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CHIEFSOFT\ameye
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<?php
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/**
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* @file classes/doi/Repository.php
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*
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* Copyright (c) 2014-2022 Simon Fraser University
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* Copyright (c) 2000-2022 John Willinsky
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* Distributed under the GNU GPL v3. For full terms see the file docs/COPYING.
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*
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* @class Repository
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*
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* @brief A repository to find and manage DOIs.
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*/
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namespace APP\doi;
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use APP\core\Request;
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use APP\facades\Repo;
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use APP\issue\Issue;
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use APP\jobs\doi\DepositIssue;
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use APP\journal\Journal;
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use APP\journal\JournalDAO;
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use APP\plugins\PubIdPlugin;
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use APP\publication\Publication;
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use APP\submission\Submission;
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use Illuminate\Support\Collection;
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use Illuminate\Support\Facades\App;
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use PKP\context\Context;
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use PKP\core\DataObject;
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use PKP\db\DAORegistry;
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use PKP\doi\Collector;
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use PKP\doi\exceptions\DoiException;
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use PKP\galley\Galley;
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use PKP\services\PKPSchemaService;
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use PKP\submission\Representation;
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class Repository extends \PKP\doi\Repository
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{
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public const TYPE_ISSUE = 'issue';
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public const CUSTOM_ISSUE_PATTERN = 'doiIssueSuffixPattern';
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public function __construct(DAO $dao, Request $request, PKPSchemaService $schemaService)
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{
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parent::__construct($dao, $request, $schemaService);
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}
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public function getCollector(): Collector
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{
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return App::makeWith(Collector::class, ['dao' => $this->dao]);
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}
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/**
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* Create a DOI for the given publication.
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*
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* @throws DoiException
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*/
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public function mintPublicationDoi(Publication $publication, Submission $submission, Context $context): int
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{
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// Default suffix does not rely on any other metadata
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if ($context->getData(Context::SETTING_DOI_SUFFIX_TYPE) === Repo::doi()::SUFFIX_DEFAULT) {
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return $this->mintAndStoreDoi($context, $this->generateDefaultSuffix());
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}
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// If not using default suffix, additional checks are required
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$issueId = $publication->getData('issueId');
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if ($issueId === null) {
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throw new DoiException(
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DoiException::PUBLICATION_MISSING_ISSUE,
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$submission->getCurrentPublication()->getLocalizedFullTitle(),
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$publication->getLocalizedFullTitle()
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);
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}
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$issue = Repo::issue()->get($publication->getData('issueId'));
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if ($issue === null) {
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throw new DoiException(
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DoiException::PUBLICATION_MISSING_ISSUE,
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$submission->getCurrentPublication()->getLocalizedFullTitle(),
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$publication->getLocalizedFullTitle()
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);
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} elseif ($issue && $context->getId() != $issue->getJournalId()) {
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throw new DoiException(
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DoiException::PUBLICATION_MISSING_ISSUE,
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$submission->getCurrentPublication()->getLocalizedFullTitle(),
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$publication->getLocalizedFullTitle()
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);
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}
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$doiSuffix = $this->generateSuffixPattern($publication, $context, $context->getData(Context::SETTING_DOI_SUFFIX_TYPE), $issue, $submission);
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return $this->mintAndStoreDoi($context, $doiSuffix);
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}
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/**
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* Create a DOI for the given galley
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*
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* @throws DoiException
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*/
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public function mintGalleyDoi(Galley $galley, Publication $publication, Submission $submission, Context $context): int
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{
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// Default suffix does not rely on any other metadata
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if ($context->getData(Context::SETTING_DOI_SUFFIX_TYPE) === Repo::doi()::SUFFIX_DEFAULT) {
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return $this->mintAndStoreDoi($context, $this->generateDefaultSuffix());
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}
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// If not using default suffix, additional checks are required
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$issue = Repo::issue()->getBySubmissionId($submission->getId());
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if ($issue === null) {
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throw new DoiException(
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DoiException::REPRESENTATION_MISSING_ISSUE,
