[REVIEW]: REDCapTidieR: Extracting complex REDCap databases into tidy tables

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@rsh52@mikemahoney218<!--end-editor-- Reviewers: @RhysPeploe, @spgarbet Archive: 10.5281/zenodo.10658773

Status

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Markdown: [![status](https://joss.theoj.org/papers/19002e0cdd99ac89e516c73c76c232bd/status.svg)](https://joss.theoj.org/papers/19002e0cdd99ac89e516c73c76c232bd)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@RhysPeploe & @spgarbet, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikemahoney218 know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @spgarbet

📝 Checklist for @RhysPeploe

editorialbot commented 10 months ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 10 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (746.5 files/s, 160403.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               31           1245           1826           4724
Markdown                        14            261              0           2468
HTML                             1             84              5            605
YAML                             6             33              9            249
Rmd                              5            355            505            146
TeX                              1             15              0            128
JSON                             1              0              0             19
-------------------------------------------------------------------------------
SUM:                            59           1993           2345           8339
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 10 months ago

Wordcount for paper.md is 1189

editorialbot commented 10 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.18637/jss.v059.i10 is OK
- 10.5281/zenodo.11826 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikemahoney218 commented 10 months ago

👋🏼 @rsh52 , @RhysPeploe , @spgarbet , this is the review thread for {REDCapTidieR}. Just about all of our communications will happen here from now on :smile: .

We might have one more reviewer join us, but I figured it made sense to get things started while I wait to hear back there :smile:

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. For best results, don't include anything else in the comment!

This will create a checklist that walks through the JOSS submission requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6277 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if you require some more time.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns.

Thank you so much for agreeing to review this submission!

mikemahoney218 commented 10 months ago

@editorialbot remind @mikemahoney218 in 2 weeks

(Setting up an automated reminder for myself to make sure this doesn't fall through the cracks 😄 )

editorialbot commented 10 months ago

Reminder set for @mikemahoney218 in 2 weeks

spgarbet commented 10 months ago

Review checklist for @spgarbet

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/CHOP-CGTInformatics/REDCapTidieR?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rsh52) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

spgarbet commented 10 months ago

How do I see the more recent edited version?

mikemahoney218 commented 10 months ago

Seems like @rsh52 has been making changes in a branch here: https://github.com/CHOP-CGTInformatics/REDCapTidieR/tree/joss-feedback-1

(I'm assuming the plan is to eventually merge this into main?)

rsh52 commented 10 months ago

Yes! I want to run the changes by the team first (an odd codecov check is currently failing) and then I was going to tag @spgarbet once I get some approvals.

spgarbet commented 10 months ago

With those it completes the checklist. Looks great.

mikemahoney218 commented 10 months ago

Thanks for the extremely speedy review @spgarbet :smile:

mikemahoney218 commented 10 months ago

:wave: @rsh52 and @RhysPeploe , just wanted to share that I'm going to be OOO from February 2nd through the 9th (so, Friday through the end of next week). I'll be around somewhat but will be much more delayed in responding on this issue; apologies in advance!

And as always, feel free to reach out if you have any questions or concerns :smile:

RhysPeploe commented 10 months ago

Review checklist for @RhysPeploe

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/CHOP-CGTInformatics/REDCapTidieR?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@rsh52) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

rsh52 commented 10 months ago

Seems like @rsh52 has been making changes in a branch here: https://github.com/CHOP-CGTInformatics/REDCapTidieR/tree/joss-feedback-1

(I'm assuming the plan is to eventually merge this into main?)

Just merged to main! Should I re-generate with the bot?

mikemahoney218 commented 10 months ago

@editorialbot generate pdf

can't hurt :smile:

editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

editorialbot commented 9 months ago

:wave: @mikemahoney218, please take a look at the state of the submission (this is an automated reminder).

RhysPeploe commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

RhysPeploe commented 9 months ago

Finished my checklist @mikemahoney218

mikemahoney218 commented 9 months ago

Awesome! Thank you so much @RhysPeploe and @spgarbet for your thoughtful reviews here.

@rsh52 , at this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

Thanks everyone :smile:

mikemahoney218 commented 9 months ago

@editorialbot generate pdf

mikemahoney218 commented 9 months ago

@editorialbot check references

editorialbot commented 9 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.18637/jss.v059.i10 is OK
- 10.5281/zenodo.10564837 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rsh52 commented 9 months ago

@mikemahoney218 Would it be ok to update the current release tag (v1.0.0) and include updated notes? Or should we bump the package version to 1.0.0.9000 and make an all-new release?

For Zenodo, do I upload the source package after build (tar.gz file)?

mikemahoney218 commented 9 months ago

We just need a GitHub release that corresponds to this version of the software, no need to do a full release -- if you make a v1.0.0-joss tag to commemorate "this is the version of the software as accepted by JOSS", that's probably easiest?

For Zenodo, I personally always have used this tutorial which will create Zenodo archives every time you create a release, because I like the idea of automatically archiving each release. If you do this, do it before creating the new tag, and you'll need to make sure the title and authors (and ORCiDs) match the JOSS submission.

If you just want to create a single archive, then upload a zipped version of your source code -- not the built version. My logic here is that things like your articles are in .Rbuildignore, so won't be in the built version, but were part of the documentation reviewed as part of your submission. If it's helpful, a recent example for what this looks like: https://zenodo.org/records/10658194

rsh52 commented 9 months ago

@mikemahoney218 Thanks so much for helping clear this up. I believe everything should be available now:

Zenodo Upload: https://zenodo.org/records/10658774
REDCapTidieR JOSS Release: https://github.com/CHOP-CGTInformatics/REDCapTidieR/releases/tag/v1.0.0-joss

mikemahoney218 commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikemahoney218 commented 9 months ago

@rsh52 not sure if it's easier for you to change things or for me to open a PR -- think there's still an issue with how the OpenSSF citation is getting rendered (sorry, my fault). Think this would fix it:

@Misc{openssf_cit,
  title = {{OpenSSF Best Practices} Badge Program},
  author = {{Open Source Security Foundation}},
  url={https://www.bestpractices.dev/},
  publisher={The Linux Foundation},
  year={2023},
  month={Oct}

(new braces in the title and author fields)

rsh52 commented 9 months ago

@mikemahoney218 Just implemented on main!

mikemahoney218 commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikemahoney218 commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Paper is not ready for acceptance yet, the archive is missing

mikemahoney218 commented 9 months ago

@editorialbot set version v1.0.0-joss

editorialbot commented 9 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

mikemahoney218 commented 9 months ago

@editorialbot set v1.0.0-joss as version

editorialbot commented 9 months ago

Done! version is now v1.0.0-joss

mikemahoney218 commented 9 months ago

@editorialbot set 10.5281/zenodo.10658773 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10658773

mikemahoney218 commented 9 months ago

@editorialbot recommend-accept

( :crossed_fingers: )

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.18637/jss.v059.i10 is OK
- 10.5281/zenodo.10564837 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5016, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

mikemahoney218 commented 9 months ago

🎉 With everything looking good on my end, it's time for me to hand this back to the EiC for last steps. Thanks @rsh52 for the submission, and thank you so much to @spgarbet and @RhysPeploe for reviewing!

openjournals / joss-reviews