Feature/sckan-250 - UI improvements for undefined values

backend/composer/api/serializers.py

@@ -486,48 +486,49 @@ def get_statement_preview(self, instance):
             self.context['journey'] = instance.get_journey()
         return self.create_statement_preview(instance, self.context['journey'])
 
+
     def create_statement_preview(self, instance, journey):
-        sex = instance.sex.name if instance.sex else ""
+        sex = instance.sex.sex_str if instance.sex else None
+
         species_list = [specie.name for specie in instance.species.all()]
         species = join_entities(species_list)
         if not species:
             species = ""
 
-        phenotype = instance.phenotype.name.lower() if instance.phenotype else ""
+        phenotype = instance.phenotype.phenotype_str if instance.phenotype else ''
         origin_names = [origin.name for origin in instance.origins.all()]
         origins = join_entities(origin_names)
         if not origins:
             origins = ""
 
-        circuit_type = instance.get_circuit_type_display().lower() if instance.circuit_type else ""
-        projection = instance.get_projection_display().lower() if instance.projection else ""
+        circuit_type = instance.get_circuit_type_display() if instance.circuit_type else None
+        projection = instance.get_projection_display() if instance.projection else None
 
         laterality_description = instance.get_laterality_description()
-        if not laterality_description:
-            laterality_description = ""
 
         apinatomy = instance.apinatomy_model if instance.apinatomy_model else ""
         journey_sentence = ', '.join(journey)
 
         # Creating the statement
-        if sex != "" or species != "":
-            statement = f"In {sex} {species}, the {phenotype} connection goes {journey_sentence}.\n"
+        if sex or species != "":
+            statement = f"In {sex or ''} {species}, the {phenotype.lower()} connection goes {journey_sentence}.\n"
         else:
-            statement = f"A {phenotype} connection goes {journey_sentence}.\n"
+            statement = f"A {phenotype.lower()} connection goes {journey_sentence}.\n"
+
         statement += f"This "
-        if projection != "not specified":
-            statement += f"{projection} "
-        if circuit_type != "not specified":
-            statement += f"{circuit_type} "
+        if projection:
+            statement += f"{projection.lower()} "
+        if circuit_type:
+            statement += f"{circuit_type.lower()} "
 
         statement += f"connection projects from the {origins}."
-        if laterality_description != "":
+        if laterality_description:
             statement = statement[:-1] + f" and is found {laterality_description}.\n"
 
         if apinatomy:
             statement += f" It is described in {apinatomy} model."
 
-        return statement.strip()
+        return statement.strip().replace("  ", " ")
 
     def get_errors(self, instance) -> List:
         return get_connectivity_errors(instance)

backend/composer/enums.py

@@ -7,14 +7,12 @@
 class Laterality(models.TextChoices):
     RIGHT = "RIGHT", "Right"
     LEFT = "LEFT", "Left"
-    UNKNOWN = "UNKNOWN", "Not specified"
 
 
 class Projection(models.TextChoices):
     IPSI = "IPSI", "Ipsilateral"
     CONTRAT = "CONTRAT", "Contralateral"
     BI = "BI", "Bilateral"
-    UNKNOWN = "UNKNOWN", "Not specified"
 
 
 # todo: motor and sensory should move to phenotype options per csv
@@ -25,7 +23,6 @@ class CircuitType(models.TextChoices):
     INTRINSIC = "INTRINSIC", "Intrinsic"
     PROJECTION = "PROJECTION", "Projection"
     ANAXONIC = "ANAXONIC", "Anaxonic"
-    UNKNOWN = "UNKNOWN", "Not specified"
 
 
 class ViaType(models.TextChoices):

backend/composer/migrations/0035_alter_connectivitystatement_circuit_type_and_more.py

