<?php

/********************************************************************************************************************************************
 *
 *	TIPS: Trends in publishing science
 *	~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 *		Maintained by Joe D: joe@cotch.net
 *		This is version 0.1b, released 2008-10-
 *
 *		TIPS is a device for creating graphs to visualise the history of terms in the PubMed database
 *
 *
 *	License
 *	~~~~~~~
 *   		This file is part of TIPS.
 *
 *    		TIPS 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.
 *
 *    		TIPS 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 TIPS.  If not, see <http://www.gnu.org/licenses/>.
 *
 *
 *  	User defined settings
 *  	~~~~~~~~~~~~~~~~~~~~~
 * 		If you wish to run TIPS on your own server, you will need to change the three settings below.
 *		You will also need to make sure that PHP is running with the sessions module installed and the HttpRequest extension available.
 *		TIPS can use a lot of memory, storage, and bandwidth -- make sure you keep an eye on these.
 *																		*/

// How should TIPS identify itself to Entrez when requesting data?
$ncbi_Tool	 = "TIPS";

/*
 *		You will also need to edit 'lib/Variables.php'
 *
 *
 *	Changelog
 *	~~~~~~~~~
 *
 *
 ********************************************************************************************************************************************/

error_reporting(E_ALL);
ini_set('display_errors', '8');
//ini_set('max_execution_time', '120');

require_once("lib/Variables.php");
include_once("lib/eSearch.php");

session_start();
if (isset($_POST['NewSession'])) session_unset();		// Check if this is a new search and, if so, delete old session variables

$PhpEntrezTool = new Tips();					// Run the object


class Tips
{
	var $PostData;		// array - Details from the search form
	var $Searches;		// array - Search terms, results, and related data
	var $Coordinates;	// array - Results, in the form of coordinates
	
	var $Stage;		// array - Our position in the search
	var $Html;
	var $Title;
	var $ImgName;
	var $GraphTitle;
	
	
	function Tips()
	{
		$this->Html;
		if (isset($_POST['NewSession'])) {				// Extract post data
			$_SESSION['began'] = microtime(true);			// Set start time
			$this->PostData = array(
				"TrendsStart" => $_POST['TrendsStart'],
				"TrendsEnd"   => $_POST['TrendsEnd'],
				"BreakDown"   => $_POST['BreakDown'],
				"GraphWidth"  => $_POST['GraphWidth'],
				"GraphHeight" => $_POST['GraphHeight'],
				"LineColours" => explode(",", $_POST['LineColours']),
				"BackGround"  => $_POST['BackGround'],
			);
			if (!empty($_POST['GraphTitle'])) $this->GraphTitle = $_POST['GraphTitle'];
			else $this->GraphTitle = "Publishing Trends";

			$this->PostData['Normalize'] = false;	
			if (!empty($_POST['Normalize'])) $this->PostData['Normalize'] = true;

			if ($this->PostData['TrendsEnd'] > date('Y')) $this->PostData['TrendsEnd'] = date('Y');
			
			for ($i = 1; $i <= 10; $i++) {
				$index = "SearchString-" . $i;
				if (!empty($_POST[$index])) $this->Searches[$i]['SearchString'] = $_POST[$index];
			}
			
			$this->Stage = array("searches", 1);
		}
		else {
			$this->PostData = $_SESSION['PostData'];
			$this->Searches = $_SESSION['Searches'];
			$this->Stage 	= $_SESSION['Stage'];
		}
		
		if ($this->Stage[0] == "searches") {
			foreach ($this->Searches as $k => $v) { 
				//if (isset($this->Stage[1]) and ($this->Stage[1] > $k)) continue;
				if ($this->PostData['BreakDown'] == "month") $this->GetCountsByMonth($k);
				else $this->GetCountsByYear($k);
				$this->Stage[1] = $k + 1;
			}
			$this->Stage[0] = "post_search";
			$this->Html .= "<p>Completed searches... building your graph...</p>";
			$this->SaveReload();	
		}
		
		if (!empty($this->PostData['Normalize'])) $this->Normalize();
		$this->MakePng();
		if ($this->PostData['BreakDown'] == "month") $this->PrintResultsMonth();
		else $this->PrintResultsYear();
	}
	
	function GetCountsByMonth($Id) {
		$Year = $this->PostData['TrendsStart'];
		$Month = 1;
		while (true) {
			if (!isset($this->Searches[$Id]['Counts'][$Year][$Month])) {
