parsing species

open-atmos · Jan 12, 2024 · c7ad061 · c7ad061
1 parent a9521a0
commit c7ad061
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Showing 8 changed files with 69 additions and 23 deletions.
diff --git a/examples/full_configuration.json b/examples/full_configuration.json
@@ -4,16 +4,20 @@
   "species": [
     {
       "name": "A",
-      "__absolute tolerance": 1.0e-30
+      "__absolute tolerance": 1.0e-30,
+      "phase": "gas"
     },
     {
-      "name": "B"
+      "name": "B",
+      "phase": "gas"
     },
     {
-      "name": "C"
+      "name": "C",
+      "phase": "gas"
     },
     {
       "name": "H2O2",
+      "phase": "gas",
       "HLC(298K) [mol m-3 Pa-1]": 1.011596348,
       "HLC exponential factor [K]": 6340,
       "diffusion coefficient [m2 s-1]": 1.46E-05,
@@ -24,25 +28,29 @@
     },
     {
       "name": "ethanol",
+      "phase": "gas",
       "diffusion coefficient [m2 s-1]": 0.95E-05,
       "N star": 2.55,
       "molecular weight [kg mol-1]": 0.04607,
       "__absolute tolerance": 1.0e-20
     },
     {
       "name": "ethanol_aq",
+      "phase": "gas",
       "molecular weight [kg mol-1]": 0.04607,
       "density [kg m-3]": 1000.0,
       "__absolute tolerance": 1.0e-20
     },
     {
       "name": "H2O2_aq",
+      "phase": "gas",
       "molecular weight [kg mol-1]": 0.0340147,
       "density [kg m-3]": 1000.0,
       "__absolute tolerance": 1.0e-10
     },
     {
       "name": "H2O_aq",
+      "phase": "gas",
       "density [kg m-3]": 1000.0,
       "molecular weight [kg mol-1]": 0.01801
     },

diff --git a/include/open_atmos/mechanism_configuration/parser.hpp b/include/open_atmos/mechanism_configuration/parser.hpp
@@ -25,12 +25,8 @@ namespace open_atmos
       InvalidKey,
       UnknownKey,
       InvalidFilePath,
-      NoConfigFilesFound,
-      DataSectionNotFound,
-      InvalidSpecies,
       ObjectTypeNotFound,
       RequiredKeyNotFound,
-      ContainsNonStandardKey,
       MutuallyExclusiveOption,
       InvalidVersion,
       DuplicateSpeciesDetected

diff --git a/src/parser.cpp b/src/parser.cpp
@@ -21,11 +21,8 @@ namespace open_atmos
         case ConfigParseStatus::InvalidKey: return "InvalidKey";
         case ConfigParseStatus::UnknownKey: return "UnknownKey";
         case ConfigParseStatus::InvalidFilePath: return "InvalidFilePath";
-        case ConfigParseStatus::NoConfigFilesFound: return "NoConfigFilesFound";
-        case ConfigParseStatus::InvalidSpecies: return "InvalidSpecies";
         case ConfigParseStatus::ObjectTypeNotFound: return "ObjectTypeNotFound";
         case ConfigParseStatus::RequiredKeyNotFound: return "RequiredKeyNotFound";
-        case ConfigParseStatus::ContainsNonStandardKey: return "ContainsNonStandardKey";
         case ConfigParseStatus::MutuallyExclusiveOption: return "MutuallyExclusiveOption";
         case ConfigParseStatus::DuplicateSpeciesDetected: return "DuplicateSpeciesDetected";
         default: return "Unknown";
@@ -136,7 +133,7 @@ namespace open_atmos
         {
           std::cerr << "Non-standard key '" << key << "' found in object" << object << std::endl;
 
-          return ConfigParseStatus::ContainsNonStandardKey;
+          return ConfigParseStatus::InvalidKey;
         }
       }
       return ConfigParseStatus::Success;
@@ -150,14 +147,12 @@ namespace open_atmos
       for (const auto& object : objects)
       {
         types::Species species;
-        auto status = ValidateSchema(object, validation::species.required_keys, validation::species.optional_keys);
+        status = ValidateSchema(object, validation::species.required_keys, validation::species.optional_keys);
         if (status != ConfigParseStatus::Success)
         {
           break;
         }
 