@@ -0,0 +1,186 @@
+# Generated by Django 4.1.4 on 2024-02-01 13:26
+
+from django.db import migrations, models
+
+
+def change_not_specified_to_null(apps, schema_editor):
+    ConnectivityStatement = apps.get_model('composer', 'ConnectivityStatement')
+    ConnectivityStatement.objects.filter(laterality='UNKNOWN').update(laterality=None)
+    ConnectivityStatement.objects.filter(projection='UNKNOWN').update(projection=None)
+    ConnectivityStatement.objects.filter(circuit_type='UNKNOWN').update(circuit_type=None)
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("composer", "0034_remove_connectivitystatement_state_valid_and_more"),
+    ]
+
+    operations = [
+        # ADD the null=True option to the circuit_type, laterality and projection fields
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="circuit_type",
+            field=models.CharField(
+                choices=[
+                    ("SENSORY", "Sensory"),
+                    ("MOTOR", "Motor"),
+                    ("INTRINSIC", "Intrinsic"),
+                    ("PROJECTION", "Projection"),
+                    ("ANAXONIC", "Anaxonic"),
+                    ("UNKNOWN", "Not specified"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="laterality",
+            field=models.CharField(
+                choices=[
+                    ("RIGHT", "Right"),
+                    ("LEFT", "Left"),
+                    ("UNKNOWN", "Not specified"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="projection",
+            field=models.CharField(
+                choices=[
+                    ("IPSI", "Ipsilateral"),
+                    ("CONTRAT", "Contralateral"),
+                    ("BI", "Bilateral"),
+                    ("UNKNOWN", "Not specified"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+
+        # CONVERT UNKNOWN TO NULL
+        migrations.RunPython(change_not_specified_to_null),
+
+
+        # Remove the UNKNOWN option from the circuit_type, laterality and projection fields
+        migrations.RemoveConstraint(
+            model_name="connectivitystatement",
+            name="circuit_type_valid",
+        ),
+        migrations.RemoveConstraint(
+            model_name="connectivitystatement",
+            name="laterality_valid",
+        ),
+        migrations.RemoveConstraint(
+            model_name="connectivitystatement",
+            name="projection_valid",
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="circuit_type",
+            field=models.CharField(
+                choices=[
+                    ("SENSORY", "Sensory"),
+                    ("MOTOR", "Motor"),
+                    ("INTRINSIC", "Intrinsic"),
+                    ("PROJECTION", "Projection"),
+                    ("ANAXONIC", "Anaxonic"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="laterality",
+            field=models.CharField(
+                choices=[("RIGHT", "Right"), ("LEFT", "Left")], max_length=20, null=True
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="projection",
+            field=models.CharField(
+                choices=[
+                    ("IPSI", "Ipsilateral"),
+                    ("CONTRAT", "Contralateral"),
+                    ("BI", "Bilateral"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AddConstraint(
+            model_name="connectivitystatement",
+            constraint=models.CheckConstraint(
+                check=models.Q(("laterality__in", ["RIGHT", "LEFT"])),
+                name="laterality_valid",
+            ),
+        ),
+        migrations.AddConstraint(
+            model_name="connectivitystatement",
+            constraint=models.CheckConstraint(
+                check=models.Q(
+                    (
+                        "circuit_type__in",
+                        ["SENSORY", "MOTOR", "INTRINSIC", "PROJECTION", "ANAXONIC"],
+                    )
+                ),
+                name="circuit_type_valid",
+            ),
+        ),
+        migrations.AddConstraint(
+            model_name="connectivitystatement",
+            constraint=models.CheckConstraint(
+                check=models.Q(("projection__in", ["IPSI", "CONTRAT", "BI"])),
+                name="projection_valid",
+            ),
+        ),
+
+
+        # add blank=True to Laterality, Projections, Circuit Type
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="circuit_type",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("SENSORY", "Sensory"),
+                    ("MOTOR", "Motor"),
+                    ("INTRINSIC", "Intrinsic"),
+                    ("PROJECTION", "Projection"),
+                    ("ANAXONIC", "Anaxonic"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="laterality",
+            field=models.CharField(
+                blank=True,
+                choices=[("RIGHT", "Right"), ("LEFT", "Left")],
+                max_length=20,
+                null=True,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="projection",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("IPSI", "Ipsilateral"),
+                    ("CONTRAT", "Contralateral"),
+                    ("BI", "Bilateral"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+
+    ]