				try {
					$MinDate = array($Year, $Month, 1);
					$MinDate = implode("/", $MinDate);
					
					$MaxDate = array($Year, $Month, lastday($Month, $Year));
					$MaxDate = implode("/", $MaxDate);
					
					$eSearch = new eSearch( 'pubmed', $this->Searches[$Id]['SearchString'], $MinDate, $MaxDate, null, 'count' );
					$eSearch->Run(2);
					
					$this->Searches[$Id]['Counts'][$Year][$Month] = $eSearch->Count;
				}
				catch (Exception $e) {
					$this->Html .= "<p><b>Warning</b>: caught an exception when trying to retreive the XML data from PubMed.  I am going to reload the page and hope that the problem goes away.  The error given was: " . $e->getMessage() . "</p>\n";
					$this->SaveReload();
					exit;
				}
			}
			$Month += 1;
			if ($Month > 12) { $Year += 1; $Month = 1; }
			if ($Year > $this->PostData['TrendsEnd']) break;
			continue;
		}
	}
	
	function GetCountsByYear($Id) {
		$Year = $this->PostData['TrendsStart'];
		while (true) {
			if (!isset($this->Searches[$Id]['Counts'][$Year])) {
				try {
					$MinDate = array($Year, "01", "01");
					$MinDate = implode("/", $MinDate);
					
					$MaxDate = array($Year, "12", "31");
					$MaxDate = implode("/", $MaxDate);
					
					$eSearch = new eSearch( 'pubmed', $this->Searches[$Id]['SearchString'], $MinDate, $MaxDate, null, 'count' );
					$eSearch->Run(2);
					
					$this->Searches[$Id]['Counts'][$Year] = $eSearch->Count;
				}
				catch (Exception $e) {
					$this->Html .= "<p><b>Warning</b>: caught an exception when trying to retreive the XML data from PubMed.  I am going to reload the page and hope that the problem goes away.  The error given was: " . $e->getMessage() . "</p>\n";
					$this->SaveReload();
					exit;
				}
			}
			$Year += 1;
			if ($Year > $this->PostData['TrendsEnd']) break;
			continue;
		}
	}

	function Normalize()
        {
                $this->Html .= "<p>Normalizing...</p>";
		if ($this->PostData['BreakDown'] == "year") {
                        $Year = $this->PostData['TrendsStart'];
                        while (true) {
                                try {
                                        $MinDate = array($Year, "01", "01");
                                        $MinDate = implode("/", $MinDate);

                                        $MaxDate = array($Year, "12", "31");
                                        $MaxDate = implode("/", $MaxDate);

                                        $eSearch = new eSearch( 'pubmed', $MinDate . ':' . $MaxDate . '[PDAT]', $MinDate, $MaxDate, null, 'count' );
                                        $eSearch->Run(2);

                                        $Normalize[$Year] = $eSearch->Count;
                                }
                                catch (Exception $e) {
                                        $this->Html .= "<p><b>Warning</b>: caught an exception when trying to retreive the XML data from PubMed.  I am going to reload the page and hope that the problem goes away.  The error given was: " . $e->getMessage() . "</p>\n";
                                        $this->SaveReload();
                                        exit;
                                }
                                $Year += 1;
          	                if ($Year > $this->PostData['TrendsEnd']) {
                  	        	foreach ($this->Searches as $Id => &$Search) {
						foreach ($Search['Counts'] as $Y => &$C) {
							$C = ($C / $Normalize[$Y]) * 100;
						}
					}
                                	break;
                        	}
                        	else continue;
			}
                }
/*
		elseif ($this->PostData['BreakDown'] == "month") {
			$Year = $this->PostData['TrendsStart'];
			$Month = 1;
			while (true) {
				try {
					$MinDate = array($Year, $Month, 1);
					$MinDate = implode("/", $MinDate);
					
					$MaxDate = array($Year, $Month, lastday($Month, $Year));
					$MaxDate = implode("/", $MaxDate);
					
					$eSearch = new eSearch( 'pubmed', '*', $MinDate, $MaxDate, null, 'count' );
					$eSearch->Run(2);
					
					$this->Searches[$Id]['Counts'][$Year][$Month] = $eSearch->Count;
