def _create_or_update_pending_sampleSetItem(
request, user, sampleSet_ids, sample, sampleGender,
sampleRelationshipRole, sampleRelationshipGroup, sampleControlType,
selectedBarcodeKit, selectedBarcode, sampleCancerType,
sampleCellularityPct, sampleNucleotideType, pcrPlateRow,
sampleBiopsyDays, sampleCellNum, sampleCoupleId, sampleEmbryoId,
sampleSetItemDescription):
if selectedBarcode:
dnabarcode = models.dnaBarcode.objects.get(name=selectedBarcodeKit,
id_str=selectedBarcode)
else:
dnabarcode = None
if sampleNucleotideType.lower() == "fusions":
sampleNucleotideType = "rna"
for sampleSet_id in sampleSet_ids:
sampleSet = get_object_or_404(SampleSet, pk=sampleSet_id)
relationshipGroup = int(
sampleRelationshipGroup) if sampleRelationshipGroup else 0
pcrPlateColumn = "1" if pcrPlateRow else ""
sampleSetItem_kwargs = {
'gender': sampleGender,
'relationshipRole': sampleRelationshipRole,
'relationshipGroup': relationshipGroup,
'controlType': sampleControlType,
'cancerType': sampleCancerType,
'cellularityPct': sampleCellularityPct,
'dnabarcode': dnabarcode,
'pcrPlateRow': pcrPlateRow,
'pcrPlateColumn': pcrPlateColumn,
'biopsyDays': sampleBiopsyDays,
'cellNum': sampleCellNum,
'coupleId': sampleCoupleId,
'embryoId': sampleEmbryoId,
'description': sampleSetItemDescription,
'lastModifiedUser': user,
}
try:
sampleSetItem = SampleSetItem.objects.get(
sample=sample,
sampleSet_id=sampleSet_id,
nucleotideType=sampleNucleotideType,
dnabarcode=dnabarcode)
except:
sampleSetItem = SampleSetItem(sample=sample,
sampleSet_id=sampleSet_id,
nucleotideType=sampleNucleotideType,
creator=user)
for field, value in sampleSetItem_kwargs.iteritems():
setattr(sampleSetItem, field, value)
sampleSetItem.save()
def _get_nucleotideType_choices(request):
nucleotideType_tuple = SampleSetItem.get_nucleotideType_choices()
nucleotideType_choices = OrderedDict()
for i, (internalValue, displayedValue) in enumerate(nucleotideType_tuple):
nucleotideType_choices[internalValue] = displayedValue
return nucleotideType_choices
def _get_pcrPlateCol_valid_values(request):
col_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_column_choices()
col_values = []
for i, (internalValue, displayedValue) in enumerate(col_choices_tuple):
col_values.append(displayedValue)
return col_values
def _get_pcrPlateRow_valid_values(request):
row_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_row_choices()
row_values = []
for i, (internalValue, displayedValue) in enumerate(row_choices_tuple):
row_values.append(displayedValue)
return row_values
def _get_pcrPlateRow_choices(request):
row_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_row_choices()
row_choices = OrderedDict()
for i, (internalValue, displayedValue) in enumerate(row_choices_tuple):
row_choices[internalValue] = displayedValue
return row_choices
def _get_pcrPlateCol_valid_values(request):
col_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_column_choices()
col_values = []
for i, (internalValue, displayedValue) in enumerate(col_choices_tuple):
col_values.append(displayedValue)
return col_values
def _get_pcrPlateRow_valid_values(request):
row_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_row_choices()
row_values = []
for i, (internalValue, displayedValue) in enumerate(row_choices_tuple):
row_values.append(displayedValue)
return row_values
def _get_pcrPlateRow_choices(request):
row_choices_tuple = SampleSetItem.get_ampliseq_plate_v1_row_choices()
row_choices = OrderedDict()
for i, (internalValue, displayedValue) in enumerate(row_choices_tuple):
row_choices[internalValue] = displayedValue
return row_choices
def _get_nucleotideType_choices(request):
nucleotideType_tuple = SampleSetItem.get_nucleotideType_choices()
nucleotideType_choices = OrderedDict()
for i, (internalValue, displayedValue) in enumerate(nucleotideType_tuple):
