[REVIEW]: OpenTera: A Framework for Telehealth Applications

[editorialbot]

Submitting author: !--author-handle-->@doumdi<!--end-author-handle-- (Dominic Létourneau) Repository: https://github.com/introlab/opentera Branch with paper.md (empty if default branch): main Version: v1.2.4-zenodo Editor: !--editor-->@galessiorob<!--end-editor-- Reviewers: @Rocsg, @tmickleydoyle Archive: 10.5281/zenodo.10078847

Status

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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

@Rocsg & @NoujoudNader, 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 @galessiorob 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 @Rocsg

📝 Checklist for @NoujoudNader

📝 Checklist for @tmickleydoyle

[editorialbot]

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

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[editorialbot]

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

OK DOIs

- 10.1109/ICVR.2017.8007524 is OK
- 10.1109/EMBC.2017.8037404 is OK
- 10.1007/s12553-021-00636-5 is OK
- 10.1145/514183.514185 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.77 s (752.0 files/s, 150764.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         390          10726           5491          46610
JavaScript                      40           2407           3006          14472
JSON                            13              1              0           8994
CSS                             16           1154            140           7248
SVG                              3              0              0           2737
PO File                         10           1400           2829           2514
Markdown                        42            818              0           2362
HTML                            22            169             90           1412
YAML                             5             62             10            327
CMake                           10             80             84            247
INI                              4             40              0            201
reStructuredText                 7             27             70             51
TeX                              1              5              0             50
Bourne Shell                     7              3              1             37
Mako                             2             14              0             34
Dockerfile                       2             21             31             33
DOS Batch                        3              9              1             32
make                             1              4              7              9
SQL                              1              1              0              8
-------------------------------------------------------------------------------
SUM:                           579          16941          11760          87378
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1321

[editorialbot]

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

[galessiorob]

@Rocsg, @NoujoudNader - thank you so much for volunteering to review this paper and software!

Please comment @editorialbot generate my checklist to generate your review checklist, and let me know if you have any questions on how to proceed. I'm really looking forward to working with you. 🚀

[NoujoudNader]

Review checklist for @NoujoudNader

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/introlab/opentera?
• [x] 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 (@doumdi) 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
• [ ] 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

• [x] 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

• [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?

[galessiorob]

Hey @NoujoudNader thanks for getting started on generating your checklist, please let me know if you have any questions.

@Rocsg let me know if you run into any issues to generate and get started on yours. Thanks!

[galessiorob]

Checking in again, I just emailed @NoujoudNader and @Rocsg to get their ETAs, I might send out a few additional review invites just in case.

[Rocsg]

Review checklist for @Rocsg

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/introlab/opentera?
• [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 (@doumdi) 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?

[galessiorob]

@NoujoudNader glad you figured out the checklist! Let me know if you run into any other issues.

@Rocsg thanks for getting started!

[Rocsg]

@galessiorob , I have a tough point, let's talk about this "in the open". I have to consider the "diff" between the previous OpenTera paper (feb. 2022) and the actual one. To me, this is not stated sharply in the paper (there is no "Here is the V2", or that kind of statement).

Given the repo contribution flow, there had been some serious job on the repo meanwhile, which match with the "rule of thumb". But for now I mainly consider the fact that opentera should now be published with JOSS as this is an opportunity to give it to a "Tech-validating" audience, which is complementary to the Springer stuff "Health and Tech", with maybe medics reviewers more involved to apply than to evaluate the Tech'.

I open this point with you as, to me, this point is more a matter for an editor, rather than a matter for a reviewer. Accordingly I mark my last check (substantial scholar effort), and let you see about it. If you want me to say something to the authors to go into that direction, I can remove my mark and ask. Or if you want to give me a clue or a way to read this point, It's welcome.

See you ! Romain

[galessiorob]

Thanks for your comment and for your review @Rocsg - I'll review it carefully considering your points and get back to you.

@doumdi Ould you mind expanding a bit as a comment as to why there's no "V2" mention on this current paper or an indication that this is an evolution from the original one? Thanks

[doumdi]

@galessiorob @Rocsg I am not sure I understand the V2 vs original version. The paper in the "main" branch did not change since our submission three months ago. Of course, development continues on OpenTera and we did merge some bug fixes and Python packages upgrade fix in the main branch. Documentation / features did not change however. How can I be of assistance to make sure you have everything you need ?

[galessiorob]

Thanks for chiming in @doumdi, I think (please correct me if wrong @Rocsg) the question came up due to the previous publishing of the software in 2022 and JOSS's guidelines that ask to disclose if co-publishing. From my purview, as long as this is disclosed and the software is a significant contribution, which in this case it is, then we are good to review and publish this paper (see: "JOSS considers submissions for which the implementation of the software itself reflects a substantial scientific effort" in the guidelines.)

I will check with the EiC about this to confirm shortly.

[Rocsg]

@galessiorob I think you understood exactly my point. @doumdi when I talk about "V2", I mean positioning the diff in OpenTera relatively to the version disclosed in the feb. 2022 paper in the health and Tech. journal. As a rule of thumb, I "measured" the activity of the github repo between the versions (since feb. 2022, and there is), and considered the diff between the journals in terms of scope, which can be substantial. From my experience, I published a paper in Bioinformatics which was NOT studied at all, and another one in JOSS which was really studied by the reviewers. So these publishing paths are significantly different, and complementary, to me. And I let this point to the editor representative, as I believe I am not in charge of that kind of questions in this process.

See you

Romain

[galessiorob]

@editorialbot ping track-eic

[editorialbot]

:bellhop_bell::exclamation:Hey @openjournals/bcm-eics, this submission requires your attention.

