File

tripal_pub/includes/importers/PMID.inc, line 311

Tripal Pub PubMed Interface

Code

function tripal_pub_PMID_parse_pubxml($pub_xml) {
  $pub = array();

  if (!$pub_xml) {
    return $pub;
  }

  // read the XML and iterate through it.
  $xml = new XMLReader();
  $xml->xml(trim($pub_xml));
  while ($xml->read()) {
    $element = $xml->name;
    if ($xml->nodeType == XMLReader::ELEMENT) {

      switch ($element) {
        case 'ERROR':
          $xml->read(); // get the value for this element
          watchdog('tripal_pub', "Error: %err", array('%err' => $xml->value), WATCHDOG_ERROR);
          break;
        case 'PMID':
          // thre are multiple places where a PMID is present in the XML and
          // since this code does not descend into every branch of the XML tree
          // we will encounter many of them here.  Therefore, we only want the
          // PMID that we first encounter. If we already have the PMID we will
          // just skip it.  Examples of other PMIDs are in the articles that
          // cite this one.
          $xml->read(); // get the value for this element
          if (!$pub['Publication Dbxref']) {
            $pub['Publication Dbxref'] = 'PMID:' . $xml->value;
          }
          break;
        case 'Article':
          $pub_model = $xml->getAttribute('PubModel');
          $pub['Publication Model'] = $pub_model;
          tripal_pub_PMID_parse_article($xml, $pub);
          break;
        case 'MedlineJournalInfo':
          tripal_pub_PMID_parse_medline_journal_info($xml, $pub);
          break;
        case 'ChemicalList':
          // TODO: handle this
          break;
        case 'SupplMeshList':
          // TODO: meant for protocol list
          break;
        case 'CitationSubset':
          // TODO: not sure this is needed.
          break;
        case 'CommentsCorrections':
          // TODO: handle this
          break;
        case 'GeneSymbolList':
          // TODO: handle this
          break;
        case 'MeshHeadingList':
          // TODO: Medical subject headings
          break;
        case 'NumberOfReferences':
          // TODO: not sure we should keep this as it changes frequently.
          break;
        case 'PersonalNameSubjectList':
          // TODO: for works about an individual or with biographical note/obituary.
          break;
        case 'OtherID':
          // TODO: ID's from another NLM partner.
          break;
        case 'OtherAbstract':
          // TODO: when the journal does not contain an abstract for the publication.
          break;
        case 'KeywordList':
          // TODO: handle this
          break;
        case 'InvestigatorList':
          // TODO: personal names of individuals who are not authors (can be used with collection)
          break;
        case 'GeneralNote':
          // TODO: handle this
          break;
        case 'DeleteCitation':
          // TODO: need to know how to handle this
          break;
        default:
          break;
      }
    }
  }
  $pub['Citation'] = tripal_pub_create_citation($pub);

  $pub['raw'] = $pub_xml;
  return $pub;
}