f/shashank-website -- Website Documentation -- Creation of Website using Python

projects/CMakeLists.txt

@@ -13,7 +13,7 @@ find_path (
         ${PROJECT_SOURCE_DIR}/../verification  
         ${PROJECT_SOURCE_DIR}/../validation 
         ${PROJECT_SOURCE_DIR}/../baselines
-  DOC "Optional directory path to hiarchial filetree of baseline archives. This will be used by Java Utilities to find Baselines"
+  DOC "Optional directory path to hiarchial filetree of baseline archives. This will be used by Python Plotters to find Baselines"
 )
 find_path (
   ${ROOT_PROJECT_NAME}_Reference_DIR
@@ -138,11 +138,7 @@ add_custom_target( prepare_runtime_dir
 #         this list
 ###############################################################################
 
-find_package(Java)
-find_package(JNI)
 verify_package(Log4cpp REQUIRED)
-option(${ROOT_PROJECT_NAME}_BUILD_JAVATOOLS     "Build Java based development tools (requires Doxygen)" OFF )
-
 add_subdirectory(biogears-common)
 add_subdirectory(biogears)
 add_subdirectory(test_driver)
@@ -151,10 +147,7 @@ add_subdirectory(unit)
 add_subdirectory(circuit_profiler)
 add_subdirectory(zip)
 add_subdirectory(cli)
-
-if(Java_FOUND AND ${ROOT_PROJECT_NAME}_BUILD_JAVATOOLS)
-  add_subdirectory(java)
-endif()
+add_subdirectory(website)
 
 ##############################################################################
 # Step 3: Global Doxygen configuration 

projects/cli/bg-cli-main.cpp

@@ -227,8 +227,10 @@ int main(int argc, char** argv)
       std::transform(table.begin(), table.end(), table.begin(), ::tolower);
       if (table == "html") {
         report_writer.gen_tables(biogears::ReportWriter::HTML);
+	report_writer.gen_patient_tables(biogears::ReportWriter::HTML);
       } else if (table == "md") {
         report_writer.gen_tables(biogears::ReportWriter::MD);
+	report_writer.gen_patient_tables(biogears::ReportWriter::MD);
       } else if (table == "xml") {
         report_writer.gen_tables(biogears::ReportWriter::XML);
       } else if (table == "web") {

projects/cli/src/exec/Driver.cpp

@@ -32,6 +32,8 @@
 #include <biogears/engine/BioGearsPhysiologyEngine.h>
 #include <biogears/engine/Controller/Scenario/BioGearsScenario.h>
 #include <biogears/engine/Controller/Scenario/BioGearsScenarioExec.h>
+#include <biogears/cdm/engine/PhysiologyEngineDynamicStabilization.h>
+#include <biogears/cdm/engine/PhysiologyEngineTimedStabilization.h>
 
 #ifdef CMD_BIO_SUPPORT_CIRCUIT_TEST
 #include <biogears/cdm/test/CommonDataModelTest.h>
@@ -285,13 +287,13 @@ void Driver::queue_Scenario(Executor exec, bool as_subprocess)
     }
   }
 
-  std::unique_ptr<mil::tatrc::physiology::datamodel::ScenarioData> scenario;
+  std::unique_ptr<CDM::ScenarioData> scenario;
   try {
     xml_schema::flags xml_flags;
     xml_schema::properties xml_properties;
 
     xml_properties.schema_location("uri:/mil/tatrc/physiology/datamodel", "xsd/BioGearsDataModel.xsd");
-    scenario = mil::tatrc::physiology::datamodel::Scenario(ifs, xml_flags, xml_properties);
+    scenario = CDM::Scenario(ifs, xml_flags, xml_properties);
   } catch (std::runtime_error e) {
     std::cout << e.what() << "\n";
     return;
@@ -362,13 +364,22 @@ void Driver::subprocess_execute(biogears::Executor& ex, bool multi_patient_run)
 {
   using namespace biogears;
   _process_count += 1;
-
+  std::cout<<"Trying this up in subprocess_execute";
   try {
     using namespace boost::process;
 
     std::string options;
 
     options = "--quiet";
+    if(ex.TrackStabilization()){
+	std::cout<<"Checking sub fun";
+        if (eng->GetConfiguration()->HasDynamicStabilizationCriteria()) {
+          const_cast<PhysiologyEngineDynamicStabilization*>(eng->GetConfiguration()->GetDynamicStabilizationCriteria())->TrackStabilization(CDM::enumOnOff::On);
+        }
+        if (eng->GetConfiguration()->HasTimedStabilizationCriteria()) {
+          const_cast<PhysiologyEngineTimedStabilization*>(eng->GetConfiguration()->GetTimedStabilizationCriteria())->TrackStabilization(CDM::enumOnOff::On);
+        }
+    }
 
