<?php

// Pubmed object

/**
 * @file pubmed.php
 *
 */

require_once("Net/HTTP/Client.php");
//require_once("XPath.class.php");


/**
 * @brief Pubmed object
 *
 * Encapsulates access to a Pubmed reference.
 *
 */
class Pubmed {

	var $pmid;
	var $data;
	
	//----------------------------------------------------------------------------
	function Pubmed ($id)
	{
		$this->pmid = $id;
		$this->data = "";
	}
	
	//----------------------------------------------------------------------------
	/**
	 * @brief Get Pubmed record in XML.
	 *
	 * If record has not yet been obtained we call Fetch to retrieve it.
	 *
	 */
	function Get () 
	{
		if ($this->data == "") 
		{
			$this->Fetch();
		}
		return $this->data;
	}

	//----------------------------------------------------------------------------
	/**
	 *
	 * Fetch Pubmed XML from a remote store 
	 */
	function Fetch () 
	{
		global $config;
		
		// Connect to Pubmed database
		$http = new Net_HTTP_Client();
		if ($config['proxy_name'] != "")
		{
			$http->setProxy ($config['proxy_name'], $config['proxy_port']);
		}
		$http->Connect( $config['ncbi_url'], 80 ) 
			or die( "Connect problem" );
		
		// Construct query NCBI for Pubmed
		$query = $config['eutils'];
		$query .= "&retmode=xml&db=pubmed&id=";
		$query .= $this->pmid;
		
		//echo $query;
			
		// Go!
		$status = $http->Get( $query );
		if( $status != 200 )
			die( "Problem : " . $http->getStatusMessage() );
		else
		{
			$this->data = $http->getBody();
		}

		//echo $this->data;
		$http->Disconnect();

	
	
	/*
		$xmlfilename = "11839199.xml";
		$myfile = @fopen($xmlfilename, "r") or die("could't open file \"$xmlfilename\"");
		$this->data = @fread($myfile, filesize ($xmlfilename));
		fclose($myfile);	
	*/
	}
	
	//----------------------------------------------------------------------------
	/**
	 * @brief Get abstract from Pubmed record
	 *
	 * Use XPath query to pull out abstract
	 *
	 */
	function GetAbstract ()
	{
		$abstract == "";
		$this->Get();
		
		if (PHP_VERSION >= 5.0)
		{
			$dom= new DOMDocument;
			$dom->loadXML($this->data);
			$xpath = new DOMXPath($dom);
			$xpath_query = "//Abstract/AbstractText";
			$nodeCollection = $xpath->query ($xpath_query);
			foreach($nodeCollection as $node)
			{
				$abstract = $node->firstChild->nodeValue;
			}
		}
		else
		{
			$xpath = new XPath();		
			$xpath->importFromString ($this->data);
			$nodeCollection = $xpath->match("//Abstract/AbstractText");
			
			if (!empty($nodeCollection))
			{
				// Get abstract
				foreach($nodeCollection as $node)
				{
					$abstract .= $xpath->getData($node);
				}
			}
		}
		return $abstract;
	}
}


?>