File

tripal_pub/includes/importers/PMID.inc, line 441

Tripal Pub PubMed Interface

Code

function tripal_pub_PMID_parse_article($xml, &$pub) {

  while ($xml->read()) {
    // get this element name
    $element = $xml->name;

    // if we're at the </Article> element then we're done with the article...
    if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Article') {
      return;
    }
    if ($xml->nodeType == XMLReader::ELEMENT) {
      switch ($element) {
        case 'Journal':
          tripal_pub_PMID_parse_journal($xml, $pub);
          break;
        case 'ArticleTitle':
          $xml->read();
          // remoave any trailing period from the title
          $pub['Title'] = trim(preg_replace('/\.$/', '', $xml->value));
          break;
        case 'Abstract':
          tripal_pub_PMID_parse_abstract($xml, $pub);
          break;
        case 'Pagination':
          tripal_pub_PMID_parse_pagination($xml, $pub);
          break;
        case 'ELocationID':
          $type = $xml->getAttribute('EIdType');
          $valid = $xml->getAttribute('ValidYN');
          $xml->read();
          $elocation = $xml->value;
          if ($type == 'doi' and $valid == 'Y') {
            $pub['DOI'] = $elocation;
          }
          if ($type == 'pii' and $valid == 'Y') {
            $pub['PII'] = $elocation;
          }
          $pub['Elocation'] = $elocation;
          break;
        case 'Affiliation':
          // the affiliation tag at this level is meant solely for the first author
          $xml->read();
          $pub['Author List'][0]['Affiliation'] = $xml->value;
          break;
        case 'AuthorList':
          $complete = $xml->getAttribute('CompleteYN');
          tripal_pub_PMID_parse_authorlist($xml, $pub);
          break;
        case 'InvestigatorList':
          // TODO: perhaps handle this one day.  The investigator list is to list the names of people who
          // are members of a collective or corporate group that is an author in the paper.
          break;
        case 'Language':
          $xml->read();
          $lang_abbr = $xml->value;
          // there may be multiple languages so we store these in an array
          $pub['Language'][] = tripal_pub_remote_search_get_language($lang_abbr);
          $pub['Language Abbr'][] = $lang_abbr;
          break;
        case 'DataBankList':
          // TODO: handle this case
          break;
        case 'GrantList':
          // TODO: handle this case
          break;
        case 'PublicationTypeList':
          tripal_pub_PMID_parse_publication_type($xml, $pub);
          break;
        case 'VernacularTitle':
          $xml->read();
          $pub['Vernacular Title'][] = $xml->value;
          break;
        case 'ArticleDate':
          // TODO: figure out what to do with this element. We already have the
          // published date in the <PubDate> field, but this date should be in numeric
          // form and may have more information.
          break;
        default:
          break;
      }
    }
  }
}