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Copy pathJatsParserPlugin.inc.php
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JatsParserPlugin.inc.php
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<?php
/**
* @file plugins/generic/jatsParser/JatsParserPlugin.inc.php
*
* Copyright (c) 2017-2018 Vitalii Bezsheiko
* Distributed under the GNU GPL v3.
*
* @class JatsParserPlugin
* @ingroup plugins_generic_jatsParser
*
*/
require_once __DIR__ . '/JATSParser/vendor/autoload.php';
import('lib.pkp.classes.plugins.GenericPlugin');
import('plugins.generic.jatsParser.classes.JATSParserDocument');
import('plugins.generic.jatsParser.classes.components.forms.PublicationJATSUploadForm');
import('lib.pkp.classes.citation.Citation');
import('lib.pkp.classes.file.PrivateFileManager');
use APP\core\Application;
use APP\core\Request;
use PKP\core\JSONMessage;
use PKP\galley\Galley;
use APP\facades\Repo;
use PKP\facades\Locale;
use PKP\i18n\LocaleMetadata;
use JATSParser\Body\Document;
use JATSParser\PDF\TCPDFDocument;
use JATSParser\HTML\Document as HTMLDocument;
use \PKP\components\forms\FormComponent;
define("CREATE_PDF_QUERY", "download=pdf");
class JatsParserPlugin extends GenericPlugin {
function register($category, $path, $mainContextId = null) {
if (parent::register($category, $path, $mainContextId)) {
if ($this->getEnabled()) {
// Add data to the publication
HookRegistry::register('Template::Workflow::Publication', array($this, 'publicationTemplateData'));
HookRegistry::register('Schema::get::publication', array($this, 'addToSchema'));
HookRegistry::register('LoadHandler', array($this, 'loadFullTextAssocHandler'));
HookRegistry::register('Publication::edit', array($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('Publication::edit', array($this, 'editPublicationDates'));
HookRegistry::register('Publication::edit', array($this, 'createPdfGalley'), HOOK_SEQUENCE_LAST);
}
return true;
}
return false;
}
/**
* Get the plugin display name.
* @return string
*/
function getDisplayName() {
return __('plugins.generic.jatsParser.displayName');
}
/**
* Get the plugin description.
* @return string
*/
function getDescription() {
return __('plugins.generic.jatsParser.description');
}
/**
* @copydoc Plugin::getActions()
*/
function getActions($request, $verb) {
$router = $request->getRouter();
import('lib.pkp.classes.linkAction.request.AjaxModal');
return array_merge(
$this->getEnabled()?array(
new LinkAction(
'settings',
new AjaxModal(
$router->url($request, null, null, 'manage', null, array('verb' => 'settings', 'plugin' => $this->getName(), 'category' => 'generic')),
$this->getDisplayName()
),
__('manager.plugins.settings'),
null
),
):array(),
parent::getActions($request, $verb)
);
}
/**
* @copydoc Plugin::manage()
*/
function manage($args, $request) {
switch ($request->getUserVar('verb')) {
case 'settings':
$context = $request->getContext();
$this->import('JatsParserSettingsForm');
$form = new JatsParserSettingsForm($this, $context->getId());
if ($request->getUserVar('save')) {
$form->readInputData();
if ($form->validate()) {
$form->execute();
return new JSONMessage(true);
}
} else {
$form->initData();
}
return new JSONMessage(true, $form->fetch($request));
}
return parent::manage($args, $request);
}
/**
* @param $article Submission
* @param $request PKPRequest
* @param $htmlDocument HTMLDocument
* @param $issue Issue
* @param
*/
private function pdfCreation(string $htmlString, Publication $publication, Request $request, string $localeKey): string
{
// HTML preparation
$context = $request->getContext(); /* @var $context Journal */
$submission = Repo::submission()->get($publication->getData('submissionId')); /* @var $submission Submission */
$issue = Repo::issue()->getBySubmissionId($submission->getId());
