Parses the section from the XML returned from PubMed that contains information about a journal

Parameters

$xml: The XML to parse

$pub: The publication object to which additional details will be added

File

tripal_chado/includes/loaders/tripal_chado.pub_importer_PMID.inc, line 744

This file provides support for importing and parsing of results from the NCBI PubMed database. The functions here are used by both the publication importer setup form and the publication importer.

Code

function tripal_pub_PMID_parse_journal($xml, &$pub) {

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

    if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Journal') {
      return;
    }
    if ($xml->nodeType == XMLReader::ELEMENT) {
      switch ($element) {
        case 'ISSN':
          $issn_type = $xml->getAttribute('IssnType');
          $xml->read();
          $issn = $xml->value;
          $pub['ISSN'] = $issn;
          if ($issn_type == 'Electronic') {
            $pub['eISSN'] = $issn;
          }
          if ($issn_type == 'Print') {
            $pub['pISSN'] = $issn;
          }
          break;
        case 'JournalIssue':
          // valid values of cited_medium are 'Internet' and 'Print'
          $cited_medium = $xml->getAttribute('CitedMedium');
          tripal_pub_PMID_parse_journal_issue($xml, $pub);
          break;
        case 'Title':
          $xml->read();
          $pub['Journal Name'] = $xml->value;
          break;
        case 'ISOAbbreviation':
          $xml->read();
          $pub['Journal Abbreviation'] = $xml->value;
          break;
        default:
          break;
      }
    }
  }
}