* 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! ***************************************************************/ require_once(PATH_t3lib.'class.t3lib_befunc.php'); require_once(PATH_t3lib.'stddb/tables.php'); require_once(t3lib_extMgm::extPath('cms','ext_tables.php')); require_once(PATH_t3lib.'class.t3lib_db.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_process.php'); /** * Class 'tx_nG6_eid' for the 'nG6' extension. * This class is in charge of all communication between the client and the server using AJAX * * @author PF bioinformatique de Toulouse <> */ class tx_nG6_eid { /** * The main function of the tx_nG6_eid, this function is the one called when using ajax */ function main() { // Connect to the databse tslib_eidtools::connectDB(); $type = trim(t3lib_div::_GP('type')); $user_id = trim(t3lib_div::_GP('user_id')); // If the type of data requested is project if ($type == 'project') { $project_id = trim(t3lib_div::_GP('id')); // Select all runs linked to the project $project_runs = tx_nG6_db::get_project_runs($user_id, $project_id, 'tx_nG6_run.date DESC'); // for each run $html_tree = ''; foreach($project_runs as $run_id => $run_values) { $html_tree .= '

'.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###', '###SPAN_NB_SEQ###', '###SPAN_SPECIES###'), array($run_values['name'], strftime('%d-%m-%y',$run_values['date']), $run_values['nb_sequences'], $run_values['species']), trim(t3lib_div::_GP('run_description'))).'

'; } // Then all project analysis $project_analysis = tx_nG6_db::get_project_analysis($user_id, $project_id, 'tx_nG6_analyze.name'); foreach($project_analysis as $analyse_id => $analyse_values) { $html_tree .= '

'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'

'; } // Return the html_tree print $html_tree; // If the type of data requested is run } else if ($type == 'run'){ $run_id = trim(t3lib_div::_GP('id')); // Select all analysis linked to the run and the run information $run_analysis = tx_nG6_db::get_run_analysis($user_id, $run_id, 'tx_nG6_analyze.name'); $run_info = tx_nG6_db::select_run($run_id); // for each analysis $html_tree = ''; $html_tree .= '

'.trim(t3lib_div::_GP("raw_data_description")).'

'; foreach($run_analysis as $analyse_id => $analyse_values) { $html_tree .= '

'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'

