+
+use APP\core\Application;
+
+$requestPath = Application::get()->getRequest()->getRequestPath();
+if (strpos($requestPath, '/stats/publications')) {
+    return new \APP\API\v1\stats\publications\StatsPublicationHandler();
+} elseif (strpos($requestPath, '/stats/editorial')) {
+    return new \APP\API\v1\stats\editorial\StatsEditorialHandler();
+} elseif (strpos($requestPath, '/stats/users')) {
+    return new \PKP\API\v1\stats\users\PKPStatsUserHandler();
+} elseif (strpos($requestPath, '/stats/issues')) {
+    return new \APP\API\v1\stats\issues\StatsIssueHandler();
+} elseif (strpos($requestPath, '/stats/contexts')) {
+    return new \PKP\API\v1\stats\contexts\PKPStatsContextHandler();
+} elseif (strpos($requestPath, '/stats/sushi')) {
+    return new \APP\API\v1\stats\sushi\StatsSushiHandler();
+} else {
+    http_response_code('404');
+    header('Content-Type: application/json');
+    echo json_encode([
+        'error' => 'api.404.endpointNotFound',
+        'errorMessage' => __('api.404.endpointNotFound'),
+    ]);
+    exit;
+}

api/v1/stats/issues/StatsIssueHandler.php

@@ -0,0 +1,463 @@
+<?php
+
+/**
+ * @file api/v1/stats/StatsIssueHandler.php
+ *
+ * Copyright (c) 2022 Simon Fraser University
+ * Copyright (c) 2022 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class StatsIssueHandler
+ *
+ * @ingroup api_v1_stats
+ *
+ * @brief Handle API requests for issue statistics.
+ *
+ */
+
+namespace APP\API\v1\stats\issues;
+
+use APP\core\Application;
+use APP\core\Services;
+use APP\facades\Repo;
+use APP\security\authorization\OjsIssueRequiredPolicy;
+use APP\statistics\StatisticsHelper;
+use PKP\core\APIResponse;
+use PKP\handler\APIHandler;
+use PKP\plugins\Hook;
+use PKP\security\authorization\ContextAccessPolicy;
+use PKP\security\authorization\PolicySet;
+use PKP\security\authorization\RoleBasedHandlerOperationPolicy;
+use PKP\security\authorization\UserRolesRequiredPolicy;
+use PKP\security\Role;
+use Slim\Http\Request as SlimHttpRequest;
+
+class StatsIssueHandler extends APIHandler
+{
+    /**
+     * Constructor
+     */
+    public function __construct()
+    {
+        $this->_handlerPath = 'stats/issues';
+        $roles = [Role::ROLE_ID_SITE_ADMIN, Role::ROLE_ID_MANAGER /*, Role::ROLE_ID_SUB_EDITOR */];
+        $this->_endpoints = [
+            'GET' => [
+                [
+                    'pattern' => $this->getEndpointPattern(),
+                    'handler' => [$this, 'getMany'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/timeline',
+                    'handler' => [$this, 'getManyTimeline'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/{issueId:\d+}',
+                    'handler' => [$this, 'get'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/{issueId:\d+}/timeline',
+                    'handler' => [$this, 'getTimeline'],
+                    'roles' => $roles
+                ],
+            ],
+        ];
+        parent::__construct();
+    }
+
+    /**
+     * @copydoc PKPHandler::authorize()
+     */
+    public function authorize($request, &$args, $roleAssignments)
+    {
+        $routeName = null;
+        $slimRequest = $this->getSlimRequest();
+
+        $this->addPolicy(new UserRolesRequiredPolicy($request), true);
+
+        $this->addPolicy(new ContextAccessPolicy($request, $roleAssignments));
+
+        $rolePolicy = new PolicySet(PolicySet::COMBINING_PERMIT_OVERRIDES);
+        foreach ($roleAssignments as $role => $operations) {
+            $rolePolicy->addPolicy(new RoleBasedHandlerOperationPolicy($request, $role, $operations));
+        }
+        $this->addPolicy($rolePolicy);
+
+        if (!is_null($slimRequest) && ($route = $slimRequest->getAttribute('route'))) {
+            $routeName = $route->getName();
+        }
+        if (in_array($routeName, ['get', 'getGalley', 'getToc'])) {
+            $this->addPolicy(new OjsIssueRequiredPolicy($request, $args));
+        }
+
+        return parent::authorize($request, $args, $roleAssignments);
+    }
+
+    /**
+     * Get usage stats for a set of issues
+     *
+     * Returns total views by toc and all galleys.
+     */
+    public function getMany(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        $request = $this->getRequest();
+        $responseCSV = str_contains($slimRequest->getHeaderLine('Accept'), APIResponse::RESPONSE_CSV) ? true : false;
+
+        $defaultParams = [
+            'count' => 30,
+            'offset' => 0,
+            'orderDirection' => StatisticsHelper::STATISTICS_ORDER_DESC,
+        ];
+
+        $requestParams = array_merge($defaultParams, $slimRequest->getQueryParams());
