Module overrides

[dehall]

Starting point for "module overrides". The idea here is that we can provide a module override file at runtime that defines parameters that override parts of the generic modules. There are a number of possible use cases for this, for example pre-defining alternative populations (think "internationalization", such as "run with this override file to produce a population matching all condition prevalence rates in Germany"). Also includes a task that can generate a base set of override files with some configurability.

The format of the overrides file is a java properties file, with format:

(module file path)::(jsonpath to value) = (new value)

example:

congestive_heart_failure.json\:\:$['states']['Age_70-79-Chance\ of\ CHF']['distributed_transition'][0]['distribution'] = 0.024
congestive_heart_failure.json\:\:$['states']['Age_80-Chance\ of\ CHF']['distributed_transition'][0]['distribution'] = 0.045
atopy.json\:\:$['states']['Initial']['complex_transition'][0]['distributions'][0]['distribution'] = 0.917
atopy.json\:\:$['states']['Initial']['complex_transition'][1]['distributions'][0]['distribution'] = 0.033

The way that this feature is used is by setting a config property:

run_synthea --module_override=path_to_properties_file

Note that I also extracted the common "for each module" logic into a new utility method since the exact same boilerplate was used in 5+ places. Apologies for the extra diffs but if you view it in "ignore whitespace mode" it's more obvious what the actual change to those files was.

[codecov]

Codecov Report

Merging #566 into master will increase coverage by <1%.
The diff coverage is 57%.

@@            Coverage Diff            @@
##             master    #566    +/-   ##
=========================================
+ Coverage        76%     76%   +<1%     
- Complexity     2202    2246    +44     
=========================================
  Files            85      86     +1     
  Lines         14546   14645    +99     
  Branches       1974    1991    +17     
=========================================
+ Hits          11088   11227   +139     
+ Misses         2887    2855    -32     
+ Partials        571     563     -8

Impacted Files	Coverage Δ	Complexity Δ
src/main/java/Graphviz.java	0% <0%> (ø)	0 <0> (ø)	⬇️
...main/java/org/mitre/synthea/helpers/Utilities.java	78% <100%> (+1%)	107 <6> (+6)	⬆️
src/main/java/org/mitre/synthea/engine/Module.java	79% <52%> (-9%)	38 <6> (-1)
...ava/org/mitre/synthea/helpers/ModuleOverrides.java	56% <56%> (ø)	20 <20> (?)
.../main/java/org/mitre/synthea/helpers/Concepts.java	84% <75%> (-1%)	16 <1> (-2)
...ain/java/org/mitre/synthea/helpers/Attributes.java	85% <75%> (-1%)	65 <1> (-2)
...in/java/org/mitre/synthea/export/TextExporter.java	92% <0%> (-2%)	79% <0%> (-6%)
...org/mitre/synthea/export/ClinicalNoteExporter.java	79% <0%> (-2%)	14% <0%> (-2%)
...ava/org/mitre/synthea/modules/EncounterModule.java	96% <0%> (-2%)	31% <0%> (-1%)
...ava/org/mitre/synthea/modules/LifecycleModule.java	90% <0%> (-1%)	127% <0%> (ø)
... and 9 more

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[dehall]

Note to self: once this is eventually complete and merged, update the README on the populations repo: https://github.com/synthetichealth/populations

[dehall]

Once this is merged I'll add a wiki page for it as well