<?php
/****************************************************************************************************************************************************
 *
 *
 *	PHP ENTREZ TOOLS
 *	~~~~~~~~~~~~~~~~~~
 *	- v0.1 - last changed 2008-10-12 by joe@cotch.net
 *	- eSearch: http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
 *
 *	License
 *	~~~~~~~
 *   		This file is part of PHP Entrez Tools (PET)
 *
 *    		PET is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
 *    		the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 *
 *    		PET is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    		MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
 *
 *    		You should have received a copy of the GNU General Public License along with PET.  If not, see <http://www.gnu.org/licenses/>.
 *
 *
 ***************************************************************************************************************************************************/

require_once("Variables.php");
require_once("HttpRequest.php");
require_once("XmlArray.php");

class eSearch
{
	var $DB;
	var $SearchTerm;
	var $MinDate;
	var $MaxDate;
	var $RelDate;
	var $RetMax;
	var $RetType;
	var $DateType;
	
	var $QueryData;
	var $CacheName;
	var $Xml;
	var $Array;
	
	var $QueryKey;
	var $WebEnv;
	var $Translation;
	var $Count;
	var $IdList;
	
	var $Html;
	var $Error;
	
	function eSearch( $DB = 'pubmed', $SearchTerm = null, $MinDate = null, $MaxDate = null, $RetMax = 20, $RetType = 'uilist', $DateType = null )
	{
		$this->DB = $DB;
		if (isset($SearchTerm)) $this->SearchTerm = $SearchTerm;
		if (isset($MinDate))	$this->MinDate	  = $MinDate;
		if (isset($MaxDate))	$this->MaxDate	  = $MaxDate;
		if (isset($RetMax))	$this->RetMax	  = $RetMax;
		$this->RetType	  = $RetType;
		if (isset($DateType))	$this->DateType	  = $DateType;
	}
	
	function Run( $Level = 0 )
	{
		if (isset($this->Xml)) unset($this->Xml);
		if (isset($this->Array)) unset($this->Array);
		$this->MakeCacheName();
		$this->MakeQueryData();						// We MUST make the query data fresh on each run, as one can run multiple searches with the same object
		$this->GetXmlFile();
		if ($Level >= 1) {
			$this->MakeArray();
			if (empty($this->Array)) {
				$this->DeleteCache();
				if (isset($this->Error)) throw new Exception( "Failed to create an Array from the XML in eSearch:" . $this->Error );
				else throw new Exception( "Failed to create an Array from the XML in eSearch->Run->MakeArray calling to XmlArray->eSearch." );
			}
		}
		if ($Level > 1) $this->ExtractResults();
		return true;
	}
	
	
	function MakeCacheName()
	{
		Global $ncbi_CachePath;
		$this->DB = str_replace("/", "", $this->DB); 	// escape slashes in the DB name for the unlikely event that this is used for filesystem attacks      
		$dir = $ncbi_CachePath . $this->DB;					// Make database specific folders
		if (!file_exists($dir)) mkdir($dir);
		$dir .= "/eSearch";
		if (!file_exists($dir)) mkdir($dir);
		$dir .= "/" . strtolower(substr(trim($this->SearchTerm, " /.(\"["), 0, 1));			// Add the first letter of the search term to the folder to prevent dirs getting too big
		if (!file_exists($dir)) mkdir($dir);
				
		$this->CacheName = $dir . "/" . (isset($this->DB) ? $this->DB : 'pubmed') . "," . $this->RetType . "," . str_replace("/", "", $this->MinDate) . "," . (isset($this->MaxDate) ? str_replace("/", "", $this->MaxDate) : date('Ymd')) . "," . (isset($this->DateType) ? $this->DateType : '') . (isset($this->RelDate) ? $this->RelDate : '') . "," . str_replace("/", "", $this->SearchTerm) . "," . str_replace("/", "", $this->RetMax) . ",.txt";
	}
	
	
	function MakeQueryData()
	{
		// Construct the Query Data
		$this->QueryData = array(
			"db"		=> "pubmed",				// Default database is pubmed -- overule by setting $this->DB
    			"usehistory" 	=> "y",
    			"term"		=> $this->SearchTerm
		);
		if (!empty($this->DB))	     $this->QueryData['db']	= $this->DB;
    		if (!empty($this->RetMax))   $this->QueryData['retmax']  = $this->RetMax;
    		if (!empty($this->MinDate))  $this->QueryData['mindate'] = $this->MinDate;
    		if (!empty($this->MaxDate))  $this->QueryData['maxdate'] = $this->MaxDate;
    		if (!empty($this->RetType))  $this->QueryData['rettype'] = $this->RetType;
    		if (!empty($this->RelDate))  $this->QueryData['reldate'] = $this->RelDate;
    		if (!empty($this->DateType)) $this->QueryData['datetype'] = $this->DateType;
	}
	
	
	function GetXmlFile()
	{
		try { $Request = new EntrezRequest( "eSearch", $this->CacheName, $this->QueryData ); }
		catch (Exception $e) { throw new Exception($e->getMessage()); }					// Pass on any errors
		if (!empty($Request->Html)) $this->Html .= $Request->Html;					// Pass on any HTML messages
		if (empty($Request->Xml)) { throw new Exception( "Empty XML file." ); }
		$this->Xml = $Request->Xml;
		unset($Request);
	}
	
	function MakeArray()
	{
		if (empty($this->Xml)) return false;
		require_once("XmlArray.php");
		try {
			$Arr = new XmlArray($this->Xml, true);
			$this->Array = $Arr->Array;
			unset($Arr);
		}
		catch (Exception $e) {
			$this->DeleteCache();				// The failure of XmlArray may be because PubMed's servers broke -- delete the cache and we could try it again
			$this->Error = $e->getMessage();		// If using Run(), this will now cause an exception to be thrown.  Applications should catch this and either try Run() again, reload, or give up
			return false;
		}
		
		return $this->Array;
	}
	
	function ExtractResults()
	{	// These all need to use 'isset' rather than '!empty' -- e.g. for Counts of 0
        	if (isset($this->Array['QueryKey']))		$this->QueryKey    = $this->Array['QueryKey'];
        	if (isset($this->Array['WebEnv']))		$this->WebEnv      = $this->Array['WebEnv'];
		if (isset($this->Array['Count']))		$this->Count	   = $this->Array['Count'];
		if (isset($this->Array['QueryTranslation']))	$this->Translation = str_replace("&quot;", "\"", $this->Array['QueryTranslation']);
		if (isset($this->Array['IdList']))		$this->IdList 	   = $this->Array['IdList'];
	}
	
	function DeleteCache() 
	{
		if (empty($this->CacheName)) $this->MakeCacheName();
		/* TEMP FIX */
		Global $ncbi_WinFiles;
		if ($ncbi_WinFiles) {						// Escape filenames when using windows
			$this->CacheName = str_replace("\"", "", $this->CacheName);
			$this->CacheName = str_replace("[", "", $this->CacheName);
			$this->CacheName = str_replace("]", "", $this->CacheName);
		}
		/* END TEMP FIX */
		if (file_exists($this->CacheName)) { unlink($this->CacheName); return true; }
		else return false;
	}
}

?>