def get(self, process_id):
process = SequencingProcess(int(process_id))
name_pieces = ["preps", process.run_name]
with BytesIO() as content:
with zipfile.ZipFile(content,
mode='w',
compression=zipfile.ZIP_DEFLATED) as zf:
# We anticipate that someday the generation of multiple
# prep files for different studies may be coming back; that
# is why this loop has not been torn out in spite of the
# fact that, given changes in the generate_*_prep_information
# methods, the dictionary will only have one item in it
# so this loop will only ever execute once.
for _, prep in process.generate_prep_information().items():
# NB: first piece is NOT the same as above: singular "prep"
# instead of plural "preps"
curr_name_pieces = ["prep", process.run_name]
name = self.generate_file_name(curr_name_pieces, process)
zf.writestr(name, prep)
self.deliver_zip(name_pieces,
process,
content.getvalue(),
extension="zip")
def get(self, process_id):
process = SequencingProcess(int(process_id))
text = process.generate_sample_sheet()
name_pieces = ["samplesheet", process.run_name]
if not process.is_amplicon_assay:
name_pieces.append(process.experiment)
self.deliver_text(name_pieces, process, text, extension="csv")
def get(self, process_id):
pid = int(process_id)
process = SequencingProcess(pid)
text = process.generate_sample_sheet()
name_pieces = ["samplesheet", process.run_name]
# TODO: Verify that the isAmplicon conditional is still needed.
assay = PoolComposition.get_assay_type_for_sequencing_process(pid)
if assay != 'Amplicon':
name_pieces.append(process.experiment)
self.deliver_text(name_pieces, process, text, extension="csv")
def get(self):
res = {"data": [[p['process_id'],
p['run_name'],
p['experiment'],
p['principal_investigator'],
p['sequencing_process_id']]
for p in SequencingProcess.list_sequencing_runs()]}
self.write(res)
def create_sequencing_process(user, pools):
seq_process = SequencingProcess.create(
user,
pools,
'New sequencing run %s' % datetime.now(),
'Run experiment %s' % datetime.now(),
Equipment(18),
151,
151,
User('*****@*****.**'),
contacts=[User('*****@*****.**'),
User('*****@*****.**')])
return seq_process
def post(self, _):
pools = self.get_argument('pools')
run_name = self.get_argument('run_name')
experiment = self.get_argument('experiment')
sequencer_id = self.get_argument('sequencer')
fwd_cycles = int(self.get_argument('fwd_cycles'))
rev_cycles = int(self.get_argument('rev_cycles'))
pi = self.get_argument('principal_investigator')
contacts = self.get_argument('additional_contacts')
pools = [PoolComposition(x) for x in json_decode(pools)]
contacts = [User(x) for x in json_decode(contacts)]
process = SequencingProcess.create(self.current_user, pools,
run_name, experiment,
Equipment(sequencer_id), fwd_cycles,
rev_cycles, User(pi), contacts)
self.write({'process': process.id})