Merge pull request #290 from MetaCell/feature/CSCKAN-293_3

restoring projections along new projection phenotype
MetaCell · Jul 18, 2024 · 4b3e745 · 4b3e745
2 parents fdac91a + bbf86d0
commit 4b3e745
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Showing 8 changed files with 61 additions and 8 deletions.
diff --git a/backend/composer/admin.py b/backend/composer/admin.py
@@ -194,7 +194,6 @@ class ConnectivityStatementAdmin(
         "sentence__pmcid",
         "knowledge_statement",
     )
-    exclude = ("projection",)
 
     fieldsets = ()
 

diff --git a/backend/composer/api/serializers.py b/backend/composer/api/serializers.py
@@ -572,6 +572,7 @@ def create_statement_preview(self, instance, journey):
             origins = ""
 
         circuit_type = instance.get_circuit_type_display() if instance.circuit_type else None
+        projection = instance.get_projection_display() if instance.projection else None
         projection_phenotype = str(instance.projection_phenotype) if instance.projection_phenotype else ''
 
         laterality_description = instance.get_laterality_description()
@@ -586,6 +587,8 @@ def create_statement_preview(self, instance, journey):
             statement = f"A {phenotype.lower()} connection goes {journey_sentence}.\n"
 
         statement += f"This "
+        if projection:
+            statement += f"{projection.lower()} "
         if projection_phenotype:
             statement += f"{projection_phenotype.lower()} "
         if circuit_type:

diff --git a/backend/composer/enums.py b/backend/composer/enums.py
@@ -10,9 +10,9 @@ class Laterality(models.TextChoices):
 
 
 class Projection(models.TextChoices):
-    IPSI = "IPSI", "Ipsilateral"
-    CONTRAT = "CONTRAT", "Contralateral"
-    BI = "BI", "Bilateral"
+    IPSI = "IPSI", "ipsilateral"
+    CONTRAT = "CONTRAT", "contralateral"
+    BI = "BI", "bilateral"
 
 
 # todo: motor and sensory should move to phenotype options per csv
@@ -78,7 +78,7 @@ class ExportRelationships(models.TextChoices):
     hasSomaPhenotype = "hasSomaPhenotype", "SomaPhenotype"
     hasAlert = "hasAlert", "Alert"
     hasSomaLocatedIn = "hasSomaLocatedIn", "Soma"
-    hasProjectionPhenotype = "hasProjectionPhenotype", "ProjectionPhenotype"
+    hasProjectionPhenotype = "hasProjection", "ProjectionPhenotype"
     hasAxonPresynapticElementIn = "hasAxonPresynapticElementIn", "Axon terminal"
     hasAxonSensorySubcellularElementIn = "hasAxonSensorySubcellularElementIn", "Afferent terminal",
     hasAxonLocatedIn = "hasAxonLocatedIn", "Axon"

diff --git a/backend/composer/migrations/0052_alter_anatomicalentity_options_and_more.py b/backend/composer/migrations/0052_alter_anatomicalentity_options_and_more.py
@@ -0,0 +1,34 @@
+# Generated by Django 4.1.4 on 2024-07-18 09:08
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("composer", "0051_alter_anatomicalentity_region_layer"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="anatomicalentity",
+            options={
+                "verbose_name": "Anatomical Entity",
+                "verbose_name_plural": "Anatomical Entities",
+            },
+        ),
+        migrations.AlterField(
+            model_name="connectivitystatement",
+            name="projection",
+            field=models.CharField(
+                blank=True,
+                choices=[
+                    ("IPSI", "ipsilateral"),
+                    ("CONTRAT", "contralateral"),
+                    ("BI", "bilateral"),
+                ],
+                max_length=20,
+                null=True,
+            ),
+        ),
+    ]
diff --git a/backend/composer/models.py b/backend/composer/models.py
@@ -668,6 +668,10 @@ class Meta:
                 check=Q(circuit_type__in=[c[0] for c in CircuitType.choices]),
                 name="circuit_type_valid",
             ),
+            models.CheckConstraint(
+                check=Q(projection__in=[p[0] for p in Projection.choices]),
+                name="projection_valid",
+            )
         ]
 
 

diff --git a/backend/composer/services/export_services.py b/backend/composer/services/export_services.py
@@ -32,7 +32,7 @@
 HAS_NERVE_BRANCHES_TAG = "Has nerve branches"
 TEMP_CIRCUIT_MAP = {
     CircuitType.INTRINSIC: "http://uri.interlex.org/tgbugs/uris/readable/IntrinsicPhenotype",
-    CircuitType.PROJECTION: "http://uri.interlex.org/tgbugs/uris/readable/ProjectionPhenotype",
+    CircuitType.PROJECTION: "http://uri.interlex.org/tgbugs/uris/readable/HasProjection",
     CircuitType.MOTOR: "http://uri.interlex.org/tgbugs/uris/readable/MotorPhenotype",
     CircuitType.SENSORY: "http://uri.interlex.org/tgbugs/uris/readable/SensoryPhenotype",
 }

diff --git a/frontend/src/components/Forms/StatementForm.tsx b/frontend/src/components/Forms/StatementForm.tsx
@@ -78,13 +78,24 @@ const StatementForm = (props: any) => {
   };
 
 
+  copiedUISchema.projection = {
+    "ui:widget": "CustomSingleSelect",
+    "ui:options": {
+      isDisabled,
+      label: "Projection laterality",
+      classNames: "col-xs-12 col-md-6",
+      placeholder: "Enter Projection Laterality",
+    },
+  };
+
+
   copiedUISchema.projection_phenotype_id = {
     "ui:widget": "CustomSingleSelect",
     "ui:options": {
       isDisabled,
-      label: "Projection",
+      label: "Projection phenotype",
       classNames: "col-xs-12 col-md-6",
-      placeholder: "Enter Projection",
+      placeholder: "Enter Projection Phenotype",
       data: projections.getProjections().map((row: any) => ({
         label: row.name,
         value: row.id,
@@ -712,6 +723,7 @@ const StatementForm = (props: any) => {
         "sex_id",
         "laterality",
         "circuit_type",
+        "projection",
         "projection_phenotype_id",
       ]}
       {...props}

diff --git a/frontend/src/components/TriageStatementSection/StatementDetailsAccordion.tsx b/frontend/src/components/TriageStatementSection/StatementDetailsAccordion.tsx
@@ -67,6 +67,7 @@ const StatementDetailsAccordion = (props: any) => {
             "apinatomy_model",
             "circuit_type",
             "laterality",
+            "projection",
             "projection_phenotype_id",
             "phenotype_id",
             "additional_information"