Adding the scenario files for testing to the repository rather than in the downloaded baseline zip

bin/run.config.in

@@ -3,6 +3,7 @@
 
 root_dir=@CMAKE_SOURCE_DIR@/
 data_dir=@CMAKE_SOURCE_DIR@/data
+scenario_dir=@CMAKE_SOURCE_DIR@/test/scenarios
 test_config_dir=@CMAKE_SOURCE_DIR@/test/config
 validation_dir=@CMAKE_SOURCE_DIR@/test/validation
 verification_dir=@CMAKE_INSTALL_PREFIX@/bin/verification
\ No newline at end of file

cdm/java/com/kitware/physiology/utilities/RunConfiguration.java

@@ -14,16 +14,18 @@ import org.jfree.util.Log;
  */
 public class RunConfiguration 
 {
-	protected String rootDirectory;
+  protected String rootDirectory;
   protected String dataDirectory;
+  protected String scenarioDirectory;
   protected String testConfigDirectory;
   protected String validationDirectory;
   protected String verificationDirectory;
   
   public    String getRootDirectory()         { return rootDirectory;         }
   public    String getDataDirectory()         { return dataDirectory;         }
+  public    String getScenarioDirectory()     { return scenarioDirectory;     }
   public    String getTestConfigDirectory()   { return testConfigDirectory;   }
-  public    String getValidationDirectory()   { return validationDirectory; }
+  public    String getValidationDirectory()   { return validationDirectory;   }
   public    String getVerificationDirectory() { return verificationDirectory; }
   
   
@@ -32,6 +34,7 @@ public class RunConfiguration
     // Default values
   	rootDirectory         = "./";
     dataDirectory         = "./";
+    scenarioDirectory     = "./";
     testConfigDirectory   = "./";
     validationDirectory   = "./";
     verificationDirectory = "./";
@@ -83,6 +86,18 @@ public class RunConfiguration
           Log.error("data_dir set to invalid directory "+val+", ignoring and using default ("+this.dataDirectory+")");
       }
     }
+    if(properties.containsKey("scenario_dir"))
+    {  
+      String val = properties.get("scenario_dir").toString();
+      if(!val.startsWith("@"))
+      {
+        File dir = new File(val);
+        if(dir.exists() && dir.isDirectory())
+          scenarioDirectory = val;
+        else
+          Log.error("scenario_dir set to invalid directory "+val+", ignoring and using default ("+this.scenarioDirectory+")");
+      }
+    }
     if(properties.containsKey("test_config_dir"))
     {  
       String val = properties.get("test_config_dir").toString();

engine/cpp/physiology/Respiratory.h

@@ -136,7 +136,7 @@ protected:
   double m_ElapsedBreathingCycleTime_min;
   double m_IEscaleFactor;
   double m_InstantaneousFunctionalResidualCapacity_L;
-  double m_MaxDriverPressure_cmH2O;    
+  double m_MaxDriverPressure_cmH2O;
   double m_PeakRespiratoryDrivePressure_cmH2O;
   double m_PreviousTargetAlveolarVentilation_L_Per_min;
   double m_VentilationFrequency_Per_min;

test/driver/java/com/kitware/physiology/testing/Rebase.java

@@ -16,162 +16,158 @@ import com.kitware.physiology.utilities.RunConfiguration;
 
