class.tx_nG6_pi1.php

<?php
/***************************************************************
*  Copyright notice
*
*  (c) 2009 PF bioinformatique de Toulouse <>
*  All rights reserved
*
*  This script is part of the TYPO3 project. The TYPO3 project 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 2 of the License, or
*  (at your option) any later version.
*
*  The GNU General Public License can be found at
*  http://www.gnu.org/copyleft/gpl.html.
*
*  This script 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.
*
*  This copyright notice MUST APPEAR in all copies of the script!
***************************************************************/
/**
 * Plugin 'nG6' for the 'nG6' extension.
 *
 * @author	PF bioinformatique de Toulouse <>
 */

require_once(PATH_tslib.'class.tslib_pibase.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_upgrade.php');
require_once(t3lib_extMgm::extPath('nG6').'/res/smarty/libs/Smarty.class.php'); 

class tx_nG6_pi1 extends tslib_pibase {
	
	var $prefixId = 'tx_nG6_pi1';		// Same as class name
	var $scriptRelPath = 'pi1/class.tx_nG6_pi1.php';	// Path to this script relative to the extension dir.
	var $extKey = 'nG6';	// The extension key.
	
	/**
	 * Main method of your PlugIn
	 *
	 * @param	string		$content: The content of the PlugIn
	 * @param	array		$conf: The PlugIn Configuration
	 * @return	The content that should be displayed on the website
	 */
	function main($content,$conf)	{
		
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
		// Setting the TypoScript passed to this function in $this->conf
		$this->conf=$conf;
		
		$this->pi_setPiVarDefaults();
		// Configuring so caching is not expected. This value means that no cHash params are ever set. We do this, because it's a USER_INT object!
		$this->pi_USER_INT_obj=1;
		// Loading the LOCAL_LANG values
		$this->pi_loadLL();		
		
		// Add the ng6 plugins css
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.core.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.cookie.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.hotkeys.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.jstree.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.dialog.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.draggable.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.resizable.min.js"></script> 
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.bgiframe.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.plugins.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.url.packed.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.venny.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.exporting.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_classes.js"></script>		
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jsphylosvg-min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/raphael-min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/unitip.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.datePicker.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.jeditable.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_table.js"></script>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/unitip.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.venny.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.dataTables.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.datePicker.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.core.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.theme.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.dialog.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.resizable.css"/>';

		// if asked to upgrade to version 1.3
		if($this->piVars['upgrade']){
			$content = tx_nG6_upgrade::upgrade($this->piVars['upgrade']);
		} else {
		
			// If the user is authorized to access the specified project/run, display the page
			if (tx_nG6_db::user_is_authorized($GLOBALS['TSFE']->fe_user->user['uid'], $this->piVars['project_id'], $this->piVars['run_id'])) {
				switch((string)$this->conf['view'])	{
					// If the plugin is configured to display results by project
					case 'project':
						if ($this->piVars['analyze_id']) {
							$content .= $this->pi_analyze_view();
						} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
							$content .= $this->pi_run_view();
						} else {
							$content .= $this->pi_project_view();
						}
						break;
					// If the plugin is configured to display results by run
					case 'run':
						if ($this->piVars['analyze_id']) {
							$content .= $this->pi_analyze_view();
						} else {
							$content .= $this->pi_run_view();
						}
						break;
					// If the plugin is not configured, display by project is default
					default:
						$content .= $this->pi_project_view();
						break;
				}
			// If the user is not authorized
			} else {
				$content .= $this->pi_getLL('not_authorized','[not_authorized]');
			}
		}
		
		return $this->pi_wrapInBaseClass($content);
	}

	/**
	 * Return the project view
	 */
	function pi_project_view()	{
		
		$projects = array();
		// If a single element
		if ($this->piVars['project_id']) {
			$projects = array('project_'.$this->piVars['project_id'] => tx_nG6_db::select_project($this->piVars['project_id']));
		} else {
			$projects = tx_nG6_db::select_all_user_projects($GLOBALS['TSFE']->fe_user->user['uid'], 'tx_nG6_project.name');
		}
		$smarty = new Smarty();
		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
		$smarty->security = true;
		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');		
		// Add some information to the table
		$project_ids = "";
		foreach($projects as $project_id => $project_values) {
			if (tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'project', $project_values['id']) ) {
				$projects[$project_id]['superuser'] = true;
			} else {
				$projects[$project_id]['superuser'] = false;
			}
			$project_ids .= $project_values['id'].",";
			$projects[$project_id]['href'] = $this->pi_list_linkSingle($project_values['name'],$project_values['id'],1, array('project_id'=>$project_values['id']));
		}
		$smarty->assign('projects', $projects);
		$smarty->assign('login_user', $GLOBALS['TSFE']->loginUser);
		$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
		$smarty->assign('data_folder', $this->conf["data"]);
		$smarty->assign('server_name', $this->conf["server_name"]);
		$smarty->assign('project_ids', substr($project_ids,0,-1));

