Parse synapse mod variables in conditions/mechanisms section (#217)

BlueBrain · Jul 12, 2022 · e0cdaf7 · e0cdaf7
1 parent 15adaae
commit e0cdaf7
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Showing 7 changed files with 111 additions and 12 deletions.
diff --git a/include/bbp/sonata/config.h b/include/bbp/sonata/config.h
@@ -29,6 +29,8 @@
 namespace bbp {
 namespace sonata {
 
+using variantValueType = nonstd::variant<bool, std::string, int, double>;
+
 /**
  * Stores population-specific network information.
  */
@@ -241,6 +243,11 @@ class SONATA_API SimulationConfig
         /// Enable legacy behavior to randomize the GABA_A rise time in the helper functions.
         /// Default is false
         bool randomizeGabaRiseTime;
+        /// Properties to assign values to variables in synapse MOD files.
+        /// The format is a dictionary with keys being the SUFFIX names and values being
+        /// dictionaries of variables' names and values.
+        std::unordered_map<std::string, std::unordered_map<std::string, variantValueType>>
+            mechanisms;
     };
     /**
      * List of report parameters collected during the simulation

diff --git a/python/bindings.cpp b/python/bindings.cpp
@@ -597,7 +597,10 @@ PYBIND11_MODULE(_libsonata, m) {
                       DOC_SIMULATIONCONFIG(Conditions, minisSingleVesicle))
         .def_readonly("randomize_gaba_rise_time",
                       &SimulationConfig::Conditions::randomizeGabaRiseTime,
-                      DOC_SIMULATIONCONFIG(Conditions, randomizeGabaRiseTime));
+                      DOC_SIMULATIONCONFIG(Conditions, randomizeGabaRiseTime))
+        .def_readonly("mechanisms",
+                      &SimulationConfig::Conditions::mechanisms,
+                      DOC_SIMULATIONCONFIG(Conditions, mechanisms));
 
     py::class_<SimulationConfig::Report> report(m, "Report", "Parameters of a report");
     report

diff --git a/python/generated/docstrings.h b/python/generated/docstrings.h
@@ -545,6 +545,11 @@ R"doc(Extracellular calcium concentration, being applied to the synapse
 uHill parameter in order to scale the U parameter of synapses. Default
 is None.)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_Conditions_mechanisms =
+R"doc(Properties to assign values to variables in synapse MOD files. The
+format is a dictionary with keys being the SUFFIX names and values
+being dictionaries of variables' names and values.)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_Conditions_minisSingleVesicle =
 R"doc(Limit spontaneous release to single vesicle when true. Default is
 false)doc";
@@ -875,19 +880,43 @@ static const char *__doc_bbp_sonata_SimulationConfig_Report_variableName = R"doc
 
 static const char *__doc_bbp_sonata_SimulationConfig_Run = R"doc(Parameters defining global simulation settings for spike reports)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_euler = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_invalid = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_nicholson = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_IntegrationMethod_nicholson_ion = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_SpikeLocation = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_SpikeLocation_AIS = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_SpikeLocation_invalid = R"doc()doc";
+
+static const char *__doc_bbp_sonata_SimulationConfig_Run_SpikeLocation_soma = R"doc()doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_Run_dt = R"doc(Integration step duration in milliseconds)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_randomSeed = R"doc(Random seed)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_forwardSkip =
+R"doc(Run without Stimulus or Reports for given duration prior to t=0 using
+a timestep computed as dt=0.1*forward_skip. Default = None)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_tstop = R"doc(Biological simulation end time in milliseconds)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_integrationMethod =
+R"doc(Selects the NEURON/CoreNEURON integration method. This parameter sets
+the NEURON global variable h.secondorder. Default 0 ('euler'))doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_spikeThreshold = R"doc(The spike detection threshold. Default is -30mV)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_randomSeed = R"doc(Random seed)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_spikeLocation = R"doc(The spike detection location. Can be either ‘soma’ or 'AIS'. Default is 'soma')doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_spikeLocation =
+R"doc(The spike detection location. Can be either ‘soma’ or 'AIS'. Default
+is 'soma')doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_integrationMethod = R"doc(Selects the NEURON/CoreNEURON integration method. This parameter sets the NEURON global variable h.secondorder. Default 0 ('euler'))doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_spikeThreshold = R"doc(The spike detection threshold. Default is -30mV)doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_Run_forwardSkip = R"doc(Run without Stimulus or Reports for given duration prior to t=0 using a timestep computed as dt=0.1*forward_skip. Default = None)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Run_tstop = R"doc(Biological simulation end time in milliseconds)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_SimulationConfig =
 R"doc(Parses a SONATA JSON simulation configuration file.
@@ -910,6 +939,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_conditions = R"doc()doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_connections = R"doc()doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_expandedJSON = R"doc()doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_fromFile =
 R"doc(Loads a SONATA JSON simulation config file from disk and returns a
 CircuitConfig object which parses it.
@@ -930,6 +961,10 @@ R"doc(Returns the given connection parameters
     SonataError if the given connection name does not correspond with
     any existing connection.)doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_getExpandedJSON =
+R"doc(Returns the configuration file JSON whose variables have been expanded
+by the manifest entries.)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_getInput =
 R"doc(Returns the given input parameters.
 