				}
				catch (Exception $e) {
					$this->Html .= "<p><b>Warning</b>: caught an exception when trying to retreive the XML data from PubMed.  I am going to reload the page and hope that the problem goes away.  The error given was: " . $e->getMessage() . "</p>\n";
					$this->SaveReload();
					exit;
				}
				$Month += 1;
				if ($Month > 12) { $Year += 1; $Month = 1; }
				if ($Year > $this->PostData['TrendsEnd']) break;
				continue;
			}
		}
*/
		return true;
        }
	
	function MakePng()
	{
		Global $ncbi_CachePath;
	
		include_once("Image/Graph.php");
		require_once 'Image/Canvas.php';

		//$Graph =& Image_Graph::factory('graph', array($this->PostData['GraphWidth'], $this->PostData['GraphHeight']));
		$Proportions = array( (int)$this->PostData['GraphWidth'], (int)$this->PostData['GraphHeight'] );
		// create a PNG canvas and enable antialiasing (canvas implementation)
		$Canvas =& Image_Canvas::factory('png', array('width' => (int)$this->PostData['GraphWidth'], 'height' => (int)$this->PostData['GraphHeight'], 'antialias' => 'native'));
		// create the graph
		$Graph =& Image_Graph::factory('graph', $Canvas);
		//$Graph =& Image_Graph::factory('graph', $Proportions);
		
		// add a TrueType font 
		
		putenv('GDFONTPATH=/usr/share/fonts/truetype');
		$Font1 =& $Graph->addNew('font', 'Vera.ttf'); 
		$Font1->setSize(11);
		$Graph->setFont($Font1);
		
		$Graph->add(
			Image_Graph::vertical(
				Image_Graph::factory('title',array($this->GraphTitle,14)),
				Image_Graph::vertical(
					$Plotarea = Image_Graph::factory('plotarea'),
					$Legend = Image_Graph::factory('legend'),
					90
				),
				5
			)
		);
		
		$Font2 =& $Graph->addNew('font', 'Vera.ttf'); 
		$Font2->setSize(8);
		$Graph->setFont($Font2);
		
		foreach ($this->Searches as $Id => $Search) {
			$Dataset[$Id] =& Image_Graph::factory('dataset');
			$Dataset[$Id]->setName($Search['SearchString']);
			foreach ($Search['Counts'] as $Year => $Value) {
				if (is_array($Value)) {
					foreach ($Value as $Month => $Count) {
						$Dataset[$Id]->addPoint("{$Year}-" . ((strlen($Month) == 1) ? '0' . $Month : $Month), $Count);
					}
				}
				else $Dataset[$Id]->addPoint($Year, $Value);
			}
			
			$Plot[$Id] =& $Plotarea->addNew('line', &$Dataset[$Id]);
			$Plot[$Id]->setLineColor(trim($this->PostData['LineColours'][$Id-1]));
		}
		if (isset($this->PostData['BackGround'])) {
			if ($this->PostData['BackGround'] == "grey") $Plot[1]->setBackgroundColor( 'lightgrey' ); 
			elseif ($this->PostData['BackGround'] == "lightgrey-grey") $Plot[1]->setBackgroundColor( Image_Graph::factory( 'gradient', array(IMAGE_GRAPH_GRAD_VERTICAL, 'gray', 'lightgrey') ) ); 
			elseif ($this->PostData['BackGround'] == "grey-lightgrey") $Plot[1]->setBackgroundColor( Image_Graph::factory( 'gradient', array(IMAGE_GRAPH_GRAD_VERTICAL, 'lightgrey', 'gray') ) ); 
			elseif ($this->PostData['BackGround'] == "blue") $Plot[1]->setBackgroundColor( 'lightblue' ); 
		}
		
		$AxisY =& $Plotarea->getAxis(IMAGE_GRAPH_AXIS_Y);
		if (!empty($this->PostData['Normalize'])) $AxisY->setTitle('Publications (percentage of total)', 'vertical');
		else $AxisY->setTitle('Publications', 'vertical');
		$GridY =& $Plotarea->addNew('line_grid', IMAGE_GRAPH_AXIS_Y); 
		$GridY->setLineColor('silver@0.5'); 
		$AxisX =& $Plotarea->getAxis(IMAGE_GRAPH_AXIS_X);
		$AxisX->setFontAngle('90');
		if (($this->PostData['BreakDown'] == "month") and (($this->PostData['TrendsEnd'] - $this->PostData['TrendsStart']) > 5)) $AxisX->setLabelInterval(12);
		
		$Graph->setBorderColor('black@0.2');
		$Legend->setPlotarea($Plotarea);
		
		$this->ImgName = md5(date('Y-m-d H:i:s'));
		$filename = $ncbi_CachePath . "tips/" . $this->ImgName . ".png";
		$Graph->done(array("filename" => $filename));
	}	
	
	
	/********************************************************************************************************************************************
	 *	Function: PrintResultsMonth() and PrintResultsYear()
	 *		- Output HTML with a link to the image script which will produce the graph
	 */	
	function PrintResultsMonth()
	{
