Removing Abstract References from XSD for the moment

Author: StevenAWhite

projects/cli/bg-cli-main.cpp

@@ -117,7 +117,9 @@ bool genRuntime(std::string pathName)
 //  This function parses the multword value list of a GENERATE
 //  keyword and proeprly queues the correct operations needed to process
 //  the command
-void parse_generate_arguments(biogears::Arguments::MultiwordValue&& args)
+void parse_generate_arguments
+
+(biogears::Arguments::MultiwordValue&& args)
 {
 
   auto is_keyword = [](const std::string& v) { return v == "data" || v == "patients" || v == "runtime" || v == "states" || v == "sepsis" || v == "tables"; };
@@ -126,6 +128,8 @@ void parse_generate_arguments(biogears::Arguments::MultiwordValue&& args)
   auto end = args.end();
   for (; current != end; ++current) {
     const auto& arg = *current;
+    std::transform(current->begin(), current->end(), current->begin(), ::tolower);
+    
     if (arg == "data") {
       g_run_generate_data = true;
     } else if (arg == "patients") {
@@ -428,8 +432,8 @@ int main(int argc, char** argv)
       if (runs) {
         driver.queue(runs, as_subprocess);
       } else {
-        std::cout << "Unable to run " << biogears::branded_version_string_str() << std::endl;
-        exit(BG_CLI_SUCCESS);
+        std::cout << "Failed to read " << arg << std::endl;
+        exit(BG_CLI_PARSE_ERROR);
       }
     }
   }

projects/cli/src/exec/Driver.cpp

@@ -380,6 +380,8 @@ void Driver::queue_Scenario(Executor exec, bool as_subprocess)
     const auto patient_file = scenario->InitialParameters()->PatientFile().get();
     std::string nc_patient_file = patient_file;
     std::transform(nc_patient_file.begin(), nc_patient_file.end(), nc_patient_file.begin(), ::tolower);
+    //When the user provides the ALL directive
+    //We will load one file for every patient in patients/
     if ("all" == nc_patient_file) {
       auto patient_files = biogears::ListFiles("patients", R"(.*\.xml)", false);
 #if BIOGEARS_IO_PRESENT
@@ -390,20 +392,27 @@ void Driver::queue_Scenario(Executor exec, bool as_subprocess)
 #endif
       queue_from_patient_files(exec, patient_files, scenario_launch);
     } 
-    else if (filesystem::exists(scenario->InitialParameters()->PatientFile().get())) {
-      if (filesystem::is_directory(scenario->InitialParameters()->PatientFile().get())) {
-        auto patient_files = biogears::ListFiles(scenario->InitialParameters()->PatientFile().get(), R"(.*\.xml)", false);
+    //When the user provides a directory we treat it as an ALL
+    //But for the directory given
+    else if (filesystem::exists(patient_file)) {
+      if (filesystem::is_directory(patient_file)) {
+        auto patient_files = biogears::ListFiles(patient_file, R"(.*\.xml)", false);
         queue_from_patient_files(exec, patient_files, scenario_launch);
         return;
-      } else {
+      }
+      else {
         exec.Patient(patient_file);
         _pool.queue_work(std::bind(scenario_launch, std::move(exec), false));
         ++_total_work;
         return;
       }
-    } else if (filesystem::exists("patients/" + scenario->InitialParameters()->PatientFile().get())) {
-      if (filesystem::is_directory("patients/" + scenario->InitialParameters()->PatientFile().get())) {
-        auto patient_files = biogears::ListFiles("patients/" + scenario->InitialParameters()->PatientFile().get(), R"(.*\.xml)", false);
+    } 
+    //Historically biogears auto falls back on a assumed directory structure
+    //If the given exist in patients/ and is a directory we will treat it as
+    //if ALL was given but for the provided directory
+    else if (filesystem::exists("patients/" + patient_file)) {
+      if (filesystem::is_directory("patients/" + patient_file)) {
+        auto patient_files = biogears::ListFiles("patients/" + patient_file, R"(.*\.xml)", false);
         queue_from_patient_files(exec, patient_files, scenario_launch);
         return;
       } else {
@@ -412,11 +421,21 @@ void Driver::queue_Scenario(Executor exec, bool as_subprocess)
         ++_total_work;
         return;
       }
-    } else {
-      auto matching_patients = find_matching_files(scenario->InitialParameters()->PatientFile().get());
+    } 
+    //As the user has not provided ALL or given a directory we will now
+    //find matching files across all the IO call backs and queue correctly.
+    //We support some wild cards so we may have more then one result. 
+    else {
+       auto matching_patients = find_matching_files(patient_file);
       if (matching_patients.empty()) {
-        matching_patients = find_matching_files("patients/" + scenario->InitialParameters()->PatientFile().get());
+        matching_patients = find_matching_files("patients/" + patient_file);
+      } 
+      if (matching_patients.empty()){
+        // As all fallback locations have failed we have no furtherways to process the patient and should abort processing.
+        std::cout << "Error unable to process InitialParameter Patient " << patient_file << " no patient specified.\n";
+        return;
       }
+
       queue_from_patient_files(exec, matching_patients, scenario_launch);
     }
   } else if (scenario->InitialParameters().present() && scenario->InitialParameters()->Patient().present()) {
@@ -460,7 +479,9 @@ void Driver::queue_from_sate_files(const Executor& exec, const std::vector<files
 void Driver::queue_from_patient_files(const Executor& exec, const std::vector<filesystem::path>& patient_files, std::function<void(Executor, bool)> scenario_launch_func)
 {
   for (auto& patient_file : patient_files) {
-    std::cout << "\t" << patient_file << std::endl;
+    if (patient_files.size() != 1) {
+        std::cout << "\t" << patient_file << std::endl;
+    }
     Executor patientEx { exec };
     patientEx.Patient(patient_file);
 
