Specialities on encounters

[eedrummer]

Adds a specialty property on the Encounter state in GMF. This will require the encounter to happen at a Provider that offers that specialty.

The preferred provider infrastructure has been updated to handle this. People now have a preferred provider by encounter class and specialty.

Checkstyle fixes added in as well. It appears that there are now checkstyle violations on master 😲

[codecov]

Codecov Report

Attention: 11 lines in your changes are missing coverage. Please review.

Comparison is base (c28eec1) 77% compared to head (a03a6fc) 80%.
Report is 40 commits behind head on master.

❗ Current head a03a6fc differs from pull request most recent head 2872fee. Consider uploading reports for the commit 2872fee to get more accurate results

Files	Patch %	Lines
src/main/java/org/mitre/synthea/engine/State.java	60%	2 Missing and 2 partials ⚠️
...tre/synthea/world/concepts/PreferredProviders.java	84%	2 Missing and 2 partials ⚠️
.../java/org/mitre/synthea/world/agents/Provider.java	33%	1 Missing and 1 partial ⚠️
.../world/agents/behaviors/ProviderFinderQuality.java	50%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             master   #1047     +/-   ##
==========================================
+ Coverage        77%     80%     +2%     
+ Complexity     3690    3212    -478     
==========================================
  Files           170     120     -50     
  Lines         24000   21779   -2221     
  Branches       3332    2959    -373     
==========================================
- Hits          18560   17458   -1102     
+ Misses         4405    3403   -1002     
+ Partials       1035     918    -117     

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[jawalonoski]

Left some comments and questions.

[jawalonoski]

@eedrummer, can you resolve the conflicts? Then I'll merge it in if it passes the unit tests.

[eedrummer]

Converting this to draft while we figure out the best way to address the underlying needs of this PR. Namely, how can we limit a provider location in Synthea to offer a subset of services. It may be something like fully enabling some of the clinical specialty infrastructure... or something else.

[eedrummer]

There have been changes in Synthea since this PR was first submitted. When this was first created, the provider files had specialities listed. An update to the provider files removed specialties.

The more recent commits attempt to add specialties back in using information from NPPES. It's unclear at the current moment whether this approach will be useable as the test suite is breaking because some patients in MA can't find a cardiologist. This may be due to me picking the wrong specialty for cardiology or it may be that the data isn't good enough for our purposes and a new approach is needed.

[eedrummer]

After attempting to do some more work, it's clear that the Healthcare Provider Taxonomy Codes in NPPES aren't going to be useful for clinical specialty information for providers in Synthea. There are a few reasons for this:

1. Most hospitals are listed with just the General Acute Care Hospital Code.
2. Although NPPES has information on provides that work at these hospitals, attempting to aggregate or "roll up" this information is difficult. Inconsistencies in organization names (Massachusetts General Hospital vs. MG) and addresses (55 Fruit St. vs. 55 Fruit Street) make require a more sophisticated approach to aggregation than plain string matching.

If specialty information is to be incorporated into Synthea, it will likely have to come from a different source.