function get_data_total($path, $dbpass) { $file_count = 0; $file_size = 0; $countQuery = "SELECT count(*) as dbcount from Genomes.xGDB_Log where {$path} !='' AND {$path} LIKE '/xGDBvm/data%' AND Status='Development'"; # non-example data paths $get_count = $countQuery; $check_get_count = mysql_query($get_count); $count = $check_get_count; $row = mysql_fetch_assoc($count); $gdb_count = $row['dbcount']; $gdbQuery = "SELECT DISTINCT {$path} from Genomes.xGDB_Log where {$path} !='' AND {$path} LIKE '/xGDBvm/data%' AND Status='Development'"; # non-example data paths $get_gdb = $gdbQuery; $check_get_gdb = mysql_query($get_gdb); $result = $check_get_gdb; $n = 0; while ($row = mysql_fetch_assoc($result)) { $input_path = $row[$path]; if ($path == "Input_Data_Path" || $path == "Update_Data_Path") { $gdb_input = create_file_list($input_path, "dir", $input_path, "", 0, $dbpass); // returns array($file_list_formatted, $n, $total_size, $file_list) # $gdb_input= create_file_list("/xGDBvm/examples/example2/new_data", "dir", "", "", 0); // requires ($input, $type, $path, $title, $cutoff); returns array($file_list_formatted, $n, $total_size, $file_list) $file_count = $file_count + $gdb_input[1]; // number of valid files $file_size = $file_size + $gdb_input[2]; // number of MB break; } elseif ($path == "CpGAT_ReferenceProt_File" || $path == "RepeatMask_File") { $gdb_cpgat = validate_refpro($input_path); // returns array($file_list, $n, $total_size) $file_count = $file_count + $gdb_cpgat[1]; // number of valid files $file_size = $file_size + $gdb_cpgat[2]; // number of MB } $n = $n + 1; } return array($file_count, $file_size, $gdb_count); // file count and MB size for all validated data of the specified class (input, update, cpgat, mask) }
$validRefPro = $CpGAT_ReferenceProt_File; //We don't store validated file other than user input. It is by definition validated or the process would not have run! } elseif ($g_exists != "Yes" && mysql_select_db("{$DBid}")) { $database_message = "<span class=\"alertnotice largerfont\">Warning: A MySQL database exists for {$DBid} but <pre>/{$XGDB_DATADIR}{$DBid}/</pre> is missing. </span>"; $create = "display_off"; // disable create button #### End GDB Exists #### } else { ############ GDB Database Not Yet Created (Status='Development').############# $archive_dirlist = archive_dir_dropdown($dataDir, "ArchiveGDB"); #this is a list of any ArchiveGDB datasets that are available. Updated 1-28-16 to include dataDir param. $display_load_archive = $archive_dirlist == "" ? "display_off" : "{$display_load_archive}"; #don't display the dropdown if there are no archives. $archive_dirlist_display = $archive_dirlist == "" ? "<option value=\"none\">-none-</option>" : $archive_dirlist; ######### Validate user-proposed Input Data Path files (note - these functions are also called elsewhere in this script for "Current" GDB. ###### $arrayList = create_file_list($Input_Data_Path, "dir", $Input_Data_Path, "Input Directory", "2", $dbpass); //create validated, formatted file list based on dir path - conf_functions.inc.php $validList = $arrayList[0]; //formatted $validCount = $arrayList[1]; $validSize = $arrayList[2]; # total bytes from valid files $validGB = round($validSize / 1000000000, 3); $validRefPro = $CpGAT_Status == "Yes" ? validate_library($CpGAT_ReferenceProt_File, "Reference Protein Library", $dbpass) : ""; //from conf_functions.inc.php $validRepMask = $RepeatMask_Status == "Yes" ? validate_library($RepeatMask_File, "Repeat Mask Library", $dbpass) : ""; //from conf_functions.inc.php $file_codes = $arrayList[4]; #single-letter code string $input_errors = input_errors($file_codes); $input_warnings = input_warnings($Input_Data_Path);
$Gth_Species_Model = $data["Gth_Species_Model"]; ######## CpGAT ######## $CpGAT_Status = $data["CpGAT_Status"]; $CpGAT_ReferenceProt_File = $data["CpGAT_ReferenceProt_File"]; $CpGAT_BGF = $data["CpGAT_BGF"]; $CpGAT_Augustus = $data["CpGAT_Augustus"]; $CpGAT_GeneMark = $data["CpGAT_GeneMark"]; $CpGAT_Skip_Mask = $data["CpGAT_Skip_Mask"]; $CpGAT_Relax_UniRef = $data["CpGAT_Relax_UniRef"]; $CpGAT_Skip_PASA = $data["CpGAT_Skip_PASA"]; $CpGAT_Filter_Genes = $data["CpGAT_Filter_Genes"]; $Update_Data_CpGAT = $data["Update_Data_CpGAT"]; $Update_Status = $data["Update_Status"]; ####### Database Update ####### ####### Get snapshot of input files (valid list) ##### $arrayList = create_file_list($Input_Data_Path, "dir", "", "", 2, $dbpass); //from conf_functions.inc.php create_file_list($input, $type, $path, $title, $cutoff) $validList = $arrayList[3]; # not formatted, just the raw list (what we will store) ####### Set up Computer Resources Parameter String (GSQ) ####### $GSQ_CompResParameter = " Local "; // Default arguments. if ($GSQ_CompResources == "Remote") { //require correct config. $remote = true; $username = $_SESSION['username']; // the user's iPlant login $refresh_token = $_SESSION['refresh_token']; // obtained from iPlant authentication URL $server = $_SERVER['SERVER_NAME']; // required for callback URL