+
+        $allowedParams = $this->_processAllowedParams($requestParams, [
+            'dateStart',
+            'dateEnd',
+            'count',
+            'offset',
+            'orderDirection',
+            'searchPhrase',
+            'issueIds',
+        ]);
+
+        Hook::call('API::stats::issues::params', [&$allowedParams, $slimRequest]);
+
+        $allowedParams['contextIds'] = [$request->getContext()->getId()];
+
+        $result = $this->_validateStatDates($allowedParams);
+        if ($result !== true) {
+            return $response->withStatus(400)->withJsonError($result);
+        }
+
+        if (!in_array($allowedParams['orderDirection'], [StatisticsHelper::STATISTICS_ORDER_ASC, StatisticsHelper::STATISTICS_ORDER_DESC])) {
+            return $response->withStatus(400)->withJsonError('api.stats.400.invalidOrderDirection');
+        }
+
+        // Identify issues which should be included in the results when a searchPhrase is passed
+        if (!empty($allowedParams['searchPhrase'])) {
+            $allowedIssueIds = empty($allowedParams['issueIds']) ? [] : $allowedParams['issueIds'];
+            $allowedParams['issueIds'] = $this->_processSearchPhrase($allowedParams['searchPhrase'], $allowedIssueIds);
+
+            if (empty($allowedParams['issueIds'])) {
+                $csvColumnNames = $this->_getIssueReportColumnNames();
+                if ($responseCSV) {
+                    return $response->withCSV([], $csvColumnNames, 0);
+                } else {
+                    return $response->withJson([
+                        'items' => [],
+                        'itemsMax' => 0,
+                    ], 200);
+                }
+            }
+        }
+
+        // Get a list (count number) of top issues by total (toc + galley) views
+        $statsService = Services::get('issueStats');
+        $totalMetrics = $statsService->getTotals($allowedParams);
+
+        // Get the stats for each issue
+        $items = [];
+        foreach ($totalMetrics as $totalMetric) {
+            $issueId = $totalMetric->issue_id;
+            $dateStart = array_key_exists('dateStart', $allowedParams) ? $allowedParams['dateStart'] : null;
+            $dateEnd = array_key_exists('dateEnd', $allowedParams) ? $allowedParams['dateEnd'] : null;
+            $metricsByType = $statsService->getTotalsByType($issueId, $this->getRequest()->getContext()->getId(), $dateStart, $dateEnd);
+
+            if ($responseCSV) {
+                $items[] = $this->getItemForCSV($issueId, $metricsByType['toc'], $metricsByType['galley']);
+            } else {
+                $items[] = $this->getItemForJSON($issueId, $metricsByType['toc'], $metricsByType['galley']);
+            }
+        }
+
+        $itemsMax = $statsService->getCount($allowedParams);
+        $csvColumnNames = $this->_getIssueReportColumnNames();
+        if ($responseCSV) {
+            return $response->withCSV($items, $csvColumnNames, $itemsMax);
+        } else {
+            return $response->withJson([
+                'items' => $items,
+                'itemsMax' => $itemsMax,
+            ], 200);
+        }
+    }
+
+    /**
+     * Get the total TOC or issue galley views for a set of issues
+     * in a timeline broken down by month or day
+     */
+    public function getManyTimeline(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        $responseCSV = str_contains($slimRequest->getHeaderLine('Accept'), APIResponse::RESPONSE_CSV) ? true : false;
+
+        $request = $this->getRequest();
+
+        $defaultParams = [
+            'timelineInterval' => StatisticsHelper::STATISTICS_DIMENSION_MONTH,
+        ];
+
+        $requestParams = array_merge($defaultParams, $slimRequest->getQueryParams());
+
+        $allowedParams = $this->_processAllowedParams($requestParams, [
+            'dateStart',
+            'dateEnd',
+            'timelineInterval',
+            'searchPhrase',
+            'type'
+        ]);
+
+        Hook::call('API::stats::issues::timeline::params', [&$allowedParams, $slimRequest]);
+
+        if (!$this->isValidTimelineInterval($allowedParams['timelineInterval'])) {
+            return $response->withStatus(400)->withJsonError('api.stats.400.wrongTimelineInterval');
+        }
+
+        $result = $this->_validateStatDates($allowedParams);
+        if ($result !== true) {
+            return $response->withStatus(400)->withJsonError($result);
+        }
+
+        $allowedParams['contextIds'] = [$request->getContext()->getId()];
+        $allowedParams['assocTypes'] = [Application::ASSOC_TYPE_ISSUE];
