[REVIEW]: Biosensor Framework: A C# Library for Affective Computing

whedon commented 3 years ago

Submitting author: @wsarce (Walker Arce) Repository: https://github.com/Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework Version: 1.0.0 Editor: @osorensen Reviewer: @professoralkmin, @AustinTSchaffer Archive: 10.5281/zenodo.5161984

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Reviewer instructions & questions

@professoralkmin & @AustinTSchaffer, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @professoralkmin

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wsarce) 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

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 and who the target audience is?
[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?

Review checklist for @AustinTSchaffer

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@wsarce) 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

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 and who the target audience is?
[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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @professoralkmin, @AustinTSchaffer it looks like you're currently assigned to review this paper :tada:.

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whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.13 s (327.2 files/s, 87353.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C#                              28            489           1410           3326
Markdown                         5           1266              0           2339
XML                              4             21              0           1569
MSBuild script                   3              7              0            349
TeX                              1              0              0            170
-------------------------------------------------------------------------------
SUM:                            41           1783           1410           7753
-------------------------------------------------------------------------------

Statistical information for the repository 'b80f3946c7962bd08b95fbd7' was
gathered on 2021/07/06.
No commited files with the specified extensions were found.

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3242969.3242985 is OK
- 10.1109/tits.2005.848368 is OK
- 10.1007/978-3-319-91262-2_16 is OK
- 10.1145/3027063.3053140 is OK
- 10.1016/j.trf.2019.09.015 is OK
- 10.24251/hicss.2020.456 is OK
- 10.37896/jxu15.3/018 is OK
- 10.1109/10.979357 is OK
- 10.3390/s121217620 is OK
- 10.1080/19315864.2019.1595233 is OK
- 10.1002/aur.1433 is OK
- 10.1145/3136755.3143025 is OK
- 10.1089/cyber.2019.0093 is OK
- 10.1186/s12984-015-0010-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

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

osorensen commented 3 years ago

@AustinTSchaffer, regarding your question in the other thread. Here is the review issue, and hopefully the information above will help get you started. Feel very welcome to contact me if you have any more questions about the review process.

whedon commented 3 years ago

:wave: @professoralkmin, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @AustinTSchaffer, please update us on how your review is going (this is an automated reminder).

professoralkmin commented 3 years ago

Looks good to me, and I have sure this work presents a genuine academic contribution.

So as reviewer, I recommend acceptance.

osorensen commented 3 years ago

Thanks for completing your review, @professoralkmin!

AustinTSchaffer commented 3 years ago

Hey all, sorry for not giving a review yet. I've set aside some time for this tomorrow.

On Fri, Jul 30, 2021, 2:11 PM Øystein Sørensen @.***> wrote:

Thanks for completing your review, @professoralkmin https://github.com/professoralkmin!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3455#issuecomment-890067111, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD3PHG2X3Q5EHFJCXECQG7TT2LTOJANCNFSM474QMZKA .

AustinTSchaffer commented 3 years ago

Testing: I don't see any unit tests or integration tests.

Installation: The project mentions NuGet and Unity for installation, though provides few details. The Readme should probably at least link to the project's page on NuGet, which provides additional help with how to get the package installed with a variety of tools. Also, the package itself is a .NET Standard 2.0 project, but the provided examples are .NET Framework 4.7, which makes it hard to tell if this project only works on Windows, or if it can be used on Mac or Linux.

This work appears to satisfy all of the requirements of acceptance, except for automated tests. Unless automated testing is a strict requirement, and barring minor confusions with installation, I recommend acceptance.

osorensen commented 3 years ago

Thanks for your review @AustinTSchaffer!

Regarding unit tests, the Review criteria say the following:

Good: An automated test suite hooked up to continuous integration (GitHub Actions, Circle CI, or similar) OK: Documented manual steps that can be followed to objectively check the expected functionality of the software (e.g., a sample input file to assert behavior) Bad (not acceptable): No way for you, the reviewer, to objectively assess whether the software works

@wsarce, could you please elaborate on how the reviewers can test the software, and if necessary, add additional unit test?

@wsarce, please also answer the issue @AustinTSchaffer raised about Installation.

wsarce commented 3 years ago

@osorensen, I've added a third example project that tests the affective computing tasks without the need for an attached body-worn sensor. It processes the WESAD dataset that is provided in the Dataset folder of the repo and reports the results in the Console output.

@AustinTSchaffer, The NuGet package link as well as installation CLI command has been added to the readme. This project was written to be OS agnostic, .NET Standard 2.0 should run on Windows, Linux, and MacOS. The examples are .NET Framework 4.7 to utilize the Console and were written on Windows 10. Instructions for installing Unity package has been added to the readme as well.

Let me know if there are any other concerns. Thank you for the feedback and your time!

osorensen commented 3 years ago

Thanks for the update @wsarce.

@AustinTSchaffer, if you find the tests/examples described in the comment by @wsarce satisfactory, please tick off the last box on the reviewer checklist.

AustinTSchaffer commented 3 years ago

LGTM!

osorensen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

osorensen commented 3 years ago

@wsarce, the paper is well written, but I noted the following issues which need to be fixed before acceptance.