//$this->imageUrlReplacement($xmlGalley, $xpath);
//$this->ojsCitationsExtraction($article, $templateMgr, $htmlDocument, $request);
// extends TCPDF object
$pdfDocument = new TCPDFDocument();
$pdfDocument->setTitle($publication->getLocalizedFullTitle($localeKey));
// get the logo
$journal = $request->getContext();
$thumb = $journal->getLocalizedData('journalThumbnail');
if (!empty($thumb)) {
$journalFilesPath = __DIR__ . '/../../../' . Config::getVar('files', 'public_files_dir') . '/journals/' . $journal->getId() . '/'; // TCPDF accepts only relative path
$pdfHeaderLogo = $journalFilesPath . $thumb['uploadName'];
} else {
$pdfHeaderLogo = __DIR__ . "/JATSParser/logo/logo.jpg";
}
$pdfDocument->SetCreator(PDF_CREATOR);
$userGroups = Repo::userGroup()->getCollector()
->filterByContextIds([$context->getId()])
->getMany();
$pdfDocument->SetAuthor($publication->getAuthorString($userGroups));
$pdfDocument->SetSubject($publication->getLocalizedData('subject', $localeKey));
$articleDataString = '';
if ($issue && $issueIdentification = $issue->getIssueIdentification()) {
$articleDataString .= $issueIdentification;
}
if ($pages = $publication->getLocalizedData('subject', $localeKey)) {
$articleDataString .= ", ". $pages;
}
if ($doi = $publication->getData('pub-id::doi')) {
$articleDataString .= "\n" . __('plugins.pubIds.doi.readerDisplayName', null, $localeKey) . ': ' . $doi;
}
$pdfDocument->SetHeaderData($pdfHeaderLogo, PDF_HEADER_LOGO_WIDTH, $journal->getName($localeKey), $articleDataString);
$pdfDocument->setHeaderFont(Array(PDF_FONT_NAME_MAIN, '', PDF_FONT_SIZE_MAIN));
$pdfDocument->setFooterFont(Array(PDF_FONT_NAME_DATA, '', PDF_FONT_SIZE_DATA));
$pdfDocument->SetDefaultMonospacedFont(PDF_FONT_MONOSPACED);
$pdfDocument->SetMargins(PDF_MARGIN_LEFT, PDF_MARGIN_TOP, PDF_MARGIN_RIGHT);
$pdfDocument->SetHeaderMargin(PDF_MARGIN_HEADER);
$pdfDocument->SetFooterMargin(PDF_MARGIN_FOOTER);
$pdfDocument->SetAutoPageBreak(TRUE, PDF_MARGIN_BOTTOM);
$pdfDocument->setImageScale(PDF_IMAGE_SCALE_RATIO);
$pdfDocument->AddPage();
// Article title
$pdfDocument->SetFillColor(255, 255, 255);
$pdfDocument->SetFont('dejavuserif', 'B', 20);
$pdfDocument->MultiCell('', '', $publication->getLocalizedFullTitle($localeKey), 0, 'L', 1, 1, '' ,'', true);
$pdfDocument->Ln(6);
// Article's authors
$authors = $publication->getData('authors');
if (count($authors) > 0) {
/* @var $author Author */
foreach ($authors as $author) {
$pdfDocument->SetFont('dejavuserif', 'I', 10);
// Calculating the line height for author name and affiliation
$authorName = htmlspecialchars($author->getGivenName($localeKey)) . ' ' . htmlspecialchars($author->getFamilyName($localeKey));
$affiliation = htmlspecialchars($author->getAffiliation($localeKey));
$authorLineWidth = 60;
$authorNameStringHeight = $pdfDocument->getStringHeight($authorLineWidth, $authorName);
$affiliationLineWidth = 110;
$afilliationStringHeight = $pdfDocument->getStringHeight(110, $affiliation);
$authorNameStringHeight > $afilliationStringHeight ? $cellHeight = $authorNameStringHeight : $cellHeight = $afilliationStringHeight;
// Writing affiliations into cells
$pdfDocument->MultiCell($authorLineWidth, 0, $authorName, 0, 'L', 1, 0, 19, '', true, 0, false, true, 0, "T", true);
$pdfDocument->SetFont('dejavuserif', '', 10);
$pdfDocument->MultiCell($affiliationLineWidth, $cellHeight, $affiliation, 0, 'L', 1, 1, '', '', true, 0, false, true, 0, "T", true);
}
$pdfDocument->Ln(6);
}
// Abstract
if ($abstract = $publication->getLocalizedData('abstract', $localeKey)) {
$pdfDocument->setCellPaddings(5, 5, 5, 5);
$pdfDocument->SetFillColor(248, 248, 255);
$pdfDocument->SetFont('dejavuserif', '', 10);
$pdfDocument->SetLineStyle(array('width' => 0.5, 'cap' => 'butt', 'join' => 'miter', 'dash' => 4, 'color' => array(255, 140, 0)));
