add synapse_with_neuron schema

emannotationschemas/__init__.py

@@ -4,6 +4,7 @@
 from emannotationschemas.schemas.synapse import BuhmannSynapseSchema
 from emannotationschemas.schemas.synapse import BuhmannEcksteinSynapseSchema
 from emannotationschemas.schemas.synapse import NoCleftSynapse
+from emannotationschemas.schemas.synapse import SynapseWithNeuron
 from emannotationschemas.schemas.bouton_shape import BoutonShape
 from emannotationschemas.schemas.presynaptic_bouton_type import PresynapticBoutonType
 from emannotationschemas.schemas.base import ReferenceAnnotation, ReferenceTagAnnotation
@@ -102,6 +103,7 @@
     "bound_tag_bool": BoundBoolAnnotation,
     "bound_tag_bool_valid": BoundBoolWithValid,
     "bound_tag_valid": BoundTagWithValid,
+    "synapse_with_neuron": SynapseWithNeuron,
 }
 
 def get_types():

emannotationschemas/schemas/synapse.py

@@ -88,3 +88,32 @@ class ValidSynapse(ReferenceAnnotation):
         required=True,
         description="Valid annotation for synapses",
     )
+
+class SynapseWithNeuron(SynapseSchema):
+    pre_neuron_pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="a point of the sample voxel of the neuron where the presynaptic compartment of the synapse is located",
+        order=3,
+    )
+    post_neuron_pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="a point of the sample voxel of the neuron where the postsynaptic compartment of the synapse is located",
+        order=4,
+    )
+
+    @mm.post_load
+    def check_root_id(self, data, **kwargs):
+        pre_neuron_id = data["pre_neuron_pt"].get("root_id", None)
+        post_neuron_id = data["post_neuron_pt"].get("root_id", None)
+        # when the root_id is present
+        # we should set the valid flag depending up on this rule
+        # when the root_id is not present
+        # (i.e. when posting new annotations with no root_id's in mind)
+        # then the valid flag should be not present
+        if pre_neuron_id is not None:
+            data["valid"] = False if pre_neuron_id == post_neuron_id else True
+        else:
+            data.pop("valid", None)
+        return data

requirements_service.txt

@@ -5,4 +5,5 @@ flask-admin==1.6.1
 flask-restx==1.3.0
 flask-accepts==0.18.4
 Werkzeug <= 2.1.2
-pandas==2.0.3
+pandas==2.0.3
+cryptography>=42.0.5

tests/test_synapse_schema.py

@@ -9,6 +9,7 @@
     NoCleftSynapse,
     PlasticSynapse,
     SynapseSchema,
+    SynapseWithNeuron,
 )
 
 good_base_synapse = {
@@ -80,6 +81,13 @@
     "plasticity": 1,
 }
 
+good_synapse_with_neuron = {
+    "pre_pt": {"position": [31, 31, 0]},
+    "ctr_pt": {"position": [32, 32, 0]},
+    "post_pt": {"position": [33, 33, 0]},
+    "pre_neuron_pt": {"position": [34, 34, 0]},
+    "post_neuron_pt": {"position": [35, 35, 0]},
+}
 # class PlasticSynapse(SynapseSchema):
 #     plasticity = mm.fields.Int(required=True,
 #                                validate=mm.validate.OneOf([0, 1, 2, 3, 4]),
@@ -203,3 +211,19 @@ def test_synapse_invalid():
     schema = SynapseSchema()
     with pytest.raises(mm.ValidationError):
         result = schema.load(supervoxel_rootId_invalid_synapse)
+
+def test_synapse_with_neuron():
+    schema = SynapseWithNeuron()
+    result = schema.load(good_synapse_with_neuron)
+    assert result["pre_pt"]["position"] == [31, 31, 0]
+    assert result["pre_neuron_pt"]["position"] == [34, 34, 0]
+    assert result["post_neuron_pt"]["position"] == [35, 35, 0]
+
+
+def test_synapse_with_neuron_postgis():
+    schema = SynapseWithNeuron(context={"postgis": True})
+    result = schema.load(good_synapse_with_neuron)
+    d = flatten_dict(result)
+    assert d["pre_pt_position"] == "POINTZ(31 31 0)"
+    assert d["pre_neuron_pt_position"] == "POINTZ(34 34 0)"
+    assert d["post_neuron_pt_position"] == "POINTZ(35 35 0)"