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Implement Pathling R API for sparklyr #1611

Merged
merged 79 commits into from
Dec 1, 2023
Merged

Implement Pathling R API for sparklyr #1611

merged 79 commits into from
Dec 1, 2023

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piotrszul
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Resolves #193.

piotrszul added 22 commits July 10, 2023 12:38
@piotrszul
Added initial version of R pathlyr package using the code from the sp…
a0732d4 
…ike.
@piotrszul
Integrated execution of tests.
e90638c 
Some cleanup of the package files to pass R CMD check.
@piotrszul
Added ChatGPT translated code for context, udfs, and functions with s…
b5655d0 
…ome initial tests.
@piotrszul
Ported unit tests for encoding functions to R.
2b2726f
@piotrszul
Scaffolding for porting udf tests.
a2af135
@piotrszul
Removing uncessary dependency on org.apache.curator and enabling JV…
c7f5439 
…M debugging for python tests.
@piotrszul
Added tests for 'translate' udf and fixed the implementation.
c72d36a
@piotrszul
Fixed implementation and tests for 'property', 'display' and 'designa…
d44dee9 
…tion'.
@piotrszul
Refactoring of udf tests: split tests into separate files.
ac00167
@piotrszul
Enabled tests for subsumption UDFs.
c3baeae
@piotrszul
Implemented queries and converted query tests.
9d28ea6
@piotrszul
Implemented and tested part of datasources.
8814c1a 
Writting and delta is still not to be done.
@piotrszul
Refactoring
6a8ef10
@piotrszul
Added renv based dependency specification.
8ae4eee
@piotrszul
Small fixed for R check.
8f0fd7e
@piotrszul
Added a script for setting version in poms and DESCRIPTION files.
8645eae
@piotrszul
Added verify step with "R CMD check"
f04e789
@piotrszul
Making changes necessary to pass 'R CMD check --as-cran'.
9fdc5d6
@piotrszul
Removed dependency on 'renv' using the basic devtools support for ins…
5a4172a 
…talling dependencies instead.

Added the github job for R verification.
Added basic readme on setting up R dev environment.
@piotrszul
Fixed the issue with writing data sources.
aa38a12
@piotrszul
Fixing a numer of TODO: items.
6b35211
@piotrszul
Updating springBoot version to: 2.7.14 and spring securty to 2.7.10 i…
5d169c2 
…n order to fix: CVE-2023-34034
@piotrszul piotrszul self-assigned this Aug 11, 2023
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codecov bot commented Aug 11, 2023 •
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Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (6d28d10) 85.53% compared to head (919b94d) 85.48%.
Report is 3 commits behind head on main.

Additional details and impacted files 
@@             Coverage Diff              @@
##               main    #1611      +/-   ##
============================================
- Coverage     85.53%   85.48%   -0.05%     
  Complexity      139      139              
============================================
  Files           340      339       -1     
  Lines          7845     7826      -19     
  Branches        525      525              
============================================
- Hits           6710     6690      -20     
  Misses          843      843              
- Partials        292      293       +1
Files Coverage Δ
lib/python/pathling/__init__.py 100.00% <ø> (ø)
lib/python/pathling/context.py 81.96% <100.00%> (+1.32%) ⬆️
.../csiro/pathling/sql/udf/TerminologyUdfHelpers.java 70.00% <100.00%> (ø)
lib/python/pathling/functions.py 94.73% <66.66%> (-5.27%) ⬇️
...u/csiro/pathling/library/io/source/FileSource.java 95.74% <75.00%> (-4.26%) ⬇️

... and 2 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@johngrimes johngrimes assigned johngrimes and unassigned piotrszul Oct 26, 2023
johngrimes and others added 26 commits October 28, 2023 12:59
@johngrimes
Add functions for creating LOINC codings
6c4aed3
@johngrimes
Add R examples to terminology functions page
c4cafc6
@piotrszul
Updating R tests to work with the new version of sparklyr (1.8.4)
7716f4b
@piotrszul
Updating R examples to work with the new version of sparklyr (1.8.4)
b165157
@johngrimes
Add R extract example to documentation
a4bd056
@johngrimes
Add R aggregate example to documentation
d20f9d2
@johngrimes
Fix closing tags
98d749e
@johngrimes
Complete remaining R examples on FHIRPath query page
6f26c0a
@johngrimes
Rename ptl_ to pathling_ and trm_ to tx_
9b796b3
@johngrimes
Pin zookeeper to 3.7.2
b161ffe
@johngrimes
Move dependency installation to initialize phase
ae79b46
@johngrimes
Update SCT version in DockerImageTest
8a1b494
@johngrimes
Fix citation configuration
0c20b6f
@johngrimes
Revert "Move dependency installation to initialize phase"
eb2a106 
This reverts commit ae79b46.
@johngrimes
Remove reference to non-existent Maven variable
5ec07fc
@johngrimes
Add R dependency steps to site job
653aa49
@johngrimes
Improve job and step names
26d5d7d
@johngrimes
Remove JAR from R package and specify as a dependency instead
9b39f2b
@johngrimes
Add missing step name to R test job
b66d589
@johngrimes
Fix documentation for to_xxx_coding variants
c194b9a
@johngrimes
Change R pom back to jar type
873dee7
@johngrimes
Remove JAR from Python package and specify as a dependency instead
b12c011
@johngrimes
Use install goal instead of verify for library builds
14abeaf
@johngrimes
Add library runtime package to Spark submit test
42f0737
@johngrimes
Incorporate dev notes into README
93f0152
@johngrimes
Update LICENSE for R package
919b94d
@johngrimes johngrimes merged commit 919b94d into main Dec 1, 2023
32 of 33 checks passed
@johngrimes johngrimes deleted the issue/193 branch December 1, 2023 07:46
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