$pdfDocument->writeHTMLCell('', '', '', '', $abstract, 'B', 1, 1, true, 'J', true);
$pdfDocument->Ln(4);
}
// Text (goes from JATSParser
$pdfDocument->setCellPaddings(0, 0, 0, 0);
$pdfDocument->SetFont('dejavuserif', '', 10);
$htmlString .= "\n" . '<style>' . "\n" . file_get_contents($this->getPluginPath() . DIRECTORY_SEPARATOR . 'resources' . DIRECTORY_SEPARATOR . 'styles' . DIRECTORY_SEPARATOR . 'default' . DIRECTORY_SEPARATOR . 'pdfGalley.css') . '</style>';
$htmlString = $this->_prepareForPdfGalley($htmlString);
$pdfDocument->writeHTML($htmlString, true, false, true, false, '');
return $pdfDocument->Output('article.pdf', 'S');
}
/**
* @param string $htmlString
* @return string Preprocessed HTML string for TCPDF
*/
private function _prepareForPdfGalley(string $htmlString): string {
$dom = new DOMDocument('1.0', 'utf-8');
$htmlHead = "\n";
$htmlHead .= '<head>';
$htmlHead .= "\t" . '<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>';
$htmlHead .= "\n";
$htmlHead .= '</head>';
$dom->loadHTML($htmlHead . $htmlString);
// set style for figures and table
$xpath = new \DOMXPath($dom);
$tableNodes = $xpath->evaluate('//table');
foreach ($tableNodes as $tableNode) {
$tableNode->setAttribute('border', '1');
$tableNode->setAttribute('cellpadding', '2');
}
$captionNodes = $xpath->evaluate('//figure/p[@class="caption"]|//table/caption');
foreach ($captionNodes as $captionNode) {
$captionParts = $xpath->evaluate('span[@class="label"]|span[@class="title"]', $captionNode);
foreach ($captionParts as $captionPart) {
$emptyTextNode = $dom->createTextNode(' ');
$captionPart->appendChild($emptyTextNode);
}
}
// TCPDF doesn't recognize display property, insert div
$tableCaptions = $xpath->evaluate('//table/caption');
foreach ($tableCaptions as $tableCaption) {
/* @var $tableNode \DOMNode */
$tableNode = $tableCaption->parentNode;
$divNode = $dom->createElement('div');
$divNode->setAttribute('class', 'caption');
$nextToTableNode = $tableNode->nextSibling;
if ($nextToTableNode) {
$tableNode->parentNode->insertBefore($divNode, $nextToTableNode);
}
$divNode->appendChild($tableCaption);
}
// Remove redundant whitespaces before caption label
$modifiedHtmlString = $dom->saveHTML();
$modifiedHtmlString = preg_replace('/<caption>\s*/', '<br>' . '<caption>', $modifiedHtmlString);
$modifiedHtmlString = preg_replace('/<p class="caption">\s*/', '<p class="caption">', $modifiedHtmlString);
return $modifiedHtmlString;
}
/**
* Add a property to the publication schema
*
* @param $hookName string `Schema::get::publication`
* @param $args [[
* @option object Publication schema
* ]]
*/
public function addToSchema($hookName, $args) {
$schema = $args[0];
$propId = '{
"type": "integer",
"multilingual": true,
"apiSummary": true,
"validation": [
"nullable"
]
}';
$propText = '{
"type": "string",
"multilingual": true,
"apiSummary": true,
"validation": [
"nullable"
]
}';
$schema->properties->{'jatsParser::fullTextFileId'} = json_decode($propId);
$schema->properties->{'jatsParser::fullText'} = json_decode($propText);
}
/**
* @param string $hookname
* @param array $args [string, TemplateManager]
*/
function publicationTemplateData(string $hookname, array $args): void {
/**
* @var $templateMgr TemplateManager
* @var $submission Submission
* @var $submissionFile SubmissionFile
*/
$templateMgr = $args[1];
$request = $this->getRequest();
$context = $request->getContext();
$submission = $templateMgr->getTemplateVars('submission');
$latestPublication = $submission->getLatestPublication();
$latestPublicationApiUrl = $request->getDispatcher()->url($request, ROUTE_API, $context->getData('urlPath'), 'submissions/' . $submission->getId() . '/publications/' . $latestPublication->getId());
$supportedSubmissionLocales = $context->getSupportedSubmissionLocales();
