[REVIEW]: CRSocket: A web app component facilitating the administration of digital trials from a separate device

[editorialbot]

Submitting author: @henrikdvn (Henrik Dvergsdal)
Repository: https://github.com/henrikdvn/CRSocket
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @britta-wstnr
Reviewers: @rabdill, @lukaszjablonski
Archive: 10.6084/m9.figshare.24009225.v3

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3becacf85e23eb6be092c08148cb4be2"><img src="https://joss.theoj.org/papers/3becacf85e23eb6be092c08148cb4be2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3becacf85e23eb6be092c08148cb4be2/status.svg)](https://joss.theoj.org/papers/3becacf85e23eb6be092c08148cb4be2)

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

@rabdill & @lukaszjablonski, 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 @britta-wstnr 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 @lukaszjablonski

📝 Checklist for @rabdill

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1427.8 files/s, 197578.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13            819            748           3059
HTML                            28            229              0           2194
PHP                             20            276            284            852
Markdown                         3            143              0            619
TeX                              1              9              0            152
CSS                              3             50              4             87
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            69           1527           1040           6981
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.1016/j.neuroimage.2022.119241 is OK
- 10.1371/journal.pone.0260695 is OK
- 10.1111/desc.13193 is OK
- 10.1016/j.infbeh.2021.101649 is OK
- 10.1080/15248372.2015.1061528 is OK
- 10.3389/fpsyg.2016.01021 is OK
- 10.1002/acp.3569 is OK
- 10.1177/0894439319851503 is OK
- 10.3233/JAD-160545 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1079

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[britta-wstnr]

Hello again! 👋

@rabdill @lukaszjablonski
FYI @henrikdvn

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to #5658 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 We aim for the review process to be completed within about 4-6 weeks* but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

*I do appreciate of course that it is summer vacation time 🏖️ - also a heads-up that I will have limited availability myself for the next two weeks.

[lukaszjablonski]

Review checklist for @lukaszjablonski

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/henrikdvn/CRSocket?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@henrikdvn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[rabdill]

Review checklist for @rabdill

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/henrikdvn/CRSocket?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@henrikdvn) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[rabdill]

The short version: This application uses PHP 7.4, which is no longer supported. Is that an issue, @britta-wstnr?

The longer version:
This is interesting work and I'm making my way through the review checklist, but I wanted to raise a question about the use of PHP: The documentation currently states that CRSocket can run on "any web server that supports PHP 7.4 and common Apache HTTP functionality... Migration to PHP 8 will require some minor adjustments."

PHP 7.4 left active support in 2021, and, as of last November, is no longer receiving even critical security patches. I don't see any journal policy about this, but I'm unsure of whether it's a good idea to publish a software paper that relies on a platform that is explicitly no longer supported, particularly when it is intended to be the foundation of larger applications that 1) will probably take a little while to develop, and 2) will probably be used for months or years at a time. So it's a little outdated right now, but it will be considerably farther removed by the time someone integrates CRSocket into their application and deploys it for a study.

On the other hand, most online PHP applications are still using PHP 7.4, so this is a common issue—indeed, using a secure and supported version of PHP seems like the more unusual situation. So sure, it isn't best practice, but it's not rare, and there's no requirement that CRSocket applications actually communicate over the internet instead of a local network.

Looking at past reviews, I can't find many examples of situations like this: A 2020 review noted a similarly unsupported version of PHP, but that wasn't the deciding factor in its eventual rejection. A reviewer noted that a 2017 submission was using Python 2.7; the submission was accepted, but Python 2 was not yet end-of-life. This was also raised in another 2019 review, but Python 2 was not EOL then either, and the issues raised were unrelated.

Anyway, I'm sorry if this is the wrong format for a question like this, but I didn't want to open an issue in the submitting repository for updating PHP if this was just an editorial call that I'm not supposed to be involved in.

[henrikdvn]

Regarding the PHP version: There was an issue with version 8.0 at some point, but it now seems to work well with 8.2.5 which is the latest supported by my ISP. Haven't tested extensively, and I don't know about all versions in between, but I have now taken the chance to state that it supports "7.4 or later".

[britta-wstnr]

Hi @radbill,

thanks for raising this - and thanks for looking into comparable cases as well. Indeed, JOSS does not have a requirement for this. I raised this with the EiC team, and there the major point was about whether the software can be easily installed and run.
Looking at those points and also at @henrikdvn's answer, what do you think about it now, @rabdill ?

