modifications as a list

BlueBrain · Jul 1, 2024 · c3897f3 · c3897f3
1 parent c1e6f17
commit c3897f3
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Showing 5 changed files with 40 additions and 49 deletions.
diff --git a/include/bbp/sonata/config.h b/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

diff --git a/python/bindings.cpp b/python/bindings.cpp
@@ -695,13 +695,8 @@ 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")
@@ -710,6 +705,8 @@ PYBIND11_MODULE(_libsonata, m) {
 
     py::class_<SimulationConfig::ModificationBase> modificationBase(simConf, "ModificationBase");
     modificationBase
+        .def_readonly("name",
+                      &SimulationConfig::ModificationBase::name)
         .def_readonly("node_set",
                       &SimulationConfig::ModificationBase::nodeSet,
                       DOC_SIMULATIONCONFIG(ModificationBase, nodeSet))

diff --git a/src/config.cpp b/src/config.cpp
@@ -613,11 +613,16 @@ 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());
@@ -629,16 +634,18 @@ 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:
@@ -1384,6 +1391,11 @@ 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;
 }
@@ -1446,20 +1458,5 @@ 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
diff --git a/tests/data/config/simulation_config.json b/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": {

diff --git a/tests/test_config.cpp b/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");