<?php
/**
* @file api/v1/dois/PKPDoiHandler.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 PKPDoiHandler
*
* @ingroup api_v1_dois
*
* @brief Handle API requests for DOI operations.
*
*/
namespace PKP\API\v1\dois;
use APP\core\Application;
use APP\facades\Repo;
use APP\submission\Submission;
use PKP\context\Context;
use PKP\core\APIResponse;
use PKP\doi\Doi;
use PKP\doi\exceptions\DoiException;
use PKP\file\TemporaryFileManager;
use PKP\handler\APIHandler;
use PKP\jobs\doi\DepositSubmission;
use PKP\plugins\Hook;
use PKP\security\authorization\ContextAccessPolicy;
use PKP\security\authorization\DoisEnabledPolicy;
use PKP\security\authorization\PolicySet;
use PKP\security\authorization\RoleBasedHandlerOperationPolicy;
use PKP\security\authorization\UserRolesRequiredPolicy;
use PKP\security\Role;
use PKP\services\PKPSchemaService;
use Slim\Http\Request as SlimRequest;
use Slim\Http\Response;
class PKPDoiHandler extends APIHandler
{
/** @var int The default number of DOIs to return in one request */
public const DEFAULT_COUNT = 30;
/** @var int The maximum number of DOIs to return in one request */
public const MAX_COUNT = 100;
/** @var array Handlers that must be authorized to access a submission */
public $requiresSubmissionAccess = [];
/** @var array Handlers that must be authorized to write to a publication */
public $requiresPublicationWriteAccess = [];
/**
* Constructor
*/
public function __construct()
{
$this->_handlerPath = 'dois';
$this->_endpoints = array_merge_recursive($this->_endpoints, [
'GET' => [
[
'pattern' => $this->getEndpointPattern(),
'handler' => [$this, 'getMany'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/{doiId:\d+}',
'handler' => [$this, 'get'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/exports/{fileId:\d+}',
'handler' => [$this, 'getExportedFile'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
]
],
'POST' => [
[
'pattern' => $this->getEndpointPattern(),
'handler' => [$this, 'add'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/assignDois',
'handler' => [$this, 'assignSubmissionDois'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
],
'PUT' => [
[
'pattern' => $this->getEndpointPattern() . '/{doiId:\d+}',
'handler' => [$this, 'edit'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/export',
'handler' => [$this, 'exportSubmissions'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/deposit',
'handler' => [$this, 'depositSubmissions'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/markRegistered',
'handler' => [$this, 'markSubmissionsRegistered'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/markUnregistered',
'handler' => [$this, 'markSubmissionsUnregistered'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/submissions/markStale',
'handler' => [$this, 'markSubmissionsStale'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
[
'pattern' => $this->getEndpointPattern() . '/depositAll',
'handler' => [$this, 'depositAllDois'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN]
],
],
'DELETE' => [
[
'pattern' => $this->getEndpointPattern() . '/{doiId:\d+}',
'handler' => [$this, 'delete'],
'roles' => [Role::ROLE_ID_MANAGER, Role::ROLE_ID_SITE_ADMIN],
],
],
]);
parent::__construct();
}
/**
* @param \APP\core\Request $request
* @param array $args
* @param array $roleAssignments
*
* @return bool
*/
public function authorize($request, &$args, $roleAssignments)
{
$this->addPolicy(new UserRolesRequiredPolicy($request), true);
// This endpoint is not available at the site-wide level
$this->addPolicy(new ContextAccessPolicy($request, $roleAssignments));
// DOIs must be enabled to access DOI API endpoints
$this->addPolicy(new DoisEnabledPolicy($request->getContext()));
$rolePolicy = new PolicySet(PolicySet::COMBINING_PERMIT_OVERRIDES);
foreach ($roleAssignments as $role => $operations) {
$rolePolicy->addPolicy(new RoleBasedHandlerOperationPolicy($request, $role, $operations));
}
$this->addPolicy($rolePolicy);
return parent::authorize($request, $args, $roleAssignments);
}
/**
* Get a single DOI
*
* @param SlimRequest $slimRequest Slim request object
* @param APIResponse $response object
* @param array $args arguments
*
*/
public function get(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$doi = Repo::doi()->get((int) $args['doiId']);
if (!$doi) {
return $response->withStatus(404)->withJsonError('api.404.resourceNotFound"');
}
// The contextId should always point to the requested contextId
if ($doi->getData('contextId') !== $this->getRequest()->getContext()->getId()) {