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$submission->getCurrentPublication()->getLocalizedFullTitle(),
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$galley->getLabel()
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);
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} elseif ($issue && $context->getId() != $issue->getJournalId()) {
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throw new DoiException(
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DoiException::REPRESENTATION_MISSING_ISSUE,
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$submission->getCurrentPublication()->getLocalizedFullTitle(),
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$galley->getLabel()
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);
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}
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$doiSuffix = $this->generateSuffixPattern($galley, $context, $context->getData(Context::SETTING_DOI_SUFFIX_TYPE), $issue, $submission, $galley);
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return $this->mintAndStoreDoi($context, $doiSuffix);
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}
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/**
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* Create a DOI for the given Issue
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*
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* @throws DoiException
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*/
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public function mintIssueDoi(Issue $issue, Context $context): int
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{
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if ($context->getId() != $issue->getJournalId()) {
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throw new DoiException(
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DoiException::INCORRECT_ISSUE_CONTEXT,
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$issue->getLocalizedTitle(),
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$issue->getLocalizedTitle()
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);
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}
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// Default suffix does not rely on any other metadata
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if ($context->getData(Context::SETTING_DOI_SUFFIX_TYPE) === Repo::doi()::SUFFIX_DEFAULT) {
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return $this->mintAndStoreDoi($context, $this->generateDefaultSuffix());
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}
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// If not using default suffix, use pattern generator
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$doiSuffix = $this->generateSuffixPattern($issue, $context, $context->getData(Context::SETTING_DOI_SUFFIX_TYPE), $issue);
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return $this->mintAndStoreDoi($context, $doiSuffix);
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}
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/**
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* Handles updating issue DOI status when metadata changes
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*
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*/
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public function issueUpdated(Issue $issue)
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{
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$doiIds = Repo::doi()->getDoisForIssue($issue->getId());
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$this->dao->markStale($doiIds);
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}
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/**
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* Generate a suffix using a provided pattern type
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*
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* @param string $patternType Repo::doi()::CUSTOM_SUFFIX_* constants
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*
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*/
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protected function generateSuffixPattern(
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DataObject $object,
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Context $context,
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string $patternType,
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?Issue $issue = null,
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?Submission $submission = null,
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?Representation $representation = null
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): string {
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$doiSuffix = '';
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switch ($patternType) {
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case self::SUFFIX_CUSTOM_PATTERN:
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$pubIdSuffixPattern = $this->getPubIdSuffixPattern($object, $context);
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$doiSuffix = PubIdPlugin::generateCustomPattern($context, $pubIdSuffixPattern, $object, $issue, $submission, $representation);
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break;
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case self::SUFFIX_MANUAL:
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break;
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}
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return $doiSuffix;
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}
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/**
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* Gets all DOI IDs related to a submission
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*
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* @return array<int> DOI IDs
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*/
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public function getDoisForSubmission(int $submissionId): array
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{
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$doiIds = Collection::make();
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$submission = Repo::submission()->get($submissionId);
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/** @var Publication[] $publications */
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$publications = $submission->getData('publications');
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/** @var JournalDAO $contextDao */
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$contextDao = DAORegistry::getDAO('JournalDAO');
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/** @var Journal $context */
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$context = $contextDao->getById($submission->getData('contextId'));
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foreach ($publications as $publication) {
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$publicationDoiId = $publication->getData('doiId');
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if (!empty($publicationDoiId) && $context->isDoiTypeEnabled(self::TYPE_PUBLICATION)) {
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$doiIds->add($publicationDoiId);
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}
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// Galleys
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$galleys = Repo::galley()->getCollector()
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->filterByPublicationIds(['publicationIds' => $publication->getId()])
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->getMany();
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foreach ($galleys as $galley) {
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$galleyDoiId = $galley->getData('doiId');
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if (!empty($galleyDoiId) && $context->isDoiTypeEnabled(self::TYPE_REPRESENTATION)) {
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$doiIds->add($galleyDoiId);
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}
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}
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}
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return $doiIds->unique()->toArray();
