Flexporter - Update randomCode fn to take output type as an optional second param

[dehall]

Updates to address flexporter issues identified by @elsaperelli :

1. I realized the randomCode function was improperly named since technically it produces a Coding not a code. Rather than rename it and break backwards compatibility, this gives it an optional second parameter for "return type". This can be "code" to return a string, "Coding" to return a Coding (ie {system, code, display}), or "CodeableConcept" to return a CodeableConcept. Default if unspecified is Coding, for backwards compatibility.

2. Adds support for defining custom ValueSets in a flexporter mapping file, so that you can select a randomCode from your handpicked set of codes rather than having to use a terminology server and pre-existing VS. The syntax is a YAML version of the ValueSet resource, to minimize inventing new things. There are some quirks to this though so I'm open to suggestions here:

   • Our YAML parser doesn't work with the HAPI FHIR model classes, so this uses a roundabout way of loading that parses the YAML to Map<String,Object>, serializes that to JSON, then parses the JSON as FHIR. The alternative here would be to define a custom new model to represent a VS, or to re-implement the ValueSet class.
   • The ValueSets need to be loaded once per mapping file, so I added a new function to be called in the main flexporter entrypoints (App and RunFlexporter). Trying to load them multiple times wouldn't break anything but I don't want to do that (YAML) -> (JSON) -> (FHIR classes) sequence multiple times unnecessarily.

3. Added some extra error handling for the value set $expand operation, to assist in debugging when it returns an OperationOutcome

[codecov]

Codecov Report

Attention: Patch coverage is 43.47826% with 13 lines in your changes missing coverage. Please review.

Project coverage is 77%. Comparing base (df8ed77) to head (e83ae2f).
Report is 173 commits behind head on master.

Files with missing lines	Patch %	Lines
...org/mitre/synthea/helpers/RandomCodeGenerator.java	15%	10 Missing and 1 partial ⚠️
...a/org/mitre/synthea/export/flexporter/Actions.java	80%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             master   #1527     +/-   ##
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  Coverage        77%     77%             
- Complexity     3710    4005    +295     
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  Files           170     178      +8     
  Lines         24077   25169   +1092     
  Branches       3351    3591    +240     
==========================================
+ Hits          18618   19485    +867     
- Misses         4418    4557    +139     
- Partials       1041    1127     +86     

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[elsaperelli]

Lgtm! Great new feature

[dehall]

Update: I'm converting this to draft and will add the ability to define custom value sets within a flexporter mapping. It's a little roundabout but it will allow for choosing from just a small set of codes rather than forcing the user to use a terminology service and real VS

[elsaperelli]

This custom value set functionality is awesome! Tested out with our qpp qicore mapping file to split the MedicationDispense status ValueSet and it worked very easily!