}
### POST actions ###
if ($_POST['action'] == 'restore_all') {
$warning = "";
$return = $_POST['return'];
$return_url = $return == "archive" ? "archive.php" : ($return == "viewall" ? "viewall.php" : "index.php");
$command = "/xGDBvm/scripts/xGDB_RestoreAll.sh";
exec($command);
header("Location: {$return_url}");
} elseif ($_POST['action'] == 'restore_one' && $_POST['id'] != '' && $_POST['xgdb'] != '') {
$warning = "";
$id = intval($_POST['id']);
// e.g. 1, the ID of the GDB requesting restoration
$xgdb = $_POST['xgdb'];
//e.g. GDB001, the GDBID of the GDB requesting restoration
$xgdb = shell_args_whitelist($xgdb);
// sanitize 2/26/15
$source_file = $_POST['source_file'];
//e.g GDB002-[description-species].tar; The archive source may be the SAME numbered GDB archive as the current GDB, or (if specified by user and stored in xGDB_Log.Restore_From_OtherGDB) a DIFFERENT-numbered GDB archive....
$pattern = "/^(GDB\\d\\d\\d)(-\\S+)(\\.tar)\$/";
# Parse the GDB ID from the source filename
if (preg_match($pattern, $source_file, $matches)) {
$xgdb_source = $matches[1];
// e.g. GDB001
} else {
$warning = "The archive source file is incorrectly named or missing, and it could not be loaded";
exit;
}
$id_source = intval(substr($xgdb_source, -3));
// e.g. 2
$return = $_POST['return'];
$file = $_POST['source_file'];
# Restore_From_File (from Genomes.xGDB_Log), a filename e.g. GDB002-Description-Species.tar
$file = shell_args_whitelist($file);
$return = "archive.php";
$return_url = $return == 'view' ? "view.php?id={$id}" : "archive.php";
$command = "/xGDBvm/scripts/xGDB_DeleteOneArchive.sh {$xgdb} {$id} {$file} >> /tmp/log & ";
exec($command);
header("Location: {$return_url}");
} elseif ($_POST['action'] == 'copy_one') {
$warning = "";
$xgdb = $_POST['xgdb'];
$xgdb = shell_args_whitelist($xgdb);
$id = intval($_POST['id']);
$file = $_POST['source_file'];
# Restore_From_File (from Genomes.xGDB_Log), a filename e.g. GDB002-Description-Species.tar
$file = shell_args_whitelist($file);
$return_url = "archive.php";
$command = "/xGDBvm/scripts/xGDB_CopyOneArchive.sh {$xgdb} {$id} {$file} >> /tmp/log & ";
exec($command);
header("Location: {$return_url}");
} elseif ($_POST['action'] == 'delete_archive_all') {
$warning = "";
$return = "archive.php";
$return_url = $return == 'view' ? "view.php?id={$id}" : "archive.php";
$command = "/xGDBvm/scripts/xGDB_DeleteArchiveAll.sh >> /tmp/log & ";
exec($command);
header("Location: {$return_url}");
} else {
$warning = "Could not proceed. Unable to archive";
exit;
}
$ID = $id;
#post result.
$DBid = 'GDB' . substr('00' . $id, -3);
#calculated from unique ID
$DBname = $data["DBname"];
$Status = $data["Status"];
$Organism = $data["Organism"];
$GSQ_CompResources = $data["GSQ_CompResources"];
$GTH_CompResources = $data["GTH_CompResources"];
####### Database Creation #######
$Input_Data_Path = $data["Input_Data_Path"];
$input_path_trim = trim($Input_Data_Path);
//trim spaces from ends
$input_path = preg_replace('/\\s/', '_', $input_path_trim);
//change any directory name spaces into "_"
$input_path = shell_args_whitelist($input_path);
//from validation_functions.inc.php 2/26/15
$GFF_Type = $data["GFF_Type"];
$gff_type = $GFF_Type == "CpGAT" ? "standard" : "other";
//specifies gff3 file type, whether CpGAT generated or "other".
####### GSQ Parameters #######
$RepeatMask_Status = $data["RepeatMask_Status"];
$RepeatMask_File = $data["RepeatMask_File"];
$Species_Model = $data["Species_Model"];
$Alignment_Stringency = $data["Alignment_Stringency"];
####### GSQ Parameters #######
$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"];
