def test_run_form_invalid_lowercase(self):
form = RunNameForm({
'run_name': '1234567_aaa'
})
self.assertFalse(form.is_valid())
try:
form.cleaned_data.get('run_name')
except forms.ValidationError as e:
self.assertEqual('BadRunName', e.code)
def test_run_form_invalid_name_date_second(self):
form = RunNameForm({
'run_name': 'M02345_191215'
})
self.assertFalse(form.is_valid())
try:
form.cleaned_data.get('run_name')
except forms.ValidationError as e:
self.assertEqual('BadRunName', e.code)
def upload_metadata(request):
form = RunNameForm()
if request.method == 'POST':
form = RunNameForm(request.POST)
if form.is_valid():
if not SequencingRun.objects.filter(
run_name=form.cleaned_data.get('run_name')).exists():
sequencing_run, created = SequencingRun.objects.update_or_create(
run_name=form.cleaned_data.get('run_name'), seqids=list())
else:
sequencing_run = SequencingRun.objects.get(
run_name=form.cleaned_data.get('run_name'))
files = [
request.FILES.get('file[%d]' % i)
for i in range(0, len(request.FILES))
]
container_name = sequencing_run.run_name.lower().replace('_', '-')
blob_client = BlockBlobService(
account_name=settings.AZURE_ACCOUNT_NAME,
account_key=settings.AZURE_ACCOUNT_KEY)
blob_client.create_container(container_name)
for item in files:
blob_client.create_blob_from_bytes(
container_name=container_name,
blob_name=item.name,
blob=item.read())
if item.name == 'SampleSheet.csv':
instance = DataFile(sequencing_run=sequencing_run,
data_file=item)
instance.save()
with open(
'olc_webportalv2/media/{run_name}/SampleSheet.csv'.
format(run_name=str(sequencing_run))) as f:
lines = f.readlines()
seqid_start = False
seqid_list = list()
for i in range(len(lines)):
if seqid_start:
seqid = lines[i].split(',')[0]
seqid_list.append(seqid)
if 'Sample_ID' in lines[i]:
seqid_start = True
SequencingRun.objects.filter(pk=sequencing_run.pk).update(
seqids=seqid_list)
return redirect('cowbat:upload_interop',
sequencing_run_pk=sequencing_run.pk)
return render(request, 'cowbat/upload_metadata.html', {'form': form})
def test_run_form_external_lab(self):
form = RunNameForm({
'run_name': '191218_CAL'
})
self.assertTrue(form.is_valid())
self.assertEqual(form.cleaned_data.get('run_name'), '191218_CAL')
def test_run_form_miseq_id(self):
form = RunNameForm({
'run_name': '191218_M02345'
})
self.assertTrue(form.is_valid())
self.assertEqual(form.cleaned_data.get('run_name'), '191218_M02345')
def upload_metadata(request):
form = RunNameForm()
if request.method == 'POST':
form = RunNameForm(request.POST)
if form.is_valid():
if not SequencingRun.objects.filter(
run_name=form.cleaned_data.get('run_name')).exists():
sequencing_run, created = SequencingRun.objects\
.update_or_create(run_name=form.cleaned_data.get('run_name'),
seqids=list())
else:
sequencing_run = SequencingRun.objects.get(
run_name=form.cleaned_data.get('run_name'))
files = [
request.FILES.get('file[%d]' % i)
for i in range(0, len(request.FILES))
]
container_name = sequencing_run.run_name.lower().replace('_', '-')
blob_client = BlockBlobService(
account_name=settings.AZURE_ACCOUNT_NAME,
account_key=settings.AZURE_ACCOUNT_KEY)
blob_client.create_container(container_name)
for item in files:
blob_client.create_blob_from_bytes(
container_name=container_name,
blob_name=item.name,
blob=item.read())
if item.name == 'SampleSheet.csv':
instance = DataFile(sequencing_run=sequencing_run,
data_file=item)
instance.save()
with open(
'olc_webportalv2/media/{run_name}/SampleSheet.csv'.
format(run_name=str(sequencing_run))) as f:
lines = f.readlines()
seqid_start = False
seqid_list = list()
realtime_dict = dict()
# Sample plate column in SampleSheet should have Lab/Whatever other ID.
# Store that data in a dictionary with SeqIDs as keys and LabIDs as values
sample_plate_dict = dict()
for i in range(len(lines)):
if seqid_start:
seqid = lines[i].split(',')[0]
labid = lines[i].split(',')[2]
sample_plate_dict[seqid] = labid
try:
realtime = lines[i].rstrip().split(',')[9]
except IndexError:
realtime = ''
seqid_list.append(seqid)
if realtime == 'TRUE' or realtime == 'VRAI':
realtime_dict[
seqid] = 'True' # Not sure JSONField this gets stored in can handle bool
else:
realtime_dict[seqid] = 'False'
if 'Sample_ID' in lines[i]:
seqid_start = True
SequencingRun.objects.filter(pk=sequencing_run.pk).update(
seqids=seqid_list,
realtime_strains=realtime_dict,
sample_plate=sample_plate_dict)
# TODO: Change this back to verify_realtime once we've gotten the OK from external labs to make them
# validate their data.
# return redirect('cowbat:verify_realtime', sequencing_run_pk=sequencing_run.pk)
return redirect('cowbat:upload_interop',
sequencing_run_pk=sequencing_run.pk)
return render(request, 'cowbat/upload_metadata.html', {'form': form})