def test_xls_key(self):
#
# Import .xlsx workbook
#
test_file = os.path.join(test_dir, "sample_gc_ms_key.xlsx")
headers, table = gc_ms.import_xlsx_metadata(open(test_file, "rb"))
assert (headers == [
'sample ID (could be vial #)',
'label to display',
'parent strain',
'plasmid/change',
'colony number',
'time point',
'media (induction, etc.)',
'sample type',
None,
'user field 1',
'user field 2',
'user field 3',
])
def process_gc_ms_form_and_parse_file(form, file):
try:
data = re.sub("\r", "", file.read())
result = gc_ms.Report(data.splitlines())
except ValueError as e:
try:
headers, table = gc_ms.import_xlsx_metadata(file)
except Exception:
raise ValueError(
"The uploaded file could not be processed as either an MSDChemStation report "
"or an Excel workbook.")
else:
return {
"data_type": "xls",
"headers": headers,
"table": table,
}
if form.get("auto_peaks") == "auto":
return result.find_peaks_automatically_and_export(include_headers=True)
else:
n_mols = form_utils.extract_integers_from_form(form, "n_mols")
rt_std_min = form_utils.extract_floats_from_form(
form, "rt_standard_min")
rt_std_max = form_utils.extract_floats_from_form(
form, "rt_standard_max")
rt_ranges_and_molecules = [(rt_std_min, rt_std_max, "standard")]
for i_mol in range(n_mols):
mol_name = form_utils.extract_non_blank_string_from_form(
form, param_name="mol_name_%d" % i_mol)
rt_min = form_utils.extract_floats_from_form(
form, param_name='rt_min_mol_%d' % i_mol)
rt_max = form_utils.extract_floats_from_form(
form, param_name='rt_max_mol_%d' % i_mol)
rt_ranges_and_molecules.append((rt_min, rt_max, mol_name))
rt_ranges_and_molecules.sort(key=lambda x: x[0])
for i_rt, (x1, y1, s1) in enumerate(rt_ranges_and_molecules[:-1]):
x2, y2, s2 = rt_ranges_and_molecules[i_rt + 1]
assert (y1 < x2) # this should really be checked server-side too
return result.find_peaks_by_range_and_export(
rt_ranges=[(x, y) for (x, y, s) in rt_ranges_and_molecules],
molecule_names=[s for (x, y, s) in rt_ranges_and_molecules])