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#24 Parse and save citations
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@Vitaliy-1
Vitaliy-1 committed Aug 14, 2020
1 parent 21425c4 commit f515d64
Showing 1 changed file with 93 additions and 43 deletions.
136 changes: 93 additions & 43 deletions JatsParserPlugin.inc.php
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
import('plugins.generic.jatsParser.classes.JATSParserDocument');
import('plugins.generic.jatsParser.classes.components.forms.PublicationJATSUploadForm');
import('lib.pkp.classes.file.SubmissionFileManager');
import('lib.pkp.classes.citation.Citation');

use JATSParser\Body\Document;
use JATSParser\PDF\TCPDFDocument;
Expand Down Expand Up @@ -45,10 +46,12 @@ function register($category, $path, $mainContextId = null) {
HookRegistry::register('Schema::get::publication', array($this, 'addToSchema'));
HookRegistry::register('TemplateManager::display', array($this, 'previewFullTextCall'));
HookRegistry::register('LoadHandler', array($this, 'loadPreviewHandler'));
HookRegistry::register('Publication::edit', array($this, 'editPublication'));
HookRegistry::register('Publication::edit', array($this, 'editPublicationFullText'));
HookRegistry::register('Templates::Article::Main', array($this, 'displayFullText'));
HookRegistry::register('TemplateManager::display', array($this, 'themeSpecificStyles'));
HookRegistry::register('Form::config::before', array($this, 'addCitationsFormFields'));
HookRegistry::register('Publication::edit', array($this, 'editPublicationReferences'));
HookRegistry::register('citationdao::getAdditionalFieldNames', array($this, 'citationFieldNames'));

return true;
}
Expand Down Expand Up @@ -490,17 +493,8 @@ public function addToSchema($hookName, $args) {
"nullable"
]
}';
$propRef = '{
"type": "boolean",
"multilingual": true,
"apiSummary": true,
"validation": [
"nullable"
]
}';
$schema->properties->{'jatsParser::fullTextFileId'} = json_decode($propId);
$schema->properties->{'jatsParser::fullText'} = json_decode($propText);
$schema->properties->{'jatsParser::references'} = json_decode($propRef);
}

/**
Expand Down Expand Up @@ -609,7 +603,7 @@ function loadPreviewHandler($hookName, $args) {
* ]
* @return bool
*/
function editPublication(string $hookname, array $args) {
function editPublicationFullText(string $hookname, array $args) {
$newPublication = $args[0];
$params = $args[2];
if (!array_key_exists('jatsParser::fullTextFileId', $params)) return false;
Expand All @@ -629,6 +623,77 @@ function editPublication(string $hookname, array $args) {
return false;
}

/**
* @param string $hookname
* @param array $args
* @return bool
* @brief modify citationsRaw property based on parsed citations from JATS XML
*/
function editPublicationReferences(string $hookname, array $args) {
$newPublication = $args[0];
$params = $args[2];
if (!array_key_exists('jatsParser::references', $params)) return false;

$fileId = $params['jatsParser::references'];
if (!$fileId) return false;

$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
$submissionFile = $submissionFileDao->getLatestRevision($fileId, SUBMISSION_FILE_PRODUCTION_READY);
$htmlDocument = $this->getFullTextFromJats($submissionFile);

$request = $this->getRequest();
$context = $request->getContext();
$citationStyle = $this->getSetting($context->getId(), 'citationStyle');
$lang = str_replace('_', '-', $submissionFile->getSubmissionLocale());
$htmlDocument->setReferences($citationStyle, $lang, false);

$this->_importCitations($htmlDocument, $newPublication);

return false;
}

/**
* @param HTMLDocument $htmlDocument
* @param Publication $newPublication
* @return void
* @brief used instead of CitationDAO::importCitations
*/
private function _importCitations(HTMLDocument $htmlDocument, Publication $newPublication): void {
$refs = $htmlDocument->getRawReferences();
$publicationId = $newPublication->getId();
$citationDao = DAORegistry::getDAO('CitationDAO'); /** @var $citationDao CitationDAO */

$citationDao->deleteByPublicationId($publicationId);
$cslRefs = $htmlDocument->citeProcReferences;
$idColumn = array_column($cslRefs, 'id');
$seq = 0;

foreach ($refs as $key => $ref) {
$citation = new Citation($ref);
$citation->setData('publicationId', $publicationId);
$citation->setSequence(++$seq);

$cslKey = array_search($key, $idColumn);
if ($cslKey !== false) {
$citation->setData('jatsParser::csl', $cslRefs[$cslKey]);
}

$citationDao->insertObject($citation);
}
}

/**
* @param $hookname string
* @param $args array
* @return bool
*/
function citationFieldNames($hookname, $args) {
$fields =& $args[1];
$fields[] = 'jatsParser::csl';

return false;
}

/**
* @param SubmissionFile $submissionFile
* @return HTMLDocument
Expand Down Expand Up @@ -942,41 +1007,26 @@ public function addCitationsFormFields(string $hookName, FormComponent $form): v

if (empty($submissionFiles)) return;

if (count($submissionFiles) > 1) {
$options = [];
foreach ($submissionFiles as $submissionFile) {
$options[] = [
'value' => $submissionFile->getId(),
'label' => $submissionFile->getLocalizedName(),
];
}

$options = [];
foreach ($submissionFiles as $submissionFile) {
$options[] = [
'value' => null,
'label' => __('common.default'),
'value' => $submissionFile->getId(),
'label' => $submissionFile->getLocalizedName(),
];

$form->addField(new \PKP\components\forms\FieldOptions('jatsParser::references', [
'label' => __('plugins.generic.jatsParser.publication.jats.references.label'),
'description' => __('plugins.generic.jatsParser.publication.jats.references.description'),
'type' => 'radio',
'options' => $options,
]));
} else {
$submissionFile = array_shift($submissionFiles);
$form->addField(new \PKP\components\forms\FieldOptions('jatsParser::references', [
'label' => __('plugins.generic.jatsParser.publication.jats.references.label'),
'description' => __('plugins.generic.jatsParser.publication.jats.references.description'),
'type' => 'checkbox',
'options' => [
[
'value' => $submissionFile->getId(),
'label' => $submissionFile->getLocalizedName(),
],
],

]));
}

$options[] = [
'value' => null,
'label' => __('common.default'),
];

$form->addField(new \PKP\components\forms\FieldOptions('jatsParser::references', [
'label' => __('plugins.generic.jatsParser.publication.jats.references.label'),
'description' => __('plugins.generic.jatsParser.publication.jats.references.description'),
'type' => 'radio',
'options' => $options,
'value' => null
]));

}
}

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