Implement SQL on FHIR views

[johngrimes]

Resolves #1438.

[codecov[bot]]

Codecov Report

Attention: 63 lines in your changes are missing coverage. Please review.

Comparison is base (1b30556) 85.35% compared to head (37c01fd) 85.23%. Report is 7 commits behind head on main.

:exclamation: Current head 37c01fd differs from pull request most recent head d306c69. Consider uploading reports for the commit d306c69 to get more accurate results

Additional details and impacted files

@@             Coverage Diff              @@
##               main    #1439      +/-   ##
============================================
- Coverage     85.35%   85.23%   -0.12%     
  Complexity      139      139              
============================================
  Files           340      347       +7     
  Lines          7845     7998     +153     
  Branches        525      520       -5     
============================================
+ Hits           6696     6817     +121     
- Misses          856      888      +32     
  Partials        293      293              

Files	Coverage Δ
...iro/pathling/aggregate/AggregateQueryExecutor.java	98.24% <100.00%> (ø)
...ro/pathling/fhirpath/parser/InvocationVisitor.java	93.22% <100.00%> (+0.11%)	:arrow_up:
.../csiro/pathling/fhirpath/parser/ParserContext.java	100.00% <100.00%> (ø)
...siro/pathling/fhirpath/parser/UnnestBehaviour.java	100.00% <100.00%> (ø)
.../java/au/csiro/pathling/views/NamedExpression.java	100.00% <100.00%> (ø)
...va/au/csiro/pathling/views/VariableExpression.java	100.00% <100.00%> (ø)
lib/python/pathling/__init__.py	100.00% <100.00%> (ø)
...src/main/java/au/csiro/pathling/QueryExecutor.java	93.82% <88.88%> (-0.30%)	:arrow_down:
...au/csiro/pathling/fhirpath/FhirPathAndContext.java	66.66% <66.66%> (ø)
...rc/main/java/au/csiro/pathling/views/FhirView.java	80.00% <80.00%> (ø)
... and 13 more

... and 39 files with indirect coverage changes

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[johngrimes]

@piotrszul Thanks for picking this up. The goal is to get au.csiro.pathling.views.FhirViewTest passing.

[johngrimes]

@piotrszul I did a bit more work on the PR, primarily so that I could do a demo for the SQL on FHIR track at the Phoenix connectathon over the weekend.

You can see it here: https://youtu.be/2Dj4fBoBmRA

There is now a submodule at sql-on-fhir, and a symlink fhirpath/src/test/resources/tests/sql-on-fhir -> ../../../../../sql-on-fhir/tests.

You might need to:

git submodule init
git submodule update

[johngrimes]

Closing this in favour of #1775.