Add new Libraries and Samples: New fields addition

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},
         }
 
@@ -80,16 +76,12 @@ def get_library_protocol_name(self, obj):
 class LibrarySerializer(BaseSerializer):
     class Meta(BaseSerializer.Meta):
         model = Library
-        fields = BaseSerializer.Meta.fields + (
-            "qpcr_result",
-            "qpcr_result_facility",
-            "mean_fragment_size",
-        )
+        fields = BaseSerializer.Meta.fields + ("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 +94,16 @@ 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

@@ -34,7 +34,6 @@ class LibraryAdmin(admin.ModelAdmin):
     list_filter = (
         ("library_protocol", RelatedDropdownFilter),
         ("library_type", RelatedDropdownFilter),
-        ("concentration_method", RelatedDropdownFilter),
         ("organism", RelatedDropdownFilter),
         ("read_length", RelatedDropdownFilter),
         ("index_type", RelatedDropdownFilter),
@@ -58,20 +57,17 @@ class LibraryAdmin(admin.ModelAdmin):
                 "fields": (
                     "library_protocol",
                     "library_type",
+                    "measuring_unit",
+                    "measured_value",
                     "concentration",
-                    "concentration_method",
-                    "organism",
+                    "volume",
                     "read_length",
                     "sequencing_depth",
-                    "mean_fragment_size",
-                    "equal_representation_nucleotides",
                     "index_type",
                     "index_reads",
                     "index_i7",
                     "index_i5",
-                    "qpcr_result",
-                    "amplification_cycles",
-                    "comments",
+                    "organism",
                 ),
             },
         ),
@@ -81,12 +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/0005_library_measuring_unit_library_volume_and_more.py

@@ -0,0 +1,45 @@
+# Generated by Django 4.2.14 on 2024-08-06 15:32
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("library", "0004_archived_feature"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="library",
+            name="measuring_unit",
+            field=models.CharField(
+                blank=True,
+                choices=[("bp", "bp (DNA)"), ("-", "Measure for Me")],
+                max_length=50,
+                null=True,
+                verbose_name="Measuring Unit",
+            ),
+        ),
+        migrations.AddField(
+            model_name="library",
+            name="volume",
+            field=models.FloatField(
+                blank=True,
+                null=True,
+                validators=[django.core.validators.MinValueValidator(10)],
+                verbose_name="Volume",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="library",
+            name="mean_fragment_size",
+            field=models.FloatField(
+                blank=True,
+                null=True,
+                validators=[django.core.validators.MinValueValidator(-1)],
+                verbose_name="Measured Value",
+            ),
+        ),
+    ]

backend/library/migrations/0006_rename_mean_fragment_size_library_measured_value.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.15 on 2024-08-22 11:36
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("library", "0005_library_measuring_unit_library_volume_and_more"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="library",
+            old_name="mean_fragment_size",
+            new_name="measured_value",
+        ),
+    ]

backend/library/migrations/0007_rename_amplification_cycles_library_removed_amplification_cycles_and_more.py

@@ -0,0 +1,53 @@
+# Generated by Django 4.2.15 on 2024-09-24 22:34
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("library", "0006_rename_mean_fragment_size_library_measured_value"),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="library",
+            old_name="amplification_cycles",
+            new_name="removed_amplification_cycles",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="comments",
+            new_name="removed_comments",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="comments_facility",
+            new_name="removed_comments_facility",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="concentration_method",
+            new_name="removed_concentration_method",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="concentration_method_facility",
+            new_name="removed_concentration_method_facility",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="equal_representation_nucleotides",
+            new_name="removed_equal_representation_nucleotides",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="qpcr_result",
+            new_name="removed_qpcr_result",
+        ),
+        migrations.RenameField(
+            model_name="library",
+            old_name="qpcr_result_facility",
+            new_name="removed_qpcr_result_facility",
+        ),
+    ]

backend/library/migrations/0008_alter_library_removed_equal_representation_nucleotides.py

@@ -0,0 +1,25 @@
+# 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/0009_alter_library_removed_concentration_method.py

@@ -0,0 +1,31 @@
+# Generated by Django 4.2.15 on 2024-09-25 00:31
+
+import library_sample_shared.models
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "library_sample_shared",
+            "0011_alter_indexi5_number_alter_indexi5_prefix_and_more",
+        ),
+        ("library", "0008_alter_library_removed_equal_representation_nucleotides"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="library",
+            name="removed_concentration_method",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=models.SET(
+                    library_sample_shared.models.get_removed_concentrationmethod
+                ),
+                to="library_sample_shared.concentrationmethod",
+                verbose_name="Concentration Method",
+            ),
+        ),
+    ]

backend/library/migrations/max_migration.txt

@@ -1 +1 @@
-0004_archived_feature
+0009_alter_library_removed_concentration_method

backend/library/models.py

@@ -1,24 +1,40 @@
+from django.core.validators import MinValueValidator
 from django.db import models
 from library_sample_shared.models import GenericLibrarySample
 
 
 class Library(GenericLibrarySample):
-    mean_fragment_size = models.PositiveIntegerField(
-        "Mean Fragment Size",
+    MEASURING_UNIT_CHOICES = [
+        ("bp (DNA)", "bp", "DNA"),
+        ("Measure for Me", "-", "Measure"),
+    ]
+
+    measuring_unit = models.CharField(
+        "Measuring Unit",
+        max_length=50,
+        choices=[
+            (unit, display_name)
+            for display_name, unit, input_type in MEASURING_UNIT_CHOICES
+        ],
         null=True,
         blank=True,
     )
 
-    qpcr_result = models.FloatField("qPCR Result", null=True, blank=True)
+    measured_value = models.FloatField(
+        "Measured Value", validators=[MinValueValidator(-1)], null=True, blank=True
+    )
+
+    archived = models.BooleanField("Archived", default=False)
+
+    removed_qpcr_result = models.FloatField(
+        "qPCR Result", null=True, blank=True
+    )  # This field is not in use
 
-    # Quality Control
-    qpcr_result_facility = models.FloatField(
+    removed_qpcr_result_facility = models.FloatField(
         "qPCR Result (facility)",
         null=True,
         blank=True,
-    )
-
-    archived = models.BooleanField("Archived", default=False)
+    )  # This field is not in use
 
     class Meta:
         verbose_name = "Library"