backend/composer/models.py

@@ -154,6 +154,10 @@ class Phenotype(models.Model):
 
     def __str__(self):
         return self.name
+
+    @property
+    def phenotype_str(self):
+        return str(self.name) if self.name else ''
 
     class Meta:
         ordering = ["name"]
@@ -182,6 +186,10 @@ class Sex(models.Model):
 
     def __str__(self):
         return self.name
+
+    @property
+    def sex_str(self):
+        return str(self.name) if self.name else ''
 
     class Meta:
         ordering = ["name"]
@@ -386,14 +394,15 @@ class ConnectivityStatement(models.Model):
     owner = models.ForeignKey(
         User, verbose_name="Curator", on_delete=models.SET_NULL, null=True, blank=True
     )
+
     laterality = models.CharField(
-        max_length=20, default=Laterality.UNKNOWN, choices=Laterality.choices
+        max_length=20, choices=Laterality.choices, null=True, blank=True
     )
     projection = models.CharField(
-        max_length=20, default=Projection.UNKNOWN, choices=Projection.choices
+        max_length=20, choices=Projection.choices, null=True, blank=True
     )
     circuit_type = models.CharField(
-        max_length=20, default=CircuitType.UNKNOWN, choices=CircuitType.choices
+        max_length=20, choices=CircuitType.choices, null=True, blank=True
     )
     # TODO for next releases we could have only 1 field for phenotype + an intermediate table with the phenotype's categories such as circuit_type, laterality, projection, functional_circuit_role, projection_phenotype among others
     phenotype = models.ForeignKey(
@@ -546,9 +555,8 @@ def get_laterality_description(self):
         laterality_map = {
             Laterality.RIGHT.value: "on the right side of the body",
             Laterality.LEFT.value: "on the left side of the body",
-            Laterality.UNKNOWN.value: "",
         }
-        return laterality_map.get(self.laterality, "")
+        return laterality_map.get(self.laterality, None)
 
     def assign_owner(self, request):
         if ConnectivityStatementService(self).should_set_owner(request):

frontend/src/components/Forms/StatementForm.tsx

@@ -62,6 +62,7 @@ const StatementForm = (props: any) => {
       isDisabled,
       label: "Circuit Type",
       classNames: "col-xs-12 col-md-6",
+      placeholder: "Enter Circuit Type",
     },
   };
 
@@ -71,6 +72,7 @@ const StatementForm = (props: any) => {
       isDisabled,
       label: "Laterality",
       classNames: "col-xs-12 col-md-6",
+      placeholder: "Enter Laterality",
     },
   };
 
@@ -80,6 +82,7 @@ const StatementForm = (props: any) => {
       isDisabled,
       label: "Projection",
       classNames: "col-xs-12 col-md-6",
+      placeholder: "Enter Projection",
     },
   };
 
@@ -653,6 +656,20 @@ const StatementForm = (props: any) => {
     },
   };
 
+  // Add null option to the fields which have null type in dropdown.
+  Object.keys(copiedSchema.properties).forEach((key) => {
+    if (copiedSchema.properties[key].type.includes("null") && copiedSchema.properties[key]?.enum && copiedSchema.properties[key]?.enumNames) {
+      copiedSchema.properties[key].enum.push(null);
+      copiedSchema.properties[key].enumNames.push("---------");
+    }
+  });
+
+  Object.keys(copiedUISchema).forEach((key) => {
+    if (copiedUISchema[key]["ui:options"] && copiedUISchema[key]["ui:options"].data) {
+      copiedUISchema[key]["ui:options"].data.push({ label: "---------", value: null })
+    }
+  });
+
   const widgets = {
     AnatomicalEntitiesField,
     CustomSingleSelect,