EntrezPubmedArticle.php in Bibliography Module 7

Provides a class for handling PubMed articles retrieved with EFetch.

Orginally writen by Stefan Freudenberg.

File

modules/pubmed/EntrezPubmedArticle.php

<?php

/**
 * @file
 * Provides a class for handling PubMed articles retrieved with EFetch.
 *
 * Orginally writen by Stefan Freudenberg.
 */

/**
 *
 */
class BiblioEntrezPubmedArticle {
  private $article;
  private $id;
  private $md5;
  private $biblio = array();

  /**
   * Stores the given SimpleXMLElement the PubMed ID and the md5 hash of the
   * serialized XML.
   *
   * @param $pubmedArticle
   *   a PubmedArticle element
   */
  public function __construct(SimpleXMLElement $pubmedArticle = NULL) {
    if ($pubmedArticle) {
      $this
        ->setArticle($pubmedArticle);
    }
  }

  /**
   * Returns the PubMed ID of the article.
   *
   * @return int
   */
  public function setArticle(SimpleXMLElement $pubmedArticle) {
    $this->biblio = array();
    $this->article = $pubmedArticle->MedlineCitation;
    $this->pubmeddata = $pubmedArticle->PubmedData;
    $this->id = (int) $pubmedArticle->MedlineCitation->PMID;
    $this->md5 = md5($pubmedArticle
      ->asXML());
    return $this;
  }

  /**
   *
   */
  public function getId() {
    return $this->id;
  }

  /**
   * Returns the md5 hash of the serialized XML.
   *
   * @return string
   */
  public function getMd5() {
    return $this->md5;
  }

  /**
   *
   */
  public function getBiblioAsObject() {
    return (object) $this
      ->getBiblio();
  }

  /**
   * Returns article elements as an associative array suitable for import into
   * a biblio node.
   *
   * @return array
   */
  public function getBiblio() {
    if (empty($this->biblio)) {
      if (variable_get('biblio_auto_citekey', 1)) {
        $citekey = '';
      }
      else {
        $citekey = $this->id;
      }

      // Attempts to extract the name of the journal from MedlineTA if
      // available.
      if (!empty($this->article->MedlineJournalInfo->MedlineTA)) {
        $journal = (string) $this->article->MedlineJournalInfo->MedlineTA;
      }
      elseif (!empty($this->article->Article->Journal->ISOAbbreviation)) {
        $journal = (string) $this->article->Article->Journal->ISOAbbreviation;
      }
      else {
        $journal = (string) $this->article->Article->Journal->Title;
      }
      $this->biblio = array(
        'title' => (string) $this->article->Article->ArticleTitle,
        'biblio_citekey' => $citekey,
        'biblio_pubmed_id' => $this->id,
        'biblio_pubmed_md5' => $this->md5,
        'biblio_contributors' => $this
          ->contributors(),
        // MedlineCitations are always articles from journals or books.
        'biblio_type' => 102,
        'biblio_date' => $this
          ->date(),
        'biblio_year' => substr($this
          ->date(), 0, 4),
        'biblio_secondary_title' => $journal,
        'biblio_alternate_title' => (string) $this->article->Article->Journal->ISOAbbreviation,
        'biblio_volume' => (string) $this->article->Article->Journal->JournalIssue->Volume,
        'biblio_issue' => (string) $this->article->Article->Journal->JournalIssue->Issue,
        'biblio_issn' => (string) $this->article->Article->Journal->ISSN,
        'biblio_pages' => (string) $this->article->Article->Pagination->MedlinePgn,
        'biblio_abst_e' => $this
          ->abst(),
        'biblio_custom1' => "https://www.ncbi.nlm.nih.gov/pubmed/{$this->id}?dopt=Abstract",
        'biblio_keywords' => $this
          ->keywords(),
        'biblio_lang' => $this
          ->lang(),
      );
      $doi = $this->article
        ->xpath('.//ELocationID[@EIdType="doi"]/text()');
      if (empty($doi)) {
        $doi = $this->pubmeddata
          ->xpath('.//ArticleId[@IdType="doi"]/text()');
      }
      if (!empty($doi)) {
        $this->biblio['biblio_doi'] = (string) $doi[0];
      }
      $pmcid = $this->pubmeddata
        ->xpath('.//ArticleId[@IdType="pmc"]/text()');
      if (!empty($pmcid)) {
        $this->biblio['biblio_pmcid'] = (string) $pmcid[0];
      }
      $grants = $this
        ->grants();
      if (!empty($grants)) {
        $this->biblio['biblio_pubmed_grants'] = $grants;
      }
    }
    return $this->biblio;
  }