+        if (array_key_exists('type', $allowedParams) && $allowedParams['type'] == 'files') {
+            $allowedParams['assocTypes'] = [Application::ASSOC_TYPE_ISSUE_GALLEY];
+        };
+
+        // Identify issues which should be included in the results when a searchPhrase is passed
+        if (!empty($allowedParams['searchPhrase'])) {
+            $allowedIssueIds = empty($allowedParams['issueIds']) ? [] : $allowedParams['issueIds'];
+            $allowedParams['issueIds'] = $this->_processSearchPhrase($allowedParams['searchPhrase'], $allowedIssueIds);
+
+            if (empty($allowedParams['issueIds'])) {
+                $dateStart = empty($allowedParams['dateStart']) ? StatisticsHelper::STATISTICS_EARLIEST_DATE : $allowedParams['dateStart'];
+                $dateEnd = empty($allowedParams['dateEnd']) ? date('Ymd', strtotime('yesterday')) : $allowedParams['dateEnd'];
+                $emptyTimeline = Services::get('issueStats')->getEmptyTimelineIntervals($dateStart, $dateEnd, $allowedParams['timelineInterval']);
+                if ($responseCSV) {
+                    $csvColumnNames = Services::get('issueStats')->getTimelineReportColumnNames();
+                    return $response->withCSV($emptyTimeline, $csvColumnNames, 0);
+                }
+                return $response->withJson($emptyTimeline, 200);
+            }
+        }
+
+        $data = Services::get('issueStats')->getTimeline($allowedParams['timelineInterval'], $allowedParams);
+        if ($responseCSV) {
+            $csvColumnNames = Services::get('issueStats')->getTimelineReportColumnNames();
+            return $response->withCSV($data, $csvColumnNames, count($data));
+        }
+        return $response->withJson($data, 200);
+    }
+
+    /**
+     * Get a single issue's usage statistics
+     */
+    public function get(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        $request = $this->getRequest();
+
+        $issue = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_ISSUE);
+
+        $allowedParams = $this->_processAllowedParams($slimRequest->getQueryParams(), [
+            'dateStart',
+            'dateEnd',
+        ]);
+
+        Hook::call('API::stats::issue::params', [&$allowedParams, $slimRequest]);
+
+        $result = $this->_validateStatDates($allowedParams);
+        if ($result !== true) {
+            return $response->withStatus(400)->withJsonError($result);
+        }
+
+        $statsService = Services::get('issueStats');
+        $dateStart = array_key_exists('dateStart', $allowedParams) ? $allowedParams['dateStart'] : null;
+        $dateEnd = array_key_exists('dateEnd', $allowedParams) ? $allowedParams['dateEnd'] : null;
+        $metricsByType = $statsService->getTotalsByType($issue->getId(), $request->getContext()->getId(), $dateStart, $dateEnd);
+
+        return $response->withJson([
+            'tocViews' => $metricsByType['toc'],
+            'issueGalleyViews' => $metricsByType['galley'],
+            'issue' => Repo::issue()->getSchemaMap()->mapToStats($issue),
+        ], 200);
+    }
+
+    /**
+     * Get the total TOC or issue galley views for an issue broken down by
+     * month or day
+     */
+    public function getTimeline(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        $request = $this->getRequest();
+
+        $issue = $this->getAuthorizedContextObject(Application::ASSOC_TYPE_ISSUE);
+
+        $defaultParams = [
+            'timelineInterval' => StatisticsHelper::STATISTICS_DIMENSION_MONTH,
+        ];
+
+        $requestParams = array_merge($defaultParams, $slimRequest->getQueryParams());
+
+        $allowedParams = $this->_processAllowedParams($requestParams, [
+            'dateStart',
+            'dateEnd',
+            'timelineInterval',
+            'type'
+        ]);
+
+        Hook::call('API::stats::issue::timeline::params', [&$allowedParams, $slimRequest]);
+
+        $allowedParams['contextIds'] = [$request->getContext()->getId()];
+        $allowedParams['issueIds'] = [$issue->getId()];
+        $allowedParams['assocTypes'] = [Application::ASSOC_TYPE_ISSUE];
+        if (array_key_exists('type', $allowedParams) && $allowedParams['type'] == 'files') {
+            $allowedParams['assocTypes'] = [Application::ASSOC_TYPE_ISSUE_GALLEY];
+        };
+
+        if (!$this->isValidTimelineInterval($allowedParams['timelineInterval'])) {
+            return $response->withStatus(400)->withJsonError('api.stats.400.wrongTimelineInterval');
+        }
+
+        $result = $this->_validateStatDates($allowedParams);
+        if ($result !== true) {