'; } // Return the html_tree print $html_tree; // If downloading data is requested } else if ($type == 'download') { $format = trim(t3lib_div::_GP('format')); // If link in home directory if ($format == 'home_link') { $ids = trim(t3lib_div::_GP('ids')); $data_folder = trim(t3lib_div::_GP('data_folder')); $user_login = trim(t3lib_div::_GP('user_login')); $user_pwd = trim(t3lib_div::_GP('user_pwd')); $user_directory = trim(t3lib_div::_GP('user_directory')); $retcode = $this->create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory); print $retcode; // If a .tar.gz file } else { $ids = trim(t3lib_div::_GP('ids')); $data_folder = trim(t3lib_div::_GP('data_folder')); $tmp_folder = trim(t3lib_div::_GP('tmp_folder')); $user_email = trim(t3lib_div::_GP('user_email')); $title_email = trim(t3lib_div::_GP('title_email')); $msg_email = trim(t3lib_div::_GP('msg_email')); $archive_info = $this->create_archive_script($user_id, $ids, $data_folder, $tmp_folder, "tar.gz", $user_email, $title_email, $msg_email); $process = new Process("tcsh ".$archive_info[0]); print "pid=".$process->getPid()."&archive_path=".$archive_info[1]; } // If asked to check a job status } else if($type == 'check_status') { $pid = trim(t3lib_div::_GP('pid')); $archive_path = trim(t3lib_div::_GP('archive_path')); $process = new Process(); $process->setPid($pid); // If the job is done if ($process->status()) { print "pid=0&archive_path=".$archive_path; // If the job is still runing } else { print "pid=".$process->getPid()."&archive_path=".$archive_path; } // If asked to hide a {project/run} } else if ($type == 'hide') { $ids = trim(t3lib_div::_GP('ids')); // {project/run}_id to array (1;2;3;...) -> [1;2;3;...] $tab_ids = explode(";",$ids); $hide_level = trim(t3lib_div::_GP('hide_level')); if ($hide_level == 'project') { foreach($tab_ids as $id => $value) { tx_nG6_db::hide_project($value, $user_id); } } else if ($hide_level == 'run') { foreach($tab_ids as $id => $value) { tx_nG6_db::hide_run($value, $user_id); } } else if ($hide_level == 'analysis') { foreach($tab_ids as $id => $value) { tx_nG6_db::hide_analysis($value, $user_id); } } // If asked to unhide a {project/run} } else if ($type == 'unhide') { $ids = trim(t3lib_div::_GP('ids')); // {project/run}_id to array (1;2;3;...) -> [1;2;3;...] $tab_ids = explode(";",$ids); $unhide_level = trim(t3lib_div::_GP('unhide_level')); if ($unhide_level == 'project') { foreach($tab_ids as $id => $value) { tx_nG6_db::unhide_project($value, $user_id); } } else if ($unhide_level == 'run') { foreach($tab_ids as $id => $value) { tx_nG6_db::unhide_run($value, $user_id); } } else if ($unhide_level == 'analysis') { foreach($tab_ids as $id => $value) { tx_nG6_db::unhide_analysis($value, $user_id); } } // If asked to delete a {project/run/analyze} } else if ($type == 'delete') { $ids = trim(t3lib_div::_GP('ids')); // {project/run}_id to array (1;2;3;...) -> [1;2;3;...] $tab_ids = explode(";",$ids); $delete_level = trim(t3lib_div::_GP('del_level')); $data_folder = trim(t3lib_div::_GP('data_folder')); $user_login = trim(t3lib_div::_GP('user_login')); $user_pwd = trim(t3lib_div::_GP('user_pwd')); $res = 0; // check login and password if (isset($user_login) && isset($user_pwd) && $user_login != 'undefined' && $user_pwd != 'undefined') { $res = 0; $connection = ssh2_connect('127.0.0.1', 22); if (!$connection) { $res = 3; } if (!ssh2_auth_password($connection, $user_login, $user_pwd)) { $res=2;} } else { $res = 3; } if ($res == 0) { if ($delete_level == 'project') { foreach($tab_ids as $id => $value) { $res = tx_nG6_db::delete_project($user_id, $value, $user_login, $user_pwd, $data_folder); if ($res != 0) { break; } } } else if ($delete_level == 'run') { foreach($tab_ids as $id => $value) { $res = tx_nG6_db::delete_run($user_id, $value, $user_login, $user_pwd, $data_folder); if ($res != 0) { break; } } } else if ($delete_level == 'analysis') { foreach($tab_ids as $id => $value) { $res = tx_nG6_db::delete_analysis($value, $user_login, $user_pwd, $data_folder); if ($res != 0) { break; } } } } print $res; // If asked to publish a project } else if ($type == 'publish') { $ids = trim(t3lib_div::_GP('ids')); // project_id to array (1;2;3;...) -> [1;2;3;...] $tab_ids = explode(";",$ids); foreach($tab_ids as $id => $value) { tx_nG6_db::publish_project($value, $user_id); } // If asked to unpublish a project } else if ($type == 'unpublish') { $ids = trim(t3lib_div::_GP('ids')); // project_id to array (1;2;3;...) -> [1;2;3;...] $tab_ids = explode(";",$ids); foreach($tab_ids as $id => $value) { tx_nG6_db::unpublish_project($value); } // If asked the size } else if ($type == 'get_size') { $ids = trim(t3lib_div::_GP('ids')); $view = trim(t3lib_div::_GP('view')); $data_folder = trim(t3lib_div::_GP('data_folder')); $tab_ids = explode(",",$ids); $full_size = 0; foreach($tab_ids as $id => $value) { if ($view == "run") { $full_size += tx_nG6_db::get_run_size($value, $data_folder, $user_id); } else if ($view == "project") { $full_size += tx_nG6_db::get_project_size($value, $data_folder, $user_id); } } print tx_nG6_utils::get_octet_string_representation($full_size); // If update a field } else if ($type == 'update_db_field') { //Retrieve infomation $table = trim(t3lib_div::_GP('table')); $id = trim(t3lib_div::_GP('id')); $field = trim(t3lib_div::_GP('field')); $value = trim(t3lib_div::_GP('value')); //If change concernes a date if( $field == "date" || $field == "crdate" ) { //Change date format $date = explode('-', $value) ; $timestamp = mktime (0, 0, 1, $date[1], $date[0], $date[2]) ; //Update the entity tx_nG6_db::update_field($table, $id, $field, $timestamp); } else { //Update the entity tx_nG6_db::update_field($table, $id, $field, $value); } print $value; // If asked the krona page } else if ($type == 'get_krona') { $data_folder = trim(t3lib_div::_GP('data_folder')); $file_name = trim(t3lib_div::_GP('file_name')); $sequence_name = trim(t3lib_div::_GP('sequence_name')); $doc = new DomDocument(); $data_root = $doc->createElement('data'); $doc->appendChild($data_root); $attr_data_root = $doc->createAttribute("xml:id"); $data_root->appendChild($attr_data_root); $t_data_root = $doc->createTextNode('data_root'); $attr_data_root->appendChild($t_data_root); $data_root->setIdAttribute("xml:id", true); $magnitude = $doc->createElement('magnitude'); $magnitude->setAttribute("attribute", "g"); $magnitude = $data_root->appendChild($magnitude); $magnitudet = $doc->createTextNode(''); $magnitudet = $magnitude->appendChild($magnitudet); $color = $doc->createElement('color'); $color = $data_root->appendChild($color); $colort = $doc->createTextNode(''); $colort = $color->appendChild($colort); $attributes = $doc->createElement('attributes'); $attributes->setAttribute("g", $sequence_name); $attributes = $data_root->appendChild($attributes); $attributest = $doc->createTextNode(''); $attributest = $attributes->appendChild($attributest); $datasets = $doc->createElement('datasets'); $datasets->setAttribute("names", $file_name); $datasets = $data_root->appendChild($datasets); $datasetst = $doc->createTextNode(''); $datasetst = $datasets->appendChild($datasetst); $file_path = trim(t3lib_div::_GP('file_path')); $file_path = $data_folder."/".$file_path; // If the file exists $total = 0; if (file_exists($file_path)) { $lines = file($file_path); // Loop through our array foreach ($lines as $line_num => $line) { if ($line != "") { $mparts = explode("\t", trim($line)); if ($mparts[0] != "taxlevel" and $mparts[0] != "0") { // If this guy doesnt exist yet $id_searched = str_replace(".", "_", "node_".$mparts[1]); if (is_null($doc->getElementById($id_searched))) { $parentl = implode("_", array_slice(explode(".", $mparts[1]), 0, -1)); // If no parent yet, this is the root if (is_null($doc->getElementById("node_".$parentl))) { $current_node = $doc->createElement('node'); $current_node->setAttribute("name", $mparts[2]); $current_node->setAttribute("g", $mparts[4]); $id = $doc->getElementById("data_root"); $id->appendChild($current_node); $attr_current_node = $doc->createAttribute("xml:id"); $current_node->appendChild($attr_current_node); $t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1])); $attr_current_node->appendChild($t_current_node); $current_node->setIdAttribute("xml:id", true); $current_nodet = $doc->createTextNode(''); $current_nodet = $current_node->appendChild($current_nodet); } else { $current_node = $doc->createElement('node'); $current_node->setAttribute("name", $mparts[2]); $current_node->setAttribute("g", $mparts[4]); $id = $doc->getElementById("node_".$parentl); $id->appendChild($current_node); $attr_current_node = $doc->createAttribute("xml:id"); $current_node->appendChild($attr_current_node); $t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1])); $attr_current_node->appendChild($t_current_node); $current_node->setIdAttribute("xml:id", true); $current_nodet = $doc->createTextNode(''); $current_nodet = $current_node->appendChild($current_nodet); } } } if ($mparts[0] == "1") { $total += (int)$mparts[4]; } } } } $color->setAttribute("attribute", "g"); $color->setAttribute("valueStart", "0"); $color->setAttribute("valueEnd", (string)$total); $color->setAttribute("hueStart", "120"); $color->setAttribute("hueEnd", "360"); $xml_string = $doc->saveXML(); $xml_parts = explode("\n", $xml_string); $val = ''; $val .= ''; $val .= ''; $val .= ''; $val .= ''; $val .= '

