adding simulatable neuron class and registering function

bluepyemodel/access_point/forge_access_point.py

@@ -37,6 +37,7 @@
 from bluepyemodel.emodel_pipeline.emodel_settings import EModelPipelineSettings
 from bluepyemodel.emodel_pipeline.emodel_workflow import EModelWorkflow
 from bluepyemodel.emodel_pipeline.memodel import MEModel
+from bluepyemodel.emodel_pipeline.simulatable_neuron import SimulatableNeuron
 from bluepyemodel.evaluation.fitness_calculator_configuration import FitnessCalculatorConfiguration
 from bluepyemodel.model.distribution_configuration import DistributionConfiguration
 from bluepyemodel.model.neuron_model_configuration import NeuronModelConfiguration
@@ -57,6 +58,7 @@
     "EModelWorkflow": "EModelWorkflow",
     "EModelScript": "EModelScript",
     "MEModel": "MEModel",
+    "SimulatableNeuron": "SimulatableNeuron",
 }
 
 CLASS_TO_RESOURCE_NAME = {
@@ -69,6 +71,7 @@
     "EModelWorkflow": "EMW",
     "EModelScript": "EMS",
     "MEModel": "MEM",
+    "SimulatableNeuron": "SN",
 }
 
 NEXUS_TYPE_TO_CLASS = {
@@ -81,6 +84,7 @@
     "EModelWorkflow": EModelWorkflow,
     "EModelScript": EModelScript,
     "MEModel": MEModel,
+    "SimulatableNeuron": SimulatableNeuron,
 }
 
 NEXUS_ENTRIES = [
@@ -437,7 +441,9 @@ def register(
         # when EModelWorkflow resource is complete
         if type_ == "EModelWorkflow":
             type_ = "Entity"
-        schema_id = self.forge._model.schema_id(type_)
+        schema_id = None
+        if type_ != "SimulatableNeuron":
+            schema_id = self.forge._model.schema_id(type_)
 
         self.forge.register(resource, schema_id=schema_id)
 

bluepyemodel/access_point/nexus.py

@@ -1486,3 +1486,54 @@ def sonata_exists(self, seed):
             return True
         except AccessPointException:
             return False
+
+    def store_simulatable_neuron(self, simulatable_neuron, is_analysis_suitable=False):
+        """Store a BPEM object on Nexus
+
+        Args:
+            simulatable_neuron (SimulatableNeuron)
+            is_analysis_suitable (bool): Should be True only when managing metatada for resources
+                of type EModel, for which all data are complete (has FCC, ETC, EMC, etc.).
+        """
+
+        metadata_dict = self.emodel_metadata_ontology.for_resource(
+            is_analysis_suitable=is_analysis_suitable
+        )
+
+        type_ = "SimulatableNeuron"
+
+        base_payload = simulatable_neuron.as_dict()
+        base_payload["type"] = ["Entity", type_]
+        if "subject" in metadata_dict:
+            base_payload["subject"] = metadata_dict["subject"]
+        if "brainLocation" in metadata_dict:
+            base_payload["brainLocation"] = metadata_dict["brainLocation"]
+        if "annotation" in metadata_dict:
+            base_payload["annotation"] = metadata_dict["annotation"]
+
+        self.access_point.register(
+            base_payload,
+            filters_existence=None,
+            legacy_filters_existence=None,
+            replace=False,
+            distributions=None,
+            images=None,
+            type_=type_,
+        )
+
+        # update EMW if any
+        workflow, workflow_id = self.get_emodel_workflow()
+
+        # wait for the object to be uploaded and fetchable
+        if workflow is not None and workflow_id is not None:
+            time.sleep(self.sleep_time)
+
+            # fetch just uploaded simulatable neuron resource to get its id
+            type_ = "SimulatableNeuron"
+            filters = {"type": type_, **simulatable_neuron.as_dict()}
+            resource = self.access_point.fetch_one(filters, strict=True)
+            simulatable_neuron_id = resource.id
+            workflow.add_simulatable_neuron_id(simulatable_neuron_id)
+
+            time.sleep(self.sleep_time)
+            self.store_or_update_emodel_workflow(workflow)