		// If it's a single project, add runs and analysis information
		if (count($projects) == 1) {

			$project_runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['uid'], $projects[key($projects)]['id']);			
			// Add some information to the table
			foreach($project_runs as $run_id => $run_values) {
				if (tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'run', $run_values['id']) ) {
					$project_runs[$run_id]['superuser'] = true;
				} else {
					$project_runs[$run_id]['superuser'] = false;
				}
				$project_runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id']));
			}
			$smarty->assign('project_runs', $project_runs);
			$project_analysis = tx_nG6_db::get_project_analysis($GLOBALS['TSFE']->fe_user->user['uid'], $projects[key($projects)]['id']);
			// Add some information to the table
			foreach($project_analysis as $analysis_id => $analysis_values) {
				if (tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'analyze', $analysis_values['id']) ) {
					$project_analysis[$analysis_id]['superuser'] = true;
				} else {
					$project_analysis[$analysis_id]['superuser'] = false;
				}
				$project_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'project_id'=>$this->piVars['project_id']));
			}
			$smarty->assign('h_project_analysis', tx_nG6_utils::trace_hierarchy($project_analysis));
			$smarty->assign('project_analysis', $project_analysis);
		}	
		
		if (isset($this->LOCAL_LANG[$this->LLkey]) && count($this->LOCAL_LANG[$this->LLkey]) > 0) {
			$smarty->assign('llang', $this->LOCAL_LANG[$this->LLkey]);
		} else {
			$smarty->assign('llang', $this->LOCAL_LANG['default']);
		}
		return $smarty->fetch('project_view.tpl');
	}
	

	/**
	 * Return the run view
	 */
    function pi_run_view() {

		$runs = array();
		// If a single element
		if ($this->piVars['run_id']) {
			$runs = array('run_'.$this->piVars['run_id'] => tx_nG6_db::select_run($this->piVars['run_id']));
		} else {
			$runs = tx_nG6_db::select_all_user_runs($GLOBALS['TSFE']->fe_user->user['uid']);
		}
		$smarty = new Smarty();
		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
		$smarty->security = true;
		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');

		// Add some information to the table
		$run_ids = "";
		foreach($runs as $run_id => $run_values) {
			if (tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'run', $run_values['id']) ) {
				$runs[$run_id]['superuser'] = true;
			} else {
				$runs[$run_id]['superuser'] = false;
			}
			$run_ids .= $run_values['id'].",";
			if ($this->piVars['project_id']) {
				$runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id']));	
			} else {
				$runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id']));
			}
		}
		$smarty->assign('runs', $runs);
		$smarty->assign('first_id', key($runs));
		$smarty->assign('login_user', $GLOBALS['TSFE']->loginUser);
		$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
		$smarty->assign('data_folder', $this->conf["data"]);
		$smarty->assign('server_name', $this->conf["server_name"]);
		$smarty->assign('run_ids', substr($run_ids,0,-1));
		
		// If it's a single run, add analysis information
		if (count($runs) == 1) {
			$run_analysis = tx_nG6_db::get_run_analysis($GLOBALS['TSFE']->fe_user->user['uid'], $runs[key($runs)]['id']);
			// Add some information to the table
			foreach($run_analysis as $analysis_id => $analysis_values) {
				if (tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'analyze', $analysis_values['id']) ) {
					$run_analysis[$analysis_id]['superuser'] = true;
				} else {
					$run_analysis[$analysis_id]['superuser'] = false;
				}
				if ($this->piVars['project_id']) {
					$run_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'project_id'=>$this->piVars['project_id'], 'run_id'=>$this->piVars['run_id']));
				} else {
					$run_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'run_id'=>$this->piVars['run_id']));
				}
			}
			$smarty->assign('h_run_analysis', tx_nG6_utils::trace_hierarchy($run_analysis));
			$smarty->assign('run_analysis', $run_analysis);
		}
		if (isset($this->LOCAL_LANG[$this->LLkey]) && count($this->LOCAL_LANG[$this->LLkey]) > 0) {
			$smarty->assign('llang', $this->LOCAL_LANG[$this->LLkey]);
		} else {
			$smarty->assign('llang', $this->LOCAL_LANG['default']);
		}			
		return $smarty->fetch('run_view.tpl');
	}
	