return $response->withStatus(403)->withJsonError('api.dois.403.contextsNotMatched');
}
return $response->withJson(Repo::doi()->getSchemaMap()->map($doi), 200);
}
/**
* Get a collection of DOIs
*/
public function getMany(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$collector = Repo::doi()->getCollector()
->limit(self::DEFAULT_COUNT)
->offset(0);
foreach ($slimRequest->getQueryParams() as $param => $val) {
switch ($param) {
case 'count':
$collector->limit(min((int) $val, self::MAX_COUNT));
break;
case 'offset':
$collector->offset((int) $val);
break;
case 'status':
$collector->filterByStatus(array_map('intval', $this->paramToArray($val)));
break;
}
}
$collector->filterByContextIds([$this->getRequest()->getContext()->getId()]);
Hook::call('API::dois::params', [$collector, $slimRequest]);
$dois = $collector->getMany();
return $response->withJson(
[
'itemsMax' => $collector->limit(null)->offset(0)->getCount(),
'items' => Repo::doi()->getSchemaMap()->summarizeMany($dois)->values(),
],
200
);
}
/**
* Add a DOI
*/
public function add(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$request = $this->getRequest();
$context = $request->getContext();
$params = $this->convertStringsToSchema(PKPSchemaService::SCHEMA_DOI, $slimRequest->getParsedBody());
$params['contextId'] = $context->getId();
$errors = Repo::doi()->validate(null, $params);
if (!empty($errors)) {
return $response->withStatus(400)->withJson($errors);
}
$doi = Repo::doi()->newDataObject($params);
$id = Repo::doi()->add($doi);
if ($id === null) {
return $response->withStatus(400)->withJsonError('api.dois.400.creationFailed');
}
$doi = Repo::doi()->get($id);
return $response->withJson(Repo::doi()->getSchemaMap()->map($doi), 200);
}
/**
* Edit a DOI.
*
* When a pub object type and id are provided as body parameters, the DOI should only be modified for that pub object.
* To prevent the DOI from being modified for other objects it may be assigned to, we must create a new DOI
* and assign it to the object instead of editing the old DOI.
*
* When a pub object type and id are NOT provided, this function will only edit the DOI with ID of `doiId`
* without any side effects.
*/
public function edit(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$doi = Repo::doi()->get((int) $args['doiId']);
if (!$doi) {
return $response->withStatus(404)->withJsonError('api.dois.404.doiNotFound');
}
// The contextId should always point to the requested contextId
if ($doi->getData('contextId') !== $this->getRequest()->getContext()->getId()) {
return $response->withStatus(403)->withJsonError('api.dois.403.editItemOutOfContext');
}
$params = $this->convertStringsToSchema(PKPSchemaService::SCHEMA_DOI, $slimRequest->getParsedBody());
$errors = Repo::doi()->validate($doi, $params);
if (!empty($errors)) {
return $response->withStatus(400)->withJson($errors);
}
$pubObjectType = $slimRequest->getParsedBodyParam('pubObjectType');
$pubObjectId = $slimRequest->getParsedBodyParam('pubObjectId');
// Default behaviour, only edits DOI
if (empty($pubObjectType) && empty($pubObjectId)) {
Repo::doi()->edit($doi, $params);
$doi = Repo::doi()->get($doi->getId());
return $response->withJson(Repo::doi()->getSchemaMap()->map($doi), 200);
}
$pubObjectHandler = $this->getPubObjectHandler($pubObjectType);
if (is_null($pubObjectHandler)) {
return $response->withStatus(403)->withJsonError('api.dois.403.pubTypeNotRecognized');
}
// Check pubObject for doiId
$pubObject = $this->getViaPubObjectHandler($pubObjectHandler, $pubObjectId);
if ($pubObject?->getData('doiId') != $doi->getId()) {
return $response->withStatus(404)->withJsonError('api.dois.404.pubObjectNotFound');
}
// Copy DOI object data
$newDoi = clone $doi;
$newDoi->unsetData('id');
$newDoi->setAllData(array_merge($newDoi->getAllData(), ['doi' => $params['doi']]));
$newDoiId = Repo::doi()->add($newDoi);
// Update pubObject with new DOI and remove elsewhere if no longer in use
$this->editViaPubObjectHandler($pubObjectHandler, $pubObject, $newDoiId);
if (!Repo::doi()->isAssigned($doi->getId(), $pubObjectType)) {
Repo::doi()->delete($doi);
}
return $response->withJson(Repo::doi()->getSchemaMap()->map($newDoi), 200);
}
/**
* Delete a DOI
*
* When a pub object type and id are provided as body parameters, the DOI should only be deleted for that object.
* To prevent the DOI from being removed for other objects it may be assigned to, we remove the doiId from the
* pubObject then check if it's in use anywhere else before removing the DOI object directly.
