Recreation

[jawalonoski]

This pull request attempts to address #752.

Recreation of data requires the use of a random seed (-s), a clinician seed (-cs), and a reference date (-r).

Things that will not be identical:

• UUIDs: these will change across runs. Sorry.
• Export History: if you run the same parameters next year, and only keep the default 10 years of history, then the data in the record will be filtered differently (i.e. the oldest one year from the first run will not be exported)..

Summary of Changes

• Randomness
  • I made the Random inside Person to be private and made a few new accessor methods (e.g. randBoolean()).
  • Except for a few places (e.g. Generator.java), that means Random objects are no longer passed around as method arguments, and there should be no use of Random in the code.
  • All random number access goes through the Person#rand* methods.
  • There should also be no System.currentTimeInMillis() calls except for a few spots (e.g. Generator.java and sometimes export paths when folder per run settings are used).
• Reference Dates
  • I added an optional -r switch for referenceDate which can be used to specify when Synthea bases all the birth dates from. In my testing I used 20200320 (or March 20th, 2020) but you can use any date. This defaults to now (System.currentTimeinMillis()) if no value is supplied.
• Modules and States
  • All modules and states are completely cloned across the patients now. The modules used to be passed directly, and only the states were cloned. Now the modules are cloned as well. This was done to remove any possibility of multi-thread race conditions on accessing modules. Possibly unnecessary.
• Wiki
  • I added this https://github.com/synthetichealth/synthea/wiki/Contributing#new-sources-of-randomness to the wiki.

[codecov]

Codecov Report

Merging #756 into master will decrease coverage by 0%.
The diff coverage is 78%.

@@           Coverage Diff            @@
##             master    #756   +/-   ##
========================================
- Coverage        81%     81%   -1%     
- Complexity     2681    2713   +32     
========================================
  Files           100     101    +1     
  Lines         16802   16853   +51     
  Branches       2317    2324    +7     
========================================
+ Hits          13699   13738   +39     
- Misses         2404    2426   +22     
+ Partials        699     689   -10     

Impacted Files	Coverage Δ	Complexity Δ
...g/mitre/synthea/modules/HealthInsuranceModule.java	96% <0%> (-2%)	17 <0> (ø)
...java/org/mitre/synthea/world/agents/Clinician.java	83% <ø> (+3%)	9 <0> (ø)
.../mitre/synthea/world/concepts/BirthStatistics.java	58% <0%> (ø)	17 <0> (ø)
src/main/java/App.java	57% <16%> (-2%)	0 <0> (ø)
.../mitre/synthea/editors/GrowthDataErrorsEditor.java	66% <26%> (-2%)	27 <4> (-1)
...g/mitre/synthea/helpers/RandomNumberGenerator.java	42% <42%> (ø)	6 <6> (?)
...ava/org/mitre/synthea/modules/EncounterModule.java	97% <50%> (+<1%)	36 <0> (+1)
src/main/java/org/mitre/synthea/engine/State.java	90% <85%> (+<1%)	18 <0> (ø)
...va/org/mitre/synthea/world/geography/Location.java	72% <87%> (+<1%)	46 <6> (+6)
src/main/java/org/mitre/synthea/engine/Module.java	81% <90%> (+1%)	43 <2> (+3)
... and 37 more

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[hadleynet]

I guess you could move this inside the if block.

[jawalonoski]

Good catch.

[hadleynet]

Rather than having the random number related methods as public Person methods, I think it would be cleaner if they were all gathered together into an interface (e.g. RandomProvider) that Person implements. Methods that need access to randomness but not other aspects of Person could then just accept a RandomProvider instead of Person and this would make it clear which methods need Person access vs just Randomness.

[jawalonoski]

An interface like RandomProvider is a good idea. I'll work on that.

[jawalonoski]

I called the interface RandomNumberGenerator because I feel like Provider is overloaded with meaning, e.g. healthcare provider.

[hadleynet]

Should this be Person(clinicianSeed) instead?

[jawalonoski]

No. I admit that it is a little hard to follow, but clinicianSeed is the seed for ALL of the clinicians that can be passed in with the GeneratorOptions. The clinicianIdentifier is the seed for THIS particular clinician.

I'll make some changes in this area when I refactor with a RandomProvider as suggested above.

[jawalonoski]

@hadleynet Ready for your re-review.

[hadleynet]

Rebased and merged.