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<?php declare(strict_types=1); |
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/** |
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* @author Nicolas CARPi <[email protected]> |
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* @copyright 2022 Nicolas CARPi |
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* @see https://www.elabftw.net Official website |
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* @license AGPL-3.0 |
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* @package elabftw |
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*/ |
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namespace Elabftw\Make; |
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use DateTimeImmutable; |
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use Elabftw\Exceptions\IllegalActionException; |
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use Elabftw\Models\AbstractEntity; |
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use Elabftw\Models\Config; |
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use League\Flysystem\UnableToReadFile; |
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use ZipStream\ZipStream; |
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/** |
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* Make an ELN archive |
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*/ |
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class MakeEln extends MakeStreamZip |
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{ |
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private const HASH_ALGO = 'sha256'; |
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protected string $extension = '.eln'; |
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private array $authors = array(); |
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// name of the folder containing everything |
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private string $root; |
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public function __construct(protected ZipStream $Zip, AbstractEntity $entity, protected array $idArr) |
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{ |
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parent::__construct($Zip, $entity, $idArr); |
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$now = new DateTimeImmutable(); |
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$this->root = $now->format('Y-m-d-His') . '-export'; |
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$this->jsonArr = array( |
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'@context' => 'https://w3id.org/ro/crate/1.1/context', |
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'@graph' => array( |
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array( |
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'@id' => 'ro-crate-metadata.json', |
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'@type' => 'CreativeWork', |
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'about' => array('@id' => './'), |
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'conformsTo' => array('@id' => 'https://w3id.org/ro/crate/1.1'), |
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'dateCreated' => $now->format(DateTimeImmutable::ATOM), |
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'sdPublisher' => array( |
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'@type' => 'Organization', |
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'name' => 'eLabFTW', |
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'logo' => 'https://www.elabftw.net/img/elabftw-logo-only.svg', |
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'slogan' => 'A free and open source electronic lab notebook.', |
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'url' => 'https://www.elabftw.net', |
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'parentOrganization' => array( |
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'@type' => 'Organization', |
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'name' => 'Deltablot', |
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'logo' => 'https://www.deltablot.com/img/logos/deltablot.svg', |
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'slogan' => 'Open Source software for research labs.', |
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'url' => 'https://www.deltablot.com', |
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), |
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), |
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'version' => '1.0', |
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), |
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), |
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); |
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} |
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public function getFileName(): string |
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{ |
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return $this->root . $this->extension; |
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} |
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/** |
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* Loop on each id and add it to our eln archive |
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*/ |
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public function getStreamZip(): void |
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{ |
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$dataEntities = array(); |
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// an array of "@id" for main datasets |
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$rootParts = array(); |
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foreach ($this->idArr as $id) { |
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$hasPart = array(); |
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try { |
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$this->Entity->setId((int) $id); |
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} catch (IllegalActionException $e) { |
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continue; |
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} |
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$e = $this->Entity->entityData; |
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$currentDatasetFolder = $this->getBaseFileName(); |
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$this->folder = $this->root . '/' . $currentDatasetFolder; |
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$rootParts[] = array('@id' => './' . $currentDatasetFolder); |
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// LINKS |
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$mentions = array(); |
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foreach ($e['items_links'] as $link) { |
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$mentions[] = array( |
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'@id' => Config::fromEnv('SITE_URL') . '/database.php?mode=view&id=' . $link['itemid'], |
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'@type' => 'Dataset', |
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'name' => $link['category'] . ' - ' . $link['title'], |
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'identifier' => $link['elabid'], |
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); |
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} |
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foreach ($e['experiments_links'] as $link) { |
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$mentions[] = array( |
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'@id' => Config::fromEnv('SITE_URL') . '/experiments.php?mode=view&id=' . $link['itemid'], |
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'@type' => 'Dataset', |
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'name' => $link['category'] . ' - ' . $link['title'], |
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'identifier' => $link['elabid'], |
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); |
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} |
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// JSON |
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$MakeJson = new MakeJson($this->Entity, array((int) $e['id'])); |
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$json = $MakeJson->getFileContent(); |
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$this->Zip->addFile($this->folder . '/' . $MakeJson->getFileName(), $json); |
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$jsonAtId = './' . $currentDatasetFolder . '/' . $MakeJson->getFileName(); |
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// add the json in the hasPart of the entry |
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$hasPart[] = array('@id' => $jsonAtId); |
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$dataEntities[] = array( |
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'@id' => $jsonAtId, |
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'@type' => 'File', |
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'description' => 'JSON export', |
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'name' => $MakeJson->getFileName(), |