@@ -967,8 +1002,6 @@ R"doc(Returns the name of simulator, default = NEURON
 
 static const char *__doc_bbp_sonata_SimulationConfig_inputs = R"doc()doc";
 
-static const char *__doc_bbp_sonata_SimulationConfig_jsonContent = R"doc()doc";
-
 static const char *__doc_bbp_sonata_SimulationConfig_listConnectionOverrideNames = R"doc(Returns the names of the connection_overrides)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_listInputNames = R"doc(Returns the names of the reports)doc";

diff --git a/python/tests/test.py b/python/tests/test.py
@@ -716,6 +716,10 @@ def test_basic(self):
         self.assertEqual(self.config.conditions.extracellular_calcium, None)
         self.assertEqual(self.config.conditions.minis_single_vesicle, False)
         self.assertEqual(self.config.conditions.randomize_gaba_rise_time, False)
+        self.assertEqual(self.config.conditions.mechanisms, {'ProbAMPANMDA_EMS': {'property2': -1,
+                                                                                  'property1': False},
+                                                             'GluSynapse': {'property4': 'test',
+                                                                            'property3': 0.025}})
 
         self.assertEqual(self.config.list_report_names,
                          { "axonal_comp_centers", "cell_imembrane", "compartment", "soma" })

diff --git a/src/config.cpp b/src/config.cpp
@@ -421,6 +421,40 @@ SimulationConfig::Input parseInputModule(const nlohmann::json& valueIt,
     }
 }
 
+void parseConditionsMechanisms(
+    const nlohmann::json& it,
+    std::unordered_map<std::string, std::unordered_map<std::string, variantValueType>>& buf) {
+    const auto mechIt = it.find("mechanisms");
+    if (mechIt == it.end()) {
+        return;
+    }
+    for (auto& scopeIt : mechIt->items()) {
+        std::unordered_map<std::string, variantValueType> map_vars;
+        for (auto& varIt : scopeIt.value().items()) {
+            variantValueType res_val;
+            switch (varIt.value().type()) {
+            case nlohmann::json::value_t::boolean:
+                res_val = varIt.value().get<bool>();
+                break;
+            case nlohmann::json::value_t::string:
+                res_val = varIt.value().get<std::string>();
+                break;
+            case nlohmann::json::value_t::number_float:
+                res_val = varIt.value().get<double>();
+                break;
+            case nlohmann::json::value_t::number_integer:
+            case nlohmann::json::value_t::number_unsigned:
+                res_val = varIt.value().get<int>();
+                break;
+            default:
+                throw SonataError("Value type not supported");
+            }
+            map_vars.insert({varIt.key(), res_val});
+        }
+        buf.insert({scopeIt.key(), map_vars});
+    }
+}
+
 }  // namespace
 
 class CircuitConfig::Parser
@@ -845,7 +879,7 @@ class SimulationConfig::Parser
                       "randomize_gaba_rise_time",
                       result.randomizeGabaRiseTime,
                       {false});
-
+        parseConditionsMechanisms(*conditionsIt, result.mechanisms);
         return result;
     }
 

diff --git a/tests/data/config/simulation_config.json b/tests/data/config/simulation_config.json
@@ -18,8 +18,18 @@
          "spikes_sort_order": "by_id"
     },
     "conditions": {
-     "celsius": 35.0,
-     "synapses_init_deleted": false
+      "celsius": 35.0,
+      "synapses_init_depleted": false,
+      "mechanisms": {
+        "ProbAMPANMDA_EMS": {
+          "property1": false,
+          "property2": -1
+        },
+        "GluSynapse" : {
+          "property3": 0.025,
+          "property4": "test"
+        }
+      }
     },
     "inputs": {
         "ex_linear": {

diff --git a/tests/test_config.cpp b/tests/test_config.cpp
@@ -327,6 +327,14 @@ TEST_CASE("SimulationConfig") {
         CHECK(config.getConditions().extracellularCalcium == nonstd::nullopt);
         CHECK(config.getConditions().minisSingleVesicle == false);
         CHECK(config.getConditions().randomizeGabaRiseTime == false);
+        CHECK(config.getConditions().mechanisms.size() == 2);
+        auto itr = config.getConditions().mechanisms.find("ProbAMPANMDA_EMS");
+        CHECK(itr != config.getConditions().mechanisms.end());
+        CHECK(nonstd::get<bool>(itr->second.find("property1")->second) == false);
+        CHECK(nonstd::get<int>(itr->second.find("property2")->second) == -1);
+        itr = config.getConditions().mechanisms.find("GluSynapse");
+        CHECK(nonstd::get<double>(itr->second.find("property3")->second) == 0.025);
+        CHECK(nonstd::get<std::string>(itr->second.find("property4")->second) == "test");
 
         CHECK_THROWS_AS(config.getReport("DoesNotExist"), SonataError);