removed field occurences from frontend and backend

backend/flowcell/serializers.py

@@ -57,7 +57,6 @@ class LaneSerializer(ModelSerializer):
     read_length_name = SerializerMethodField()
     index_i7_show = SerializerMethodField()
     index_i5_show = SerializerMethodField()
-    equal_representation = SerializerMethodField()
     quality_check = CharField(required=False)
     request = SerializerMethodField()
     protocol = SerializerMethodField()
@@ -73,7 +72,6 @@ class Meta:
             "read_length_name",
             "index_i7_show",
             "index_i5_show",
-            "equal_representation",
             "loading_concentration",
             "phix",
             "quality_check",
@@ -168,13 +166,6 @@ def get_index_i5_show(self, obj):
             return ""
         # return None
 
-    def get_equal_representation(self, obj):
-        records = list(
-            itertools.chain(obj.pool.libraries.all(), obj.pool.samples.all())
-        )
-        ern = [x.equal_representation_nucleotides for x in records].count(True)
-        return len(records) == ern
-
 
 class FlowcellListSerializer(ModelSerializer):
     flowcell = SerializerMethodField()

backend/flowcell/views.py

@@ -117,13 +117,13 @@ def get_queryset(self):
         libraries_qs = (
             Library.objects.filter(~Q(status=-1))
             .prefetch_related("read_length", "index_type")
-            .only("read_length", "index_type", "equal_representation_nucleotides")
+            .only("read_length", "index_type")
         )
 
         samples_qs = (
             Sample.objects.filter(~Q(status=-1))
             .prefetch_related("read_length", "index_type")
-            .only("read_length", "index_type", "equal_representation_nucleotides")
+            .only("read_length", "index_type")
         )
 
         lanes_qs = (

backend/incoming_libraries/serializers.py

@@ -49,15 +49,12 @@ class Meta:
             "record_type",
             "library_protocol",
             "concentration",
-            "concentration_method",
             "dilution_factor",
             "concentration_facility",
-            "concentration_method_facility",
             "sample_volume_facility",
             "amount_facility",
             "quality_check",
             "size_distribution_facility",
-            "comments_facility",
             "sequencing_depth",
             "library_protocol_name",
         )
@@ -66,7 +63,6 @@ class Meta:
             "barcode": {"required": False},
             "library_protocol": {"required": False},
             "concentration": {"required": False},
-            "concentration_method": {"required": False},
             "sequencing_depth": {"required": False},
         }
 
@@ -81,15 +77,14 @@ class LibrarySerializer(BaseSerializer):
     class Meta(BaseSerializer.Meta):
         model = Library
         fields = BaseSerializer.Meta.fields + (
-            "qpcr_result",
-            "qpcr_result_facility",
-            "mean_fragment_size",
+            "measuring_unit",
+            "measured_value"
         )
         extra_kwargs = {
             **BaseSerializer.Meta.extra_kwargs,
             **{
-                "qpcr_result": {"required": False},
-                "mean_fragment_size": {"required": False},
+                "measuring_unit": {"required": False},
+                "measured_value": {"required": False},
             },
         }
 
@@ -102,14 +97,17 @@ class Meta(BaseSerializer.Meta):
         fields = BaseSerializer.Meta.fields + (
             "nucleic_acid_type",
             "nucleic_acid_type_name",
-            "rna_quality",
-            "rna_quality_facility",
+            "measuring_unit",
+            "measured_value"
+            "measuring_unit_facility",
+            "measured_value_facility"
         )
         extra_kwargs = {
             **BaseSerializer.Meta.extra_kwargs,
             **{
                 "nucleic_acid_type": {"required": False},
-                "rna_quality": {"required": False},
+                "measuring_unit": {"required": False},
+                "measured_value": {"required": False},
             },
         }
 

backend/incoming_libraries/views.py

@@ -28,11 +28,9 @@ def list(self, request):
         """Get the list of all incoming libraries and samples."""
         libraries_qs = Library.objects.select_related(
             "library_protocol",
-            "concentration_method",
         ).filter(status=1)
         samples_qs = Sample.objects.select_related(
             "library_protocol",
-            "concentration_method",
             "nucleic_acid_type",
         ).filter(status=1)
 

backend/library/admin.py

@@ -77,12 +77,9 @@ class LibraryAdmin(admin.ModelAdmin):
                 "fields": (
                     "dilution_factor",
                     "concentration_facility",
-                    "concentration_method_facility",
                     "sample_volume_facility",
                     "amount_facility",
                     "size_distribution_facility",
-                    "qpcr_result_facility",
-                    "comments_facility",
                 ),
             },
         ),

backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('library', '0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='library',
+            name='removed_equal_representation_nucleotides',
+            field=models.BooleanField(blank=True, default=False, verbose_name='Equal Representation of Nucleotides'),
+        ),
+    ]

backend/library/migrations/max_migration.txt

@@ -1 +1 @@
-0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more
+0008_alter_library_removed_equal_representation_nucleotides

backend/library/tests.py

@@ -25,9 +25,6 @@ def create_library(name, status=0, save=True, read_length=None, index_type=None)
     organism = Organism(name="Organism")
     organism.save()
 
-    concentration_method = ConcentrationMethod(name="Concentration Method")
-    concentration_method.save()
-
     if read_length is None:
         read_length = ReadLength(name="Read Length")
         read_length.save()
@@ -56,12 +53,10 @@ def create_library(name, status=0, save=True, read_length=None, index_type=None)
         status=status,
         organism_id=organism.pk,
         concentration=1.0,
-        concentration_method_id=concentration_method.pk,
         read_length_id=read_length.pk,
         sequencing_depth=1,
         library_protocol_id=library_protocol.pk,
         library_type_id=library_type.pk,
-        amplification_cycles=1,
         index_type_id=index_type.pk,
         index_reads=0,
         mean_fragment_size=1,
@@ -214,12 +209,10 @@ def test_add_library(self):
                             "name": name,
                             "organism": library.organism.pk,
                             "concentration": 1.0,
-                            "concentration_method": library.concentration_method.pk,
                             "read_length": library.read_length.pk,
                             "sequencing_depth": 1,
                             "library_protocol": library.library_protocol.pk,
                             "library_type": library.library_type.pk,
-                            "amplification_cycles": 1,
                             "index_type": library.index_type.pk,
                             "index_reads": 0,
                             "mean_fragment_size": 1,
@@ -246,12 +239,10 @@ def test_add_library_contains_invalid(self):
                             "name": name,
                             "organism": self.library.organism.pk,
                             "concentration": 1.0,
-                            "concentration_method": self.library.concentration_method.pk,
                             "read_length": self.library.read_length.pk,
                             "sequencing_depth": 1,
                             "library_protocol": self.library.library_protocol.pk,
                             "library_type": self.library.library_type.pk,
-                            "amplification_cycles": 1,
                             "index_type": self.library.index_type.pk,
                             "index_reads": 0,
                             "mean_fragment_size": 1,
@@ -260,7 +251,6 @@ def test_add_library_contains_invalid(self):
                             "name": self._get_random_name(),
                             "concentration": 1.0,
                             "sequencing_depth": 1,
-                            "amplification_cycles": 1,
                             "index_reads": 0,
                             "mean_fragment_size": 1,
                         },
@@ -317,12 +307,10 @@ def test_update_library(self):
                             "name": new_name,
                             "organism": library.organism.pk,
                             "concentration": 1.0,
-                            "concentration_method": library.concentration_method.pk,
                             "read_length": library.read_length.pk,
                             "sequencing_depth": 1,
                             "library_protocol": library.library_protocol.pk,
                             "library_type": library.library_type.pk,
-                            "amplification_cycles": 1,
                             "index_type": library.index_type.pk,
                             "index_reads": 0,
                             "mean_fragment_size": 1,
@@ -352,12 +340,10 @@ def test_update_library_contains_invalid(self):
                             "name": new_name1,
                             "organism": library1.organism.pk,
                             "concentration": 1.0,
-                            "concentration_method": library1.concentration_method.pk,
                             "read_length": library1.read_length.pk,
                             "sequencing_depth": 1,
                             "library_protocol": library1.library_protocol.pk,
                             "library_type": library1.library_type.pk,
-                            "amplification_cycles": 1,
                             "index_type": library1.index_type.pk,
                             "index_reads": 0,
                             "mean_fragment_size": 1,
@@ -367,7 +353,6 @@ def test_update_library_contains_invalid(self):
                             "name": new_name2,
                             "concentration": 2.0,
                             "sequencing_depth": 2,
-                            "amplification_cycles": 2,
                             "index_reads": 0,
                             "mean_fragment_size": 2,
                         },

backend/library_preparation/migrations/0005_rename_qpcr_result_librarypreparation_removed_qpcr_result.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('library_preparation', '0004_librarypreparation_smear_analysis'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='librarypreparation',
+            old_name='qpcr_result',
+            new_name='removed_qpcr_result',
+        ),
+    ]

backend/library_preparation/migrations/max_migration.txt

@@ -1 +1 @@
-0004_librarypreparation_smear_analysis
+0005_rename_qpcr_result_librarypreparation_removed_qpcr_result

backend/library_preparation/models.py

@@ -51,11 +51,11 @@ class LibraryPreparation(DateTimeMixin):
         blank=True,
     )
 