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'encodingFormat' => $MakeJson->getContentType(), |
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'contentSize' => (string) $MakeJson->getContentSize(), |
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'sha256' => hash('sha256', $json), |
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); |
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// COMMENTS |
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$comments = array(); |
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foreach ($e['comments'] as $comment) { |
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$firstname = $comment['firstname'] ?? ''; |
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$lastname = $comment['lastname'] ?? ''; |
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$dateCreated = (new DateTimeImmutable($e['created_at']))->format(DateTimeImmutable::ATOM); |
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$comments[] = array( |
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'@id' => 'comment://' . urlencode($dateCreated), |
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'dateCreated' => $dateCreated, |
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'text' => $comment['comment'], |
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'author' => array('@id' => $this->getAuthorId($comment['userid'], $firstname, $lastname, $comment['orcid'])), |
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); |
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} |
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// UPLOADS |
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$uploadedFilesArr = $e['uploads']; |
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if (!empty($uploadedFilesArr)) { |
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try { |
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// this gets modified by the function so we have the correct real_names |
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$uploadedFilesArr = $this->addAttachedFiles($uploadedFilesArr); |
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} catch (UnableToReadFile $e) { |
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continue; |
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} |
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foreach ($uploadedFilesArr as $file) { |
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$uploadAtId = './' . $currentDatasetFolder . '/' . $file['real_name']; |
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$hasPart[] = array('@id' => $uploadAtId); |
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$dataEntities[] = array( |
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'@id' => $uploadAtId, |
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'@type' => 'File', |
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'description' => $file['comment'] ?? '', |
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'name' => $file['real_name'], |
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'alternateName' => $file['long_name'], |
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'contentSize' => $file['filesize'], |
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'sha256' => $file['hash'] ?? hash_file('sha256', $uploadAtId), |
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); |
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} |
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} |
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// TAGS |
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$keywords = array(); |
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if ($this->Entity->entityData['tags']) { |
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$keywords = explode('|', (string) $this->Entity->entityData['tags']); |
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} |
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// MAIN ENTRY |
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$firstname = $e['firstname'] ?? ''; |
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$lastname = $e['lastname'] ?? ''; |
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$dataEntities[] = array( |
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'@id' => './' . $currentDatasetFolder, |
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'@type' => 'Dataset', |
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'author' => array('@id' => $this->getAuthorId($e['userid'], $firstname, $lastname, $e['orcid'])), |
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'dateCreated' => (new DateTimeImmutable($e['created_at']))->format(DateTimeImmutable::ATOM), |
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'dateModified' => (new DateTimeImmutable($e['modified_at']))->format(DateTimeImmutable::ATOM), |
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'identifier' => $e['elabid'] ?? '', |
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'comment' => $comments, |
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'keywords' => $keywords, |
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'name' => $e['title'], |
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'text' => $e['body'] ?? '', |
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'url' => Config::fromEnv('SITE_URL') . '/' . $this->Entity->page . '.php?mode=view&id=' . $e['id'], |
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'hasPart' => $hasPart, |
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'mentions' => $mentions, |
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); |
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} |
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// add the description of root with hasPart property |
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$dataEntities[] = array( |
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'@id' => './', |
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'@type' => array('Dataset'), |
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'hasPart' => $rootParts, |
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); |
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// merge all, including authors |
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$this->jsonArr['@graph'] = array_merge($this->jsonArr['@graph'], $dataEntities, $this->authors); |
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// add the metadata json file containing references to all the content of our crate |
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$this->Zip->addFile($this->root . '/ro-crate-metadata.json', json_encode($this->jsonArr, JSON_THROW_ON_ERROR, 512)); |
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$this->Zip->finish(); |
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} |
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/** |
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* Generate an author node unless it exists already |
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*/ |
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private function getAuthorId(int $userid, string $firstname, string $lastname, ?string $orcid): string |
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{ |
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// add firstname and lastname to the hash to get more entropy. Use the userid too so similar names won't collide. |
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$id = sprintf('person://%s?hash_algo=%s', hash(self::HASH_ALGO, (string) $userid . $firstname . $lastname), self::HASH_ALGO); |
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$node = array( |
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'@id' => $id, |
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'@type' => 'Person', |
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'familyName' => $lastname, |
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'givenName' => $firstname, |
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); |
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// only add an identifier property if there is an orcid |
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if ($orcid !== null) { |
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$node['identifier'] = 'https://orcid.org/' . $orcid; |
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} |
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// only add it if it doesn't exist yet in our list of authors |
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if (!in_array($id, array_column($this->authors, '@id'), true)) { |
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$this->authors[] = $node; |
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} |
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return $id; |
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} |
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} |
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elabftw /
elabftw
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The issue could also be caused by a filter entry in the build configuration. If the path has been excluded in your configuration, e.g.
excluded_paths: ["lib/*"], you can move it to the dependency path list as follows:For further information see https://scrutinizer-ci.com/docs/tools/php/php-scrutinizer/#list-dependency-paths