def import_from_local_path(path, target_dir, fsc=None):
fns = glob(os.path.join(path, '**', '*.*'), recursive=True)
fns = [fn for fn in fns if is_ms_file(fn)]
fns_out = []
n_files = len(fns)
for i, fn in enumerate(tqdm(fns)):
if fsc is not None: fsc.set('progress', int(100 * (1 + i) / n_files))
fn_out = P(target_dir) / P(fn).with_suffix('.feather').name
if P(fn_out).is_file(): continue
fns_out.append(fn_out)
try:
convert_ms_file_to_feather(fn, fn_out)
except:
logging.warning(f'Could not convert {fn}')
return fns_out
def parse_ms_files(contents, filename, date, target_dir):
content_type, content_string = contents.split(',')
decoded = base64.b64decode(content_string)
fn_abs = os.path.join(target_dir, filename)
with lock(fn_abs):
with open(fn_abs, 'wb') as file:
file.write(decoded)
new_fn = convert_ms_file_to_feather(fn_abs)
if os.path.isfile(new_fn): os.remove(fn_abs)
def ms_convert(n_clicks, rows, wdir):
target_dir = os.path.join(wdir, 'ms_files')
if n_clicks is None:
raise PreventUpdate
fns = [row['MS-file'] for row in rows]
fns = [fn for fn in fns if not fn.endswith('.feather')]
fns = [os.path.join(target_dir, fn) for fn in fns]
n_total = len(fns)
for i, fn in enumerate(fns):
fsc.set('progress', int(100 * (i + 1) / n_total))
new_fn = convert_ms_file_to_feather(fn)
if os.path.isfile(new_fn): os.remove(fn)
return dbc.Alert('Files converted to feather format.', color='info')
def test_convert_mzml_to_feather(tmp_path):
fn_out = P(TEST_MZML).with_suffix('.feather')
convert_ms_file_to_feather(TEST_MZML, fn_out)
assert fn_out.is_file()