  /**
   * Returns the list of contributors for import obtained from the given
   * MedlineCitation element.
   *
   * @return array
   *   the contributors of the article
   */
  private function contributors() {
    $contributors = array();
    if (isset($this->article->Article->AuthorList->Author)) {
      foreach ($this->article->Article->AuthorList->Author as $author) {
        $name = '';
        if (isset($author->CollectiveName)) {

          // Corporate author.
          $category = 5;
          $name = (string) $author->CollectiveName;
        }
        else {

          // Primary (human) author.
          $category = 1;
          $lastname = (string) $author->LastName;
          if (isset($author->ForeName)) {
            $name = $lastname . ', ' . (string) $author->ForeName;
          }
          elseif (isset($author->FirstName)) {
            $name = $lastname . ', ' . (string) $author->FirstName;
          }
          elseif (isset($author->Initials)) {
            $name = $lastname . ', ' . (string) $author->Initials;
          }
        }
        if (!empty($name)) {
          $contributors[] = array(
            'name' => $name,
            'auth_category' => $category,
          );
        }
      }
    }
    return $contributors;
  }

  /**
   *
   */
  private function grants() {
    $grants = array();
    if (isset($this->article->Article->GrantList->Grant)) {
      foreach ($this->article->Article->GrantList->Grant as $grant) {
        $grants[] = array(
          'grantid' => (string) $grant->GrantID,
          'acronym' => (string) $grant->Acronym,
          'agency' => (string) $grant->Agency,
          'country' => (string) $grant->Country,
        );
      }
    }
    return $grants;
  }

  /**
   * Returns the publication date obtained from the given MedlineCitation's
   * PubDate element. See the reference documentation for possible values:
   * https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html#pubdate
   * According to the above source it always begins with a four digit year.
   *
   * @return string
   *   the publication date of the article
   */
  private function date() {
    $pubDate = $this->article->Article->Journal->JournalIssue->PubDate;
    if (isset($pubDate->MedlineDate)) {
      $date = (string) $pubDate->MedlineDate;
    }
    else {
      $date = implode(' ', (array) $pubDate);
    }
    return $date;
  }

  /**
   *
   */
  private function keywords() {
    $keywords = array();
    if (isset($this->article->MeshHeadingList->MeshHeading)) {
      foreach ($this->article->MeshHeadingList->MeshHeading as $heading) {
        $keywords[] = (string) $heading->DescriptorName;
      }
    }
    return $keywords;
  }

  /**
   *
   */
  private function lang() {
    if (isset($this->article->Article->Language)) {
      return (string) $this->article->Article->Language;
    }
  }

  /**
   *
   */
  private function abst() {
    if (isset($this->article->Article->Abstract)) {
      $abst = '';
      foreach ($this->article->Article->Abstract->AbstractText as $text) {
        $abst .= "<p>";
        $attrs = $text
          ->attributes();
        if (isset($attrs['Label'])) {
          $abst .= '<b>' . $attrs['Label'] . ': </b>';
        }
        $abst .= (string) $text . '</p>';
      }
      return $abst;
    }
  }

}

Classes

Name	Description
BiblioEntrezPubmedArticle