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Commit ae5b93d1 authored by Aaron Bray's avatar Aaron Bray
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Merge branch 'feature/java_updates' into '3.x' 

Update Extended Language API's

See merge request !46
parents 4da304b5 cbdf6f70
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.gitignore
View file @ ae5b93d1
......@@ -9,10 +9,10 @@
src/schema/schema_last_built
/src/cpp/bind
/src/csharp/pulse/bind
/src/java/com
/src/java/pulse/cdm/bind
/src/java/pulse/cpm/bind
/src/java/pulse/study/bind
/src/java/com/google
/src/java/com/kitware/pulse/cdm/bind
/src/java/com/kitware/pulse/cpm/bind
/src/java/com/kitware/pulse/study/bind
/src/python/pulse/cdm/bind
/src/python/pulse/cpm/bind
/src/python/pulse/study/bind
......
NOTICE
View file @ ae5b93d1
......@@ -61,18 +61,6 @@ Licensed under BSD 3-clause
https://opensource.org/licenses/BSD-3-Clause
------------------------------------------------------------------------------
This product uses the log4cpp package
http://log4cpp.sourceforge.net/
Licensed under the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
https://www.gnu.org/licenses/lgpl.html
------------------------------------------------------------------------------
When on Windows machines, this product uses the dirent.h package
......
bin/EngineState.json
View file @ ae5b93d1
{
"Name":"BasicStandard",
"Description":"Basic scenario measuring patient vitals with no insults or interventions",
"EngineStateFile":"./states/StandardMale@0s.json",
"EngineStateFile":"./states/StandardMale@0s.pbb",
"DataRequestManager": {"DataRequest":[
{"DecimalFormat":{"Precision":1},"Category":"Patient", "PropertyName":"Weight", "Unit":"kg"},
......
bin/InitialPatientState.json
View file @ ae5b93d1
......@@ -3,12 +3,13 @@
"Name": "InitialStableState",
"Description": "Stabilize a patient and save out the engines state at time zero",
"PatientConfiguration": { "PatientFile": "StandardMale.json" },
"AnyAction": [{
"Serialize": {
}
"AnyAction":
[{
"Serialize": { "Type": "Save" }
}]
},
"Configuration": {
"Configuration":
{
"WritePatientBaselineFile": "On"
}
}
bin/run.cmake.in
View file @ ae5b93d1
# Scripts to assist developers
# Mostly these are calling the test suite driver and validator classes in Java
# TODO More Test Targets
# Rebasing
# com.kitware.physiology.utilities.testing.Rebase [from to (config|ALL)]
#
# Ploting
# com.kitware.physiology.utilities.csv.plots.PlotDriver
#
# Reconfigure the config file (in memory) so we can test serialization
# com.kitware.physiology.utilities.testing.Reconfiguration
find_package(Java REQUIRED)
include(UseJava)
......@@ -23,24 +14,19 @@ endif()
#set(Java_JAVA_EXECUTABLE "/the_jdk_I_want/bin/java)
set(JAVA_CLASSPATH Pulse.jar
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist-3.16.1-GA.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jcommon-1.0.16.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jdom-2.0.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.0.13.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.5.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-26.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/log4j-1.2.17.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/pdfbox-2.0.0-RC3.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.9-RC1-uberjar.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-2.6.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/zip4j-1.3.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/org.eclipse.jgit-4.11.0.201803080745-r.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-api-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-simple-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.2.jar")
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-collections4-4.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-compress-1.19.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-math3-3.6.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.6.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-29.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.5.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.12.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-3.1.0.jar")
if(NOT WIN32)
string(REPLACE ";" ":" JAVA_CLASSPATH "${JAVA_CLASSPATH}")
......@@ -48,22 +34,22 @@ endif()
if(TYPE STREQUAL "tests" OR TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "PatientValidation")
if(TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ScenarioVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ScenarioVerification.config)
endif()
if(TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation TEST)
endif()
if(TYPE STREQUAL "PatientValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation TEST)
endif()
elseif(TYPE STREQUAL "genData")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.dataset.DataSetReader)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.dataset.DataSetReader)
elseif(TYPE STREQUAL "genStates")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver InitialPatientStates.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver InitialPatientStates.config)
elseif(TYPE STREQUAL "doxygen")
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/header.html HEADER)
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/footer.html FOOTER)
......@@ -90,13 +76,13 @@ elseif(TYPE STREQUAL "doxygen")
file(WRITE @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER_PANEL}")
file(APPEND @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER}")
# These are run above
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND doxygen ./docs/full.doxy)
# Build our landing files
setup_landing_page(index.html)
......@@ -112,12 +98,30 @@ elseif(TYPE STREQUAL "protoc")
-P "@CMAKE_SOURCE_DIR@/src/schema/GenerateBindings.cmake")
elseif(TYPE STREQUAL "updateBaselines")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target UpdateVerification)
elseif(TYPE STREQUAL "jar")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target PulseJava)
elseif(TYPE STREQUAL "rebase")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.Rebase)
# find Git and if available set GIT_HASH variable
find_package(Git QUIET)
if(GIT_FOUND)
execute_process(
COMMAND ${GIT_EXECUTABLE} log -1 --pretty=format:%h
OUTPUT_VARIABLE GIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_QUIET
WORKING_DIRECTORY
@CMAKE_SOURCE_DIR@
)
endif()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.Rebase ${GIT_HASH})
elseif(TYPE STREQUAL "FullReport")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SEReportResults)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SEReportResults)
elseif(TYPE STREQUAL "plotter")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
else()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ${TYPE}.config)
if(${TYPE} MATCHES "Plot")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver ${TYPE}.config)
else()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ${TYPE}.config)
endif()
endif()
data/config/CDMUnitTests.config
View file @ ae5b93d1
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm/
@group Simple Circuits
......