Thanks for your thorough work!
Britta

[lukaszjablonski]

I think it's OK if it is not tested on all available PHP versions and if it works with still supported 8.2.5 it should be fine.

@henrikdvn, maybe you could add note in the documentation on which versions of PHP it was tested?

[henrikdvn]

@henrikdvn, maybe you could add note in the documentation on which versions of PHP it was tested?

Done

[henrikdvn]

@rabdill, @lukaszjablonski
Hopefully, I have now addressed all issues mentioned above

[lukaszjablonski]

@henrikdvn: Just not to open an issue for something that small, there is a typo in CONTRIBUTING.md: is "respoind", should be "respond".

[henrikdvn]

"respoind", should be "respond".

Fixed :)

[henrikdvn]

Issue #3 fixed

[lukaszjablonski]

@henrikdvn: In paper.md please change "eg." to "e.g." and "well defined set" to "well-defined set".

[lukaszjablonski]

@henrikdvn: In paper.md I would also recommend checking consistency between terms in main text and figure: "CRSocket" vs "crSocket ", "CREvent" vs "crEvent", "clientid" vs "clientId". One could also try to use for those terms inline code quotes markup in main text but I don't know what is JOSS style guide saying here (@britta-wstnr, would ytou know?).

[henrikdvn]

Have fixed spelling mistakes, added a figure caption and included a section on basic naming conventions in the paper and on the Terminology page.

[britta-wstnr]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[britta-wstnr]

@editorialbot set 10.6084/m9.figshare.24009225.v3 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.24009225.v3

[britta-wstnr]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[britta-wstnr]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[britta-wstnr]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1016/j.neuroimage.2022.119241 is OK
- 10.1371/journal.pone.0260695 is OK
- 10.1111/desc.13193 is OK
- 10.1016/j.infbeh.2021.101649 is OK
- 10.1080/15248372.2015.1061528 is OK
- 10.3389/fpsyg.2016.01021 is OK
- 10.1002/acp.3569 is OK
- 10.1177/0894439319851503 is OK
- 10.3233/JAD-160545 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[britta-wstnr]

Hi @henrikdvn - I added the new DOI and all looks good to me now - handing this off to the EiC team for acceptance
@rabdill and @lukaszjablonski - thank you very much for your work in reviewing this!
Thanks everyone for a smooth process 🙏 🌱

PS: @henrikdvn I could not find you in our reviewer database - we'd be very grateful if you considered signing up to pay it forward ✨ you can do that here: https://reviewers.joss.theoj.org/join

[britta-wstnr]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.neuroimage.2022.119241 is OK
- 10.1371/journal.pone.0260695 is OK
- 10.1111/desc.13193 is OK
- 10.1016/j.infbeh.2021.101649 is OK
- 10.1080/15248372.2015.1061528 is OK
- 10.3389/fpsyg.2016.01021 is OK
- 10.1002/acp.3569 is OK
- 10.1177/0894439319851503 is OK
- 10.3233/JAD-160545 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4521, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[henrikdvn]

Thanks again @rabdill, @lukaszjablonski and @britta-wstnr. I have now signed up as a reviewer. Don't feel like an expert on paper writing, but I'll do my best ツ

[lukaszjablonski]

@britta-wstnr and @henrikdvn, thank you for the opportunity to review that one for JOSS!

[oliviaguest]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Dvergsdal
  given-names: Henrik
  orcid: "https://orcid.org/0000-0002-8515-1670"
doi: 10.6084/m9.figshare.24009225.v3
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Dvergsdal
    given-names: Henrik
    orcid: "https://orcid.org/0000-0002-8515-1670"
  date-published: 2023-09-08
  doi: 10.21105/joss.05658
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5658
  title: "CRSocket: A web app component facilitating the administration
    of digital trials from a separate device"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05658"
  volume: 8
title: "CRSocket: A web app component facilitating the administration of
  digital trials from a separate device"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05658 joss-papers#4536
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05658
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[britta-wstnr]

Thanks @oliviaguest !

[oliviaguest]

[Sorry, I had to leave my computer for a small emergency, and then it was the weekend.]
Huge thanks to the reviewers @rabdill, @lukaszjablonski and editor @britta-wstnr! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to @henrikdvn ! 🥳 🍾

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05658/status.svg)](https://doi.org/10.21105/joss.05658)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05658">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05658/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05658/status.svg
   :target: https://doi.org/10.21105/joss.05658

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss