Commit 7354f32c authored by Aaron Bray's avatar Aaron Bray
Browse files

Fix validation bugs from adding scenarios to repo

parent b72af522
......@@ -244,7 +244,7 @@ public class SETestConfiguration
}
else if(job.executor.getClass().getName().indexOf("Scenario")!=-1)//Is a Scenario File test
{
deriveScenarioResultNames(job, job.name);
deriveScenarioResultNames(job, job.name);
}
else
{
......@@ -260,7 +260,7 @@ public class SETestConfiguration
List<String> patientFileNames;
if(patientFiles.equalsIgnoreCase("all"))
patientFileNames = FileUtils.findFiles("./patients", sce_ext, true);
patientFileNames = FileUtils.findFiles("./patients", sce_ext, true);
else
{
String[] patientFiles = this.patientFiles.split(",");
......@@ -290,7 +290,7 @@ public class SETestConfiguration
jobs.add(job);
continue;
}
copy = job.clone();
copy = job.clone();
copy.patientFile = pFileName;
deriveScenarioResultNames(copy, copy.name.replaceAll(sce_ext, "-"+pFileName));
jobs.add(copy);
......
......@@ -102,13 +102,13 @@ public class SETestDriver
job.state = SETestJob.State.Comparing;
cThread.job = job;
activeThreads++;
cThread.start();
cThread.start();
break;
}
else
{
job.state = SETestJob.State.Complete;
}
}
}
}
}
......@@ -125,7 +125,7 @@ public class SETestDriver
activeThreads++;
}
if(activeThreads == engineThreads)
break;
break;
}
}
if(activeThreads==0)
......@@ -211,8 +211,8 @@ public class SETestDriver
{
CSVComparison compare = new CSVComparison();
compare.limit = job.percentDifference;
compare.reportDifferences = false;
compare.setFullReportPath(job.reportFiles.get(i));
compare.reportDifferences = false;
compare.setFullReportPath(job.reportFiles.get(i));
if(new File(job.computedFiles.get(i)).exists())
{
Set<String> failures = null;
......
......@@ -49,6 +49,8 @@ public class SETestJob extends LogListener
copy.PlottableResults = this.PlottableResults;
copy.plotType = this.plotType;
copy.percentDifference = this.percentDifference;
copy.scenarioFiles.addAll(this.scenarioFiles);
copy.scenarioDirectory = this.scenarioDirectory;
copy.baselineFiles.addAll(this.baselineFiles);
copy.baselineDirectory = this.baselineDirectory;
copy.computedFiles.addAll(this.computedFiles);
......
{
"Name": "RespiratoryValidation",
"Description": "Validation of Respiratory Ssytem data.",
"StartType": { "PatientConfiguration": { "PatientFile": "StandardMale.json" } },
"DataRequestManager":
{
"DataRequest":
[
{ "DecimalFormat": { "Precision": 4 }, "PropertyName": "Weight", "Unit": "g" },
{ "DecimalFormat": { "Precision": 4 }, "PropertyName": "IdealBodyWeight", "Unit": "g" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "AlveolarArterialGradient", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "AlveolarDeadSpace", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "AnatomicDeadSpace", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "CarricoIndex", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ChestWallCompliance", "Unit": "L/cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ElasticWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "EndTidalCarbonDioxideFraction", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "EndTidalCarbonDioxidePressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "EndTidalOxygenFraction", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "EndTidalOxygenPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ExpiratoryFlow", "Unit": "L/s" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ImposedPowerOfBreathing", "Unit": "W" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ImposedWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "InspiratoryExpiratoryRatio", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "InspiratoryFlow", "Unit": "L/s" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "IntrapleuralPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "LungCompliance", "Unit": "L/cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "MaximalInspiratoryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PatientPowerOfBreathing", "Unit": "W" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PatientWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PeakInspiratoryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PhysiologicDeadSpace", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PositiveEndExpiratoryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PulmonaryCompliance", "Unit": "L/cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PulmonaryElastance", "Unit": "cmH2O/L" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "PulmonaryResistance", "Unit": "cmH2O s/L" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ResistiveExpiratoryWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "ResistiveInspiratoryWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "RespiratoryMuscleFatigue", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "RespiratoryMusclePressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "SpecificVentilation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalAlveolarVentilation", "Unit": "L/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalDeadSpaceVentilation", "Unit": "L/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalLungVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalPowerOfBreathing", "Unit": "W" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalPulmonaryVentilation", "Unit": "L/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TotalWorkOfBreathing", "Unit": "J" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TransairwayPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TransalveolarPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TransChestWallPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TranspulmonaryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TransrespiratoryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "TransthoracicPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "Carina", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftPleuralCavity", "PropertyName": "Pressure", "Unit": "cmH2O"},
