def post(self):
# We will receive as many files as plates the user has selected
# The key of the self.request.files dictionary is of the form
# plate-file-<PLATE_ID> so use the keys to know the plates
# that we need to quantify
plates = []
for key in self.request.files:
plate_id = key.rsplit('-', 1)[1]
# The 0 is because for each key we have a single file
file_content = self.request.files[key][0]['body'].decode('utf-8')
plate = Plate(plate_id)
pc = plate.plate_configuration
concentrations = QuantificationProcess.parse(file_content,
rows=pc.num_rows,
cols=pc.num_columns)
names = np.empty_like(plate.layout, dtype='object')
blanks = np.zeros_like(plate.layout, dtype=bool)
# fetch the sample names and whether or not the samples are blanks
# by default these are set to be None and False.
for i, full_row in enumerate(plate.layout):
for j, well in enumerate(full_row):
# some wells have no compositions at all so skip those
if well is None:
continue
comp = well.composition
# cache the sample compositions to avoid extra intermediate
# queries
if isinstance(comp, GDNAComposition):
smp = comp.sample_composition
elif isinstance(comp, (CompressedGDNAComposition,
LibraryPrep16SComposition)):
smp = comp.gdna_composition.sample_composition
elif isinstance(comp, LibraryPrepShotgunComposition):
smp = comp.normalized_gdna_composition\
.compressed_gdna_composition.gdna_composition\
.sample_composition
else:
raise ValueError('This composition type is not '
'supported')
blanks[i][j] = smp.sample_composition_type == 'blank'
names[i][j] = smp.sample_id
plates.append({
'plate_name': plate.external_id,
'plate_id': plate_id,
'concentrations': concentrations.tolist(),
'names': names.tolist(),
'blanks': blanks.tolist(),
'type': plate.process._process_type
})
self.render('quantification.html', plates=plates)
def post(self):
plate_id = self.get_argument('plate-select')
# Magic number 0 -> there is only 1 file attached
file_content = self.request.files['plate-reader-fp'][0]['body'].decode(
'utf-8')
concentrations = QuantificationProcess.parse(file_content)
plate = Plate(plate_id)
self.render('quantification.html',
concentrations=concentrations.tolist(),
plate_name=plate.external_id,
plate_id=plate.id,
plate_conf=plate.plate_configuration.description)
def post(self):
# We will receive as many files as plates the user has selected
# The key of the self.request.files dictionary is of the form
# plate-file-<PLATE_ID> so use the keys to know the plates
# that we need to quantify
plates = []
for key in self.request.files:
plate_id = key.rsplit('-', 1)[1]
# The 0 is because for each key we have a single file
file_content = self.request.files[key][0]['body'].decode('utf-8')
plate = Plate(plate_id)
pc = plate.plate_configuration
concentrations = QuantificationProcess.parse(
file_content, rows=pc.num_rows, cols=pc.num_columns)
plates.append({'plate_name': plate.external_id,
'plate_id': plate_id,
'concentrations': concentrations.tolist()})
self.render('quantification.html', plates=plates)