0063 Move examples for internal functions to unit tests

ShiyuC commented 1 month ago

This PR moves all the example sections for internal functions to unit tests. Closes #63

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github-actions[bot] commented 1 month ago

Package	Line Rate	Health
sdtm.oak	93%	✔
Summary	93% (949 / 1022)	✔

ShiyuC commented 1 month ago

@ramiromagno @edgar-manukyan May I request your review of this MR? Thanks in advance

ShiyuC commented 1 month ago

@ShiyuC: great job! Thank you so much.

I think the only remaining bit is really to fix the test failures from the testing of derive_blfl(). But I am guessing Kamil or Ram are better equipped to give you feedback here as they worked on this function.

And also still on derive_blfl(), I would convert expect_snapshot_error() to expect_snapshot(..., error = TRUE) as expect_snapshot_error() is under "questioning" status (check its documentation).

Test failures related to `derive_blfl()`

==> Testing R file using 'testthat'

ℹ Loading sdtm.oak
[ FAIL 8 | WARN 0 | SKIP 0 | PASS 7 ]

── Failure (test-derive_blfl.R:47:3): derive_blfl sdmt_in validations work ─────
Snapshot of `derive_blfl(...)` has changed:
old vs new
- Required variable `DOMAIN` is missing
+ Required variable `DOMAIN` is missing in `sdtm_in`

* Run testthat::snapshot_accept('derive_blfl') to accept the change.
* Run testthat::snapshot_review('derive_blfl') to interactively review the change.

── Failure (test-derive_blfl.R:58:3): derive_blfl sdmt_in validations work ─────
Snapshot of `derive_blfl(...)` has changed:
old vs new
- Required variables `oak_id`, `raw_source` and `patient_number` are missing
+ Required variables `oak_id`, `raw_source`, and `patient_number` are missing in `sdtm_in`

* Run testthat::snapshot_accept('derive_blfl') to accept the change.
* Run testthat::snapshot_review('derive_blfl') to interactively review the change.

── Failure (test-derive_blfl.R:74:3): derive_blfl sdmt_in validations work ─────
Snapshot of `derive_blfl(...)` has changed:
old vs new
- Required variables `VSORRES`, `VSSTAT`, `VSTESTCD` and `VSDTC` are missing
+ Required variables `VSORRES`, `VSSTAT`, `VSTESTCD`, and `VSDTC` are missing in `sdtm_in`

* Run testthat::snapshot_accept('derive_blfl') to accept the change.
* Run testthat::snapshot_review('derive_blfl') to interactively review the change.

Confirmed that the failed test will be addressed in a separate PR.

ShiyuC commented 1 month ago

@rammprasad I'm still not authorized to merge this PR after all conversations and conflicts are resolved.

galachad commented 1 month ago

@rammprasad I'm still not authorized to merge this PR after all conversations and conflicts are resolved.

@ShiyuC I will merge this PR, we can check in another one why.

kamilsi commented 1 month ago

EDIT: nevermind, I see that @galachad fixed this in https://github.com/pharmaverse/sdtm.oak/pull/73, thanks (and indeed it was caused by admiraldev)!

I think the only remaining bit is really to fix the test failures from the testing of derive_blfl(). But I am guessing Kamil or Ram are better equipped to give you feedback here as they worked on this function.

Hi @ramiromagno, the changes in test behavior are not justified by any codebase changes in this PR. Perhaps admiraldev was updated on the machine where the tests were run, allowing it to identify the object where the problem is detected. Regardless, these are good changes and should be accepted using testthat::snapshot_accept('derive_blfl').

Confirmed that the failed test will be addressed in a separate PR.

@ShiyuC which issue is that?

pharmaverse / sdtm.oak