'; $val .= '

'; $val .= ''; $val .= $xml_parts[1]; $val .= '

'; $val .= ''; $val .= ''; print $val; } } /** * Creates an archiving script to archive data from ids * * @param string $user_id the user id * @param array $ids list of ids to download * @param string $data_folder the data folder where are stored the data * @param string $tmp_folder the output directory * @param string $format the archiving format (tar.gz) * @param string $user_email the user email * @param string $title_email the email title to send * @param string $msg_email the email message to send * @return array (the path to the script, the url path to the final archive) */ private function create_archive_script($user_id, $ids, $data_folder, $tmp_folder, $format, $user_email, $title_email, $msg_email) { // First get the archive name where will be stored the data $random_key = tx_nG6_utils::create_random_key(10); $archive_path = $tmp_folder."/ng6_".$random_key; while( file_exists($archive_path) ) $archive_path = $tmp_folder."/ng6_".$random_key; // Then get the directories structure $directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $archive_path); $archive_script_path = $tmp_folder."/ng6_".$random_key.".sh"; // And write down the script in charge to create the archive $fp = fopen($archive_script_path, 'w'); foreach($directories[0] as $index => $src_directory) { if (!file_exists( $directories[1][$index])) { fwrite($fp, "mkdir -p ".$directories[1][$index]."\n"); } // For each files in the source directory foreach(scandir($src_directory) as $file) { if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") { fwrite($fp, "cp ".$src_directory."/".$file." ".$directories[1][$index]."\n"); } } } fwrite($fp, "cd ".$tmp_folder."\n"); fwrite($fp, "tar -czf ng6_".$random_key.".tar.gz ng6_".$random_key."\n"); fwrite($fp, "rm -rf ".$archive_path."\n"); fwrite($fp, 'echo "'.str_replace(array('SPAN_ARCHIVE_NAME'), array("ng6_".$random_key.".tar.gz"), $msg_email).'" | mail -s "'.$title_email.'" '.$user_email."\n"); fclose($fp); return array($archive_script_path, "ng6_".$random_key.".tar.gz"); } /** * Creates symbolic links between ids from data_folder into user_directory * * @param string $user_id the user id * @param string $user_login the user login to make ssh * @param string $user_pwd the user pwd to make ssh * @param array $ids list of ids to download * @param string $data_folder the data folder where are stored the data * @param string $user_directory the output directory * @return 0=>everything ok, 1=>user rigth problem, 2=>wrong authentification, 3=>connection error */ private function create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory) { // First try to connect the specified user using ssh $connection = ssh2_connect('127.0.0.1', 22); if (!$connection) return 3; if (!ssh2_auth_password($connection, $user_login, $user_pwd)) return 2; // Then get the directories structure $directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $user_directory); // And process the directories structure $creation = true; foreach($directories[0] as $index => $src_directory) { if (!file_exists("ssh2.sftp://".$connection.$directories[1][$index])) { if (!mkdir("ssh2.sftp://".$connection.$directories[1][$index], 0755, true)) { $creation = false; break; } // For each files in the source directory foreach(scandir($src_directory) as $file) { if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") { if (!ssh2_exec($connection, 'ln -s '.$src_directory.'/'.$file.' '.$directories[1][$index].'/'.$file)) { $creation = false; break; } } } } } if (!$creation) return 1; return 0; } /** * Returns a table with the right directories structure considering ids * * @param string $user_id the user id * @param array $ids List of ids to download * @param string $data_folder The data folder where are stored the data * @param string $output_folder The output directory * @return array [0] => source_directories, [1] => dest_directories */ private function get_directories_structure_and_content($user_id, $ids, $data_folder, $output_folder) { $src_directories = array(); $dest_directories = array(); $vals = preg_split("/;/", $ids); // Characters to be replaced in the names of the run, the analyses ... $char_to_replace = array(' ','/'); // For each project/run/analysis foreach($vals as $val) { if ($val != "undefined" && $val != "") { $id = preg_split("/_/", $val); if ($id[0] == "data") { $run = tx_nG6_db::select_run($id[1]); if (!in_array($data_folder.$run["directory"], $src_directories)) { $src_directories[] = $data_folder.$run["directory"]; $ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]); $ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData"; $dest_directories[] = $ddest; } } else if ($id[0] == "run") { $run = tx_nG6_db::select_run($id[1]); if (!in_array($data_folder.$run["directory"], $src_directories)) { $src_directories[] = $data_folder.$run["directory"]; $ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]); $ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData"; $dest_directories[] = $ddest; } foreach(tx_nG6_db::get_run_analysis($user_id, $id[1], 'tx_nG6_analyze.name') as $analyse_id => $analyse_values) { $aid = preg_split("/_/", $analyse_id); if (!in_array($data_folder.$analyse_values["directory"], $src_directories)) { $src_directories[] = $data_folder.$analyse_values["directory"]; $ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]); $ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]); $ddest .= ".".$id[1]."/Analyse_".str_replace($char_to_replace, '_', $analyse_values["name"]).".".$aid[1]; $dest_directories[] = $ddest; } } } else if ($id[0] == "analyse") { $analyse = tx_nG6_db::select_analyse($id[1]); if (!in_array($data_folder.$analyse["directory"], $src_directories)) { $src_directories[] = $data_folder.$analyse["directory"]; // If it's a project analyse if ($analyse["run_id"] == 'None') { $ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]); $ddest .= ".".$analyse["project_id"]."/Project_analyses/".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1]; $dest_directories[] = $ddest; } else { $ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]); $ddest .= ".".$analyse["project_id"]."/Run_".str_replace($char_to_replace, '_', $analyse["run_name"]); $ddest .= ".".$analyse["run_id"]."/Analyse_".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1]; $dest_directories[] = $ddest; } } } } } return array($src_directories, $dest_directories); } } if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']) { include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']); } // Instanciation $SOBE = t3lib_div::makeInstance('tx_nG6_eid'); $SOBE->main(); ?>