$localeNames = Locale::getFormattedDisplayNames(null, null, LocaleMetadata::LANGUAGE_LOCALE_ONLY);
$locales = array_map(function($localeKey) use ($localeNames) {
return ['key' => $localeKey, 'label' => $localeNames[$localeKey]];
}, $supportedSubmissionLocales);
$submissionFiles = Repo::submissionFile()
->getCollector()
->filterBySubmissionIds([$submission->getId()])
->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PRODUCTION_READY])
->getMany();
$submissionFilesXML = array();
foreach ($submissionFiles as $submissionFile) {
if (in_array($submissionFile->getData('mimetype'), array("application/xml", "text/xml"))) {
$submissionFilesXML[] = $submissionFile;
}
}
$dispatcher = $request->getDispatcher();
$submissionProps = Repo::submission()->getSchemaMap()->summarizeWithoutPublication($submission);
$currentPath = $dispatcher->url($request, ROUTE_PAGE, null, 'workflow', 'fullTextPreview', $submission->getId(), $submissionProps);
if (!empty($submissionFiles)) {
$msg = $templateMgr->smartyTranslate(array(
'key' => 'plugins.generic.jatsParser.publication.jats.description',
'params' => array("previewPath" => $currentPath)
), $templateMgr);
} else {
$msg = $templateMgr->smartyTranslate(array(
'key' => 'plugins.generic.jatsParser.publication.jats.descriptionEmpty'
), $templateMgr);
}
$form = new PublicationJATSUploadForm($latestPublicationApiUrl, $locales, $latestPublication, $submissionFilesXML, $msg);
$state = $templateMgr->getTemplateVars('state');
$state['components'][FORM_PUBLICATION_JATS_FULLTEXT] = $form->getConfig();
$templateMgr->assign('state', $state);
$templateMgr->display($this->getTemplateResource("workflowJatsFulltext.tpl"));
}
/**
* @param $hookName string
* @param $args array
* @brief Handle associated files of the full-text, only images are supported
*/
function loadFullTextAssocHandler($hookName, $args) {
$page = $args[0];
$op = $args[1];
if ($page == 'article' && $op == 'downloadFullTextAssoc') {
define('HANDLER_CLASS', 'FullTextArticleHandler');
define('JATSPARSER_PLUGIN_NAME', $this->getName());
$args[2] = $this->getPluginPath() . DIRECTORY_SEPARATOR . 'FullTextArticleHandler.inc.php';
}
}
/**
* @param string $hookname
* @param array $args [
* Publication -> new publication
* Publication
* array parameters/publication properties to be saved
* Request
* ]
* @return bool
*/
function editPublicationFullText(string $hookname, array $args) {
$newPublication = $args[0];
$params = $args[2];
if (!array_key_exists('jatsParser::fullTextFileId', $params)) return false;
$localePare = $params['jatsParser::fullTextFileId'];
foreach ($localePare as $localeKey => $fileId) {
if (empty($fileId)) {
$newPublication->setData('jatsParser::fullText', null, $localeKey);
$newPublication->setData('jatsParser::fullTextFileId', null, $localeKey);
continue;
}
$submissionFile = Repo::submissionFile()->get($fileId);
$htmlDocument = $this->getFullTextFromJats($submissionFile);
$newPublication->setData('jatsParser::fullText', $htmlDocument->saveAsHTML(), $localeKey);
}
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;
$submissionFile = Repo::submissionFile()->get($fileId);
$htmlDocument = $this->getFullTextFromJats($submissionFile);
$request = $this->getRequest();
$context = $request->getContext();
// Get citations style, define default if not set
$citationStyle = $this->getCitationStyle($context);
$lang = str_replace('_', '-', $submissionFile->getSubmissionLocale());
$htmlDocument->setFootnotes();
$htmlDocument->setReferences($citationStyle, $lang, false);
$this->_importCitations($htmlDocument, $newPublication);
return false;
}
/** --------OPUS--------
* @param string $hookname
* @param array $args
* @return false
* @brief Updates submission, decision, and publication dates from JATS file data for a given publication.
