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<?php |
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namespace PubPeerFoundation\PublicationDataExtractor\Resources\Extractors; |
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use PubPeerFoundation\PublicationDataExtractor\Helpers\DateHelper; |
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class EutilsEfetch implements Extractor, ProvidesPublicationData, ProvidesIdentifiersData, ProvidesAuthorsData, ProvidesJournalData |
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{ |
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private $document; |
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private $searchTree; |
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private $output = []; |
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private $identifier; |
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public function __construct($document, $identifier) |
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{ |
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$this->document = $document; |
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$this->identifier = $identifier; |
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} |
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public function extract(): array |
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{ |
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$this->getDataFromDocument(); |
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$this->extractAuthorsData(); |
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$this->extractIdentifiersData(); |
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$this->extractJournalData(); |
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$this->extractPublicationData(); |
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return $this->output; |
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} |
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protected function getDataFromDocument() |
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{ |
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$this->searchTree = $this->document->{'PubmedArticle'}; |
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} |
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/** |
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* Extract and format data needed for the Publication Model. |
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*/ |
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public function extractPublicationData() |
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{ |
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$this->output['publication'] = [ |
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'title' => (string) $this->searchTree->MedlineCitation->Article->ArticleTitle ?? null, |
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'url' => (string) 'http://www.ncbi.nlm.nih.gov/pubmed/'.$this->searchTree->MedlineCitation->PMID, |
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'published_at' => (new DateHelper)->dateFromPubDate($this->searchTree->MedlineCitation->Article->Journal->JournalIssue->PubDate), |
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'abstract' => (string) $this->searchTree->MedlineCitation->Article->Abstract->AbstractText ?? null, |
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]; |
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} |
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/** |
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* Extract and format data needed for the Identifiers Relationship |
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* on the Publication Model. |
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*/ |
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public function extractIdentifiersData() |
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{ |
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foreach ($this->searchTree->PubmedData->ArticleIdList->ArticleId as $identifier) { |
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$this->output['identifiers'][] = [ |
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'value' => (string) $identifier, |
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'type' => (string) $identifier['IdType'], |
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]; |
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} |
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if ($this->searchTree->MedlineCitation->Article->Journal->ISSN) { |
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$this->output['identifiers'][] = [ |
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'value' => (string) $this->searchTree->MedlineCitation->Article->Journal->ISSN, |
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'type' => 'issn', |
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]; |
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} |
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} |
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/** |
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* Extract and format data needed for the Journals Relationship |
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* on the Publication Model. |
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*/ |
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public function extractJournalData() |
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{ |
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$this->output['journals'] = [ |
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'title' => (string) $this->searchTree->MedlineCitation->Article->Journal->Title ?? null, |
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'issn' => $this->getIssns(), |
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]; |
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} |
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/** |
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* Extract and format data needed for the Authors Relationship |
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* on the Publication Model. |
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*/ |
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public function extractAuthorsData() |
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{ |
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try { |
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foreach ($this->searchTree->MedlineCitation->Article->AuthorList->Author as $author) { |
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$this->output['authors'][] = [ |
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'first_name' => (string) $author->ForeName, |
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'last_name' => (string) $author->LastName, |
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'affiliation' => (string) $author->AffiliationInfo->Affiliation, |
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]; |
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} |
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} catch (\Exception $e) { |
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// If can't find authors, just don't do anything. |
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} |
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} |
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protected function getIssns() |
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{ |
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$issn = []; |
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if ($this->searchTree->MedlineCitation->Article->Journal->ISSN) { |
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$issn[] = (string) $this->searchTree->MedlineCitation->Article->Journal->ISSN; |
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} |
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if ($this->searchTree->MedlineCitation->MedlineJournalInfo->ISSNLinking) { |
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$issn[] = (string) $this->searchTree->MedlineCitation->MedlineJournalInfo->ISSNLinking; |
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} |
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return $issn; |
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} |
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} |
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PubPeerFoundation /
PublicationDataExtractor