+            return $response->withStatus(400)->withJsonError($result);
+        }
+
+        $statsService = Services::get('issueStats');
+        $data = $statsService->getTimeline($allowedParams['timelineInterval'], $allowedParams);
+        return $response->withJson($data, 200);
+    }
+
+    /**
+     * A helper method to filter and sanitize the request params
+     *
+     * Only allows the specified params through and enforces variable
+     * type where needed.
+     */
+    protected function _processAllowedParams(array $requestParams, array $allowedParams): array
+    {
+        $returnParams = [];
+        foreach ($requestParams as $requestParam => $value) {
+            if (!in_array($requestParam, $allowedParams)) {
+                continue;
+            }
+            switch ($requestParam) {
+                case 'dateStart':
+                case 'dateEnd':
+                case 'timelineInterval':
+                case 'searchPhrase':
+                case 'type':
+                    $returnParams[$requestParam] = $value;
+                    break;
+
+                case 'count':
+                    $returnParams[$requestParam] = min(100, (int) $value);
+                    break;
+
+                case 'offset':
+                    $returnParams[$requestParam] = (int) $value;
+                    break;
+
+                case 'orderDirection':
+                    $returnParams[$requestParam] = strtoupper($value);
+                    break;
+
+                case 'issueIds':
+                    if (is_string($value) && strpos($value, ',') > -1) {
+                        $value = explode(',', $value);
+                    } elseif (!is_array($value)) {
+                        $value = [$value];
+                    }
+                    $returnParams[$requestParam] = array_map('intval', $value);
+                    break;
+            }
+        }
+        return $returnParams;
+    }
+
+    /**
+     * A helper method to get the issueIds param when a searchPhase
+     * param is also passed.
+     *
+     * If the searchPhrase and issueIds params were both passed in the
+     * request, then we only return IDs that match both conditions.
+     */
+    protected function _processSearchPhrase(string $searchPhrase, array $issueIds = []): array
+    {
+        $searchPhraseIssueIds = Repo::issue()
+            ->getCollector()
+            ->filterByContextIds([Application::get()->getRequest()->getContext()->getId()])
+            ->filterByPublished(true)
+            ->searchPhrase($searchPhrase)
+            ->getIds()
+            ->toArray();
+
+        if (!empty($issueIds)) {
+            return array_intersect($issueIds, $searchPhraseIssueIds);
+        }
+        return $searchPhraseIssueIds;
+    }
+
+    /**
+     * Get column names for the issue CSV report
+     */
+    protected function _getIssueReportColumnNames(): array
+    {
+        return [
+            __('common.id'),
+            __('editor.issues.issueIdentification'),
+            __('stats.total'),
+            __('stats.views'),
+            __('stats.downloads')
+        ];
+    }
+
+    /**
+     * Get CSV row with issue metrics
+     */
+    protected function getItemForCSV(int $issueId, int $tocViews, int $issueGalleyViews): array
+    {
+        $totalViews = $tocViews + $issueGalleyViews;
+        // Get issue identification for display
+        $issue = Repo::issue()->get($issueId);
+        $identification = $issue->getIssueIdentification();
+        return [
+            $issueId,
+            $identification,
+            $totalViews,
+            $tocViews,
+            $issueGalleyViews
+        ];
+    }
+
+    /**
+     * Get JSON data with issue metrics
+     */
+    protected function getItemForJSON(int $issueId, int $tocViews, int $issueGalleyViews): array
+    {
+        $totalViews = $tocViews + $issueGalleyViews;
+        // Get basic issue details for display
+        $issue = Repo::issue()->get($issueId);
+        $issueProps = Repo::issue()->getSchemaMap()->mapToStats($issue);
+        return [
+            'totalViews' => $totalViews,
+            'tocViews' => $tocViews,
+            'issueGalleyViews' => $issueGalleyViews,
+            'issue' => $issueProps,
+        ];
+    }
+
+    /**
+     * Check if the timeline interval is valid
+     */
+    protected function isValidTimelineInterval(string $interval): bool
+    {
+        return in_array($interval, [
+            StatisticsHelper::STATISTICS_DIMENSION_DAY,
+            StatisticsHelper::STATISTICS_DIMENSION_MONTH
+        ]);
+    }
+}