data/config/DebugPlots.config
View file @ ae5b93d1
......@@ -17,7 +17,9 @@
# ImageDimensions - Specify the image width and height in pixels (i.e. ImageDimesions=1600,800) Default is 1600x800, but ActionEventPlots can stretch automatically
# RemoveLegends - Removes all legends from the generated plot
# FontSize - Set the font size of axis labels and chart title (FontSize=22 by default)
# LegendFontSize - Set the font size of the legend (LegendFontSize=15 by default)
# OutputFilename - Set the desired filename for the generated plot (no spaces allowed; will default to the chart title if nothing is set for this)
# PercentOfBaseline - All values will be set to Value@TimeX / Values@Time0
#FLAGS FOR ACTIONEVENTPLOTTER ONLY
# Header - Specify the header(s) that you want to plot on the Y axis
......@@ -47,14 +49,18 @@
# FLAGS FOR RESPIRATORY PFT PLOTTER ONLY
# PFTFile - Specify the path and filename for the .pba containing the PFT data you want to plot (No spaces allowed)
Plotter=pulse.utilities.csv.plots.ActionEventPlotter
Plotter=pulse.utilities.csv.plots.MultiPlotter
Plotter=pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ActionEventPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiSourcePlotter
#ScenarioName=PlotterType Flag1=Stuff Flag2=Stuff Flag3 FlagN
#PralidoximeValidation=ActionEventPlotter Title=Pralidoxime NoActions NoEvents LogAxis Header=Pralidoxime-PlasmaConcentration(ug/L) DataPathOverride=./Scenarios/Validation/ DataFileOverride=PralidoximeValidationResults.csv ExperimentalData=../docs/Validation/Pharmacokinetic/CSVs/Pralidoxime.csv OutputOverride=..\docs\Doxygen\html\plots\Drugs
#VentricularSystolicDysfunction=ActionEventPlotter NoGrid Title=None Header=BloodVolume(L) OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=HeartFailure.jpg
CardiacShock=MultiPlotter X1Label=Percent_Of_Blood_Loss X1=BloodVolume(L) Y1=CardiacOutput(L/min) Y1LowerBound=0 X2=BloodVolume(L) Y2=MeanArterialPressure(mmHg) Y2LowerBound=0 X1LowerBound=0 X1UpperBound=0.5 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageClass4NoFluidResults.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=CardiacShock.jpg
#RespiratoryValidation=RespiratoryPFTPlotter Header=TotalLungVolume(mL) VerificationDir=validation/systems/ PFTFile=RespiratoryValidationPFT@120.02s.json Title=Pulmonary_Function_Test_Results OutputOverride=./docs/html/plots/Respiratory/
CardiacShock=MultiPlotter Title=Cardiovascular_Response_To_Hemorrhage PercentOfBaseline X1Label=Percent_Of_Blood_Loss X1=BloodVolume(L) Y1=CardiacOutput(L/min) Y1LowerBound=0 X2=BloodVolume(L) Y2=MeanArterialPressure(mmHg) Y2LowerBound=0 X1LowerBound=0 X1UpperBound=50 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageClass4NoFluidResults.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=CardiacShock.jpg
HemorrhageGroups=MultiSourcePlotter Title=Cardiovascular_Hemorrhage_Groups PercentOfBaseline X1=Time(s) Y1=MeanArterialPressure(mmHg) Y1Label=Mean_Arterial_Pressure_Delta Y1LowerBound=0 Y1UpperBound=100 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageGroup1Results.csv,HemorrhageGroup2Results.csv,HemorrhageGroup3Results.csv,HemorrhageGroup4Results.csv,HemorrhageGroup5Results.csv,HemorrhageGroup6Results.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=HemorrhageGroups.jpg
HemorrhageClass3NoFluid=ActionEventPlotter LegendOnly ActionsOnly Header=RightAfferentArterioleResistance(mmHg_min/mL) Title=HemorrhageClass4NoFluidLegend VerificationDir=patient OutputOverride=./docs/html/plots/Renal/ NoEvents ImageDimensions=1500,160
data/config/DebugRun.config
View file @ ae5b93d1
......@@ -22,9 +22,9 @@ Threads=-1
# Time stamp periods is creating a file per save and using the time stamp as naming convention
#AutoSerialization=./states/testing/,5,On,On,On
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm
Macro EngineUnitTest=EngineUnitTestDriver FastPlot Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse
......
