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CHIEFSOFT\ameye
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<?php
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use Illuminate\Database\Query\Builder;
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use Illuminate\Support\Collection;
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use Illuminate\Support\Facades\DB;
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require(dirname(__FILE__) . '/bootstrap.php');
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class resolveAgencyDuplicates extends \PKP\cliTool\CommandLineTool
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{
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private string|null $command = null;
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private string|null $agency_name = null;
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private bool $forceFlag = false;
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/**
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* List of potential agencies to choose from along with related fields for resolution.
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*
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* Array shape should look like:
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* `['agency_name' => [
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* 'status' => 'agency_name::status',
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* 'additionalFields': [...],
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* ]
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* ]`
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*/
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private array $agencies = [
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'crossref' => [
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'status' => 'crossref::status',
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'additionalFields' => [
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'crossref::registeredDoi',
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'crossref::batchId',
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'crossref::failedMsg',
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],
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],
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'datacite' => [
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'status' => 'datacite::status',
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'additionalFields' => [
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'datacite::registeredDoi',
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],
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],
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'medra' => [
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'status' => 'medra::status',
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'additionalFields' => [
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'medra::registeredDoi',
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],
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],
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];
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public function __construct($argv = [])
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{
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parent::__construct($argv);
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$forceFlagIndex = array_search('--force', $this->argv);
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if ($forceFlagIndex) {
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$this->forceFlag = true;
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array_splice($this->argv, $forceFlagIndex, 1);
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}
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if (sizeof($this->argv) == 0) {
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$this->exitWithUsageMessage();
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}
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$this->command = array_shift($this->argv);
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$this->agency_name = array_shift($this->argv);
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if (
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$this->command === 'resolve' &&
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($this->agency_name === null || !in_array($this->agency_name, array_keys($this->agencies)))
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) {
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$this->exitWithUsageMessage();
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}
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}
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public function usage()
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{
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$agencies = implode(', ', array_keys($this->agencies));
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echo "Script to resolve DOI registration agency duplication pre-3.4.\n"
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. "NB: If a conflict exists for a submission, the corresponding publication objects (galleys, etc.) will also be cleaned up.\n\n"
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. "Usage:\n"
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. "{$this->scriptName} resolve [agency_name] --force : Remove conflicting DOI registration info, keeping agency_name.\n"
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. "{$this->scriptName} test : Returns list of conflicting items\n\n"
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. "Options:\n"
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. "agency_name One of: {$agencies}.\n"
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. "--force Force resolve operation. Will not delete data without it.\n";
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}
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public function execute(): void
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{
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switch ($this->command) {
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case 'resolve':
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$this->resolve();
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break;
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case 'test':
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$this->test();
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break;
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default:
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$this->exitWithUsageMessage();
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break;
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}
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}
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private function resolve(): void
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{
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if (!$this->forceFlag) {
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$this->print('Warning! This is a destructive operation. Ensure you have a database backup and re-run this command with the `--force` flag.');
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exit(0);
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}
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$agencies = array_filter($this->agencies, fn ($key) => $key !== $this->agency_name, ARRAY_FILTER_USE_KEY);
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$this->print('Removing duplicate registration info for ' . implode(', ', array_keys($agencies)) . '...');
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$agencyFields = array_reduce($agencies, fn ($carry, $item) => array_merge($carry, [$item['status']], $item['additionalFields']), []);
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$submissionIds = $this->getSubmissionIds();
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$galleyIds = $this->getGalleyIds();
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$issueIds = $this->getIssueIds();
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DB::table('submission_settings')
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->whereIn('setting_name', $agencyFields)
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->whereIn('submission_id', $submissionIds)
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->delete();
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$this->print("Removed duplicates for {$submissionIds->count()} submission(s)");
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DB::table('publication_galley_settings')
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->whereIn('setting_name', $agencyFields)
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->whereIn('galley_id', $galleyIds)
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->delete();
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$this->print("Removed duplicates for {$galleyIds->count()} galley(s)");
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DB::table('issue_settings')
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->whereIn('setting_name', $agencyFields)
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->whereIn('issue_id', $issueIds)
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->delete();
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$this->print("Removed duplicates for {$issueIds->count()} issues(s)");
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}
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private function test(): void
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{
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$this->print('IDs with duplicate DOI registration metadata:');
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$this->print("Submissions: {$this->getSubmissionIds()}");
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$this->print("Galleys: {$this->getGalleyIds()}");
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$this->print("Issues: {$this->getIssueIds()}");
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}
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private function getSubmissionIds(): Collection
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{
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return DB::table('submission_settings')
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->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
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->groupBy('submission_id')
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->havingRaw('COUNT(submission_id) > 1')
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->pluck('submission_id');
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}
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/**
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* Gets galley IDs that have duplicates OR are associated with submissions with conflicts
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*/
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private function getGalleyIds(): Collection
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{
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return DB::table('publication_galley_settings')
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->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
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->orWhereIn('galley_id', function (Builder $q) {
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$q->select('pg.galley_id')
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->from('publication_galleys', 'pg')
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->leftJoin('publications as p', 'pg.publication_id', '=', 'p.publication_id')
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->leftJoin('submissions as s', 'p.submission_id', '=', 's.submission_id')
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->whereIn('s.submission_id', $this->getSubmissionIds());
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})
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->groupBy('galley_id')
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->havingRaw('COUNT(galley_id) > 1')
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->pluck('galley_id');
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}
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private function getIssueIds(): Collection
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{
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return DB::table('issue_settings')
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->whereIn('setting_name', array_map(fn ($item) => $item['status'], $this->agencies))
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->groupBy('issue_id')
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->havingRaw('COUNT(issue_id) > 1')
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->pluck('issue_id');
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}
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protected function print(string $message): void
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{
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echo $message . PHP_EOL;
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}
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}
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$tool = new resolveAgencyDuplicates($argv ?? []);
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$tool->execute();
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