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}
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/**
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* Gets all DOIs associated with an issue
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* NB: Assumes only enabled DOI types are allowed
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*
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* @param bool $enabledDoiTypesOnly
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*
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* @throws \Exception
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*
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* @return array<int> DOI IDs
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*
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*/
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public function getDoisForIssue(int $issueId, $enabledDoiTypesOnly = false): array
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{
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$doiIds = [];
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$issue = Repo::issue()->get($issueId);
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$issueDoiId = $issue->getData('doiId');
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/** @var JournalDAO $contextDao */
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$contextDao = DAORegistry::getDAO('JournalDAO');
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/** @var Journal $context */
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$context = $contextDao->getById($issue->getData('journalId'));
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if (!empty($issueDoiId)) {
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if ($enabledDoiTypesOnly == false || ($enabledDoiTypesOnly && $context->isDoiTypeEnabled(self::TYPE_ISSUE))) {
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$doiIds[] = $issueDoiId;
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}
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}
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return $doiIds;
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}
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/**
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* Schedules DOI deposits with the active registration agency for all valid and
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* unregistered/stale publication items. Items are added as a queued job to be
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* completed asynchronously.
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*
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*
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*/
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public function depositAll(Context $context)
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{
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parent::depositAll($context);
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if (in_array(Repo::doi()::TYPE_ISSUE, $context->getData(Context::SETTING_ENABLED_DOI_TYPES) ?? [])) {
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// If there is no configured registration agency, nothing can be deposited.
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$agency = $context->getConfiguredDoiAgency();
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if (!$agency) {
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return;
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}
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/** @var DAO */
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$dao = $this->dao;
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$issuesCollection = $dao->getAllDepositableIssueIds($context);
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$issueData = $issuesCollection->reduce(function ($carry, $item) {
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$carry['issueIds'][] = $item->issue_id;
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$carry['doiIds'][] = $item->doi_id;
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return $carry;
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}, ['issueIds' => [], 'doiIds' => []]);
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// Schedule/queue jobs for issues
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foreach ($issueData['issueIds'] as $issueId) {
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dispatch(new DepositIssue($issueId, $context, $agency));
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}
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// Mark issue DOIs as submitted
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Repo::doi()->markSubmitted($issueData['doiIds']);
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}
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}
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/**
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* Checks whether a DOI object is referenced by ID on any pub objects for a given pub object type.
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*
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* @param string $pubObjectType One of Repo::doi()::TYPE_* constants
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*/
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public function isAssigned(int $doiId, string $pubObjectType): bool
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{
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$isAssigned = match ($pubObjectType) {
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Repo::doi()::TYPE_REPRESENTATION => Repo::galley()
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->getCollector()
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->filterByDoiIds([$doiId])
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->getIds()
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->count(),
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default => false,
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};
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return $isAssigned || parent::isAssigned($doiId, $pubObjectType);
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}
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/**
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* Get app-specific DOI type constants to check when scheduling deposit for submissions
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*/
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protected function getValidSubmissionDoiTypes(): array
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{
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return [
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self::TYPE_PUBLICATION,
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self::TYPE_REPRESENTATION,
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];
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}
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/**
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* Gets legacy, user-generated suffix pattern associated with object type and context
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*
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*
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* @return mixed|null
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*/
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private function getPubIdSuffixPattern(DataObject $object, Context $context)
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{
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if ($object instanceof Issue) {
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return $context->getData(Repo::doi()::CUSTOM_ISSUE_PATTERN);
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} elseif ($object instanceof Representation) {
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return $context->getData(Repo::doi()::CUSTOM_REPRESENTATION_PATTERN);
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} else {
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return $context->getData(Repo::doi()::CUSTOM_PUBLICATION_PATTERN);
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}
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}
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}
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