def zip_jcamp_n_img():
file = FileContainer(request.files['file'])
molfile = FileContainer(request.files.get('molfile'))
params = extract_params(request)
if file: # and allowed_file(file):
cmpsr = TraModel(file, molfile=molfile, params=params).to_composer()
tf_jcamp, tf_img = cmpsr.tf_jcamp(), cmpsr.tf_img()
spc_type = cmpsr.core.ncl if cmpsr.core.typ == 'NMR' else cmpsr.core.typ
memory = to_zip_response([tf_jcamp, tf_img])
rsp = make_response(
send_file(
memory,
attachment_filename='spectrum.zip',
as_attachment=True
)
)
rsp.headers['X-Extra-Info-JSON'] = json.dumps({'spc_type': spc_type})
return rsp
def chemspectra_molfile_convert():
molfile = FileContainer(request.files.get('molfile'))
mm = MoleculeModel(molfile)
return jsonify(
status=True,
smi=mm.smi,
mass=mm.mass,
svg=mm.svg,
)
def chemspectra_file_save():
src = FileContainer(request.files['src'])
dst = FileContainer(request.files['dst'])
molfile = FileContainer(request.files.get('molfile'))
filename = request.form.get('filename', default=None)
params = extract_params(request)
if dst: # and allowed_file(file):
tm = TraModel(dst, molfile=molfile, params=params)
tf_jcamp, tf_img = tm.convert2jcamp_img()
tf_arr = [
src.temp_file(),
tf_jcamp,
tf_img,
tm.tf_predict(),
]
memory = to_zip_response(tf_arr, filename, src_idx=0)
return send_file(memory,
attachment_filename='spectrum.zip',
as_attachment=True)
def chemspectra_predict_by_peaks_json():
payload = request.json
layout = payload.get('layout')
peaks = payload.get('peaks')
shift = payload.get('shift')
molfile = FileContainer().from_str(payload.get('molfile'))
mm = MoleculeModel(molfile, layout, decorate=True)
outcome = InferModel.predict_nmr(
mm=mm,
layout=layout,
peaks=peaks,
shift=shift
)
if outcome:
return jsonify(outcome)
abort(400)
def test_ms_mzml_converter_composer():
params = {'mass': 230.079907196}
with open(target_dir + source_dir + '/ms/svs813f1.mzML', 'rb') as f:
file = FileStorage(f)
file = FileContainer(file)
mscv = MSConverter(file, params)
mscp = MSComposer(mscv)
lines = mscp.tf_jcamp().read()[:800] \
.decode('utf-8', errors='ignore').split('\n')
assert '##$CSSCANAUTOTARGET=3' in lines
assert '##$CSSCANEDITTARGET=3' in lines
assert '##$CSSCANCOUNT=24' in lines
assert '##$CSTHRESHOLD=0.05' in lines
assert '51.012176513671875, 34359.0' in lines