 public class Rebase
 {
-	public static void main(String[] args)
-	{
-	  jniBridge.initialize();
-	  rebase();
-	  jniBridge.deinitialize();
-	}
-	
-	public static void rebase()
-	{
-		RunConfiguration cfg = new RunConfiguration();
-		Log.setFileName("Rebase.log");    
-		String toDir = "./test_results/rebase/";
-		List<String> configFiles = new ArrayList<String>();
-		try
-		{
-			File file = new File(cfg.getTestConfigDirectory()+"/Rebase.config");
-			FileReader fileReader = new FileReader(file);
-			BufferedReader bufferedReader = new BufferedReader(fileReader);
-			String line;
-			while ((line = bufferedReader.readLine()) != null) 
-			{
-				line = line.trim();
-				if(line.indexOf("#")>-1)
-					continue;
-				if(line.indexOf(".config")==-1)
-						continue;
-				configFiles.add(line);
-			}
-			fileReader.close();
-		}
-		catch(IOException ex)
-		{
-			Log.error("Unable to open Rebase.config, check your run.config file test_config_dir");
-			return;
-		}
-		
-		// Replace back slashes with forward slashes
-		toDir = toDir.replaceAll("\\\\", "/");
-		toDir += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
-		// Ask git what the current revision hash is
-		try
-		{
-			FileRepository repo = new FileRepository(cfg.getRootDirectory()+"/.git");
-			ObjectId head = repo.resolve("HEAD");
-			if(head!=null)
-				toDir += " - "+head.getName().substring(0,8);
-			repo.close();
-		}
-		catch(IOException ex)
-		{
-			Log.error("Unable to read git hash, check your run.config file root_dir");
-		}
-		toDir += "/";
+  public static void main(String[] args)
+  {
+    jniBridge.initialize();
+    rebase();
+    jniBridge.deinitialize();
+  }
+  
+  public static void rebase()
+  {
+    RunConfiguration cfg = new RunConfiguration();
+    Log.setFileName("Rebase.log");    
+    String toDir = "./test_results/rebase/";
+    List<String> configFiles = new ArrayList<String>();
+    try
+    {
+      File file = new File(cfg.getTestConfigDirectory()+"/Rebase.config");
+      FileReader fileReader = new FileReader(file);
+      BufferedReader bufferedReader = new BufferedReader(fileReader);
+      String line;
+      while ((line = bufferedReader.readLine()) != null) 
+      {
+        line = line.trim();
+        if(line.indexOf("#")>-1)
+          continue;
+        if(line.indexOf(".config")==-1)
+            continue;
+        configFiles.add(line);
+      }
+      fileReader.close();
+    }
+    catch(IOException ex)
+    {
+      Log.error("Unable to open Rebase.config, check your run.config file test_config_dir");
+      return;
+    }
+    
+    // Replace back slashes with forward slashes
+    toDir = toDir.replaceAll("\\\\", "/");
+    toDir += new SimpleDateFormat("yyyy-MM-dd").format(new Date());
+    // Ask git what the current revision hash is
+    try
+    {
+      FileRepository repo = new FileRepository(cfg.getRootDirectory()+"/.git");
+      ObjectId head = repo.resolve("HEAD");
+      if(head!=null)
+        toDir += " - "+head.getName().substring(0,8);
+      repo.close();
+    }
+    catch(IOException ex)
+    {
+      Log.error("Unable to read git hash, check your run.config file root_dir");
+    }
+    toDir += "/";
 
-		Log.info("Rebasing to "+toDir);
+    Log.info("Rebasing to "+toDir);
 
-		// Make sure from/to dir ends with a slash
-		if(!toDir.endsWith("/"))
-			toDir = toDir + "/";
-		try
-		{
-			FileUtils.delete(toDir);
-			FileUtils.createDirectory(toDir);
-		}
-		catch(Exception ex)
-		{
-			Log.error("Could not create to Directory : "+toDir,ex);
-			return;
-		}
+    // Make sure from/to dir ends with a slash
+    if(!toDir.endsWith("/"))
+      toDir = toDir + "/";
+    try
+    {
+      FileUtils.delete(toDir);
+      FileUtils.createDirectory(toDir);
+    }
+    catch(Exception ex)
+    {
+      Log.error("Could not create to Directory : "+toDir,ex);
+      return;
+    }
 
-		String log_file;
-		String scenario_file;
-		String result_path;
-		List<String> result_files = new ArrayList<String>();
+    String log_file;
+    String result_path;
+    List<String> result_files = new ArrayList<String>();
 
-		for(String configFile : configFiles)
-		{
-			Log.info("Rebasing config "+configFile);
-			SETestConfiguration config = new SETestConfiguration();
-			config.processConfigFile(new File(cfg.getTestConfigDirectory()+"/"+configFile), cfg);
+    for(String configFile : configFiles)
+    {
+      Log.info("Rebasing config "+configFile);
+      SETestConfiguration config = new SETestConfiguration();
+      config.processConfigFile(new File(cfg.getTestConfigDirectory()+"/"+configFile), cfg);
 