api/v1/stats/publications/StatsPublicationHandler.php

@@ -0,0 +1,59 @@
+<?php
+
+/**
+ * @file api/v1/stats/publications/StatsPublicationHandler.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 StatsPublicationHandler
+ *
+ * @ingroup api_v1_stats
+ *
+ * @brief Handle API requests for publication statistics.
+ *
+ */
+
+namespace APP\API\v1\stats\publications;
+
+class StatsPublicationHandler extends \PKP\API\v1\stats\publications\PKPStatsPublicationHandler
+{
+    /** @var string The name of the section ids query param for this application */
+    public $sectionIdsQueryParam = 'sectionIds';
+
+    public function getSectionIdsQueryParam()
+    {
+        return $this->sectionIdsQueryParam;
+    }
+
+    protected function getManyAllowedParams()
+    {
+        $params = parent::getManyAllowedParams();
+        $params[] = 'issueIds';
+        return $params;
+    }
+
+    protected function getManyTimelineAllowedParams()
+    {
+        $params = parent::getManyTimelineAllowedParams();
+        $params[] = 'issueIds';
+        return $params;
+    }
+
+    protected function _processParam(string $requestParam, mixed $value): array
+    {
+        if ($requestParam == 'issueIds') {
+            $returnParams = [];
+            if (is_string($value) && str_contains($value, ',')) {
+                $value = explode(',', $value);
+            } elseif (!is_array($value)) {
+                $value = [$value];
+            }
+            $returnParams[$requestParam] = array_map('intval', $value);
+        } else {
+            $returnParams = parent::_processParam($requestParam, $value);
+        }
+        return $returnParams;
+    }
+}