	/**
	 * Return the analysis view
	 */
	function pi_analyze_view() {
		// First select the analyse
		$analyse = tx_nG6_db::select_analyse($this->piVars['analyze_id']);
		
		// Handle old fashion
		if (file_exists($this->conf['data'].$analyse['directory'].'/index.html' )) {
			// Add the analyse description
			$content = '<div id="img_dialog" title=""></div>';
			$content .= '<input type="hidden" id="analyse_name" value="'.$analyse['name'].'" />';
			$content .= '<div'.$this->pi_classParam('singleView').'>';
			$content .= '<h2>Analyse '.$analyse['name'].' : <span>'.$analyse['description'].'</span></h2></div>';
			$fp = fopen((string)$this->conf['data'].$analyse['directory'].'/index.html',"r");
			while (!feof($fp)) {
				$content .= fgets($fp, 4096);
			}
			return $content;
		// Else meaning using smarty
		} else {
			
			$smarty = new Smarty();
			$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1/analyzes');
			$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
			$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
			$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
			$smarty->security = true;
			$smarty->security_settings['MODIFIER_FUNCS'] = array('count');

			$smarty->assign('analyse', $analyse);
			$analysis_size = tx_nG6_db::get_analysis_size($this->piVars['analyze_id'], $this->conf['data']);
			$smarty->assign('analyse_size', tx_nG6_utils::get_octet_string_representation($analysis_size));
			$smarty->assign('data_folder', $this->conf["data"]);
			
			// Then select analyse results
			$results = tx_nG6_db::select_analyse_results($this->piVars['analyze_id']);		
			$smarty->assign('analyse_results', $results);
			
			// Select the run file description	
			if ($analyse['run_id'] != 'None') {
				$descriptions = tx_nG6_db::select_mid_descriptions($analyse['run_id']);
			} else {
				$descriptions = array();
			}
			$smarty->assign('descriptions', $descriptions);
			$smarty->assign('data_folder', $this->conf['data']);
			if (isset($this->LOCAL_LANG[$this->LLkey]) && count($this->LOCAL_LANG[$this->LLkey]) > 0) {
				$smarty->assign('llang', $this->LOCAL_LANG[$this->LLkey]);
			} else {
				$smarty->assign('llang', $this->LOCAL_LANG['default']);
			}			
			// Try to process the analyse template
			try {
				if (file_exists(t3lib_extMgm::extPath($this->extKey).'pi1/analyzes/'.$analyse['class'].'.js')) {
					$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] .= '<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'pi1/analyzes/'.$analyse['class'].'.js"></script>';
				}
				return $smarty->fetch($analyse['class'].'.tpl'); 
			} catch (Exception $e) { 
				return str_replace(array('###ANALYSE_CLASS###'), array($analyse['class']), $this->pi_getLL('no_template_found','[no_template_found:###ANALYSE_CLASS###]')); 
			}
		}
	}
	
	/**
	 * Overloading of the tslib_pibase->pi_list_linkSingle function so piVars[showUid] is not set.
	 * Uses pi_linkTP for the linking
	 *
	 * @param	string		The content string to wrap in <a> tags
	 * @param	integer		UID of the record for which to display details (basically this will become the value of [showUid]
	 * @param	boolean		See pi_linkTP_keepPIvars
	 * @param	array		Array of values to override in the current piVars. Same as $overrulePIvars in pi_linkTP_keepPIvars
	 * @param	boolean		If true, only the URL is returned, not a full link
	 * @param	integer		Alternative page ID for the link. (By default this function links to the SAME page!)
	 * @return	string		The input string wrapped in <a> tags
	 * @see pi_linkTP(), pi_linkTP_keepPIvars()
	 */
	function pi_list_linkSingle($str,$uid,$cache=FALSE,$mergeArr=array(),$urlOnly=FALSE,$altPageId=0)	{
		if ($this->prefixId)	{
			if ($cache)	{
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP($str,Array($this->prefixId=>$overrulePIvars),$cache,$altPageId);
			} else {
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP_keepPIvars($str,$overrulePIvars,$cache,0,$altPageId);
			}

				// If urlOnly flag, return only URL as it has recently be generated.
			if ($urlOnly)	{
				$str = $this->cObj->lastTypoLinkUrl;
			}
		}
		return $str;
	}
	
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php'])	{
	include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php']);
}

?>