single-stranded library web interface support #145

samples/forms.py

@@ -537,12 +537,14 @@ def __init__(self, *args, **kwargs):
 		for option in ['rotated']:
 			self.fields[option].disabled = True
 		# ensure current values are allowed form values
-		if self.instance.protocol:
-			self.fields['protocol'].queryset = LibraryProtocol.objects.filter(Q(active=True) | Q(id=self.instance.protocol.id) ).order_by('-start_date')
-			if self.instance.protocol.library_type == 'ss':
-				self.fields['p7_offset'].required = False
-		if self.instance.control_set:
-			self.fields['control_set'].queryset = ControlSet.objects.filter(Q(active=True) | Q(id=self.instance.control_set.id)).order_by('layout_name')
+		self.fields['p7_offset'].required = False
+		if self.instance:
+			if self.instance.protocol:
+				self.fields['protocol'].queryset = LibraryProtocol.objects.filter(Q(active=True) | Q(id=self.instance.protocol.id) ).order_by('-start_date')
+				if self.instance.protocol.library_type == 'ds':
+					self.fields['p7_offset'].required = True
+			if self.instance.control_set:
+				self.fields['control_set'].queryset = ControlSet.objects.filter(Q(active=True) | Q(id=self.instance.control_set.id)).order_by('layout_name')
 
 	# to view fields without being able to modify prior to deletion
 	def disable_fields(self):
@@ -573,13 +575,14 @@ class Meta:
 	def __init__(self, *args, **kwargs):
 		super().__init__(*args, **kwargs)
 		self.fields['reich_lab_library_id'].disabled = True
-		for option in ['nanodrop', 'qpcr_ds', 'qpcr_assay_a_1_ss', 'qpcr_assay_a_2_ss', 'qpcr_assay_b_1_ss', 'qpcr_assay_b_2_ss', 'assay_a_percent_inhibition', 'assay_b_total_molecules']:
+		for option in ['p5_index', 'p7_index', 'p5_barcode', 'p7_barcode', 'nanodrop', 'qpcr_ds', 'qpcr_assay_a_1_ss', 'qpcr_assay_a_2_ss', 'qpcr_assay_b_1_ss', 'qpcr_assay_b_2_ss', 'assay_a_percent_inhibition', 'assay_b_total_molecules']:
 			self.fields[option].required = False
 		if self.instance:
 			layout_elements = self.instance.librarybatchlayout_set
 			layout_element = layout_elements.get(library=self.instance)
 			self.initial['well_position'] = str(layout_element)
 
+
 LibraryFormset = modelformset_factory(Library, form=LibraryForm, extra=0)
 
 # raise validation error if capture batch name already exists

samples/models.py

@@ -1731,9 +1731,7 @@ def create_library_from_extract(layout_element, user, *, i5=None, i7=None, ul_ex
 			p5_barcode = Barcode.objects.get(label = p5_qstr)
 			p7_barcode = Barcode.objects.get(label = p7_qstr)
 		elif library_batch.protocol.library_type == 'ss':
-			# indices are assigned in arguments
-			if i5 is None or i7 is None:
-				raise ValueError(f'single stranded needs assigned indices')
+			# indices are assigned in arguments, or deferred and loaded later
 			p5_barcode = None
 			p7_barcode = None
 		else:
@@ -1753,7 +1751,8 @@ def create_library_from_extract(layout_element, user, *, i5=None, i7=None, ul_ex
 						p5_barcode = p5_barcode,
 						p7_barcode = p7_barcode
 					)
-		library.clean()
+		if library_batch.protocol.library_type != 'ss': # ss indices can be assigned later
+			library.clean()
 		library.save(save_user=user)
 		layout_element.library = library
 		layout_element.ul_extract_used = library.ul_extract_used
@@ -1841,8 +1840,9 @@ def create_libraries(self, user):
 		layout = self.layout_elements()
 		duplicate_positions_check_db(layout)
 
-		for layout_element in layout:
-			create_library_from_extract(layout_element, user)
+		with transaction.atomic():
+			for layout_element in layout:
+				create_library_from_extract(layout_element, user)
 
 	def get_robot_layout(self):
 		self.check_p7_offset()
@@ -1885,6 +1885,7 @@ def set_controls(self, user):
 			layout_element.ul_extract_used = 0
 			layout_element.save(save_user=user)
 
+	@transaction.atomic
 	def libraries_from_spreadsheet(self, spreadsheet, user):
 		headers, data_rows = spreadsheet_headers_and_data_rows(spreadsheet)
 
@@ -2120,6 +2121,8 @@ def clean(self):
 			raise ValidationError(_('Library must have either indices or barcodes')) 
 		if self.sample and self.extract and self.sample != self.extract.get_sample():
 			raise ValidationError(_('Library has sample mismatch'))
+		if self.library_type == 'ss' and self.p5_index is None or self.p7_index is None:
+			raise ValidationError(_('single-stranded library is missing indices'))
 
 	# barcodes and indices are unique, so we only need to check ids, not DNA sequences
 	def barcodes_are_distinct(self, other):
@@ -2247,7 +2250,7 @@ def from_spreadsheet_row(self, headers, arg_array, user):
 		except Barcode.DoesNotExist:
 			library.p7_barcode = None
 
-		library.nanodrop = float(arg_array[headers.index('nanodrop')])
+		library.nanodrop = value_convert_or_none(arg_array[headers.index('nanodrop')], float)
 		library.qpcr_ds = value_convert_or_none(arg_array[headers.index('qpcr_ds')], decimal.Decimal)
 		library.qpcr_assay_a_1_ss = value_convert_or_none(arg_array[headers.index('qpcr_assay_a_1_ss')], decimal.Decimal)
 		library.qpcr_assay_a_2_ss = value_convert_or_none(arg_array[headers.index('qpcr_assay_a_2_ss')], decimal.Decimal)

samples/views.py

@@ -1090,6 +1090,8 @@ def libraries_in_batch(request):
 		if library_batch_form.is_valid() and libraries_formset.is_valid():
 			if library_batch.status == library_batch.OPEN:
 				return redirect(f'{reverse("library_batch_assign_extract")}?library_batch_name={library_batch_name}')
+			elif library_batch.status == library_batch.CLOSED:
+				library_batch.clean()
 
 	elif request.method == 'GET':
 		library_batch_form = LibraryBatchForm(instance=library_batch, user=request.user)

screening/settings.py

@@ -115,6 +115,8 @@
 
 USE_TZ = True
 
+DATA_UPLOAD_MAX_NUMBER_FIELDS = 2000
+
 
 # Static files (CSS, JavaScript, Images)
 # https://docs.djangoproject.com/en/1.8/howto/static-files/