api/v1/stats/sushi/StatsSushiHandler.php

@@ -0,0 +1,135 @@
+<?php
+
+/**
+ * @file api/v1/stats/sushi/StatsSushiHandler.php
+ *
+ * Copyright (c) 2022 Simon Fraser University
+ * Copyright (c) 2022 John Willinsky
+ * Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
+ *
+ * @class StatsSushiHandler
+ *
+ * @ingroup api_v1_stats
+ *
+ * @brief Handle API requests for COUNTER R5 SUSHI statistics.
+ *
+ */
+
+namespace APP\API\v1\stats\sushi;
+
+use APP\sushi\IR;
+use APP\sushi\IR_A1;
+use APP\sushi\TR;
+use APP\sushi\TR_J3;
+use PKP\core\APIResponse;
+use Slim\Http\Request as SlimHttpRequest;
+
+class StatsSushiHandler extends \PKP\API\v1\stats\sushi\PKPStatsSushiHandler
+{
+    /**
+     * Get this API's endpoints definitions
+     */
+    protected function getGETDefinitions(array $roles = null): array
+    {
+        return array_merge(
+            parent::getGETDefinitions($roles),
+            [
+                [
+                    'pattern' => $this->getEndpointPattern() . '/reports/tr',
+                    'handler' => [$this, 'getReportsTR'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/reports/tr_j3',
+                    'handler' => [$this, 'getReportsTRJ3'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/reports/ir',
+                    'handler' => [$this, 'getReportsIR'],
+                    'roles' => $roles
+                ],
+                [
+                    'pattern' => $this->getEndpointPattern() . '/reports/ir_a1',
+                    'handler' => [$this, 'getReportsIRA1'],
+                    'roles' => $roles
+                ],
+            ]
+        );
+    }
+
+    /**
+     * COUNTER 'Title Master Report' [TR].
+     * A customizable report detailing activity at the journal level
+     * that allows the user to apply filters and select other configuration options for the report.
+     */
+    public function getReportsTR(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        return $this->getReportResponse(new TR(), $slimRequest, $response, $args);
+    }
+
+    /**
+     * COUNTER 'Journal Usage by Access Type' [TR_J3].
+     * This is a Standard View of Title Master Report that reports on usage of journal content for all Metric_Types broken down by Access_Type.
+     */
+    public function getReportsTRJ3(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        return $this->getReportResponse(new TR_J3(), $slimRequest, $response, $args);
+    }
+
+    /**
+     * COUNTER 'Item Master Report' [IR].
+     * A customizable report detailing activity at the article level
+     * that allows the user to apply filters and select other configuration options for the report.
+     */
+    public function getReportsIR(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        return $this->getReportResponse(new IR(), $slimRequest, $response, $args);
+    }
+
+    /**
+     * COUNTER 'Journal Article Requests' [IR_A1].
+     * This is a Standard View of Item Master Report that reports on journal article requests at the article level.
+     */
+    public function getReportsIRA1(SlimHttpRequest $slimRequest, APIResponse $response, array $args): APIResponse
+    {
+        return $this->getReportResponse(new IR_A1(), $slimRequest, $response, $args);
+    }
+
+    /**
+     * Get the application specific list of reports supported by the API
+     */
+    protected function getReportList(): array
+    {
+        return array_merge(parent::getReportList(), [
+            [
+                'Report_Name' => 'Title Master Report',
+                'Report_ID' => 'TR',
+                'Release' => '5',
+                'Report_Description' => __('sushi.reports.tr.description'),
+                'Path' => 'reports/tr'
+            ],
+            [
+                'Report_Name' => 'Journal Usage by Access Type',
+                'Report_ID' => 'TR_J3',
+                'Release' => '5',
+                'Report_Description' => __('sushi.reports.tr_j3.description'),
+                'Path' => 'reports/tr_j3'
+            ],
+            [
+                'Report_Name' => 'Item Master Report',
+                'Report_ID' => 'IR',
+                'Release' => '5',
+                'Report_Description' => __('sushi.reports.ir.description'),
+                'Path' => 'reports/ir'
+            ],
+            [
+                'Report_Name' => 'Journal Article Requests',
+                'Report_ID' => 'IR_A1',
+                'Release' => '5',
+                'Report_Description' => __('sushi.reports.ir_a1.description'),
+                'Path' => 'reports/ir_a1'
+            ],
+        ]);
+    }
+}