     if (ex.Name().size()) {
       auto name = biogears::trim(ex.Name());
@@ -542,7 +553,6 @@ void Driver::async_execute(biogears::Executor& ex, bool multi_patient_run)
   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";
   std::string log_file = base_file_name + "Results.log";
@@ -556,14 +566,23 @@ void Driver::async_execute(biogears::Executor& ex, bool multi_patient_run)
     file_logger.SetConsolesetConversionPattern("%d{%H:%M} [%p] " + ex.Name() + " %m%n");
     console_logger.SetConsolesetConversionPattern("%d{%H:%M} [%p] %m%n");
     console_logger.FormatMessages(false);
-
     eng = CreateBioGearsEngine(&file_logger);
   } catch (std::exception e) {
     std::cout << e.what();
     _thread_count -= 1;
     return;
   }
-
+   if(ex.TrackStabilization()){
+	   std::cout<<"Checking the function\n";
+        if (eng->GetConfiguration()->HasDynamicStabilizationCriteria()) {
+		std::cout<<"Checking the function 2 \n";
+          const_cast<PhysiologyEngineDynamicStabilization*>(eng->GetConfiguration()->GetDynamicStabilizationCriteria())->TrackStabilization(CDM::enumOnOff::On);
+        }
+        if (eng->GetConfiguration()->HasTimedStabilizationCriteria()) {
+		std::cout<<"Checking the function 3 \n";
+          const_cast<PhysiologyEngineTimedStabilization*>(eng->GetConfiguration()->GetTimedStabilizationCriteria())->TrackStabilization(CDM::enumOnOff::On);
+        }
+    }
   BioGearsScenario sce(eng->GetSubstanceManager());
   if (!sce.Load(trim(trimed_scenario_path))) {
     console_logger.Info(biogears::asprintf("Error[%d]: %s failed to find the specified scenario file %s", ExecutionErrors::SCENARIO_IO_ERROR, ex.Name().c_str(), ex.Scenario().c_str()));
@@ -581,13 +600,13 @@ void Driver::async_execute(biogears::Executor& ex, bool multi_patient_run)
       return;
     }
 
-    std::unique_ptr<mil::tatrc::physiology::datamodel::ScenarioData> scenario;
+    std::unique_ptr<CDM::ScenarioData> scenario;
     try {
       xml_schema::flags xml_flags;
       xml_schema::properties xml_properties;
       std::cout << "Reading " << ex.Scenario() << std::endl;
       xml_properties.schema_location("uri:/mil/tatrc/physiology/datamodel", "xsd/BioGearsDataModel.xsd");
-      scenario = mil::tatrc::physiology::datamodel::Scenario(ifs, xml_flags, xml_properties);
+      scenario = CDM::Scenario(ifs, xml_flags, xml_properties);
     } catch (std::runtime_error e) {
       std::cout << e.what() << std::endl;
       console_logger.Info(biogears::asprintf("Error[%d]: %s failed parse the specified scenario file %s", ExecutionErrors::SCENARIO_PARSE_ERROR, ex.Name().c_str(), ex.Scenario().c_str()));

projects/cli/src/utils/Config.cpp

@@ -652,6 +652,8 @@ bool handle_driver_paramaters(Tokenizer::token_list::iterator& tokenItr, Tokeniz
       continue;
     } else if (token == "nocompare") {
       rhs.NoCompare(true);
+    } else if (token == "track_stabilization") {
+      rhs.TrackStabilization(true);  
     } else if (token == "fastplot") {
       rhs.PlotStyle(EPlotStyle::FastPlot);
     } else if (token == "fullplot") {

projects/cli/src/utils/Executor.cpp

@@ -15,6 +15,7 @@ Executor::Executor(std::string n, EDriver d)
   , driver(d)
   , plot_style(EPlotStyle::FastPlot)
   , no_compare(false)
+  , track_stabilization(false)
   , group("Other")
   , patient("")
   , state("")
@@ -33,6 +34,11 @@ bool Executor::NoCompare() const
   return no_compare;
 }
 //-----------------------------------------------------------------------------
+bool Executor::TrackStabilization() const
+{
+  return track_stabilization;
+}
+//-----------------------------------------------------------------------------
 std::string Executor::Baselines() const { return baselines; }
 //-----------------------------------------------------------------------------
 std::string Executor::Computed() const { return computed; }
@@ -68,6 +74,11 @@ void Executor::NoCompare(bool nc)
   no_compare = nc;
 }
 //-----------------------------------------------------------------------------
+void Executor::TrackStabilization(bool t)
+{
+  track_stabilization=t;
+}
+//-----------------------------------------------------------------------------
 void Executor::Baselines(const std::string& b)
 {
   baselines = b;

projects/cli/src/utils/Executor.h

@@ -61,6 +61,7 @@ class Executor {
   EDriver Driver() const;
   EPlotStyle PlotStyle() const;
   bool NoCompare() const;
+  bool TrackStabilization() const;
   std::string Baselines() const;
   std::string Computed() const;
   std::string Group() const;
@@ -73,6 +74,7 @@ class Executor {
   void Driver(EDriver);
   void PlotStyle(EPlotStyle);
   void NoCompare(bool);
+  void TrackStabilization(bool);
   void Baselines(const std::string&);
   void Computed(const std::string&);
   void Group(const std::string&);
@@ -88,6 +90,7 @@ class Executor {
   EDriver driver;
   EPlotStyle plot_style;
   bool no_compare;
+  bool track_stabilization;
   std::string name;
   std::string baselines;
   std::string computed;
@@ -104,4 +107,5 @@ std::ostream& operator<<(std::ostream&, const EPlotter&);
 std::ostream& operator<<(std::ostream&, const EPlotStyle&);
 } //namespace biogears
 
-#endif //CMD_BIO_UTILS_EXECUTOR_H
+#endif //CMD_BIO_UTILS_EXECUTOR_H
+