<?php
/**
* @file classes/search/ArticleSearchIndex.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 ArticleSearchIndex
*
* @ingroup search
*
* @brief Class to maintain the article search index.
*/
namespace APP\search;
use APP\facades\Repo;
use APP\journal\Journal;
use APP\journal\JournalDAO;
use APP\submission\Submission;
use Exception;
use PKP\config\Config;
use PKP\core\PKPApplication;
use PKP\db\DAORegistry;
use PKP\jobs\submissions\UpdateSubmissionSearchJob;
use PKP\plugins\Hook;
use PKP\search\SearchFileParser;
use PKP\search\SubmissionSearch;
use PKP\search\SubmissionSearchIndex;
use PKP\submissionFile\SubmissionFile;
use Throwable;
class ArticleSearchIndex extends SubmissionSearchIndex
{
private const MINIMUM_DATA_LENGTH = 80 * 1024;
/**
* @copydoc SubmissionSearchIndex::submissionMetadataChanged()
*/
public function submissionMetadataChanged($submission)
{
// Check whether a search plug-in jumps in.
if (Hook::ABORT === Hook::call('ArticleSearchIndex::articleMetadataChanged', [$submission])) {
return;
}
$publication = $submission->getCurrentPublication();
// Build author keywords
$authorText = [];
foreach ($publication->getData('authors') as $author) {
$authorText = array_merge(
$authorText,
array_values((array) $author->getData('givenName')),
array_values((array) $author->getData('familyName')),
array_values((array) $author->getData('preferredPublicName')),
array_values(array_map('strip_tags', (array) $author->getData('affiliation'))),
array_values(array_map('strip_tags', (array) $author->getData('biography')))
);
}
// Update search index
$submissionId = $submission->getId();
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_AUTHOR, $authorText);
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_TITLE, $publication->getFullTitles());
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_ABSTRACT, $publication->getData('abstract'));
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_SUBJECT, (array) $this->_flattenLocalizedArray($publication->getData('subjects')));
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_KEYWORD, (array) $this->_flattenLocalizedArray($publication->getData('keywords')));
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_DISCIPLINE, (array) $this->_flattenLocalizedArray($publication->getData('disciplines')));
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_TYPE, (array) $publication->getData('type'));
$this->_updateTextIndex($submissionId, SubmissionSearch::SUBMISSION_SEARCH_COVERAGE, (array) $publication->getData('coverage'));
// FIXME Index sponsors too?
}
/**
* @copydoc SubmissionSearchIndex::submissionMetadataChanged()
*/
public function articleMetadataChanged($article)
{
if (Config::getVar('debug', 'deprecation_warnings')) {
trigger_error('Deprecated call to articleMetadataChanged. Use submissionMetadataChanged instead.');
}
$this->submissionMetadataChanged($article);
}
/**
* Delete keywords from the search index.
*
* @param int $articleId
* @param int $type optional
* @param int $assocId optional
*/
public function deleteTextIndex($articleId, $type = null, $assocId = null)
{
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
return $searchDao->deleteSubmissionKeywords($articleId, $type, $assocId);
}
/**
* Signal to the indexing back-end that an article file changed.
*
* @see ArticleSearchIndex::submissionMetadataChanged() above for more
* comments.
*
* @param int $articleId
* @param int $type
* @param SubmissionFile $submissionFile
*/
public function submissionFileChanged($articleId, $type, $submissionFile)
{
// Check whether a search plug-in jumps in.
if (Hook::ABORT === Hook::call('ArticleSearchIndex::submissionFileChanged', [$articleId, $type, $submissionFile->getId()])) {
return;
}
// If no search plug-in is activated then fall back to the default database search implementation.
$parser = SearchFileParser::fromFile($submissionFile);
if (!$parser) {
error_log("Skipped indexation: No suitable parser for the submission file \"{$submissionFile->getData('path')}\"");
return;
}
try {
$parser->open();
try {
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
$objectId = $searchDao->insertObject($articleId, $type, $submissionFile->getId());
do {
for ($buffer = ''; ($chunk = $parser->read()) !== false && strlen($buffer .= $chunk) < static::MINIMUM_DATA_LENGTH;);
if (strlen($buffer)) {
$this->_indexObjectKeywords($objectId, $buffer);
}
} while ($chunk !== false);
} finally {
$parser->close();
}
} catch (Throwable $e) {
throw new Exception("Indexation failed for the file: \"{$submissionFile->getData('path')}\"", 0, $e);
}
}
/**
* Remove indexed file contents for a submission
*
* @param Submission $submission
*/
public function clearSubmissionFiles($submission)
{
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
$searchDao->deleteSubmissionKeywords($submission->getId(), SubmissionSearch::SUBMISSION_SEARCH_GALLEY_FILE);
}
/**
* Signal to the indexing back-end that all files (supplementary
* and galley) assigned to an article changed and must be re-indexed.
*
* @see ArticleSearchIndex::submissionMetadataChanged() above for more
* comments.