*/
function editPublicationDates(string $hookname, array $args) {
$newPublication = $args[0];
$params = $args[2];
if (!array_key_exists('jatsParser::dates', $params)) return false;
$fileId = $params['jatsParser::dates'];
if (!$fileId) return false;
$submissionFile = Repo::submissionFile()->get($fileId);
$datesDocument = $this->getDatesFromJats($submissionFile);
// error_log("===========================");
// error_log(var_export($datesDocument,true));
$request = $this->getRequest();
$context = $request->getContext();
// Update submission date
$submission = Repo::submission()->get($newPublication->getData('submissionId'));
$submission->setData('dateSubmitted', $datesDocument['received']);
$params = [
'date_submitted' => $datesDocument['received'],
];
// error_log("-0-");
// error_log(var_export($submissionFile->getAllData(),true));
// error_log("-1-");
// error_log(var_export($submission->getAllData(),true));
Repo::submission()->edit($submission, $params);
// error_log(var_export($submission->getAllData(),true));
// Update decision date
$editorDecisions = Repo::decision()->getCollector()
->filterBySubmissionIds([$submission->getId()])
->filterByStageIds([WORKFLOW_STAGE_ID_EXTERNAL_REVIEW])
->getMany();
if (!empty($editorDecisions) && array_key_exists('accepted', $datesDocument)) {
$editorDecision = $editorDecisions->first();
// error_log("-2-");
// error_log(var_export($editorDecision->getAllData(),true));
$editorDecision->setData('dateDecided', $datesDocument['accepted']);
// error_log(var_export($editorDecision->getAllData(),true));
}
// Update publication date
$newPublication->setData('datePublished', $datesDocument['pub']);
$params = [
'date_published' => $datesDocument['pub'],
];
// error_log("-3-");
// error_log(var_export($newPublication->getAllData(),true));
Repo::publication()->edit($newPublication, $params);
// error_log(var_export($newPublication->getAllData(),true));
// error_log("===========================");
return false;
}
/** --------OPUS--------
* @param SubmissionFile $submissionFile The submission file object, expected to be a JATS XML document.
* @return array Associative array containing 'pub', 'received', and 'accepted' dates (if available) from the JATS file, formatted in ISO 8601 standard.
* @brief Extracts significant publication dates from a JATS XML document.
*/
public function getDatesFromJats(SubmissionFile $submissionFile) {
import('lib.pkp.classes.file.PrivateFileManager');
$fileMgr = new PrivateFileManager();
$dom = new DOMDocument;
$dom->load($fileMgr->getBasePath() . DIRECTORY_SEPARATOR . $submissionFile->getData('path'));
$dates = [];
// Get the 'pub' date
$pubDates = $dom->getElementsByTagName('pub-date');
if ($pubDates->length > 0) {
$dates['pub'] = $pubDates->item(0)->getAttribute('iso-8601-date');
}
// Get the 'received' and 'accepted' dates
$historyDates = $dom->getElementsByTagName('date');
foreach ($historyDates as $historyDate) {
$dateType = $historyDate->getAttribute('date-type');
if ($dateType == 'received' || $dateType == 'accepted') {
$dates[$dateType] = $historyDate->getAttribute('iso-8601-date');
}
}
return $dates;
}
/**
* @param string $hookname
* @param array $args
* @return false
* @brief creates a PDF file and saves as a galley
*/
function createPdfGalley(string $hookname, array $args) {
$newPublication = $args[0]; /* @var $newPublication Publication */
$params = $args[2];
$request = $args[3];
if (!array_key_exists('jatsParser::pdfGalley', $params)) return false;
if (!$this->getSetting($request->getContext()->getId(), 'convertToPdf')) return false;
$localePare = $params['jatsParser::pdfGalley'];
foreach ($localePare as $localeKey => $createPdf) {
$fullText = $newPublication->getData('jatsParser::fullText', $localeKey);
if (empty($fullText)) continue;
if (!$createPdf) continue;
// Set real path to images, attached to the original JATS XML file
$jatsFileId = $newPublication->getData('jatsParser::fullTextFileId', $localeKey);
$jatsSubmissionFile = Repo::submissionFile()->get($jatsFileId);
if ($jatsSubmissionFile) {
$fullText = $this->_setSupplImgPath($jatsSubmissionFile, $fullText);
}
// Add required locale components
//AppLocale::requireComponents(LOCALE_COMPONENT_PKP_SUBMISSION, $localeKey);
//AppLocale::registerLocaleFile($localeKey, 'plugins/pubIds/doi/locale/' . $localeKey . '/locale.po');
// Set references
$fullText = $this->_setReferences($newPublication, $localeKey, $fullText);
