Module Metrics

[jawalonoski]

This branch revamps the module, state, and transition metrics.

Previously, use of the generate.track_detailed_transition_metrics property outputted metrics to system out. Using this feature roughly quadrupled the runtime.

This change outputs the metrics as JSON (./output/metrics/**), one file per module. Using this feature will roughly double the runtime.

Sample output looks something like this for each state, where the name of the state (e.g., Chance_of_Stroke matches a state name in the corresponding GMF module):

  "Chance_of_Stroke": {
    "entered": 58987,
    "duration": 152635104000000,
    "population": 101,
    "current": 100,
    "destinations": {
      "Stroke": 1,
      "Chance_of_Stroke": 58886
    }
  }

Field	Description
entered	Count, how many times this state was entered.
duration	Sum of time (milliseconds) spent in this state.
population	Count, how many unique individuals entered this state (this count is not reliable for submodules).
current	Count, how many individuals are currently in this state at simulation end.
destinations	Map of states and counts that processing transitioned to.

[codecov]

Codecov Report

Attention: Patch coverage is 38.59649% with 35 lines in your changes are missing coverage. Please review.

Project coverage is 77%. Comparing base (94ca67d) to head (b44b6bd).
Report is 3 commits behind head on master.

Files	Patch %	Lines
...a/org/mitre/synthea/helpers/TransitionMetrics.java	35%	25 Missing and 1 partial ⚠️
src/main/java/org/mitre/synthea/engine/Module.java	53%	7 Missing ⚠️
...c/main/java/org/mitre/synthea/export/Exporter.java	0%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##             master   #1438    +/-   ##
=========================================
  Coverage        76%     77%            
- Complexity     3868    3948    +80     
=========================================
  Files           178     178            
  Lines         25041   25279   +238     
  Branches       3547    3624    +77     
=========================================
+ Hits          19249   19486   +237     
- Misses         4667    4677    +10     
+ Partials       1125    1116     -9     

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[hadleynet]

Tested and verified locally, just one suggestion that you can ignore if you'd prefer to keep things as is.

[hadleynet]

Just a thought but if you modified List<ModuleSupplier> getModuleSuppliers(Predicate<String> predicate) in Module.java to take a Predicate<ModuleSupplier> instead then you could get rid of the loop that follows while also making that method more flexible.

[jawalonoski]

That sounds like a good idea. I'll take a look at it.

[jawalonoski]

OK, I made a change. Everything should be ready to go.