*/
public function delete(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$doi = Repo::doi()->get((int) $args['doiId']);
if (!$doi) {
return $response->withStatus(404)->withJsonError('api.dois.404.doiNotFound');
}
// The contextId should always point to the requested contextId
if ($doi->getData('contextId') !== $this->getRequest()->getContext()->getId()) {
return $response->withStatus(403)->withJsonError('api.dois.403.editItemOutOfContext');
}
$doiProps = Repo::doi()->getSchemaMap()->map($doi);
$pubObjectType = $slimRequest->getParsedBodyParam('pubObjectType');
$pubObjectId = $slimRequest->getParsedBodyParam('pubObjectId');
// Default behaviour, directly delete DOI
if (empty($pubObjectType) && empty($pubObjectId)) {
Repo::doi()->delete($doi);
return $response->withJson($doiProps, 200);
}
$pubObjectHandler = $this->getPubObjectHandler($pubObjectType);
if (is_null($pubObjectHandler)) {
return $response->withStatus(403)->withJsonError('api.dois.403.pubTypeNotRecognized');
}
// Check pubObject for doiId
$pubObject = $this->getViaPubObjectHandler($pubObjectHandler, $pubObjectId);
if ($pubObject?->getData('doiId') != $doi->getId()) {
return $response->withStatus(404)->withJsonError('api.dois.404.pubObjectNotFound');
}
// Remove reference to DOI from pubObject and remove DOI object if no longer in use elsewhere
$this->editViaPubObjectHandler($pubObjectHandler, $pubObject, null);
if (!Repo::doi()->isAssigned($doi->getId(), $pubObjectType)) {
Repo::doi()->delete($doi);
}
return $response->withJson($doiProps, 200);
}
/**
* Export XML for configured DOI registration agency
*/
public function exportSubmissions(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve and validate submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if (!count($requestIds)) {
return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
}
$context = $this->getRequest()->getContext();
$validIds = Repo::submission()
->getCollector()
->filterByContextIds([$context->getId()])
->filterByStatus([Submission::STATUS_PUBLISHED])
->getIds()
->toArray();
$invalidIds = array_diff($requestIds, $validIds);
if (count($invalidIds)) {
return $response->withStatus(400)->withJsonError('api.dois.400.invalidPubObjectIncluded');
}
/** @var Submission[] $submissions */
$submissions = [];
foreach ($requestIds as $id) {
$submissions[] = Repo::submission()->get($id);
}
if (empty($submissions[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::exportSubmissions
$responseData = $agency->exportSubmissions($submissions, $context);
if (!empty($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 depositSubmissions(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve and validate the submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if (!count($requestIds)) {
return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
}
/** @var Context $context */
$context = $this->getRequest()->getContext();
$validIds = Repo::submission()
->getCollector()
->filterByContextIds([$context->getId()])
->filterByStatus([Submission::STATUS_PUBLISHED])
->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');
}
$doiIdsToUpdate = [];
foreach ($requestIds as $submissionId) {
dispatch(new DepositSubmission($submissionId, $context, $agency));
$doiIdsToUpdate = array_merge($doiIdsToUpdate, Repo::doi()->getDoisForSubmission($submissionId));
}
Repo::doi()->markSubmitted($doiIdsToUpdate);
return $response->withStatus(200);
}
/**
* Mark submission DOIs as registered with a DOI registration agency.
*/
public function markSubmissionsRegistered(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if (!count($requestIds)) {
return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
}
$context = $this->getRequest()->getContext();
$validIds = Repo::submission()
->getCollector()
->filterByContextIds([$context->getId()])
->filterByStatus([Submission::STATUS_PUBLISHED])
->getIds()
->toArray();
$invalidIds = array_diff($requestIds, $validIds);
if (count($invalidIds)) {
$failedDoiActions = array_map(function (int $id) {
$submissionTitle = Repo::submission()->get($id)?->getCurrentPublication()->getLocalizedFullTitle() ?? '[' . __('api.dois.404.submissionNotFound') . ']';
return new DoiException(DoiException::SUBMISSION_NOT_PUBLISHED, $submissionTitle, $submissionTitle);
}, $invalidIds);
return $response->withJson(
[
'failedDoiActions' => array_map(
function (DoiException $item) {
return $item->getMessage();
},
$failedDoiActions
)
],
400
);
}
foreach ($requestIds as $id) {
$doiIds = Repo::doi()->getDoisForSubmission($id);
foreach ($doiIds as $doiId) {
Repo::doi()->markRegistered($doiId);
}
}
return $response->withStatus(200);
}
public function depositAllDois(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$context = $this->getRequest()->getContext();
Repo::doi()->depositAll($context);
return $response->withStatus(200);
}
/**
* Mark submission DOIs as no longer registered with a DOI registration agency.