nucleotideType_choices[internalValue] = displayedValue
return nucleotideType_choices
def _create_or_update_pending_sampleSetItem(request, user, sampleSet_ids, sample, sampleGender, sampleRelationshipRole, sampleRelationshipGroup, sampleControlType,
selectedBarcodeKit, selectedBarcode, sampleCancerType, sampleCellularityPct, sampleNucleotideType,
pcrPlateRow, sampleBiopsyDays, sampleCellNum, sampleCoupleId, sampleEmbryoId, sampleSetItemDescription):
if selectedBarcode:
dnabarcode = models.dnaBarcode.objects.get(name=selectedBarcodeKit, id_str=selectedBarcode)
else:
dnabarcode = None
if sampleNucleotideType.lower() == "fusions":
sampleNucleotideType = "rna"
for sampleSet_id in sampleSet_ids:
sampleSet = get_object_or_404(SampleSet, pk=sampleSet_id)
relationshipGroup = int(sampleRelationshipGroup) if sampleRelationshipGroup else 0
pcrPlateColumn = "1" if pcrPlateRow else ""
sampleSetItem_kwargs = {
'gender': sampleGender,
'relationshipRole': sampleRelationshipRole,
'relationshipGroup': relationshipGroup,
'controlType': sampleControlType,
'cancerType': sampleCancerType,
'cellularityPct': sampleCellularityPct,
'dnabarcode': dnabarcode,
'pcrPlateRow': pcrPlateRow,
'pcrPlateColumn': pcrPlateColumn,
'biopsyDays': sampleBiopsyDays,
'cellNum': sampleCellNum,
'coupleId': sampleCoupleId,
'embryoId': sampleEmbryoId,
'description': sampleSetItemDescription,
'lastModifiedUser': user,
}
try:
sampleSetItem = SampleSetItem.objects.get(sample=sample, sampleSet_id=sampleSet_id, nucleotideType=sampleNucleotideType, dnabarcode=dnabarcode)
except:
sampleSetItem = SampleSetItem(sample=sample, sampleSet_id=sampleSet_id, nucleotideType=sampleNucleotideType, creator=user)
for field, value in sampleSetItem_kwargs.iteritems():
setattr(sampleSetItem, field, value)
sampleSetItem.save()
def _get_nucleotideType_choices(sampleGroupType=""):
nucleotideType_choices = []
for internalValue, displayedValue in SampleSetItem.get_nucleotideType_choices():
if internalValue == "rna" and "fusions" in sampleGroupType.lower():
continue
else:
nucleotideType_choices.append((internalValue, displayedValue))
if "fusions" in sampleGroupType.lower() or not sampleGroupType:
nucleotideType_choices.append(('fusions', 'Fusions'))
return nucleotideType_choices
def _get_nucleotideType_choices(sampleGroupType=""):
nucleotideType_choices = []
for internalValue, displayedValue in SampleSetItem.get_nucleotideType_choices():
if internalValue == "rna" and "fusions" in sampleGroupType.lower():
continue
else:
nucleotideType_choices.append((internalValue, displayedValue))
if "fusions" in sampleGroupType.lower() or not sampleGroupType:
nucleotideType_choices.append(("fusions", "Fusions"))
return nucleotideType_choices
def _create_or_update_sampleSetItem(
queryDict, user, item_id=None, sampleSet_id=None, sample=None
):
# use case 1: if item_id is defined we are editing existing SampleSetItem
# use case 2: if sampleSet_id is defined we are editing or adding a new SampleSetItem
sampleSetItem_kwargs = _get_sampleSetItem_kwargs(queryDict, sampleSet_id)
if item_id:
sampleSetItem = get_object_or_404(SampleSetItem, pk=item_id)
elif sampleSet_id:
sampleSet = get_object_or_404(SampleSet, pk=sampleSet_id)
try:
sampleSetItem = SampleSetItem.objects.get(
sample=sample,
sampleSet_id=sampleSet_id,
nucleotideType=sampleSetItem_kwargs["nucleotideType"],
dnabarcode=sampleSetItem_kwargs["dnaBarcode"],
)
except Exception:
sampleSetItem = SampleSetItem(
sample=sample,
sampleSet_id=sampleSet_id,
nucleotideType=sampleSetItem_kwargs["nucleotideType"],
creator=user,
)
else:
raise Exception(
"Unable to update sample: missing SampleSetItem id or SampleSet id"
)
for field, value in sampleSetItem_kwargs.items():
setattr(sampleSetItem, field, value)
logger.debug(
"views_helper._create_or_update_sampleSetItem sampleSetItem_kwargs=%s"
% (sampleSetItem_kwargs)
)
sampleSetItem.save()
