0063 Move examples for internal functions to unit tests

[ShiyuC]

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

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• Update NEWS.md if the changes pertain to a user-facing function (i.e. it
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[github-actions]

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

[ShiyuC]

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

[edgar-manukyan]

Thanks so much @ShiyuC for massive cleanup and awesome test 👍 I left one question for your kind consideration.

[ramiromagno]

@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.

[ShiyuC]

@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]

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

[galachad]

@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]

EDIT: nevermind, I see that @galachad fixed this in #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?