-			for(SETestJob job : config.jobs)
-			{
-				if(job.computedFiles.size()<=0)
-				{
-					Log.error("A job has no expected result files!?!?");
-					continue;
-				}
-				if(!job.PlottableResults && !job.isAssessment)
-					continue;// Nothing to plot/compare, nothing to zip	
-				// We assume all json will have something to zip...
-				
-				log_file = "";
-				scenario_file = "";
-				result_files.clear();
-				result_path = job.computedFiles.get(0);
-				if(!new File(result_path).exists())
-				{
-				  Log.error("Unable to find file to rebase for "+job.name+" at path "+result_path);
-				  continue;
-				}
-				
-				// If there is no baselineDirectory, then this must be an assessment...
-				if(job.name.endsWith(".json") && !job.isAssessment)
-				{
-					scenario_file = job.baselineDirectory+job.name;
-					if(job.computedFiles.size()>1)
-					{
-						Log.error("A scenario file has more than one result file!?!?");
-						continue;
-					}
-					result_files.add(result_path);
-					log_file = result_files.get(0).replaceAll("Results"+SETestConfiguration.ext, ".log");   
-					result_files.add(log_file);
-					result_files.add(scenario_file);
-          Log.info("Adding scenario file"+scenario_file);
-				}    	
-				else
-				{
-					// Its a unit test, only zip up the results
-					result_files.addAll(job.computedFiles);
-				}
+      for(SETestJob job : config.jobs)
+      {
+        if(job.computedFiles.size()<=0)
+        {
+          Log.error("A job has no expected result files!?!?");
+          continue;
+        }
+        if(!job.PlottableResults && !job.isAssessment)
+          continue;// Nothing to plot/compare, nothing to zip  
+        // We assume all json will have something to zip...
+        
+        log_file = "";
+        result_files.clear();
+        result_path = job.computedFiles.get(0);
+        if(!new File(result_path).exists())
+        {
+          Log.error("Unable to find file to rebase for "+job.name+" at path "+result_path);
+          continue;
+        }
+        
+        // If there is no baselineDirectory, then this must be an assessment...
+        if(job.name.endsWith(".json") && !job.isAssessment)
+        {
+          if(job.computedFiles.size()>1)
+          {
+            Log.error("A scenario file has more than one result file!?!?");
+            continue;
+          }
+          result_files.add(result_path);
+          log_file = result_files.get(0).replaceAll("Results"+SETestConfiguration.ext, ".log");   
+          result_files.add(log_file);
+          Log.info("Creating zip for "+result_files.get(0));
+        }      
+        else
+        {
+          // Its a unit test, only zip up the results
+          result_files.addAll(job.computedFiles);
+        }
 
-				String prepend = result_path.substring(result_path.indexOf("test_results/")+13,result_path.lastIndexOf("."));
-				int ridx = prepend.indexOf("Results");
-				if(ridx>-1)
-					prepend = prepend.substring(0,ridx);
-				String newFile = toDir + prepend + ".zip";
+        String prepend = result_path.substring(result_path.indexOf("test_results/")+13,result_path.lastIndexOf("."));
+        int ridx = prepend.indexOf("Results");
+        if(ridx>-1)
+          prepend = prepend.substring(0,ridx);
+        String newFile = toDir + prepend + ".zip";
 
-				Log.info("Creating new file "+newFile);
-				String rPath = "";
-				for(String rDir : newFile.split("/"))
-				{
-					if(rDir.endsWith(".zip"))
-					{
-						break;
-					}
-					rPath += rDir + "/";
-				}
-				try
-				{
+        Log.info("Creating new file "+newFile);
+        String rPath = "";
+        for(String rDir : newFile.split("/"))
+        {
+          if(rDir.endsWith(".zip"))
+          {
+            break;
+          }
+          rPath += rDir + "/";
+        }
+        try
+        {
           Log.info("Creating "+rPath);
-					FileUtils.createDirectory(rPath);
-				} 
-				catch (IOException ex)
-				{
-					Log.error("Could not create directory : "+rPath, ex);
-				}
-				File oldZip = new File(newFile);
-				if(oldZip.exists())
-					oldZip.delete();
-				String[] files = new String[result_files.size()];
-				files = result_files.toArray(files);
-				FileUtils.zipFiles(files, newFile,prepend+".zip");
-			}
-		}
-	}
+          FileUtils.createDirectory(rPath);
+        } 
+        catch (IOException ex)
+        {
+          Log.error("Could not create directory : "+rPath, ex);
+        }
+        File oldZip = new File(newFile);
+        if(oldZip.exists())
+          oldZip.delete();
+        String[] files = new String[result_files.size()];
+        files = result_files.toArray(files);
+        FileUtils.zipFiles(files, newFile,prepend+".zip");
+      }
+    }
+  }
 
