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structured citations #32

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53 changes: 21 additions & 32 deletions CrossrefReferenceLinkingPlugin.php
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Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@
/**
* @file CrossrefReferenceLinkingPlugin.inc.php
*
* Copyright (c) 2013-2023 Simon Fraser University
* Copyright (c) 2003-2023 John Willinsky
* Copyright (c) 2013-2025 Simon Fraser University
* Copyright (c) 2003-2025 John Willinsky
* Distributed under the GNU GPL v3. For full terms see the file LICENSE.
*
* @class CrossrefReferenceLinkingPlugin
Expand All @@ -20,17 +20,19 @@
use APP\publication\Publication;
use APP\submission\Submission;
use DOMDocument;
use PKP\citation\CitationDAO;
use GuzzleHttp\Exception\RequestException;
use PKP\citation\Citation;
use PKP\context\Context;
use PKP\core\JSONMessage;
use PKP\db\DAORegistry;
use PKP\doi\Doi;
use PKP\linkAction\LinkAction;
use PKP\linkAction\request\AjaxModal;
use PKP\plugins\GenericPlugin;
use PKP\plugins\Hook;
use PKP\plugins\PluginRegistry;
use PKP\plugins\interfaces\HasTaskScheduler;
use PKP\scheduledTask\PKPScheduler;
use Smarty;

class CrossrefReferenceLinkingPlugin extends GenericPlugin implements HasTaskScheduler
{
Expand All @@ -54,7 +56,6 @@ public function register($category, $path, $mainContextId = null): bool

// Additional fields added
Hook::add('Schema::get::submission', [$this, 'addSubmissionSchema']);
Hook::add('citationdao::getAdditionalFieldNames', [$this, 'getAdditionalCitationFieldNames']);

if (!$this->getEnabled($mainContextId)) {
return true;
Expand All @@ -72,7 +73,7 @@ public function register($category, $path, $mainContextId = null): bool
Hook::add('crossrefexportplugin::deposited', [$this, 'getCitationsDiagnosticId']);

// Citation changed hook
Hook::add('CitationDAO::afterImportCitations', [$this, 'citationsChanged']);
Hook::add('Citation::importCitations::after', [$this, 'citationsChanged']);

// Article page hooks
Hook::add('Templates::Article::Details::Reference', [$this, 'displayReferenceDOI']);
Expand Down Expand Up @@ -203,7 +204,6 @@ public function addCrossrefCitationsElements(string $hookName, array $params): b
$context = $request->getContext();
// Crossref export cannot be executed via CLI any more, thus there will always be a context
$contextId = $context->getId();
$citationDao = DAORegistry::getDAO('CitationDAO'); /** @var CitationDAO $citationDao */

$rfNamespace = 'http://www.crossref.org/schema/5.3.1';
$articleNodes = $preliminaryOutput->getElementsByTagName('journal_article');
Expand All @@ -222,17 +222,16 @@ public function addCrossrefCitationsElements(string $hookName, array $params): b
return false;
}
$submission = Repo::submission()->get($publications->first()->getData('submissionId'));
$articleCitations = $citationDao->getByPublicationId($submission->getCurrentPublication()->getId());
$articleCitationsArray = $articleCitations->toArray();
if (!empty($articleCitationsArray)) {
$citations = Repo::citation()->getByPublicationId($submission->getCurrentPublication()->getId());
if (!empty($citations)) {
$citationListNode = $preliminaryOutput->createElementNS($rfNamespace, 'citation_list');
foreach ($articleCitationsArray as $citation) {
foreach ($citations as $citation) {
$rawCitation = $citation->getRawCitation();
if (!empty($rawCitation)) {
$citationNode = $preliminaryOutput->createElementNS($rfNamespace, 'citation');
$citationNode->setAttribute('key', $citation->getId());
// if Crossref DOI already exists for this citation, include it
// else include unstructred raw citation
// else include unstructured raw citation
if ($citation->getData($this->getCitationDoiSettingName())) {
$node = $preliminaryOutput->createElementNS($rfNamespace, 'doi');
$node->appendChild($preliminaryOutput->createTextNode($citation->getData($this->getCitationDoiSettingName())));
Expand All @@ -256,7 +255,7 @@ public function addCrossrefCitationsElements(string $hookName, array $params): b
* @param $hookName string Hook name 'crossrefexportplugin::deposited'
* @param array [
* @option CrossrefExportPlugin
* @option string XML reposonse from Crossref deposit
* @option string XML response from Crossref deposit
* @option Submission
* ]
*/
Expand All @@ -275,7 +274,7 @@ public function getCitationsDiagnosticId(string $hookName, array $params): bool
//set the citations diagnostic code and the setting for the automatic check
$submission->setData($this->getCitationsDiagnosticIdSettingName(), $citationsDiagnosticCode);
$submission->setData($this->getAutoCheckSettingName(), true);
$submission = Repo::submission()->edit($submission, [], Application::get()->getRequest());
Repo::submission()->edit($submission, []);
}
return Hook::CONTINUE;
}
Expand Down Expand Up @@ -306,20 +305,11 @@ public function addSubmissionSchema(string $hookName, array $args): bool
return Hook::CONTINUE;
}