-        // std::cout << "object:\n" << object.dump(4) << std::endl;
-
         std::string name = object[validation::keys.name].get<std::string>();
         std::string phase = object[validation::keys.phase].get<std::string>();
 
@@ -167,11 +162,13 @@ namespace open_atmos
         {
           if (object.contains(key))
           {
-            if (key == validation::keys.tracer_type) {
+            if (key == validation::keys.tracer_type)
+            {
               std::string val = object[key].get<std::string>();
               string_properties[key] = val;
             }
-            else {
+            else
+            {
               double val = object[key].get<double>();
               numerical_properties[key] = val;
             }
@@ -197,14 +194,18 @@ namespace open_atmos
       }
 
       // check for duplicate species
-      for(size_t i = 0; i < all_species.size(); ++i) {
-        for(size_t j = i+1; j < all_species.size(); ++j) {
-          if (all_species[i].name == all_species[j].name) {
+      for (size_t i = 0; i < all_species.size(); ++i)
+      {
+        for (size_t j = i + 1; j < all_species.size(); ++j)
+        {
+          if (all_species[i].name == all_species[j].name)
+          {
             status = ConfigParseStatus::DuplicateSpeciesDetected;
           }
           break;
         }
-        if (status != ConfigParseStatus::Success) break;
+        if (status != ConfigParseStatus::Success)
+          break;
       }
 
       return { status, all_species };
@@ -274,4 +275,4 @@ namespace open_atmos
       return { status, mechanism };
     }
   }  // namespace mechanism_configuration
-}  // namespace open_atmos
+}  // namespace open_atmos
diff --git a/test/unit/test_parse_species.cpp b/test/unit/test_parse_species.cpp
@@ -46,4 +46,20 @@ TEST(JsonParser, DetectsDuplicateSpecies)
   auto [status, mechanism] = parser.Parse(std::string("unit_configs/duplicate_species.json"));
 
   EXPECT_EQ(status, ConfigParseStatus::DuplicateSpeciesDetected);
+}
+
+TEST(JsonParser, DetectsMissingRequiredKeys)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/missing_required_key.json"));
+
+  EXPECT_EQ(status, ConfigParseStatus::RequiredKeyNotFound);
+}
+
+TEST(JsonParser, DetectsInvalidKeys)
+{
+  JsonParser parser;
+  auto [status, mechanism] = parser.Parse(std::string("unit_configs/invalid_key.json"));
+
+  EXPECT_EQ(status, ConfigParseStatus::InvalidKey);
 }
diff --git a/test/unit/unit_configs/duplicate_species.json b/test/unit/unit_configs/duplicate_species.json
@@ -1,6 +1,6 @@
 {
   "version": "1.0.0",
-  "name": "Full Configuration",
+  "name": "Duplicate Species",
   "species": [
     {
       "name": "A",

diff --git a/test/unit/unit_configs/invalid_key.json b/test/unit/unit_configs/invalid_key.json
@@ -0,0 +1,13 @@
+{
+  "version": "1.0.0",
+  "name": "Invalid key",
+  "species": [
+    {
+      "name": "A",
+      "phase": "gas",
+      "_absolute tolerance": 1.0e-30
+    }
+  ],
+  "phases": [ ],
+  "reactions": [ ]
+}
diff --git a/test/unit/unit_configs/missing_required_key.json b/test/unit/unit_configs/missing_required_key.json
@@ -0,0 +1,12 @@
+{
+  "version": "1.0.0",
+  "name": "Invalid key",
+  "species": [
+    {
+      "Name": "A",
+      "Phase": "gas"
+    }
+  ],
+  "phases": [ ],
+  "reactions": [ ]
+}
diff --git a/test/unit/unit_configs/valid_species.json b/test/unit/unit_configs/valid_species.json
@@ -1,6 +1,6 @@
 {
   "version": "1.0.0",
-  "name": "Full Configuration",
+  "name": "Valid species configuration",
   "species": [
     {
       "name": "A",