ncbi = new ncbi();
$this->xmlCache = new plugin_cache("ncbi_esummary","pubmed","xml.gz");
if($this->ncbi == Null) print("NCBI is null !");
if($this->xmlCache == Null) print("this->xmlCache is null !");
}
function getType(){ return 'substition'; }
function getSort(){ return 158; }
function connectTo($mode){$this->Lexer->addSpecialPattern('\{\{pubmed>[^}]*\}\}',$mode,'plugin_pubmed');}
/**
* Handle the match
*/
function handle($match, $state, $pos, Doku_Handler $handler){
$match = substr($match,9,-2);
if(str_contains($match,':')){
list($cmd,$pmid) = explode(':',$match);
}else{
$cmd = $match;
$pmid = '';
}
return array($state,array($cmd,$pmid));
}
/**
* Create output
*/
function render($mode, Doku_Renderer $renderer, $data) {
if ($mode!='xhtml')
return false;
list($state, $query) = $data;
list($cmd, $pmid) = $query;
$cmd = strtolower($cmd);
if ($cmd=='long' || $cmd=='short'){
if (!is_numeric($pmid)){
$renderer->doc.=sprintf($this->getLang('pubmed_wrong_format'));
return false;
}
$xml = $this->getSummaryXML($pmid);
if(empty($xml)){
$renderer->doc.=sprintf($this->getLang('pubmed_not_found'),$pmid);
return false;
}
$href_url = sprintf($this->ncbi->pubmedURL,$pmid);
$journal = $this->ncbi->GetSummaryItem ("Source",$xml);
$date = $this->ncbi->GetSummaryItem ("PubDate",$xml);
$volume = $this->ncbi->GetSummaryItem ("Volume",$xml);
$pages = $this->ncbi->GetSummaryItem ("Pages",$xml);
$authors = $this->ncbi->GetSummaryItems("Author",$xml);
$title = $this->ncbi->GetSummaryItem ("Title",$xml);
if ($cmd=='long'||$cmd=='short'){
$renderer->doc.='';
if ($cmd=='long'){
$renderer->doc.= '
'.$title.'';
$renderer->doc.= implode(', ',$authors).'
';
$renderer->doc.= '
'.$journal.'';
}elseif($cmd=='short'){
if (count($authors)>1) $etal = '
et al.';
$renderer->doc.= '
'.$authors[0].$etal;
$renderer->doc.= ''.$journal.'';
}
$renderer->doc.= '
'.$volume.'';
$renderer->doc.= '
p'.$pages.'';
$renderer->doc.= '
('.$date.')".htmlspecialchars($xml)."
";
return true;
case 'clear_summary':
$this->xmlCache->ClearCache();
$renderer->doc .= 'Cleared.';
return true;
case 'remove_dir':
$this->xmlCache->RemoveDir();
$renderer->doc .= 'Directory cleared.';
return true;
default:
// Command was not found..
$renderer->doc.=''.sprintf($this->getLang('plugin_cmd_not_found'),$cmd).'
';
$renderer->doc.=''.$this->getLang('pubmed_available_cmd').'
';
return true;
$renderer->doc.=sprintf($this->getLang('pubmed_wrong_format'));
return true;
}
}
}
/**
* Get summary XML from cache or NCBI
*/
function getSummaryXml($pmid){
global $conf;
if($this->xmlCache == Null){
print("Null !!");}
$cachedXml = $this->xmlCache->GetMediaText($pmid);
if ($cachedXml!==false){ return $cachedXml; }
// Get summary XML
$summary = $this->ncbi->SummaryXml('pubmed',$pmid);
$cachePath = $this->xmlCache->GetMediaPath($pmid);
if (!empty($summary)){
if(io_saveFile($cachePath,$summary)){
chmod($cachePath,$conf['fmode']);
}
}
return $summary;
}
}
// TODO: Implement search results !
?>