/**
* Consider the additional citation setting name 'crossref::doi'.
*/
public function getAdditionalCitationFieldNames(string $hookName, CitationDAO $citationDao, array &$additionalFields): bool
{
$additionalFields[] = $this->getCitationDoiSettingName();
return Hook::CONTINUE;
}

/**
* Resets the submission data related to Reference Linking Plugin.
* Used every time the citations for a certain publication are imported.
*
* @param $hookName string 'CitationDAO::afterImportCitations'
* @param $hookName string 'Citation::importCitations::after'
* @param $params array [
* @option integer The publication ID for which the citations are imported
* ]
Expand All @@ -335,7 +325,7 @@ public function citationsChanged(string $hookName, array $params): bool
if ($submission->getData($this->getCitationsDiagnosticIdSettingName())) {
$submission->setData($this->getCitationsDiagnosticIdSettingName(), null);
$submission->setData($this->getAutoCheckSettingName(), null);
$submission = Repo::submission()->edit($submission, [], Application::get()->getRequest());
Repo::submission()->edit($submission, []);
}
return Hook::CONTINUE;
}
Expand All @@ -350,11 +340,10 @@ public function considerFoundCrossrefReferencesDOIs(Publication $publication): v
return;
}

$citationDao = DAORegistry::getDAO('CitationDAO'); /** @var CitationDAO $citationDao */
$citations = $citationDao->getByPublicationId($publication->getId())->toAssociativeArray();
$citations = Repo::citation()->getByPublicationId($publication->getId());

$citationsToCheck = [];
foreach ($citations as $citation) { /** @var Citation $citation */
foreach ($citations as $citation) {
if (!$citation->getData($this->getCitationDoiSettingName())) {
$citationsToCheck[$citation->getId()] = $citation;
}
Expand All @@ -377,12 +366,12 @@ public function considerFoundCrossrefReferencesDOIs(Publication $publication): v
foreach ($filteredMatchedReferences as $matchedReference) {
$citation = $citationsToCheck[$matchedReference['key']];
$citation->setData($this->getCitationDoiSettingName(), $matchedReference['doi']);
$citationDao->updateObject($citation);
Repo::citation()->edit($citation, []);
}

// remove auto check setting
$submission->setData($this->getAutoCheckSettingName(), null);
$submission = Repo::submission()->edit($submission, [], Application::get()->getRequest());
Repo::submission()->edit($submission, []);
}
}

Expand Down Expand Up @@ -426,7 +415,7 @@ public function getCitationsDiagnosticIdSettingName(): string
*/
public function getCitationDoiSettingName(): string
{
return 'crossref::doi';
return 'doi';
}

/**
Expand Down Expand Up @@ -478,7 +467,7 @@ protected function getResolvedRefs(string $doi, int $contextId): ?array
$httpClient = Application::get()->getHttpClient();
try {
$response = $httpClient->request('POST', $url);
} catch (\GuzzleHttp\Exception\RequestException $e) {
} catch (RequestException $e) {
return null;
}

Expand Down