SimulationConfig: modifications as a list to preserve the order (#359)

Author: Weina Ji

include/bbp/sonata/config.h

@@ -324,6 +324,8 @@ class SONATA_API SimulationConfig
         std::string nodeSet;
         /// Name of the manipulation. Supported values are “TTX” and “ConfigureAllSections”.
         ModificationType type;
+        /// Name of the modification setting.
+        std::string name;
     };
 
     struct ModificationTTX: public ModificationBase {};
@@ -337,8 +339,6 @@ class SONATA_API SimulationConfig
 
     using Modification = nonstd::variant<ModificationTTX, ModificationConfigureAllSections>;
 
-    using ModificationMap = std::unordered_map<std::string, Modification>;
-
     /**
      * Parameters defining global experimental conditions.
      */
@@ -366,14 +366,10 @@ class SONATA_API SimulationConfig
         /// dictionaries of variables' names and values.
         std::unordered_map<std::string, std::unordered_map<std::string, variantValueType>>
             mechanisms;
-        /// Collection of dictionaries with each member decribing a modification that mimics
-        /// experimental manipulations to the circuit.
-        ModificationMap modifications;
-        /// Returns the names of the modifications
-        std::set<std::string> listModificationNames() const;
-        /// Returns the given modification parameters
-        /// \throws SonataError if the given modification name does not exist
-        const Modification& getModification(const std::string& name) const;
+        /// List of modifications that mimics experimental manipulations to the circuit.
+        std::vector<Modification> modifications;
+        /// Method to return the full list of modifications in the Conditions section.
+        const std::vector<Modification>& getModifications() const noexcept;
     };
     /**
      * List of report parameters collected during the simulation

python/bindings.cpp

@@ -695,21 +695,15 @@ PYBIND11_MODULE(_libsonata, m) {
         .def_readonly("mechanisms",
                       &SimulationConfig::Conditions::mechanisms,
                       DOC_SIMULATIONCONFIG(Conditions, mechanisms))
-        .def_property_readonly("list_modification_names",
-                               &SimulationConfig::Conditions::listModificationNames,
-                               DOC_SIMULATIONCONFIG(Conditions, listModificationNames))
-        .def("modification",
-             &SimulationConfig::Conditions::getModification,
-             "name"_a,
-             DOC_SIMULATIONCONFIG(Conditions, getModification));
+        .def("modifications", &SimulationConfig::Conditions::getModifications);
 
 
     py::enum_<SimulationConfig::Conditions::SpikeLocation>(conditions, "SpikeLocation")
         .value("soma", SimulationConfig::Conditions::SpikeLocation::soma)
         .value("AIS", SimulationConfig::Conditions::SpikeLocation::AIS);
 
     py::class_<SimulationConfig::ModificationBase> modificationBase(simConf, "ModificationBase");
-    modificationBase
+    modificationBase.def_readonly("name", &SimulationConfig::ModificationBase::name)
         .def_readonly("node_set",
                       &SimulationConfig::ModificationBase::nodeSet,
                       DOC_SIMULATIONCONFIG(ModificationBase, nodeSet))

python/generated/docstrings.h

@@ -713,22 +713,18 @@ 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_getModification =
-R"doc(Returns the given modification parameters
-
-Throws:
-    SonataError if the given modification name does not exist)doc";
-
-static const char *__doc_bbp_sonata_SimulationConfig_Conditions_listModificationNames = R"doc(Returns the names of the modifications)doc";
+static const char *__doc_bbp_sonata_SimulationConfig_Conditions_getModifications =
+R"doc(Method to return the full list of modifications in the Conditions
+section.)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_modifications =
-R"doc(Collection of dictionaries with each member decribing a modification
-that mimics experimental manipulations to the circuit.)doc";
+R"doc(List of modifications that mimics experimental manipulations to the
+circuit.)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_Conditions_randomizeGabaRiseTime =
 R"doc(Enable legacy behavior to randomize the GABA_A rise time in the helper
@@ -1022,6 +1018,8 @@ static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_Modificati
 
 static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_ModificationType_invalid = R"doc()doc";
 
+static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_name = R"doc(Name of the modification setting.)doc";
+
 static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_nodeSet = R"doc(Node set which receives the manipulation)doc";
 
 static const char *__doc_bbp_sonata_SimulationConfig_ModificationBase_type =

python/tests/test_config.py

@@ -434,14 +434,12 @@ def test_basic(self):
                                                                                   'property1': False},
                                                              'GluSynapse': {'property4': 'test',
                                                                             'property3': 0.025}})
-        self.assertEqual(self.config.conditions.list_modification_names, {"applyTTX", "no_SK_E2"})
-        self.assertEqual(self.config.conditions.modification("applyTTX").type.name, "TTX")
-        self.assertEqual(self.config.conditions.modification("applyTTX").node_set, "single")
-        self.assertEqual(self.config.conditions.modification("no_SK_E2").type.name,
-                         "ConfigureAllSections")
-        self.assertEqual(self.config.conditions.modification("no_SK_E2").node_set, "single")
-        self.assertEqual(self.config.conditions.modification("no_SK_E2").section_configure,
-                         "%s.gSK_E2bar_SK_E2 = 0")
+        modifications = {o.name: o for o in self.config.conditions.modifications()}
+        self.assertEqual(modifications["applyTTX"].type.name, "TTX")
+        self.assertEqual(modifications["applyTTX"].node_set, "single")
+        self.assertEqual(modifications["no_SK_E2"].type.name, "ConfigureAllSections")
+        self.assertEqual(modifications["no_SK_E2"].node_set, "single")
+        self.assertEqual(modifications["no_SK_E2"].section_configure, "%s.gSK_E2bar_SK_E2 = 0")
 