-    qpcr_result = models.FloatField(
+    removed_qpcr_result = models.FloatField(
         "qPCR Result",
         null=True,
         blank=True,
-    )
+    )  # This field is not in use
 
     comments = models.TextField(
         "Comments",

backend/library_sample_shared/models.py

@@ -412,7 +412,8 @@ def index_i5_id(self):
 
     removed_equal_representation_nucleotides = models.BooleanField(
         "Equal Representation of Nucleotides",
-        default=True,
+        blank=True,
+        default=False,
     )  # This field is not in use
 
     removed_comments = models.TextField(

backend/library_sample_shared/tests.py

@@ -66,15 +66,6 @@ def test_organism_name(self):
         self.assertEqual(self.organism.__str__(), self.organism.name)
 
 
-class ConcentrationMethodTest(TestCase):
-    def setUp(self):
-        self.method = ConcentrationMethod(name=get_random_name())
-
-    def test_concentration_method_name(self):
-        self.assertTrue(isinstance(self.method, ConcentrationMethod))
-        self.assertEqual(self.method.__str__(), self.method.name)
-
-
 class ReadLengthTest(TestCase):
     def setUp(self):
         self.read_length = ReadLength(name=get_random_name())
@@ -229,23 +220,6 @@ def test_organisms_list(self):
         self.assertIn(self.read_length.name, read_lengths)
 
 
-class TestConcentrationMethods(BaseTestCase):
-    def setUp(self):
-        self.create_user("[email protected]", "foo-foo")
-        self.client.login(email="[email protected]", password="foo-foo")
-
-        self.concentration_method = ConcentrationMethod(name=self._get_random_name())
-        self.concentration_method.save()
-
-    def test_organisms_list(self):
-        """Ensure get concentration methods behaves correctly."""
-        response = self.client.get(reverse("concentration-method-list"))
-        data = response.json()
-        concentration_methods = [x["name"] for x in data]
-        self.assertEqual(response.status_code, 200)
-        self.assertIn(self.concentration_method.name, concentration_methods)
-
-
 class TestIndexTypes(BaseTestCase):
     def setUp(self):
         self.create_user("[email protected]", "foo-foo")

backend/request/views.py

@@ -1093,14 +1093,10 @@ def export_request(request):
         dataset = Dataset()
         dataset.headers = (
             # The following are not submitted by user...
-            # id barcode create_time update_time status concentration concentration_method
-            # equal_representation_nucleotides comments is_pooled amplification_cycles
-            # dilution_factor concentration_facility concentration_method_facility archived
+            # id barcode create_time update_time status concentration
+            # is_pooled dilution_factor concentration_facility archived
             # sample_volume_facility amount_facility size_distribution_facility comments_facility
-            ##libraries-exclusively:
-            # qpcr_result qpcr_result_facility
-            ##sample-exclusively:
-            # is_converted
+            ## sample-exclusively: is_converted
             "id",
             "name",
             "barcode",

backend/sample/admin.py

@@ -102,14 +102,13 @@ class SampleAdmin(admin.ModelAdmin):
             "Determined by Facility",
             {
                 "fields": (
+                    "measuring_unit_facility",
+                    "measured_value_facility",
                     "dilution_factor",
                     "concentration_facility",
-                    "concentration_method_facility",
                     "sample_volume_facility",
                     "amount_facility",
                     "size_distribution_facility",
-                    "rna_quality_facility",
-                    "comments_facility",
                 ),
             },
         ),

backend/sample/migrations/0012_alter_sample_removed_equal_representation_nucleotides.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-09-24 23:54
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('sample', '0011_alter_sample_measured_value_facility'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='sample',
+            name='removed_equal_representation_nucleotides',
+            field=models.BooleanField(blank=True, default=False, verbose_name='Equal Representation of Nucleotides'),
+        ),
+    ]

backend/sample/migrations/max_migration.txt

@@ -1 +1 @@
-0011_alter_sample_measured_value_facility
+0012_alter_sample_removed_equal_representation_nucleotides