@@ -740,9 +761,9 @@ void Driver::async_execute(biogears::Executor& ex, bool multi_patient_run)
   // NOTE: This loses non relative prefixes as the split will eat the leading path_separator
   filesystem::path parent_dir = split_scenario_path.parent_path();
 
-  //if (multi_patient_run) {
-  //  ex.Name(ex.Name() + "-" + patient_no_extension);
-  //}
+  // if (multi_patient_run) {
+  //   ex.Name(ex.Name() + "-" + patient_no_extension);
+  // }
 
   std::string base_file_name = (multi_patient_run) ? scenario_no_extension + "-" + patient_no_extension : scenario_no_extension;
   std::string console_file = base_file_name + ".log";

projects/cli/src/utils/Config.cpp

@@ -858,7 +858,6 @@ bool grab_next_word_or_fail(Tokenizer::token_list::iterator& tokenItr, Tokenizer
     ++next;
     if (next == end) {
       std::cerr << "Error: Unexpected EOF after " << error_context << "\n";
-
     } else if (next->type == ETokenClass::Whitespace) {
       continue;
     } else if (next->type == ETokenClass::Newline) {

share/xsd/cdm/AnesthesiaActions.xsd

@@ -16,7 +16,7 @@ specific language governing permissions and limitations under the License.
   <xs:include schemaLocation="Anesthesia.xsd"/>
 
   <!-- @brief Base anesthesia machine action type. -->
-  <xs:complexType name="AnesthesiaMachineActionData" abstract="true">
+  <xs:complexType name="AnesthesiaMachineActionData" >
     <xs:complexContent>
       <xs:extension base="ActionData"/>
     </xs:complexContent>

share/xsd/cdm/Circuit.xsd

@@ -32,7 +32,7 @@ specific language governing permissions and limitations under the License.
     </xs:restriction>
   </xs:simpleType>
 
-  <xs:complexType name="CircuitData" abstract="true">
+  <xs:complexType name="CircuitData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:sequence>
@@ -42,7 +42,8 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="CircuitNodeData" abstract="true">
+  
+  <xs:complexType name="CircuitNodeData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:sequence>
@@ -51,7 +52,8 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="CircuitPathData" abstract="true">
+  
+  <xs:complexType name="CircuitPathData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:sequence>

share/xsd/cdm/Compartment.xsd

@@ -25,7 +25,7 @@ specific language governing permissions and limitations under the License.
     </xs:restriction>
   </xs:simpleType>
 