On page 1, line 21, there should be a full stop (i.e., ".") at the end of the paragraph.
On page 1, line 40, and page 2, line 1, please make sure the parenthesized references are in alphabetic order.
On page 2, line 1, please fix the reference "gjoreski2016continuous".
On page 2, line 51, please make sure the reference "Jennifer Anne Healey, 2000" has the format (Last name, Year).
On page 2, line 77, the name is missing from the reference.
On page 4, lines 121-125: the citation does not appear correctly.
On page 4, lines 130-132: please add DOI 10.2196/13725.
On page 5, lines 150-153: please make sure WESAD is written in capital letters. You can fix this by putting curly braces around the word "wesad" in your source .bib file, i.e., "{WESAD}".

osorensen commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3242969.3242985 is OK
- 10.1109/tits.2005.848368 is OK
- 10.1007/978-3-319-91262-2_16 is OK
- 10.1145/3027063.3053140 is OK
- 10.1016/j.trf.2019.09.015 is OK
- 10.24251/hicss.2020.456 is OK
- 10.37896/jxu15.3/018 is OK
- 10.1109/10.979357 is OK
- 10.3390/s121217620 is OK
- 10.1080/19315864.2019.1595233 is OK
- 10.1002/aur.1433 is OK
- 10.1145/3136755.3143025 is OK
- 10.1089/cyber.2019.0093 is OK
- 10.1186/s12984-015-0010-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

wsarce commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

wsarce commented 3 years ago

@osorensen, I think I addressed all of the changes needed. Let me know if I missed anything. Thank you!

osorensen commented 3 years ago

Thank you @wsarce! I noticed that also the paper Gjoreski et al. (2016) is missing a doi. Please add https://doi.org/10.1145/2968219.2968306 to this one.

wsarce commented 3 years ago

@osorensen, the bib file has been updated. Thank you!

osorensen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

osorensen commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3242969.3242985 is OK
- 10.1109/tits.2005.848368 is OK
- 10.1007/978-3-319-91262-2_16 is OK
- 10.1145/3027063.3053140 is OK
- 10.1016/j.trf.2019.09.015 is OK
- 10.2196/13725 is OK
- 10.24251/hicss.2020.456 is OK
- 10.37896/jxu15.3/018 is OK
- 10.1109/10.979357 is OK
- 10.3390/s121217620 is OK
- 10.1080/19315864.2019.1595233 is OK
- 10.1002/aur.1433 is OK
- 10.1145/3136755.3143025 is OK
- 10.1089/cyber.2019.0093 is OK
- 10.1186/s12984-015-0010-z is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1145/2968219.2968306 is INVALID because of 'https://doi.org/' prefix

osorensen commented 3 years ago

@wsarce, please see the error message from @whedon above. The DOI 10.1145/2968219.2968306 probably has an incorrect format in your .bib file.

wsarce commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3242969.3242985 is OK
- 10.1109/tits.2005.848368 is OK
- 10.1007/978-3-319-91262-2_16 is OK
- 10.1145/2968219.2968306 is OK
- 10.1145/3027063.3053140 is OK
- 10.1016/j.trf.2019.09.015 is OK
- 10.2196/13725 is OK
- 10.24251/hicss.2020.456 is OK
- 10.37896/jxu15.3/018 is OK
- 10.1109/10.979357 is OK
- 10.3390/s121217620 is OK
- 10.1080/19315864.2019.1595233 is OK
- 10.1002/aur.1433 is OK
- 10.1145/3136755.3143025 is OK
- 10.1089/cyber.2019.0093 is OK
- 10.1186/s12984-015-0010-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

wsarce commented 3 years ago

@osorensen, okay, now I think I got everything. Sorry about that!

osorensen commented 3 years ago

Thanks @wsarce! Before we proceed, could you please do the following?

Make a tagged release of the software.
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.

wsarce commented 3 years ago

@osorensen, alright, I got it working. The DOI from Zenodo is: 10.5281/zenodo.5161984. All of the metadata looks correct and a citation file was generated for the repo. Let me know if anything doesn't look right. Thank you!

osorensen commented 3 years ago

@whedon set 10.5281/zenodo.5161984 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5161984 is the archive.

osorensen commented 3 years ago

@whedon set 1.0.0 as version

whedon commented 3 years ago

OK. 1.0.0 is the version.

osorensen commented 3 years ago

@wsarce, I noticed that the title of the zenodo archive is "Munroe-Meyer-Institute-VR-Laboratory/Biosensor-Framework: Biosensor-Framework" whereas the title of the paper is "Biosensor Framework: A C# Library for Affective Computing". Could you please edit the title of the archive so it matches the paper?

wsarce commented 3 years ago

@osorensen, the title of the archive has been updated.

osorensen commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

osorensen commented 3 years ago

@wsarce, I noticed one reference which does not appear correctly, cf. line 37 on page 1 of the article proof.

wsarce commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.1145/3242969.3242985 is OK
- 10.1109/tits.2005.848368 is OK
- 10.1007/978-3-319-91262-2_16 is OK
- 10.1145/2968219.2968306 is OK
- 10.1145/3027063.3053140 is OK
- 10.1016/j.trf.2019.09.015 is OK
- 10.2196/13725 is OK
- 10.24251/hicss.2020.456 is OK
- 10.37896/jxu15.3/018 is OK
- 10.1109/10.979357 is OK
- 10.3390/s121217620 is OK
- 10.1080/19315864.2019.1595233 is OK
- 10.1002/aur.1433 is OK
- 10.1145/3136755.3143025 is OK
- 10.1089/cyber.2019.0093 is OK
- 10.1186/s12984-015-0010-z is OK

MISSING DOIs

- None

INVALID DOIs

- None

wsarce commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

wsarce commented 3 years ago

@osorensen, that reference issue should be fixed.

osorensen commented 3 years ago

@whedon recommend-accept

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