api/v1/submissions/SubmissionHandler.php

@@ -0,0 +1,43 @@
+<?php
+
+/**
+ * @file api/v1/submissions/SubmissionHandler.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 SubmissionHandler
+ *
+ * @ingroup api_v1_submission
+ *
+ * @brief Handle API requests for submission operations.
+ *
+ */
+
+namespace APP\API\v1\submissions;
+
+use APP\submission\Collector;
+
+class SubmissionHandler extends \PKP\API\v1\submissions\PKPSubmissionHandler
+{
+    /** @copydoc PKPSubmissionHandler::getSubmissionCollector() */
+    protected function getSubmissionCollector(array $queryParams): Collector
+    {
+        $collector = parent::getSubmissionCollector($queryParams);
+
+        if (isset($queryParams['issueIds'])) {
+            $collector->filterByIssueIds(
+                array_map('intval', $this->paramToArray($queryParams['issueIds']))
+            );
+        }
+
+        if (isset($queryParams['sectionIds'])) {
+            $collector->filterBySectionIds(
+                array_map('intval', $this->paramToArray($queryParams['sectionIds']))
+            );
+        }
+
+        return $collector;
+    }
+}

api/v1/submissions/index.php

@@ -0,0 +1,24 @@
+<?php
+
+/**
+ * @defgroup api_v1_submissions Submission API requests
+ */
+
+/**
+ * @file api/v1/submissions/index.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.
+ *
+ * @ingroup api_v1_submissions
+ *
+ * @brief Handle requests for submission API functions.
+ *
+ */
+$urlParts = explode('/', trim($_SERVER['PATH_INFO'], '/'));
+if (count($urlParts) >= 6 && $urlParts[5] == 'files') {
+    return new \PKP\API\v1\submissions\PKPSubmissionFileHandler();
+} else {
+    return new \APP\API\v1\submissions\SubmissionHandler();
+}

api/v1/temporaryFiles/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_temporaryFiles Temporary file upload API requests
+ */
+
+/**
+ * @file api/v1/temporaryFiles/index.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.
+ *
+ * @ingroup api_v1_temporaryFiles
+ *
+ * @brief Handle API requests for temporary file uploading.
+ */
+
+return new \PKP\API\v1\temporaryFiles\PKPTemporaryFilesHandler();

api/v1/users/UserHandler.php

@@ -0,0 +1,22 @@
+<?php
+
+/**
+ * @file api/v1/users/UserHandler.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 UserHandler
+ *
+ * @ingroup api_v1_users
+ *
+ * @brief Handle API requests for user operations.
+ *
+ */
+
+namespace APP\API\v1\users;
+
+class UserHandler extends \PKP\API\v1\users\PKPUserHandler
+{
+}

api/v1/users/index.php

@@ -0,0 +1,20 @@
+<?php
+
+/**
+ * @defgroup api_v1_users User API requests
+ */
+
+/**
+ * @file api/v1/users/index.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.
+ *
+ * @ingroup api_v1_users
+ *
+ * @brief Handle requests for user API functions.
+ *
+ */
+
+return new \APP\API\v1\users\UserHandler();

api/v1/vocabs/index.php

@@ -0,0 +1,18 @@
+<?php
+/**
+ * @defgroup api_v1_vocabs Controlled vocabulary API requests
+ */
+
+/**
+ * @file api/v1/vocabs/index.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.
+ *
+ * @ingroup api_v1_vocabs
+ *
+ * @brief Handle API requests for vocabs.
+ */
+
+return new \PKP\API\v1\vocabs\PKPVocabHandler();