def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[param] != '' and param not in exclude: if 'uth_' in param: uth_type = param.split('_', 1) command += ' -uth ' + uth_type[1] + ' ' + str(data[param]) elif 'lth_' in param: lth_type = param.split('_', 1) command += ' -lth ' + lth_type[1] + ' ' + str(data[param]) else: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'text', result_dir)
def parse_arg(self, code, parser): tmp_dir = make_tmp_dir(self._data_dir) js_path = hash_val(code) + '.js' js_path = os.path.join(tmp_dir, js_path) write(js_path, code) ast_path = parser.parse(js_path) return tmp_dir, ast_path
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] exclude += ['markov_order'] command = utils.rsat_bin + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[param] != '' and param not in exclude: if param == 'org' and data[param] is not None and data[param] != '': len = 1 if 'markov_order' in data and data['markov_order'] is not None and data['markov_order'] != '': len = data['markov_order'] + 1 command += ' -bgfile ' + utils.get_backgroundfile(data['org'], len) + '.gz' elif 'uth_' in param: uth_type = param.split('_', 1) command += ' -uth ' + uth_type[1] + ' ' + str(data[param]) elif 'lth_' in param: lth_type = param.split('_', 1) command += ' -lth ' + lth_type[1] + ' ' + str(data[param]) else: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'ft', result_dir)
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters ) = utils.get_boolean_file_params(service_dir + '/' + tool.replace('-', '_') + '.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[ param] != '' and param not in exclude: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') command += ' -o ' + result_dir + '/position_analysis.tab' return utils.run_command_background(command, tool, result_dir, 'position_analysis_index.html')
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters ) = utils.get_boolean_file_params(service_dir + '/' + tool.replace('-', '_') + '.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[ param] != '' and param not in exclude: if param == 'return': return_fields = data[param].split(',') for i in return_fields: command += ' -return ' + i.strip() elif param == 'q': q_fields = data[param].split(',') for i in q_fields: command += ' -q ' + i.strip() else: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'tab', result_dir)
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters ) = utils.get_boolean_file_params(service_dir + '/' + tool.replace('-', '_') + '.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.rsat_bin + '/' + tool result_dir = utils.make_tmp_dir(tool) options_var = [ 'maxspacing', 'minspacing', 'sites', 'collect', 'seedmatrix', 'strand' ] for param in data: if param in boolean_var: if data[param] == True: if param == 'zoops': command += ' --zoops' else: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[ param] != '' and param not in exclude: if param in options_var: command += ' ---' + param + '=' + str(data[param]) else: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'tab', result_dir)
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters ) = utils.get_boolean_file_params(service_dir + '/' + tool.replace('-', '_') + '.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) matrix_title = dict() matrix_format = dict() for param in data: if 'matrix_title_' in param and data[param] != '': p = re.compile('matrix_title_(\d)') num = p.search(param) matrix_title[int(num.group(1)) - 1] = data[param] elif 'matrix_format_' in param and data[param] != '': p = re.compile('matrix_format_(\d)') num = p.search(param) matrix_format[int(num.group(1)) - 1] = data[param] elif param == 'o': command += ' -o ' + result_dir + '/' + data[param] elif param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[ param] != '' and param not in exclude: if 'uth_' in param: uth_type = param.split('_', 1) command += ' -uth ' + uth_type[1] + ' ' + str(data[param]) elif 'lth_' in param: lth_type = param.split('_', 1) command += ' -lth ' + lth_type[1] + ' ' + str(data[param]) else: command += ' -' + param + ' ' + str(data[param]) upload_str = utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') upload_str = re.sub(r"matrix_\d+", "matrix", upload_str) matrix_file = re.split('\s*-matrix\s*', upload_str) upload_str = '' for key in matrix_title: if matrix_title[key] != '': upload_str += ' -matrix ' + matrix_title[ key] + ' ' + matrix_file[key + 1] + ' ' + matrix_format[key] command += upload_str command += ' -outdir ' + result_dir + ' -prefix ' + tool return utils.run_command_background(command, tool, result_dir, data['o'] + '_SUMMARY.html')
def _run(self,data): output_choice = 'display' fileupload_parameters = ['i'] exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if data[param] is not None and data[param] != '' and param not in exclude: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, 'fasta', result_dir)
def _run(self,data): output_choice = 'display' (boolean_var, fileupload_parameters) = utils.get_boolean_file_params(service_dir+'/' + tool.replace('-','_') +'.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] result_dir = utils.make_tmp_dir(tool) command = utils.perl_scripts + '/' + tool for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif data[param] is not None and data[param] != '' and not param in exclude: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, fileupload_parameters, tool, result_dir, ',') return utils.run_command(command, output_choice, tool, data['out_format'], result_dir)
def _run(self, data): output_choice = 'display' (boolean_var, fileupload_parameters ) = utils.get_boolean_file_params(service_dir + '/' + tool.replace('-', '_') + '.yml') exclude = fileupload_parameters + ['content-type'] for x in fileupload_parameters: exclude = exclude + [x + '_string', x + '_string_type'] # background model exclude += ['markov_order', 'org', 'seq_type', 'seq_type_2'] command = utils.perl_scripts + '/' + tool result_dir = utils.make_tmp_dir(tool) for param in data: if param in boolean_var: if data[param] == True: command += ' -' + param elif data[param] == False: continue elif param == 'seq_type' and data[ param] is not None and data[param] != '': seq_file = utils.parse_fileupload_parameters( data, ['seq_file'], tool, result_dir, ',') seq_file_ops = seq_file.strip().split(' ') command += ' -seq ' + data['seq_type'] + ' ' + seq_file_ops[1] elif param == 'seq_type_2' and data[ param] is not None and data[param] != '': seq_file = utils.parse_fileupload_parameters( data, ['seq_file_2'], tool, result_dir, ',') seq_file_ops = seq_file.strip().split(' ') command += ' -seq ' + data['seq_type_2'] + ' ' + seq_file_ops[1] elif param == 'perm' and data[ param] is not None and data[param] != '': command += ' -perm ' + data['seq_type'] + ' ' + str( data[param]) elif param == 'plot' and data[ param] is not None and data[param] != '': command += ' -plot ' + data['seq_type'] + ' ' + data[param] elif param == 'perm_2' and data[ param] is not None and data[param] != '': command += ' -perm ' + data['seq_type_2'] + ' ' + str( data[param]) elif param == 'plot_2' and data[ param] is not None and data[param] != '': command += ' -plot ' + data['seq_type_2'] + ' ' + data[param] elif param == 'org' and data[ param] is not None and data[param] != '': len = 1 if 'markov_order' in data and data[ 'markov_order'] is not None and data[ 'markov_order'] != '': len = data['markov_order'] + 1 command += ' -bgfile ' + utils.get_backgroundfile( data['org'], len) + '.gz' elif data[param] is not None and data[ param] != '' and param not in exclude: command += ' -' + param + ' ' + str(data[param]) command += utils.parse_fileupload_parameters(data, ['m', 'ms', 'bgfile'], tool, result_dir, ',') command += ' -o ' + result_dir + '/' + tool return utils.run_command_background(command, tool, result_dir, tool + '_synthesis.html')