-  <xs:complexType name="CompartmentData" abstract="true">
+  <xs:complexType name="CompartmentData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:sequence>
@@ -36,7 +36,7 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="CompartmentLinkData" abstract="true">
+  <xs:complexType name="CompartmentLinkData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:sequence>
@@ -49,7 +49,7 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="CompartmentGraphData" abstract="true">
+  <xs:complexType name="CompartmentGraphData" >
     <xs:sequence>
       <xs:element name="Name" type="xs:string" minOccurs="1" maxOccurs="1"/>
 
@@ -58,7 +58,7 @@ specific language governing permissions and limitations under the License.
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="FluidCompartmentData" abstract="true">
+  <xs:complexType name="FluidCompartmentData" >
     <xs:complexContent>
       <xs:extension base="CompartmentData">
         <xs:sequence>
@@ -70,7 +70,7 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="FluidCompartmentLinkData" abstract="true">
+  <xs:complexType name="FluidCompartmentLinkData" >
     <xs:complexContent>
       <xs:extension base="CompartmentLinkData">
         <xs:sequence>
@@ -79,7 +79,7 @@ specific language governing permissions and limitations under the License.
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
-  <xs:complexType name="FluidCompartmentGraphData" abstract="true">
+  <xs:complexType name="FluidCompartmentGraphData" >
     <xs:complexContent>
       <xs:extension base="CompartmentGraphData">
         <xs:sequence>

share/xsd/cdm/EngineConfiguration.xsd

@@ -37,14 +37,14 @@ specific language governing permissions and limitations under the License.
 
 
 
-  <xs:complexType name="PhysiologyEngineStabilizationData" abstract="true">
+  <xs:complexType name="PhysiologyEngineStabilizationData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
       </xs:extension>
     </xs:complexContent>
   </xs:complexType>
 
-  <xs:complexType name="PhysiologyEngineConditionStabilizationData" abstract="true">
+  <xs:complexType name="PhysiologyEngineConditionStabilizationData" >
     <xs:complexContent>
       <xs:extension base="ObjectData">
         <xs:attribute name="Name" type="xs:string" use="required"/>
@@ -110,4 +110,4 @@ specific language governing permissions and limitations under the License.
   </xs:complexType>
   <xs:element name="PhysiologyEngineDynamicStabilization" type="PhysiologyEngineDynamicStabilizationData"/>
 
-</xs:schema>
+</xs:schema>

share/xsd/cdm/EnvironmentActions.xsd

@@ -16,7 +16,7 @@ specific language governing permissions and limitations under the License.
   <xs:include schemaLocation="Scenario.xsd"/>
 
   <!-- @brief Base Environmental Action type -->
-  <xs:complexType name="EnvironmentActionData" abstract="true">
+  <xs:complexType name="EnvironmentActionData" >
     <xs:complexContent>
       <xs:extension base="ActionData"/>
     </xs:complexContent>

share/xsd/cdm/EnvironmentConditions.xsd

@@ -16,7 +16,7 @@ specific language governing permissions and limitations under the License.
   <xs:include schemaLocation="Scenario.xsd"/>
 
   <!-- @brief Base environmental condition type -->
-  <xs:complexType name="EnvironmentConditionData" abstract="true">
+  <xs:complexType name="EnvironmentConditionData" >
     <xs:complexContent>
       <xs:extension base="ConditionData"/>
     </xs:complexContent>

share/xsd/cdm/InhalerActions.xsd

@@ -16,7 +16,7 @@ specific language governing permissions and limitations under the License.
   <xs:include schemaLocation="Inhaler.xsd"/>
 
   <!-- @brief Base inhaler action type. -->
-  <xs:complexType name="InhalerActionData" abstract="true">
+  <xs:complexType name="InhalerActionData" >
     <xs:complexContent>
       <xs:extension base="ActionData"/>
     </xs:complexContent>