		$this->Html .= "<div style=\"text-align:center;\"><p><img src=\"cache/tips/" . $this->ImgName . ".png\"/></p>
				<p><i>Cached images are regularly deleted: save a copy if you want to keep it!</i></p>\n";
		$this->Html .= "<table cellpadding=4 cellspacing=0 border=1><tr><th>&nbsp;</th>\n";
		foreach ($this->Searches as $k => $v) {	$this->Html .= "<th>" . $v['SearchString'] . "</th>\n";	}
		$this->Html .= "</tr>\n";
		
		$Year = $this->PostData['TrendsStart'];
		$Month = 1;
		while (true) {
			$this->Html .= "<tr><td>{$Year}-{$Month}</td>\n";
			foreach ($this->Searches as $k => $v) { $this->Html .= "<td>" . $v['Counts'][$Year][$Month] . "</td>\n"; }
			$this->Html .= "</tr>\n";

			$Month += 1;
			if ($Month > 12) { $Year += 1; $Month = 1; }
			if ($Year > $this->PostData['TrendsEnd']) break;
			continue;
		}
		
		$this->Html .= "</table>\n";
		$this->Html .= "<p style=\"text-align: center;\">Content from pubmed used under NLM terms of use (<a href=\"http://www.ncbi.nlm.nih.gov/About/disclaimer.html\">NLM disclaimer</a>).</p></div>\n";
	
		$this->Title = "TiPS: Search complete.";
		$this->OutputHtml();
	}
	function PrintResultsYear()
	{
		$this->Html .= "<div style=\"text-align:center;\"><p><img src=\"cache/tips/" . $this->ImgName . ".png\"/></p>
				<p><i>Cached images are regularly deleted: save a copy if you want to keep it!</i></p>\n";
		$this->Html .= "<table cellpadding=4 cellspacing=0 border=1><tr><th>&nbsp;</th>\n";
		foreach ($this->Searches as $k => $v) {	$this->Html .= "<th>" . $v['SearchString'] . "</th>\n";	}
		$this->Html .= "</tr>\n";
		
		$Year = $this->PostData['TrendsStart'];
		while (true) {
			$this->Html .= "<tr><td>{$Year}</td>\n";
			foreach ($this->Searches as $k => $v) { $this->Html .= "<td>" . $v['Counts'][$Year] . "</td>\n"; }
			$this->Html .= "</tr>\n";

			$Year += 1;
			if ($Year > $this->PostData['TrendsEnd']) break;
			continue;
		}
		
		$this->Html .= "</table>\n";
		$this->Html .= "<p style=\"text-align: center;\">Content from pubmed used under NLM terms of use (<a href=\"http://www.ncbi.nlm.nih.gov/About/disclaimer.html\">NLM disclaimer</a>).</p></div>\n";
	
		$this->Title = "TiPS: Search complete.";
		$this->OutputHtml();
	}		

	/********************************************************************************************************************************************
	 *	Function: SaveReload()
	 *		- Saves session variables and then outputs HTML with the reload clause set
	 */
	function SaveReload()
	{
		$_SESSION['PostData'] = $this->PostData;
		$_SESSION['Searches'] = $this->Searches;
		$_SESSION['Stage']    = $this->Stage;
		
		$this->Title = "Error!";
		$this->OutputHtml(true);
	}


	/********************************************************************************************************************************************
	 *	Function: OutputHtml( Reload )
	 *		Formats the page as HTML
	 */
	function OutputHtml($Reload = false)
	{
		$Title  = $this->Title;
		$Html   = $this->Html;
		
		if ($Reload) $Reload = "<meta http-equiv=\"refresh\" content=\"0;url=Tips-0.2.php?s=" . session_id() . "\">\n";
		else $Reload = "";
		$NavBar = file_get_contents("NavBar.php");
		
		$Time = round((microtime(true) - $_SESSION['began']), 2);	// Calculate the time elapsed

echo <<<END
			<html>
				<head>
					<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
					<title>$Title</title>
					<link rel="stylesheet" type="text/css" href="style.css"/>					
					$Reload
				</head>
				<body>
					$NavBar
					<div id="main">
					<h1>TiPS<sup>beta</sup>: Trends in publishing science</h1>
					$Html
					<p style="text-align: center;">... time elapsed: $Time seconds.</p>
					</div>
				</body>
			<html>
END;
		exit;


	}	

}

// CC-NC-BY-SA -- There is probably a better way of doing things than this, but it will do for testing purposes
function lastday($month = '', $year = '') {
   if (empty($month)) {
      $month = date('m');
   }
   if (empty($year)) {
      $year = date('Y');
   }
   $result = strtotime("{$year}-{$month}-01");
   $result = strtotime('-1 second', strtotime('+1 month', $result));
   return date('d', $result);
}

?>