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightPleuralCavity", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "PulmonaryLungs", "PropertyName": "Volume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftLungPulmonary", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightLungPulmonary", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAlveoli", "PropertyName": "Volume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAlveoli", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAlveoli", "PropertyName": "Volume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAlveoli", "PropertyName": "Pressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAnatomicDeadSpace", "PropertyName": "Volume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAnatomicDeadSpace", "PropertyName": "Volume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "Carina", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "Carina", "SubstanceName": "CarbonDioxide", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAlveoli", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAlveoli", "SubstanceName": "CarbonDioxide", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAlveoli", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAlveoli", "SubstanceName": "CarbonDioxide", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAnatomicDeadSpace", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "LeftAnatomicDeadSpace", "SubstanceName": "CarbonDioxide", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAnatomicDeadSpace", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "GasCompartment", "CompartmentName": "RightAnatomicDeadSpace", "SubstanceName": "CarbonDioxide", "PropertyName": "PartialPressure", "Unit": "mmHg" }
]
"Description": "Validation of Respiratory data.",
"StartType": {
"PatientConfiguration": {
"PatientFile": "StandardMale.json"
}
},
"AnyAction":
[
{ "AdvanceTime": { "Time": { "ScalarTime": { "Value": 2.0, "Unit": "min" }}}},
{ "PatientAction": { "Assessment": { "Type": "PulmonaryFunctionTest" }}}
]
}
\ No newline at end of file
"DataRequestManager": {
"DataRequest": [{
"DecimalFormat": {
"Precision": 4
},
"PropertyName": "Weight",
"Unit": "g"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "AlveolarArterialGradient",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "CarricoIndex",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "EndTidalCarbonDioxideFraction",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "EndTidalCarbonDioxidePressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "ExpiratoryFlow",
"Unit": "L/s"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "InspiratoryExpiratoryRatio",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "InspiratoryFlow",
"Unit": "L/s"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "PulmonaryCompliance",
"Unit": "L/cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "PulmonaryResistance",
"Unit": "cmH2O s/L"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "RespirationMusclePressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "RespirationRate",
"Unit": "1/min"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "SpecificVentilation",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TidalVolume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TotalAlveolarVentilation",
"Unit": "L/min"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TotalDeadSpaceVentilation",
"Unit": "L/min"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TotalLungVolume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TotalPulmonaryVentilation",
"Unit": "L/min"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "TranspulmonaryPressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "Carina",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "Carina",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "Carina",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftPleuralCavity",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightPleuralCavity",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "PulmonaryLungs",
"PropertyName": "Volume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftLungPulmonary",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightLungPulmonary",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"PropertyName": "Volume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"PropertyName": "Volume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftDeadSpace",
"PropertyName": "Volume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftDeadSpace",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "LeftDeadSpace",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightDeadSpace",
"PropertyName": "Volume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightDeadSpace",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "GasCompartment",
"CompartmentName": "RightDeadSpace",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}]
},
"AnyAction": [{
"AdvanceTime": {
"Time": {
"ScalarTime": {
"Value": 2.0,
"Unit": "min"
}
}
}
}, {
"PatientAction": {
"Assessment": {
"Type": "PulmonaryFunctionTest"
}
}
}]
}
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