 }

test/driver/java/com/kitware/physiology/testing/SETestJob.java

@@ -26,6 +26,8 @@ public class SETestJob extends LogListener
   public boolean      PlottableResults = false;
   public PlotType     plotType = PlotType.FastPlot;//Only plot every nth data point
   public double       percentDifference;
+  public List<String> scenarioFiles = new ArrayList<String>();
+  public String       scenarioDirectory = null;
   public List<String> baselineFiles = new ArrayList<String>();
   public String       baselineDirectory = null;
   public List<String> computedFiles = new ArrayList<String>();

test/engine/java/com/kitware/physiology/pulse/testing/ScenarioTestDriver.java

@@ -22,10 +22,10 @@ public class ScenarioTestDriver implements SETestDriver.Executor
     String outputFile = job.computedDirectory+"/"+job.name;
     String log;
     String results;
-    String json = FileUtils.readFile(job.baselineDirectory+"/"+job.name);
+    String json = FileUtils.readFile(job.scenarioDirectory+"/"+job.name);
     if(json==null)
     {
-      Log.error("Could not read file : "+job.baselineDirectory+"/"+job.name);
+      Log.error("Could not read file : "+job.scenarioDirectory+"/"+job.name);
       return false;
     }
     ScenarioData.Builder builder;
@@ -44,7 +44,7 @@ public class ScenarioTestDriver implements SETestDriver.Executor
 	    }
 	    catch(InvalidProtocolBufferException ex2)
 	    {
-	    	Log.error("Unable to read scenario"+job.baselineDirectory+"/"+job.name,ex2);
+	    	Log.error("Unable to read scenario"+job.scenarioDirectory+"/"+job.name,ex2);
 	    	return false;
 	    }
     }

test/scenarios/combined/Cynthia.json

+{
+  "Name": "Cynthia",
+  "Description": "Inject Cynthia with Midazolam. Reaction to sedative causes an airway obstruction. An anesthesia machine mask is applied to attempt to supply Oxygen. Ketamine is administered and the airway obstruction is cleared. Rocuronium is administered. Patient is then intubated.",
+  "StartType": {
+    "PatientConfiguration": {
+      "PatientFile": "Cynthia.json"
+    }
+  },
+  "DataRequestManager": {
+    "DataRequest": [{
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "PropertyName": "Weight",
+      "Unit": "kg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "HeartRate",
+      "Unit": "1/min"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "HeartStrokeVolume",
+      "Unit": "mL"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "BloodVolume",
+      "Unit": "L"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "ExtravascularFluidVolume",
+      "Unit": "L"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "ArterialPressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "MeanArterialPressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+      },
+      "Category": "Physiology",
+      "PropertyName": "SystolicArterialPressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "DiastolicArterialPressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "CardiacOutput",
+      "Unit": "L/min"
+    }, {
+      "DecimalFormat": {
+      },
+      "Category": "Physiology",
+      "PropertyName": "HemoglobinContent",
+      "Unit": "g"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "CentralVenousPressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "PulmonaryCapillariesWedgePressure",
+      "Unit": "mmHg"
+    }, {
+      "DecimalFormat": {
+        "Precision": 3
+      },
+      "Category": "Physiology",
+      "PropertyName": "TidalVolume",
+      "Unit": "mL"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "TotalLungVolume",
+      "Unit": "L"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "RespirationRate",
+      "Unit": "1/min"
+    }, {
+      "DecimalFormat": {
+        "Precision": 3
+      },
+      "Category": "Physiology",
+      "PropertyName": "OxygenSaturation",
+      "Unit": "unitless"
+    }, {
+      "DecimalFormat": {
+        "Precision": 3
+      },
+      "Category": "Physiology",
+      "PropertyName": "CarbonDioxideSaturation",
+      "Unit": "unitless"
+    }, {
+      "DecimalFormat": {
+        "Precision": 4
+      },
+      "Category": "Physiology",
+      "PropertyName": "EndTidalCarbonDioxideFraction",
+      "Unit": "unitless"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "TotalAlveolarVentilation",
+      "Unit": "L/min"
+    }, {
+      "DecimalFormat": {
+        "Precision": 2
+      },
+      "Category": "Physiology",
+      "PropertyName": "TranspulmonaryPressure",
+      "Unit": "cmH2O"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "CoreTemperature",
+      "Unit": "degC"
+    }, {
+      "DecimalFormat": {
+        "Precision": 1
+      },
+      "Category": "Physiology",
+      "PropertyName": "SkinTemperature",
+      "Unit": "degC"
+    }, {
+      "DecimalFormat": {
+        "Precision": 3