Added CodeSystemRef and updated CodeSystem type

[elsaperelli]

Summary

This PR addresses #259 to add capability for CodeSystemRef. It also adds name to the CodeSystem type, something that was introduced in CQL 1.5.

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• [✔] This pull request describes why these changes were made
• [✔] Code diff has been done and been reviewed (it does not contain: additional white space, not applicable code changes, debug statements, etc.)
• [✔] Tests are included and test edge cases
• [✔] Tests have been run locally and pass
• [✔] Code coverage has not gone down and all code touched or added is covered.
• [✔] Code passes lint and prettier (hint: use npm run test:plus to run tests, lint, and prettier)
• [✔] All dependent libraries are appropriately updated or have a corresponding PR related to this change
• [✔] cql4browsers.js built with npm run build:browserify if source changed.

Reviewer:

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• Code is maintainable and reusable, reuses existing code and infrastructure where appropriate, and accomplishes the task’s purpose
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[codecov-commenter]

Codecov Report

❌ Patch coverage is 85.71429% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 87.46%. Comparing base (2a3dfb2) to head (4395de4).

Files with missing lines	Patch %	Lines
src/elm/clinical.ts	83.33%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #346      +/-   ##
==========================================
- Coverage   87.47%   87.46%   -0.01%     
==========================================
  Files          52       52              
  Lines        4550     4555       +5     
  Branches     1284     1285       +1     
==========================================
+ Hits         3980     3984       +4     
  Misses        361      361              
- Partials      209      210       +1     

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[cmoesel]

This is looking pretty good. I've left a few comments:

• one about the CodeSystem constructor and backwards-compatibility
• and a couple about one of the tests

Looking for feedback on the constructor and backwards compatibility.

[hossenlopp]

CodeSystemRef should be able to reference a CodeSystem in another library. If CQL-to-ELM can't translate that right then maybe either not implement it or just not test it.

[hossenlopp]

ELM specification says this could reference CodeSystems in other libraries. The optional libraryName should be pulled out of the json and used when getting the code system from the context. Which will require changes to the Context (and Library) getCodeSystem function to support the library parameter. ValueSetRef and getValueSet can be used as a good reference for this.

http://cql.hl7.org/04-logicalspecification.html#codesystemref

[cmoesel]

Ooooh. Good call, @hossenlopp. I just tested this and confirmed that the translator does support referencing CodeSystems from another library.

[cmoesel]

I've updated this branch to add support for code systems from other libraries. Along the way I noticed a couple of related things that needed to be fixed:

• CodeSystems from included libraries were being put into the main library codesystems collection -- and overwriting the ones from the main library in cases where the name was the same! Whoops!
• When resolving ValueSetRefs, the logic was only looking at the specified library name if it couldn't find a ValueSet with the requested name in the main library. Which means that if you had a VS in the main library and a VS in an included library with the same name, it always gave you the former, even if you asked for the latter! Whoops (again)!

[elsaperelli]

Reviewed @cmoesel's updates and they all look good to me! Approved!

[hossenlopp]

Additional changes and tests look good.