data/config/DrugPKVerification.config
View file @ ae5b93d1
......@@ -20,7 +20,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/EngineUnitTests.config
View file @ ae5b93d1
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Macro EngineUnitTest=EngineUnitTestDriver FastPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
Macro FullPlotEngineUnitTest=EngineUnitTestDriver FullPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
......@@ -44,6 +44,10 @@ RespiratoryDriver = EngineUnitTest Results=RespiratoryDriverOutput
AnesthesiaMachineCircuitAndTransport = EngineUnitTest Results=AnesthesiaMachineCircuitOutput,AnesthesiaMachineTransportOutput
RespiratoryWithAnesthesiaMachineCircuitAndTransport = EngineUnitTest Results=RespiratoryAndAnesthesiaMachineCircuitOutput,RespiratoryAndAnesthesiaMachineTransportOutput
@group MechanicalVentilator
MechanicalVentilatorCircuitAndTransport = EngineUnitTest Results=MechanicalVentilatorCircuitOutput,MechanicalVentilatorTransportOutput
RespiratoryWithMechanicalVentilatorCircuitAndTransport = EngineUnitTest Results=RespiratoryAndMechanicalVentilatorCircuitOutput,RespiratoryAndMechanicalVentilatorTransportOutput
@group Inhaler
RespiratoryWithInhalerCircuitAndTransport = EngineUnitTest Results=RespiratoryAndInhalerCircuitOutput,RespiratoryAndInhalerTransportOutput,AerosolInhalerTransportOutput
......
data/config/InitialPatientStates.config
View file @ ae5b93d1
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioRun=ScenarioTestDriver NoPlot Scenario=./ Computed=./test_results/scenarios/
......
data/config/LongVerificationScenarios.config
View file @ ae5b93d1
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PatientVerification.config
View file @ ae5b93d1
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PlotRun.config
View file @ ae5b93d1
This diff is collapsed.
data/config/ScenarioVerification.config
View file @ ae5b93d1
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......@@ -129,6 +129,11 @@ equipment/NasalCannula.json = ScenarioTest
equipment/NonRebreatherMask.json = ScenarioTest
equipment/SimpleMask.json = ScenarioTest
@group Nutrition
nutrition/Nutrition.json = ScenarioTest
nutrition/SodiumIngestion.json = ScenarioTest
nutrition/WaterIngestion.json = ScenarioTest
@group Drugs
drug/Albuterol.json = ScenarioTest
drug/Desflurane.json = ScenarioTest
......@@ -172,13 +177,13 @@ miscellaneous/ImpairedAlveolarExchangeFraction.json = ScenarioTest
miscellaneous/ImpairedAlveolarExchangeSeverity.json = ScenarioTest
miscellaneous/ImpairedAlveolarExchangeSurfaceArea.json = ScenarioTest
miscellaneous/MultiDrug.json = ScenarioTest
miscellaneous/Nutrition.json = ScenarioTest
miscellaneous/PulmonaryShunt.json = ScenarioTest
miscellaneous/SpirometryComparison.json = ScenarioTest
miscellaneous/SpirometryHealthy.json = ScenarioTest
miscellaneous/SpirometryPulmonaryFibrosis.json = ScenarioTest
miscellaneous/TBIandDrugs.json = ScenarioTest
@group Compartments
#compartments/UserSpecific.json = ScenarioTest
compartments/AnesthesiaMachineCompartments.json = ScenarioTest
......
data/config/SystemVerification.config
View file @ ae5b93d1
......@@ -16,7 +16,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/human/adult/baselines/scenarios/equipment/MechanicalVentilatorPressureControlledARDS.zip.sha512
View file @ ae5b93d1
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data/human/adult/baselines/scenarios/equipment/MechanicalVentilatorPressureControlledVaried.zip.sha512
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