// Finally, convert and receive TCPDF output as a binary string
$pdf = $this->pdfCreation($fullText, $newPublication, $request, $localeKey);
// Create a PDF Galley
$galleyId = $this->createGalley($localeKey, $newPublication);
$galley = Repo::galley()->getByBestId($galleyId, $newPublication);
// Create associated submission file and update the galley
$submissionFile = $this->_setPdfSubmissionFile($pdf, $newPublication, $galley);
if ($submissionFile) {
$galley->setData('fileId', $submissionFile->getData('fileId'));
Repo::galley()->edit($galley, []);
}
// remove galley if submission file is missing
else {
Repo::galley()->delete($galley);
}
}
return false;
}
/**
* @param string $galleyLocale
* @param Publication $publication
* @return int
* @brief create an empty galley
*/
function createGalley(string $galleyLocale, Publication $publication): int {
$articleGalley = Repo::galley()->newDataObject();
$articleGalley->setlocale($galleyLocale);
$articleGalley->setData('publicationId', $publication->getId());
$articleGalley->setLabel(__('plugins.generic.jatsParser.publication.galley.pdf.label'));
return Repo::galley()->add($articleGalley);
}
/**
* @param string $pdfBinaryString output of the TCPDF, binary string
* @param Publication $publication publication associated with a submission file
* @brief creates a new PDF submission file
*/
private function _setPdfSubmissionFile(string $pdfBinaryString, Publication $publication, Galley $galley) {
$submission = Repo::submission()->get($publication->getData('submissionId')); /* @var $submission Submission */
$request = $this->getRequest();
// Create a temporary file
$tmpFile = tempnam(sys_get_temp_dir(), 'jatsParser');
file_put_contents($tmpFile, $pdfBinaryString);
// Set main Submission File data
$submissionDir = Repo::submissionFile()->getSubmissionDir($submission->getData('contextId'), $submission->getId());
$fileId = Services::get('file')->add(
$tmpFile,
$submissionDir . DIRECTORY_SEPARATOR . uniqid() . '.pdf'
);
// Set original filename, get it from the JATS XML file
$jatsFileId = $publication->getData('jatsParser::fullTextFileId', $galley->getLocale());
$jatsFile = Repo::submissionFile()->get($jatsFileId);
$name = [];
foreach ($jatsFile->getData('name') as $locale => $sourceName) {
$name[$locale] = pathinfo($sourceName)['filename'] . '.pdf';
}
// Finally transfer data to PDF galley
$genreDAO = DAORegistry::getDAO('GenreDAO');
$genre = $genreDAO->getByKey('SUBMISSION', $submission->getData('contextId'));
$submissionFile = Repo::submissionFile()->newDataObject([
'fileId' => $fileId,
'assocType' => ASSOC_TYPE_GALLEY,
'assocId' => $galley->getId(),
'fileStage' => SUBMISSION_FILE_PROOF,
'mimetype' => 'application/pdf',
'locale' => $galley->getData('locale'),
'genreId' => $genre->getId(),
'name' => $name,
'submissionId' => $submission->getId(),
]);
$submissionFileId = Repo::submissionFile()->add($submissionFile);
$submissionFile = Repo::submissionFile()->get($submissionFileId);
unlink($tmpFile); // remove temporary file
return $submissionFile;
}
/**
* @param Publication $publication
* @param string $locale
* @param string $htmlString
* @return string
* @brief set references for PDF galley
*/
private function _setReferences(Publication $publication, string $locale, string $htmlString): string {
$rawCitations = $publication->getData('citationsRaw');
if (empty($rawCitations)) return $htmlString;
// Use OJS raw citations tokenizer
import('lib.pkp.classes.citation.CitationListTokenizerFilter');
$citationTokenizer = new CitationListTokenizerFilter();
$citationStrings = $citationTokenizer->execute($rawCitations);
if (!is_array($citationStrings) || empty($citationStrings)) return $htmlString;
$htmlString .= '<h2 class="article-section-title" id="reference-title">' . __('submission.citations', null, $locale) . '</h2>';
$htmlString .= "\n";
$htmlString .= '<ol id="references">';
$htmlString .= "\n";
foreach ($citationStrings as $citationString) {
$htmlString .= "\t";
$htmlString .= '<li>' . $citationString . '</li>';
$htmlString .= "\n";
}
$htmlString .= '</ol>';
return $htmlString;
}
/**
* @param Journal $context Journal
* @return string
* @brief Retrieve citation style format that should be supported by citeproc-php
* use own format defined in settings if set
* use CitationStyleLanguagePlugin if set
* use vancouver style otherwise
*/