*/
public function markSubmissionsUnregistered(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if (!count($requestIds)) {
return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
}
$context = $this->getRequest()->getContext();
$validIds = Repo::submission()
->getCollector()
->filterByContextIds([$context->getId()])
->getIds()
->toArray();
$invalidIds = array_diff($requestIds, $validIds);
if (count($invalidIds)) {
$failedDoiActions = array_map(function (int $id) {
return new DoiException(DoiException::INCORRECT_SUBMISSION_CONTEXT, $id, $id);
}, $invalidIds);
return $response->withJson(
[
'failedDoiActions' => array_map(
function (DoiException $item) {
return $item->getMessage();
},
$failedDoiActions
)
],
400
);
}
foreach ($requestIds as $id) {
$doiIds = Repo::doi()->getDoisForSubmission($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 markSubmissionsStale(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if (!count($requestIds)) {
return $response->withStatus(404)->withJsonError('api.dois.404.noPubObjectIncluded');
}
$context = $this->getRequest()->getContext();
$validIds = Repo::submission()
->getCollector()
->filterByContextIds([$context->getId()])
->filterByStatus([Submission::STATUS_PUBLISHED])
// 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) {
$submissionTitle = Repo::submission()->get($id)?->getCurrentPublication()->getLocalizedFullTitle() ?? '[' . __('api.dois.404.submissionNotFound') . ']';
return new DoiException(DoiException::INCORRECT_STALE_STATUS, $submissionTitle, $submissionTitle);
}, $invalidIds);
return $response->withJson(
[
'failedDoiActions' => array_map(
function (DoiException $item) {
return $item->getMessage();
},
$failedDoiActions
)
],
400
);
}
foreach ($requestIds as $id) {
$doiIds = Repo::doi()->getDoisForSubmission($id);
Repo::doi()->markStale($doiIds);
}
return $response->withStatus(200);
}
/**
* Assign DOIs to submissions
*/
public function assignSubmissionDois(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
// Retrieve submissions
$requestIds = $slimRequest->getParsedBody()['ids'] ?? [];
if ($requestIds == null) {
return $response->withStatus(404)->withJsonError('api.404.resourceNotFound');
}
$context = $this->getRequest()->getContext();
$doiPrefix = $context->getData(Context::SETTING_DOI_PREFIX);
if (empty($doiPrefix)) {
return $response->withStatus(403)->withJsonError('api.dois.403.prefixRequired');
}
$failedDoiActions = [];
// Assign DOIs
foreach ($requestIds as $id) {
$submission = Repo::submission()->get($id);
if ($submission !== null) {
if ($submission->getData('contextId') !== $context->getId()) {
$creationFailureResults = [
new DoiException(
DoiException::INCORRECT_SUBMISSION_CONTEXT,
$id,
$id
)
];
} else {
$creationFailureResults = Repo::submission()->createDois($submission);
}
$failedDoiActions = array_merge($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);
}
/**
* Download exported DOI XML from temporary file ID
*/
public function getExportedFile(SlimRequest $slimRequest, APIResponse $response, array $args): Response
{
$fileId = $args['fileId'];
$currentUser = Application::get()->getRequest()->getUser();
$tempFileManager = new TemporaryFileManager();
$isSuccess = $tempFileManager->downloadById($fileId, $currentUser->getId());
if (!$isSuccess) {
return $response->withStatus(403)->withJsonError('api.403.unauthorized');
}
return $response->withStatus(200);
}
/**
* Gets a "handler" (either a repo or DAO) for a pub object to perform DOI-related operations.
* See PKPDoiHandler::edit() and PKPDoiHandler::delete().
*
* @param string $type One of Repo::doi()::TYPE_*
*
* @return mixed Returns either a repo or, for pub objects without repos, a DAO
*/
protected function getPubObjectHandler(string $type): mixed
{
return match ($type) {
Repo::doi()::TYPE_PUBLICATION => Repo::publication(),
Repo::doi()::TYPE_REPRESENTATION => Repo::galley(),
default => null,
};
}
/**
* Retrieve the pub object with the given ID.
*
* @param mixed $pubObjectHandler Either a repo or DAO for the pub object type
*
* @return mixed The actual pub object
*/
protected function getViaPubObjectHandler(mixed $pubObjectHandler, int $pubObjectId): mixed
{
return $pubObjectHandler->get($pubObjectId);
}
/**
* Edit the DOI ID for the given pub object via the "handler" (repo or DAO).
*
* @param mixed $pubObjectHandler Either a repo or DAO for the pub object type
* @param mixed $pubObject The pub object th edit
*/
protected function editViaPubObjectHandler(mixed $pubObjectHandler, mixed $pubObject, ?int $doiId): void
{
$pubObjectHandler->edit($pubObject, ['doiId' => $doiId]);
}
}
|