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Command line interfaces
bg-cli [HELP, GENDATA, GENSTATES, GENSEPSIS, VERIFY, VERSION, THREADED]
[JOBS N]
[CONFIG [FILE]...], [SCENARIO [FILE]...], [TEST cdm|bge], [VALIDATE patient|drug|system|all]
[GENTABLES html|md|xml|web|all]
Flags:
-v : Print Version
-j N : Adjust maximum parallel job count from default of Total-1
-h : Print this message
-t : Use Threads instead of Subprocess
This project is a command line implementation of BioGears for processing Scenario files it also had the ability to run Circuit Test and control threading
HELP: Print out help dialog.
GENDATA: Generate data XMLs from CSV files located in the runtime directory.
GENSTATES: Generate stabilized patient states for all patients.
GENSEPSIS: Generate stabilized sepsis states at various levels of infection and progression.
VERIFY: Run VerificationScenarios.config.
VERSION: Print out version string.
THREADED: Prefer threads of subprocesses when compiled against boost; Requires Boost
JOBS: Takes an integer to control the number of threads the pool will use when running multiple scenarios.
CONFIG: Take a number of config files which will be loaded and run.
SCENARIO: Takes a number of scenario files which will be loaded and run. Global settings in the files will overwrite previous entries.
TEST: Run a series of predetermined Circuit Test. Arguments are cdm or bge.
VALIDATE Run one ore more validate senarios arguments include drug,patient,system or all. Where VALIDATE all is the same as providing the following VALIDATE drug patient system VERIFY.
GENTABLES: Generate validation tables for BioGears documentation. Inputs are html, md, xml, web, or all.
The system will execute as many command line arguments as you give in a predetermined order. HELP or VERSION however will immediately stop a run if they are included in the arguments.
Examples
bg-cli THREADS 1 GENDATA GENSTATES -- Generate Data and States bg-cli TEST cdm VALIDATE all -- Run CDM Test followed by all validations bg-cli SCENARIO RunBGETest.config -- Read in RunBGETest.config and process it
If CMake can detect Boost when building bg-cli it will compile with the BIOGEARS_SUBPROCES_SUPPORT definition. With this enabled bg-cli will launch subprocess for each simulation instead of threads. This is intended to harden bg-cli against unexpected crashes of biogears instances with in the thread pool and mitigate the disruption caused by an unhandled exception in the code base. When built against Boost bg-cli can still run simulations in the threadpoll when the THREADED flag is given.
The BioGears build system provides a helpful STAGE target to run cmakes fixup_bundle utility for consolidating all external DLLs to a single runtime directory. This is inteneded to assist users in avoiding putting all of their third party development DLLs in their system path.
After BioGears has completed building run the STAGE target one time to ensure all the third party DLLS will be moved in to the output directory before attempting to launch the application. This functionality should only needed to be run once per build configuration.
bg-scenario [options] scenario
Allowed options:
-h [ --help ] produce help message
-n [ --name ] arg Set Scenario Name
-g [ --group ] arg Set Name of Scenario Group
-p [ --patient ] arg Specifcy the Initial Patient File
--state arg Specifcy the Initial Patient State File
-r [ --results ] arg Specifcy the Resoults File
-q [ --quiet ] Supress most log messages
***Examples***
bg-scenario Patient/Cough.xml
bg-scenario --patient Cyntha.xml Showcase/AsthmaAttack.xml -- Run AsthmaAttack.xml override specified initialization with Cynthia Patient file
bg-scenario --state [email protected] Showcase/AsthmaAttack.xml -- Run ASthmaAttack.xml overide specificed initialization with Joel@0s State file