PubPeerFoundation\PublicationDataExtractor\Resources\Extractors\EutilsEfetch

Complexity

Total Complexity

18

Size/Duplication

Total Lines	142
Duplicated Lines	0 %

Test Coverage

Coverage

100%

Importance

Changes

0

10 Methods

Rating	Name	Duplication	Size	Complexity
A	extractIdentifiersData()	0	12	3
A	extractPublicationData()	0	7	1
A	getDataFromDocument()	0	3	1
A	extractJournalData()	0	5	1
A	getIssns()	0	13	3
A	getEmailsFromAffiliations()	0	3	1
A	loopOverAuthors()	0	4	2
A	loopOverAffiliations()	0	8	2
A	createAuthorEntry()	0	10	2
A	extractAuthorsData()	0	5	2

<?php

namespace PubPeerFoundation\PublicationDataExtractor\Resources\Extractors;

use Tightenco\Collect\Support\Arr;

class EutilsEfetch extends Extractor implements ProvidesPublicationData, ProvidesIdentifiersData, ProvidesAuthorsData, ProvidesJournalData
{
    /**
     * Create search tree.
     */
    protected function getDataFromDocument()
    {
        $this->searchTree = $this->document->{'PubmedArticle'};
    }

    /**
     * Extract and format data needed for the Publication Model.
     */
    public function extractPublicationData()
    {
        $this->output['publication'] = [
            'title' => get_string($this->searchTree, 'MedlineCitation.Article.ArticleTitle'),
            'url' => (string) 'http://www.ncbi.nlm.nih.gov/pubmed/'.get_string($this->searchTree, 'MedlineCitation.PMID'),
            'published_at' => date_from_pub_date(data_get($this->searchTree, 'MedlineCitation.Article.Journal.JournalIssue.PubDate')),
            'abstract' => get_string($this->searchTree, 'MedlineCitation.Article.Abstract.AbstractText'),
        ];
    }

    /**
     * Extract and format data needed for the Identifiers Relationship
     * on the Publication Model.
     */
    public function extractIdentifiersData()
    {
        foreach ($this->searchTree->PubmedData->ArticleIdList->ArticleId as $identifier) {
            $this->output['identifiers'][] = [
                'value' => (string) $identifier,
                'type' => (string) $identifier['IdType'],
            ];
        }
        if ($value = get_string($this->searchTree, 'MedlineCitation.Article.Journal.ISSN')) {
            $this->output['identifiers'][] = [
                'value' => $value,
                'type' => 'issn',
            ];
        }
    }

    /**
     * Extract and format data needed for the Journals Relationship
     * on the Publication Model.
     */
    public function extractJournalData()
    {
        $this->output['journal'] = [
            'title' => get_string($this->searchTree, 'MedlineCitation.Article.Journal.Title'),
            'issn' => $this->getIssns(),
        ];
    }

    /**
     * Extract and format data needed for the Authors Relationship
     * on the Publication Model.
     */
    public function extractAuthorsData()
    {
        try {
            $this->loopOverAuthors();
        } catch (\Exception $e) {
            // Empty catch block, don't want anything to happen in case of exception.
        }
    }

    /**
     * Get all available ISSNs values from the tree.
     *
     * @return array
     */
    protected function getIssns()
    {
        $issn = [];

        if ($number = get_string($this->searchTree, 'MedlineCitation.Article.Journal.ISSN')) {
            $issn[] = $number;
        }

        if ($number = get_string($this->searchTree, 'MedlineCitation.MedlineJournalInfo.ISSNLinking')) {
            $issn[] = $number;
        }

        return $issn;
    }

    /**
     * Loop over authors array.
     */
    protected function loopOverAuthors(): void
    {
        foreach ($this->searchTree->MedlineCitation->Article->AuthorList->Author as $author) {
            $this->createAuthorEntry($author);
        }
    }

    /**
     * Create an author entry in output.
     *
     * @param $author
     */
    protected function createAuthorEntry($author): void
    {
        if (! empty($lastName = get_string($author, 'LastName'))) {
            $affiliations = $this->loopOverAffiliations($author);

            $this->output['authors'][] = [
                'first_name' => get_string($author, 'ForeName'),
                'last_name' => $lastName,
                'email' => $this->getEmailsFromAffiliations($affiliations),
                'affiliation' => $affiliations,
            ];
        }
    }

    /**
     * Loop over affiliations.
     *
     * @param  array $author
     * @return array
     */
    protected function loopOverAffiliations($author): array
    {
        $affiliations = [];
        foreach ($author->AffiliationInfo as $affiliation) {
            $affiliations[]['name'] = get_string($affiliation, 'Affiliation');
        }

        return $affiliations;
    }

    /**
     * Get emails from affiliations array.
     *
     * @param  array  $affiliations
     * @return string
     */
    protected function getEmailsFromAffiliations($affiliations): string
    {
        return get_string(find_emails_in_array(Arr::pluck($affiliations, 'name')), 0);
    }
}