*
* @param Submission $article
*/
public function submissionFilesChanged($article)
{
// If a search plug-in is activated then skip the default database search implementation.
if (Hook::ABORT === Hook::call('ArticleSearchIndex::submissionFilesChanged', [$article])) {
return;
}
$submissionFiles = Repo::submissionFile()
->getCollector()
->filterBySubmissionIds([$article->getId()])
->filterByFileStages([SubmissionFile::SUBMISSION_FILE_PROOF])
->getMany();
$exceptions = [];
foreach ($submissionFiles as $submissionFile) {
try {
$this->submissionFileChanged($article->getId(), SubmissionSearch::SUBMISSION_SEARCH_GALLEY_FILE, $submissionFile);
} catch (Throwable $e) {
$exceptions[] = $e;
}
$dependentFiles = Repo::submissionFile()->getCollector()
->filterByAssoc(
PKPApplication::ASSOC_TYPE_SUBMISSION_FILE,
[$submissionFile->getId()]
)
->filterBySubmissionIds([$article->getId()])
->filterByFileStages([SubmissionFile::SUBMISSION_FILE_DEPENDENT])
->includeDependentFiles()
->getMany();
foreach ($dependentFiles as $dependentFile) {
try {
$this->submissionFileChanged($article->getId(), SubmissionSearch::SUBMISSION_SEARCH_SUPPLEMENTARY_FILE, $dependentFile);
} catch (Throwable $e) {
$exceptions[] = $e;
}
}
}
if (count($exceptions)) {
$errorMessage = implode("\n\n", $exceptions);
throw new Exception("The following errors happened while indexing the submission ID {$article->getId()}:\n{$errorMessage}");
}
}
/**
* Signal to the indexing back-end that a file was deleted.
*
* @see ArticleSearchIndex::submissionMetadataChanged() above for more
* comments.
*
* @param int $articleId
* @param int $type optional
* @param int $assocId optional
*/
public function submissionFileDeleted($articleId, $type = null, $assocId = null)
{
// If a search plug-in is activated then skip the default database search implementation.
if (Hook::ABORT === Hook::call('ArticleSearchIndex::submissionFileDeleted', [$articleId, $type, $assocId])) {
return;
}
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
return $searchDao->deleteSubmissionKeywords($articleId, $type, $assocId);
}
/**
* Signal to the indexing back-end that the metadata of
* a supplementary file changed.
*
* @see ArticleSearchIndex::submissionMetadataChanged() above for more
* comments.
*
* @param int $articleId
*/
public function articleDeleted($articleId)
{
// Trigger a hook to let the indexing back-end know that
// an article was deleted.
Hook::call(
'ArticleSearchIndex::articleDeleted',
[$articleId]
);
// The default indexing back-end does nothing when an
// article is deleted (FIXME?).
}
/**
* @copydoc SubmissionSearchIndex::submissionChangesFinished()
*/
public function submissionChangesFinished()
{
// Trigger a hook to let the indexing back-end know that
// the index may be updated.
Hook::call(
'ArticleSearchIndex::articleChangesFinished'
);
// The default indexing back-end works completely synchronously
// and will therefore not do anything here.
}
/**
* @copydoc SubmissionSearchIndex::submissionChangesFinished()
*/
public function articleChangesFinished()
{
if (Config::getVar('debug', 'deprecation_warnings')) {
trigger_error('Deprecated call to articleChangesFinished. Use submissionChangesFinished instead.');
}
$this->submissionChangesFinished();
}
/**
* Rebuild the search index for one or all journals.
*
* @param bool $log Whether to display status information
* to stdout.
* @param Journal $journal If given the user wishes to
* re-index only one journal. Not all search implementations
* may be able to do so. Most notably: The default SQL
* implementation does not support journal-specific re-indexing
* as index data is not partitioned by journal.
* @param array $switches Optional index administration switches.
*/
public function rebuildIndex($log = false, $journal = null, $switches = [])
{
// If a search plug-in is activated then skip the default database search implementation.
if (Hook::ABORT === Hook::call('ArticleSearchIndex::rebuildIndex', [$log, $journal, $switches])) {
return;
}
// Clear index
if ($log) {
echo __('search.cli.rebuildIndex.clearingIndex') . ' ... ';
}
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
$searchDao->clearIndex($journal ? $journal->getId() : null);
if ($log) {
echo __('search.cli.rebuildIndex.done') . "\n";
}
// Build index
$journalDao = DAORegistry::getDAO('JournalDAO'); /** @var JournalDAO $journalDao */
$journals = $journal ? [$journal] : $journalDao->getAll()->toArray();
foreach ($journals as $journal) {
$numIndexed = 0;
if ($log) {
echo __('search.cli.rebuildIndex.indexing', ['journalName' => $journal->getLocalizedName()]) . ' ... ';
}
$submissions = Repo::submission()
->getCollector()
->filterByContextIds([$journal->getId()])
->getMany();
foreach ($submissions as $submission) {
dispatch(new UpdateSubmissionSearchJob($submission->getId()));
++$numIndexed;
}
if ($log) {
echo __('search.cli.rebuildIndex.result', ['numIndexed' => $numIndexed]) . "\n";
}
}
}
//
// Private helper methods
//
/**
* Index a block of text for an object.
*
* @param int $objectId
* @param string|array $text
*/
protected function _indexObjectKeywords($objectId, $text)
{
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
$keywords = $this->filterKeywords($text);
$searchDao->insertObjectKeywords($objectId, $keywords);
}
/**
* Add a block of text to the search index.
*
* @param int $articleId
* @param int $type
* @param string|array $text
* @param int $assocId optional
*/
protected function _updateTextIndex($articleId, $type, $text, $assocId = null)
{
$searchDao = DAORegistry::getDAO('ArticleSearchDAO'); /** @var ArticleSearchDAO $searchDao */
$objectId = $searchDao->insertObject($articleId, $type, $assocId);
$this->_indexObjectKeywords($objectId, $text);
}
/**
* Flattens array of localized fields to a single, non-associative array of items
*
* @param array $arrayWithLocales Array of localized fields
*
* @return array
*/
protected function _flattenLocalizedArray($arrayWithLocales)
{
$flattenedArray = [];
foreach ($arrayWithLocales as $localeArray) {
$flattenedArray = array_merge(
$flattenedArray,
$localeArray
);
}
return $flattenedArray;
}
}
if (!PKP_STRICT_MODE) {
class_alias('\APP\search\ArticleSearchIndex', '\ArticleSearchIndex');
}
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