0.4 Small Updates

[rsh52]

Description

This PR builds on top of #154 and addresses some behavior caught by @skadauke in Teams.

Proposed Changes

List changes below in bullet format:

• Tweak suprtbl_recode() using label capture and re-establishment similar to what's used in make_labelled() to re-establish labels after loss due to data reformatting
  • This was causing logical data for yesno and checkbox fields to lose their labels
• Add a new check function check_file_exists() (name could be updated, this is also a checkmate function name) which checks if arg overwrite is FALSE in write_redcap_xlsx() and arg file already exists. Provides a helpful reminder to change overwrite.
• Minor changes to tests and snapshots. Minor change to NAMESPACE due to removal of lifecycle deprecated functions

Additional Changes

• Update cli_message_examples.R with new warnings and checks, rerun reprex
• Documentation updated as requested in Teams
• New internal release_questions() function added that gets called when running devtools::release(). See image below for example output once all standard release() questions have been answered:
  • We can easily add more to the character vector, these are just some to start with

Issue Addressed

NA

PR Checklist

Before submitting this PR, please check and verify below that the submission meets the below criteria:

• [x] New/revised functions have associated tests
• [NA] New/revised functions that update downstream outputs have associated static testing files (.RDS) updated under inst/testdata/create_test_data.R
• [NA] New tests that make API calls use httptest::with_mock_api and any new mocks were added to tests/testthat/fixtures/create_httptest_mocks.R
• [x] New/revised functions use appropriate naming conventions
• [ ] New/revised functions don't repeat code

  Possibility here to generalize repeated code from make_labelled(), but unsure if worth it

• [x] Code changes are less than 250 lines total
• [x] Issues linked to the PR using GitHub's list of keywords
• [x] The appropriate reviewer is assigned to the PR
• [x] The appropriate developers are assigned to the PR
• [x] Pre-release package version incremented using usethis::use_dev_version()

Code Review

This section to be used by the reviewer and developers during Code Review after PR submission

Code Review Checklist

• [ ] I checked that new files follow naming conventions and are in the right place
• [ ] I checked that documentation is complete, clear, and without typos
• [ ] I added/edited comments to explain "why" not "how"
• [ ] I checked that all new variable and function names follow naming conventions
• [ ] I checked that new tests have been written for key business logic and/or bugs that this PR fixes
• [ ] I checked that new tests address important edge cases

[skadauke]

I think a warning is probably the way to go here. If no extension is supplied, should we automatically add ".xlsx"?

Get Outlook for iOShttps://aka.ms/o0ukef

---

From: Rich Hanna @.> Sent: Wednesday, May 31, 2023 10:28:22 PM To: CHOP-CGTInformatics/REDCapTidieR @.> Cc: Stephan Kadauke @.>; Mention @.> Subject: [External]Re: [CHOP-CGTInformatics/REDCapTidieR] 0.4 Small Updates (PR #155)

@rsh52 commented on this pull request.

---

In utility/cli_message_examples_reprex.mdhttps://github.com/CHOP-CGTInformatics/REDCapTidieR/pull/155#discussion_r1212274756:

+#> Warning: Empty string detected for a given multiple choice label. +#> Error in write_redcap_xlsx(): +#> ✖ add_labelled_column_headers declared TRUE, but no variable labels +#> detected. +#> ℹ Did you run make_labelled() on the supertibble? + +read_redcap(redcap_uri, classic_token) %>%

• write_redcap_xlsx(file = "temp.pdf") +#> Warning in read_redcap(redcap_uri, classic_token): ! Multiple values are mapped to the label A in field radio_duplicate_label +#> ℹ Consider making the labels for radio_duplicate_label unique in your REDCap +#> project +#> Warning: ! The field radio_dtxt_error in data_field_types is a radio field type, however +#> it does not have any categories. +#> Warning: Empty string detected for a given multiple choice label. +#> Error in write_redcap_xlsx(): +#> ✖ Invalid file extension supplied to file: pdf

Using wb$save() will execute for pretty much any extension, but the files themselves will be corrupted, produce warnings, or be not be openable. In testing, CSV and XLS save but they open with warnings. docx and pdf will save, but the files won't open. When I tested no file extension it was an empty file.

I guess it's a determination of if we want to fail loudly or silently and let users discover for themselves if their files work. CSV and XLS will be openable, but users will have to convert the files to XLSX to retain the XLSX features we have in our output.

— Reply to this email directly, view it on GitHubhttps://github.com/CHOP-CGTInformatics/REDCapTidieR/pull/155#discussion_r1212274756, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACTGHWUS4JNN6ZXUFQB6QTTXI6SWNANCNFSM6AAAAAAYUOJE4M. You are receiving this because you were mentioned.Message ID: @.***>

This email originated from an EXTERNAL sender to CHOP. Proceed with caution when replying, opening attachments, or clicking links. Do not disclose your CHOP credentials, employee information, or protected health information to a potential hacker.

[rsh52]

I think a warning is probably the way to go here. If no extension is supplied, should we automatically add ".xlsx"?

Sounds good. Changed to warning, slight update to message. Up to you, FWIW this isn't behavior seen in base R write.* or readr write_*. For each of those a nondescript file gets made unless you specify an extension, despite the name of the function, but we've typically broken the mold with this package anyway.

[skadauke]

I think a warning is probably the way to go here. If no extension is supplied, should we automatically add ".xlsx"?

Sounds good. Changed to warning, slight update to message. Up to you, FWIW this isn't behavior seen in base R write.* or readr write_*. For each of those a nondescript file gets made unless you specify an extension, despite the name of the function, but we've typically broken the mold with this package anyway.

Yes you're right. Just one place where we're doing a better job than posit :)

[rsh52]

I think a warning is probably the way to go here. If no extension is supplied, should we automatically add ".xlsx"?

Sounds good. Changed to warning, slight update to message. Up to you, FWIW this isn't behavior seen in base R write.* or readr write_*. For each of those a nondescript file gets made unless you specify an extension, despite the name of the function, but we've typically broken the mold with this package anyway.

Yes you're right. Just one place where we're doing a better job than posit :)

Cool 👍 Solution implemented, corresponding warning messages updated using ChatGPT ✨