Implement SQL on FHIR views #1439

johngrimes · 2023-05-09T16:05:07Z

Resolves #1438.

codecov · 2023-05-17T01:53:11Z

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.

❗ 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%)`	⬆️
.../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%)`	⬇️
...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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# Conflicts: # encoders/pom.xml # fhir-server/pom.xml # fhirpath/pom.xml # fhirpath/src/main/java/au/csiro/pathling/fhirpath/function/NamedFunction.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/LiteralPath.java # fhirpath/src/main/java/au/csiro/pathling/fhirpath/literal/StringLiteralPath.java # lib/import/pom.xml # lib/js/pom.xml # lib/python/Dockerfile # lib/python/pom.xml # library-api/pom.xml # pom.xml # site/pom.xml # terminology/pom.xml # utilities/pom.xml

johngrimes · 2023-09-10T12:57:30Z

@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

…ments to Spark/Catalyst. Initial concept of annotation fhipath based function definition.

Refactoring of ParserTest and related assertion classes, to work with column based approach (WIP).

…Test expectations.

…tions.

Implementation of 'union' and 'forEach' clauses. Separation of 'v1' FHIRView test from our custom enhanced tests.

Implemented 'getResourceKey()' function.

Implementing `join()` function.

…g deserialization of WhereClause.

…nteger`)

Implementing 'collection' and singular value selection semantics for DirectSelection.

…ons. Implementing 'r-keys' functions: getReferenceKey() and getResourceKey(). Cleaning up our extended FhirView tests.

…repostory.

…to allow FHIRView paths like: forEach = 'where(gender='male').name,

…al result.

johngrimes · 2024-07-04T05:53:06Z

Closing this in favour of #1775.

Implement initial part of query, and test stub

e59d062

johngrimes added the new feature New feature or request label May 9, 2023

johngrimes self-assigned this May 9, 2023

johngrimes changed the base branch from main to release/6.2.0 May 9, 2023 16:15

Get test #2 working

6ecad1b

johngrimes added 6 commits May 18, 2023 13:12

Get test #3 working

f0bf7ce

Add test #4

74d0822

Ensure determinism in ordering of join columns

14b0229

Add test purpose comments

c0c059d

Add tests #5-7

5b33f53

Add test 8

fd25b92

Base automatically changed from release/6.2.0 to main May 23, 2023 03:29

johngrimes added 6 commits May 23, 2023 14:46

Merge branch 'main' into fhir-views

be78820

Merge remote-tracking branch 'origin/main' into fhir-views

d936b10

Update version to 6.3.0-SNAPSHOT

9c3cd02

Replace extract column joining logic with view executor method

37c01fd

Add ExtractQueryTest#multipleIndependentUnnestings

b4f2db0

Add ExtractQueryTest#toleranceOfColumnOrdering

b321ead

johngrimes changed the title ~~SQL on FHIR view layer - POC implementation~~ Implement optional and per-column unnesting May 29, 2023

johngrimes added 3 commits May 29, 2023 16:31

Enable structured extract results within library

414f4be

Add string coercion

5493c67

Implement joining with topological sorting

69d7c3b

johngrimes added this to the SQL on FHIR Views milestone Jul 6, 2023

johngrimes added 6 commits July 9, 2023 11:12

Fix import within NamedFunction

71da037

Add additional tests

aebef99

Remove column joins

44f61bc

Get ExtractQueryTest passing

108922e

Add comments and remove unnecessary classes

f050a58

johngrimes added 3 commits September 10, 2023 21:55

Use expect instead of expected

b9ec589

Add formatting to pre-commit hook

1274efc

Make column aliases optional

f0d79d7

piotrszul added 22 commits September 11, 2023 15:25

Updating the pointer to sql-on-fhir

a9fec44

Delegating singularity tracking for column representation of FHIR ele…

afb652b

…ments to Spark/Catalyst. Initial concept of annotation fhipath based function definition.

Updating the sql-on-fire test cases

b478a2b

Making the entire code compilable.

af744ee

Refactoring of ParserTest and related assertion classes, to work with column based approach (WIP).

Reverting test data for Patient resource to be compatible with Parser…

9a80a95

…Test expectations.

Implemented first(), empty(), where(), and count() as collection func…

5174a7f

…tions.

Added first draft of new binary operators.

e10e6f0

Implementing extension support and 'typeOf' operation.

31d6310

Refactoring of FHIRViews execution.

76f6bcf

Implementation of 'union' and 'forEach' clauses. Separation of 'v1' FHIRView test from our custom enhanced tests.

Added (temporarily) new 'v1' tests to extended tests.

4e0dd31

Implemented 'getResourceKey()' function.

Implementing optional arguments to FHIR functions.

c1771b8

Implementing `join()` function.

Implemented 'not()', 'empty()' and 'exists()' for non-resource paths.

eb1a4f8

Adding support for empty results in FhirView test cases and correctin…

c7ee10b

…g deserialization of WhereClause.

Added direct traversal to nested choice element by name (e.g. `valueI…

e104a08

…nteger`)

Fixing the fn_rkeys test.

fe8a1bc

Updating the sql-on-fire pointer

82aea7a

Implementing 'expectError' and 'expectCount' for FhirViewTests.

ae4cbd8

Implementing 'collection' and singular value selection semantics for DirectSelection.

Re-implementing type specifiers as special cases of FhirPath expressi…

1f15872

…ons. Implementing 'r-keys' functions: getReferenceKey() and getResourceKey(). Cleaning up our extended FhirView tests.

Updating the sql-on-fhir pointer after merging changes from the main …

764b7ad

…repostory.

Replacing 'where()' with 'exists()' in FHIRView where clauses.

1e1e306

Adding support for FHIR operations on singular ResoureceCollections, …

272b301

…to allow FHIRView paths like: forEach = 'where(gender='male').name,

Updating test cases for 'forEach' removing the null rows from the fin…

d306c69

…al result.

johngrimes assigned johngrimes and unassigned piotrszul Oct 26, 2023

johngrimes closed this Jul 4, 2024

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Implement SQL on FHIR views #1439

Implement SQL on FHIR views #1439

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codecov bot commented May 17, 2023 •

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johngrimes commented Jul 4, 2024

Implement SQL on FHIR views #1439

Implement SQL on FHIR views #1439

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