bluepyemodel/emodel_pipeline/emodel_workflow.py

@@ -32,6 +32,7 @@ def __init__(
         fitness_configuration_id=None,
         emodels=None,
         emodel_scripts_id=None,
+        simulatable_neuron_ids=None,
         state="not launched",
     ):
         """Init
@@ -42,6 +43,8 @@ def __init__(
             emodel_configuration (str): NeuronModelConfiguration id
             fitness_configuration_id (str): FitnessCalculatorConfiguration id
             emodels (list): list of EModel ids
+            emodel_scripts_id (list): list of EModelScript ids
+            simulatable_neuron_ids (list): list of SimulatableNeuron ids
             state (str): can be "not launched", "running" or "done"
         """
         self.targets_configuration_id = targets_configuration_id
@@ -50,16 +53,21 @@ def __init__(
         self.fitness_configuration_id = fitness_configuration_id
         self.emodels = emodels if emodels else []
         self.emodel_scripts_id = emodel_scripts_id if emodel_scripts_id else []
+        self.simulatable_neuron_ids = simulatable_neuron_ids if simulatable_neuron_ids else []
         self.state = state
 
     def add_emodel_id(self, emodel_id):
         """Add an emodel id to the list of emodels"""
         self.emodels.append(emodel_id)
 
     def add_emodel_script_id(self, emodel_script_id):
-        """Add an emodel id to the list of emodels"""
+        """Add an emodel script id to the list of emodel scripts"""
         self.emodel_scripts_id.append(emodel_script_id)
 
+    def add_simulatable_neuron_id(self, simulatable_neuron_id):
+        """Add an simulatable neuron id to the list of simulatable neurons"""
+        self.emodel_scripts_id.append(simulatable_neuron_id)
+
     def get_configuration_ids(self):
         """Return all configuration id parameters"""
         ids = (
@@ -75,7 +83,10 @@ def get_configuration_ids(self):
     def get_related_nexus_ids(self):
         emodels_ids = [{"id": id_, "type": "EModel"} for id_ in self.emodels]
         emodel_scripts_ids = [{"id": id_, "type": "EModelScript"} for id_ in self.emodel_scripts_id]
-        generates = emodels_ids + emodel_scripts_ids
+        simulatable_neuron_ids = [
+            {"id": id_, "type": "SimulatableNeuron"} for id_ in self.simulatable_neuron_ids
+        ]
+        generates = emodels_ids + emodel_scripts_ids + simulatable_neuron_ids
         if self.fitness_configuration_id:
             generates.append(
                 {

bluepyemodel/emodel_pipeline/simulatable_neuron.py

@@ -0,0 +1,62 @@
+"""SimulatableNeuron class"""
+
+"""
+Copyright 2025 Open Brain Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+"""
+
+
+class SimulatableNeuron:
+    """Whole neuron model, including links to morphology, ion channels models and hoc."""
+
+    def __init__(
+        self,
+        name,
+        description,
+        emodel_script_id,
+        mechanism_ids,
+        morphology_id,
+        holding_current=None,
+        threshold_current=None,
+        validated=False,
+    ):
+        """Init
+
+        from_circuit and synaptomes, that might be present in the database,
+        are not implemented here.
+        subject, brainRegion are coming emodel_metadata
+
+        Args:
+            name (str): name
+            description (str): description of the model
+            emodel_script_id (str): ID of the hoc model in the database
+            mechanism_ids (list of str): IDs of the ion channel models in the database
+            morphology_id (str): ID of the morphology in the database
+            holding_current (float): holding current to use in protocols (in nA)
+            threshold_current (float): current at which the cell starts firing (in nA)
+            validated (bool): whether the model has been validated by user
+        """
+        # check if brain region and subject are automatically added
+        self.name = name
+        self.description = description
+        self.emodel_script_id = emodel_script_id
+        self.mechanism_ids = mechanism_ids
+        self.morphology_id = morphology_id
+        self.holding_current = holding_current
+        self.threshold_current = threshold_current
+        self.validated = validated
+
+    def as_dict(self):
+        """Used for the storage of the object"""
+        return vars(self)