         self.assertEqual(self.config.list_report_names,
                          { "axonal_comp_centers", "cell_imembrane", "compartment", "soma", "lfp" })

src/config.cpp

@@ -612,11 +612,16 @@ void parseConditionsMechanisms(
 }
 
 void parseConditionsModifications(const nlohmann::json& it,
-                                  SimulationConfig::ModificationMap& buf) {
+                                  std::vector<SimulationConfig::Modification>& buf) {
     const auto sectionIt = it.find("modifications");
-    if (sectionIt == it.end()) {
+    if (sectionIt == it.end() || sectionIt->is_null()) {
         return;
     }
+    if (!sectionIt->is_array()) {
+        throw SonataError("`modifications` must be an array");
+    }
+    buf.reserve(sectionIt->size());
+
     for (auto& mIt : sectionIt->items()) {
         const auto valueIt = mIt.value();
         const auto debugStr = fmt::format("modification {}", mIt.key());
@@ -628,16 +633,18 @@ void parseConditionsModifications(const nlohmann::json& it,
         case SimulationConfig::ModificationBase::ModificationType::TTX: {
             SimulationConfig::ModificationTTX result;
             result.type = type;
+            parseMandatory(valueIt, "name", debugStr, result.name);
             parseMandatory(valueIt, "node_set", debugStr, result.nodeSet);
-            buf[mIt.key()] = result;
+            buf.push_back(std::move(result));
             break;
         }
         case SimulationConfig::ModificationBase::ModificationType::ConfigureAllSections: {
             SimulationConfig::ModificationConfigureAllSections result;
             result.type = type;
+            parseMandatory(valueIt, "name", debugStr, result.name);
             parseMandatory(valueIt, "node_set", debugStr, result.nodeSet);
             parseMandatory(valueIt, "section_configure", debugStr, result.sectionConfigure);
-            buf[mIt.key()] = result;
+            buf.push_back(std::move(result));
             break;
         }
         default:
@@ -1383,6 +1390,11 @@ const SimulationConfig::Conditions& SimulationConfig::getConditions() const noex
     return _conditions;
 }
 
+const std::vector<SimulationConfig::Modification>& SimulationConfig::Conditions::getModifications()
+    const noexcept {
+    return modifications;
+}
+
 const std::string& SimulationConfig::getNetwork() const noexcept {
     return _network;
 }
@@ -1445,20 +1457,5 @@ const std::string& SimulationConfig::getExpandedJSON() const {
     return _expandedJSON;
 }
 
-std::set<std::string> SimulationConfig::Conditions::listModificationNames() const {
-    return getMapKeys(modifications);
-}
-
-const SimulationConfig::Modification& SimulationConfig::Conditions::getModification(
-    const std::string& name) const {
-    const auto it = modifications.find(name);
-    if (it == modifications.end()) {
-        throw SonataError(
-            fmt::format("The modification '{}' is not present in the simulation config file",
-                        name));
-    }
-    return it->second;
-}
-
 }  // namespace sonata
 }  // namespace bbp

tests/data/config/simulation_config.json

@@ -48,17 +48,19 @@
           "property4": "test"
         }
       },
-      "modifications": {
-        "applyTTX": {
+      "modifications": [
+        {
             "node_set": "single",
-            "type": "TTX"
+            "type": "TTX",
+            "name": "applyTTX"
         },
-        "no_SK_E2": {
+        {
             "node_set": "single",
             "type": "ConfigureAllSections",
-            "section_configure": "%s.gSK_E2bar_SK_E2 = 0"
+            "section_configure": "%s.gSK_E2bar_SK_E2 = 0",
+            "name": "no_SK_E2"
         }
-      }
+        ]
     },
     "inputs": {
         "ex_linear": {

tests/test_config.cpp

@@ -345,15 +345,14 @@ TEST_CASE("SimulationConfig") {
         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(config.getConditions().listModificationNames() ==
-              std::set<std::string>{"applyTTX", "no_SK_E2"});
-        const auto TTX = nonstd::get<SimulationConfig::ModificationTTX>(
-            config.getConditions().getModification("applyTTX"));
-        const auto configAllSects = nonstd::get<SimulationConfig::ModificationConfigureAllSections>(
-            config.getConditions().getModification("no_SK_E2"));
-        CHECK_THROWS_AS(config.getConditions().getModification("DoesNotExist"), SonataError);
+        const auto modifications = config.getConditions().getModifications();
+        CHECK(modifications.size() == 2);
+        const auto TTX = nonstd::get<SimulationConfig::ModificationTTX>(modifications[0]);
+        CHECK(TTX.name == "applyTTX");
         CHECK(TTX.type == SimulationConfig::ModificationBase::ModificationType::TTX);
         CHECK(TTX.nodeSet == "single");
+        const auto configAllSects = nonstd::get<SimulationConfig::ModificationConfigureAllSections>(modifications[1]);
+        CHECK(configAllSects.name == "no_SK_E2");
         CHECK(configAllSects.type ==
               SimulationConfig::ModificationBase::ModificationType::ConfigureAllSections);
         CHECK(configAllSects.sectionConfigure == "%s.gSK_E2bar_SK_E2 = 0");