function getCitationStyle(Journal $context): string {
$contextId = $context->getId();
$citationStyle = $this->getSetting($contextId, 'citationStyle');
if ($citationStyle) return $citationStyle;
$pluginSettingsDAO = DAORegistry::getDAO('PluginSettingsDAO');
$cslPluginSettings = $pluginSettingsDAO->getPluginSettings($contextId, 'CitationStyleLanguagePlugin');
if ($cslPluginSettings &&
array_key_exists('enabled', $cslPluginSettings) &&
$cslPluginSettings['enabled'] &&
array_key_exists('primaryCitationStyle', $cslPluginSettings) &&
$cslPrimaryCitStyle = $cslPluginSettings['primaryCitationStyle']
) $citationStyle = $cslPrimaryCitStyle;
if ($citationStyle) return $citationStyle;
$lastCslKey = array_key_last(self::getSupportedCitationStyles());
return self::getSupportedCitationStyles()[$lastCslKey]['id']; // vancouver
}
/**
* @param HTMLDocument $htmlDocument
* @param Publication $newPublication
* @return void
* @brief saves parsed citeproc references as raw citations
*/
private function _importCitations(HTMLDocument $htmlDocument, Publication $newPublication): void {
$refs = $htmlDocument->getRawReferences();
$publicationId = $newPublication->getId();
$citationDao = DAORegistry::getDAO('CitationDAO'); /** @var $citationDao CitationDAO */
$citationDao->deleteByPublicationId($publicationId);
$rawCitations = '';
foreach ($refs as $key => $ref) {
$rawCitations .= $ref . "\n";
}
$newPublication->setData('citationsRaw', $rawCitations);
}
/**
* @param SubmissionFile $submissionFile
* @return HTMLDocument
* @brief retrieves PHP DOM representation of the article's full-text
*/
public function getFullTextFromJats (SubmissionFile $submissionFile): HTMLDocument {
import('lib.pkp.classes.file.PrivateFileManager');
$fileMgr = new PrivateFileManager();
$htmlDocument = new HTMLDocument(new Document($fileMgr->getBasePath() . DIRECTORY_SEPARATOR . $submissionFile->getData('path')));
return $htmlDocument;
}
/**
* @param string $hookname
* @param array $args
* @return bool
* @brief Displays full-text on article landing page
*/
function displayFullText(string $hookname, array $args) {
$templateMgr =& $args[1];
$output =& $args[2];
$publication = $templateMgr->getTemplateVars('publication');
$submission = $templateMgr->getTemplateVars('article');
$fullTexts = $publication->getData('jatsParser::fullText');
$submissionFileId = 0;
$submissionFile = null;
$request = $this->getRequest();
$html = null;
$context = $request->getContext();
if (empty($fullTexts)) return false;
$currentLocale = Locale::getLocale();
if (array_key_exists($currentLocale, $fullTexts)) {
$html = $fullTexts[$currentLocale];
$submissionFileId = $publication->getData('jatsParser::fullTextFileId', $currentLocale);
$submissionFile = Repo::submissionFile()->get($submissionFileId);
} else {
$locales = $request->getJournal()->getSupportedLocaleNames();
$msg = __('plugins.generic.jatsParser.article.fulltext.availableLocale');
if (count($fullTexts) > 1) {
$msg = __('plugins.generic.jatsParser.article.fulltext.availableLocales');
}
$html = '<p>' . $msg;
foreach ($fullTexts as $localeKey => $fullText) {
$html .= ' <a href="' . $request->url(null, 'user', 'setLocale', $localeKey) . '">' . $locales[$localeKey] . '</a>';
if ($fullText !== end($fullTexts)) {
$html .= ', ';
} else {
$html .= '.';
}
}
$html .= '</p>';
}
if (is_null($html)) return false;
if ($submissionFileId && $submissionFile) {
$html = $this->_setSupplImgPath($submissionFile, $html);
}
$templateMgr->assign('fullText', $html);
$output .= $templateMgr->fetch($this->getTemplateResource('articleMainView.tpl'));
return false;
}
/**
* @param SubmissionFile $submissionFile
* @param string $htmlString
* @return string
* @brief Substitute path to attached images for full-text HTML
*/
function _setSupplImgPath(SubmissionFile $submissionFile, string $htmlString): string {
///-------------------------------------------------///
$dependentFiles = Repo::submissionFile()
->getCollector()
->filterByAssoc(
Application::ASSOC_TYPE_SUBMISSION_FILE,
[$submissionFile->getId()]
)
->filterBySubmissionIds([$submissionFile->getData('submissionId')])
->filterByFileStages([SubmissionFile::SUBMISSION_FILE_DEPENDENT])
->includeDependentFiles()
->getMany();
$request = $this->getRequest();
$imageFiles = [];
$privateFileManager = new PrivateFileManager();
$genreDao = DAORegistry::getDAO('GenreDAO');
foreach ($dependentFiles as $dependentFile) {
