single-stranded library fields for qpcr assays A,B #145

samples/forms.py

@@ -565,15 +565,15 @@ class LibraryForm(UserModelForm):
 
 	class Meta:
 		model = Library
-		fields = ['well_position', 'reich_lab_library_id', 'p5_index', 'p7_index', 'p5_barcode', 'p7_barcode', 'nanodrop', 'qpcr_ds', 'plate_id', 'fluidx_barcode', 'notes']
+		fields = ['well_position', 'reich_lab_library_id', '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', 'plate_id', 'fluidx_barcode', 'notes']
 		widgets = {
 			'notes': Textarea(attrs={'cols': 60, 'rows': 2}),
 		}
 
 	def __init__(self, *args, **kwargs):
 		super().__init__(*args, **kwargs)
 		self.fields['reich_lab_library_id'].disabled = True
-		for option in ['nanodrop', 'qpcr_ds']:
+		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']:
 			self.fields[option].required = False
 		if self.instance:
 			layout_elements = self.instance.librarybatchlayout_set

samples/migrations/0181_auto_20240502_1523.py

@@ -0,0 +1,48 @@
+# Generated by Django 3.0.3 on 2024-05-02 19:23
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('samples', '0180_auto_20240502_1517'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='library',
+            name='assay_a_percent_inhibition',
+            field=models.FloatField(null=True),
+        ),
+        migrations.AddField(
+            model_name='library',
+            name='assay_b_total_molecules',
+            field=models.BigIntegerField(null=True),
+        ),
+        migrations.AddField(
+            model_name='library',
+            name='qpcr_assay_a_1_ss',
+            field=models.DecimalField(decimal_places=2, help_text='SS qpcr Assay A_1', max_digits=4, null=True),
+        ),
+        migrations.AddField(
+            model_name='library',
+            name='qpcr_assay_a_2_ss',
+            field=models.DecimalField(decimal_places=2, help_text='SS qpcr Assay A_2', max_digits=4, null=True),
+        ),
+        migrations.AddField(
+            model_name='library',
+            name='qpcr_assay_b_1_ss',
+            field=models.DecimalField(decimal_places=2, help_text='SS qpcr Assay B_1', max_digits=4, null=True),
+        ),
+        migrations.AddField(
+            model_name='library',
+            name='qpcr_assay_b_2_ss',
+            field=models.DecimalField(decimal_places=2, help_text='SS qpcr Assay B_2', max_digits=4, null=True),
+        ),
+        migrations.AlterField(
+            model_name='library',
+            name='qpcr_ds',
+            field=models.DecimalField(decimal_places=2, help_text='DS qpcr value', max_digits=4, null=True),
+        ),
+    ]

samples/models.py

@@ -22,6 +22,7 @@
 from .spreadsheet import *
 from .validation import *
 
+import decimal
 import re, string
 
 REICH_LAB = 'Reich Lab'
@@ -65,6 +66,13 @@ def get_value(obj, *property_name_chain, default=''):
 		if callable(current_object):
 			current_object = current_object()
 	return current_object
+
+# convert a non-empty string using a coversion function
+# or return None
+def value_convert_or_none(value_str, conversion_function):
+	if len(value_str) > 0:
+		return conversion_function(value_str)
+	return None
 
 class Timestamped(models.Model):
 	creation_timestamp = models.DateTimeField(default=timezone.now, null=True)
@@ -2089,7 +2097,13 @@ class Library(Timestamped):
 	fluidx_barcode = models.CharField(max_length=12, blank=True, help_text='Physical barcode on FluidX tube')
 
 	nanodrop = models.DecimalField(max_digits=5, decimal_places=2, null=True)
-	qpcr_ds = models.DecimalField(max_digits=4, decimal_places=2, null=True)
+	qpcr_ds = models.DecimalField(max_digits=4, decimal_places=2, null=True, help_text='DS qpcr value')
+	qpcr_assay_a_1_ss = models.DecimalField(max_digits=4, decimal_places=2, null=True, help_text='SS qpcr Assay A_1')
+	qpcr_assay_a_2_ss = models.DecimalField(max_digits=4, decimal_places=2, null=True, help_text='SS qpcr Assay A_2')
+	qpcr_assay_b_1_ss = models.DecimalField(max_digits=4, decimal_places=2, null=True, help_text='SS qpcr Assay B_1')
+	qpcr_assay_b_2_ss = models.DecimalField(max_digits=4, decimal_places=2, null=True, help_text='SS qpcr Assay B_2')
+	assay_a_percent_inhibition = models.FloatField(null=True)
+	assay_b_total_molecules = models.BigIntegerField(null=True)
 
 	# single stranded libraries have indices directly assigned
 	p5_index = models.ForeignKey(P5_Index, on_delete=models.PROTECT, null=True)
@@ -2161,6 +2175,12 @@ def spreadsheet_header(cumulative=False):
 			'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',
 			'plate_id',
 			'fluidx_barcode',
 			'notes',
@@ -2179,6 +2199,12 @@ def to_spreadsheet_row(self, cumulative=False):
 			get_value(self.library, 'p7_barcode', 'label'),
 			get_value(self.library, 'nanodrop'),
 			get_value(self.library, 'qpcr_ds'),
+			get_value(self.library, 'qpcr_assay_a_1_ss'),
+			get_value(self.library, 'qpcr_assay_a_2_ss'),
+			get_value(self.library, 'qpcr_assay_b_1_ss'),
+			get_value(self.library, 'qpcr_assay_b_2_ss'),
+			get_value(self.library, 'assay_a_percent_inhibition'),
+			get_value(self.library, 'assay_b_total_molecules'),
 			get_value(self.library, 'plate_id'),
 			get_value(self.library, 'fluidx_barcode'),
 			get_value(self.library, 'notes')
@@ -2222,7 +2248,13 @@ def from_spreadsheet_row(self, headers, arg_array, user):
 			library.p7_barcode = None
 
 		library.nanodrop = float(arg_array[headers.index('nanodrop')])
-		library.qpcr = float(arg_array[headers.index('qpcr_ds')])
+		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)
+		library.qpcr_assay_b_1_ss = value_convert_or_none(arg_array[headers.index('qpcr_assay_b_1_ss')], decimal.Decimal)
+		library.qpcr_assay_b_2_ss = value_convert_or_none(arg_array[headers.index('qpcr_assay_b_2_ss')], decimal.Decimal)
+		library.assay_a_percent_inhibition = value_convert_or_none(arg_array[headers.index('assay_a_percent_inhibition')], float)
+		library.assay_b_total_molecules = value_convert_or_none(arg_array[headers.index('assay_b_total_molecules')], int)
 		library.plate_id = arg_array[headers.index('plate_id')]
 		library.fluidx_barcode = arg_array[headers.index('fluidx_barcode')]
 		library.notes = arg_array[headers.index('notes')]