$genre = $genreDao->getById($dependentFile->getData('genreId'));
if ($genre->getCategory() !== GENRE_CATEGORY_ARTWORK) continue; // only art works are supported
if (!in_array($dependentFile->getData('mimetype'), self::getSupportedSupplFileTypes())) continue; // check if MIME type is supported
$submissionId = $submissionFile->getData('submissionId');
switch ($request->getRequestedOp()) {
case 'view':
$filePath = $request->url(null, 'article', 'downloadFullTextAssoc', array($submissionId, $dependentFile->getData('assocId'), $dependentFile->getData('fileId')));
break;
case 'editPublication':
// API Handler cannot process $op, $path or $anchor in url()
$image = file_get_contents($privateFileManager->getBasePath() . DIRECTORY_SEPARATOR . $dependentFile->getData('path'));
$imageBase64 = base64_encode($image);
$filePath = '@' . $imageBase64; // Format, supported by TCPDF
break;
}
$imageFileNames = array_values($dependentFile->getData('name')); // localized
foreach ($imageFileNames as $imageFileName) {
if (empty($imageFileName)) continue;
if (array_key_exists($imageFileName, $imageFiles)) continue;
$imageFiles[$imageFileName] = $filePath;
}
}
if (empty($imageFiles)) return $htmlString;
// Solution from HtmlArticleGalleyPlugin::_getHTMLContents
foreach ($imageFiles as $originalFileName => $filePath) {
$pattern = preg_quote(rawurlencode($originalFileName));
$htmlString = preg_replace(
'/([Ss][Rr][Cc]|[Hh][Rr][Ee][Ff]|[Dd][Aa][Tt][Aa])\s*=\s*"([^"]*' . $pattern . ')"/',
'\1="' . $filePath . '"',
$htmlString
);
}
return $htmlString;
}
/**
* @return array
* @brief get the list of types of files that are dependent from an original JATS XML (from which full-text was generated) and are accessible to public
*/
public static function getSupportedSupplFileTypes() {
return [
'image/png',
'image/jpeg'
];
}
public static function getSupportedCitationStyles() {
return [
[
'id' => 'acm-sig-proceedings',
'title' => 'plugins.generic.jatsParser.style.acm-sig-proceedings',
],
[
'id' => 'acs-nano',
'title' => 'plugins.generic.jatsParser.style.acs-nano',
],
[
'id' => 'apa',
'title' => 'plugins.generic.jatsParser.style.apa',
],
[
'id' => 'associacao-brasileira-de-normas-tecnicas',
'title' => 'plugins.generic.jatsParser.style.associacao-brasileira-de-normas-tecnicas',
],
[
'id' => 'chicago-author-date',
'title' => 'plugins.generic.jatsParser.style.chicago-author-date',
],
[
'id' => 'harvard-cite-them-right',
'title' => 'plugins.generic.jatsParser.style.harvard-cite-them-right',
],
[
'id' => 'ieee',
'title' => 'plugins.generic.jatsParser.style.ieee',
],
[
'id' => 'modern-language-association',
'title' => 'plugins.generic.jatsParser.style.modern-language-association',
],
[
'id' => 'turabian-fullnote-bibliography',
'title' => 'plugins.generic.jatsParser.style.turabian-fullnote-bibliography',
],
[
'id' => 'vancouver',
'title' => 'plugins.generic.jatsParser.style.vancouver',
],
];
}
/**
* @param string $hookname
* @param array $args
* @return bool
* @brief theme-specific styles for galley and article landing page
*/
function themeSpecificStyles(string $hookname, array $args) {
$templateMgr = $args[0];
$template = $args[1];
if ($template !== "frontend/pages/article.tpl") return false;
$request = $this->getRequest();
$baseUrl = $request->getBaseUrl() . '/' . $this->getPluginPath();
$themePlugins = PluginRegistry::getPlugins('themes');
foreach ($themePlugins as $themePlugin) {
if ($themePlugin->isActive()) {
$parentTheme = $themePlugin->parent;
// Chances are that child theme of a Default also need this styling
if ($themePlugin->getName() == "defaultthemeplugin" || ($parentTheme && $parentTheme->getName() == "defaultthemeplugin")) {
$templateMgr->addStyleSheet('jatsParserThemeStyles', $baseUrl . '/resources/styles/default/article.css');
}
}
}
return false;
}
/**
* @return void
* @brief iterate through all submissions and add full-text from galleys
*/
public function importGalleys() {
$request = $this->getRequest();
$context = $request->getContext();
$user = $request->getUser();
$fileManager = new PrivateFileManager();
$submissions = Repo::submission()->getCollector()
->filterByContextIds([$context->getId()])
->filterByStageIds([WORKFLOW_STAGE_ID_PRODUCTION])
->getMany();
foreach ($submissions as $submission) {
$publication = $submission->getCurrentPublication();
$galleys = $publication->getData('galleys');
if (empty($galleys)) continue;
foreach ($galleys as $galley) {