[doumdi]

@Rocsg, @galessiorob thanks for the clarifications. The focus of the two papers is different. The first paper aimed to describe specific applications related to COVID with a preliminary implementation of OpenTera. The current paper presents the implementation and design choices for a more generic OpenTera framework with a focus on open source implementation. Code quality, documentation, examples and usability have been greatly improved between these versions. There is little overlap between the two papers.

[galessiorob]

Thanks for clarifying above @doumdi, and understood about the different scopes and applications. I think even just adding a line that acknowledges the previous publication and, as @Rocsg mentions, explains the "diff", just like you did in your comment above, would be very beneficial as there might be users that look up this paper or the package by name and could be confused by the previous one surfacing. I don't see any conflict in having both publications, but I do think it's worth mentioning them.

@NoujoudNader mind updating us with the ETA for your review - thanks!

[doumdi]

@galessiorob from what I understand, you are suggesting to add more information in the JOSS paper clarifying the difference between the two papers. I would change this sentence and clarify as mentioned above: "OpenTera has been deployed for robot teleoperation during COVID [@panchea_opentera_2022] and is currently used for multiple rehabilitation projects." Should I make the change in another branch of the project in the joss-paper directory ? I am a little confused about the process here and what I need to do. Maybe this justification needs to be written somewhere else?

[galessiorob]

@editorialbot generate pdf

[editorialbot]

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

[galessiorob]

@doumdi yes, I think that the clarification you mention is enough to clarify the difference between the two papers. You can make the change either in a branch or since it's so small and only for the text, directly on your main since you're the author. Editors and reviewers will make suggested changes in issues in your repo, or if they are specific changes in a branch if you are okay with this type of review.

[galessiorob]

@doumdi I put together a few edit suggestions for the paper here, please adapt as you see fit. I have emailed @NoujoudNader to ask what their ETA on the review is.

[galessiorob]

@doumdi checking in on the paper, any updates or changes?

@NoujoudNader please update us on your ETA, thanks.

[doumdi]

@galessiorob, Thank you for the review and suggestions. I am working in the "joss-paper-review" branch. You can see the full changes here.

[doumdi]

@galessiorob, Do you have an update for the review of the paper ? Thank you!

[Kevin-Mattheus-Moerman]

@galessiorob please pick this up and continue to work with the authors/reviewers to proceed.

[Kevin-Mattheus-Moerman]

@doumdi it looks like @galessiorob had suggestions, and asked you to update the paper. Did you work on those aspects? Could you respond to @galessiorob ?

[Kevin-Mattheus-Moerman]

@NoujoudNader thanks for agreeing to review for JOSS. The editors have asked for an update from you regarding this review. It has been some time since you've checked in here. Please can you pick this review up at your earliest convenience? Unfortunately we need to remove you as a reviewer and recruit an alternative reviewer if you are no longer available.

[doumdi]

@Kevin-Mattheus-Moerman @galessiorob, Yes I have integrated the suggestions from @Rocsg and @galessiorob in this branch as I already mentioned in my comment August 29th. @galessiorob reacted to this post with a heart. Changes can be tracked here. I though the only thing missing was @NoujoudNader's review, that is why I asked for an update three weeks ago. Did I miss something else?

Best Regards,

Dominic

[Kevin-Mattheus-Moerman]

@doumdi okay thanks for the update. I wasn't sure if a full response was needed, and I think I missed the "heart" response too. Anyway, thanks, and good to hear that from your end things are all set.

[galessiorob]

@editorialbot generate pdf

[editorialbot]

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

[galessiorob]

@doumdi I apologize for the very late response! Thank you for reviewing the suggestions and adopting those that help.

IMO this paper is ready to be published, however, @NoujoudNader has been unresponsive and I'm not confident we'll get their review. I have asked @tmickleydoyle to do an additional review, and after that is completed we should be good to go.

Thanks for your patience, and I apologize again for the delayed reply.

[galessiorob]

@editorialbot add @tmickleydoyle as reviewer

[editorialbot]

@tmickleydoyle added to the reviewers list!

[galessiorob]

@tmickleydoyle thank you so much for volunteering to review this paper! Please let me know if you have any questions.

[tmickleydoyle]

Hey krewe 👋 I will prioritize this work this week or next. Feel free to ping me for updates 🙇

[tmickleydoyle]

@galessiorob 👋 What is the best way to generate my checklist for reviewing this body of work? Thank you 🙇

[galessiorob]

@tmickleydoyle you can comment @editorialbot generate my checklist 🙇‍♀️

[tmickleydoyle]

Review checklist for @tmickleydoyle

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/introlab/opentera?
• [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 (@doumdi) 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?

[tmickleydoyle]

Hey team 👋 Great work! Two notes:

• The installation process is more complex and requires a decent knowledge of a lot of technologies. It would be great if there were a much simpler way to deploy this application, maybe via Docker? I am putting myself in the shoes of a semi-technical IT person at a medical center, and the number of steps required to install this software would be challenging. There are a lot of opportunities for errors, and unless the user is well versed in digesting error logs, they might get tripped up with the install.
• The writing in the paper might need another pass. For English readers, several sections could be read more smoothly. I am happy to take a pass at editing if you all would like. I will not change the references or the essence of the paper. Let me know! If you do not think this is a necessary step, I can be convinced to check the Quality of writing box.

Cheers 🎉

[tmickleydoyle]

☝️ cc @galessiorob @doumdi

[doumdi]

@tmickleydoyle Thank you for the quick response and the review. Please make sure you make your review (and pull request) on this branch : https://github.com/introlab/opentera/tree/joss-paper-review. Meanwhile, we will update the documentation with Docker instructions. Regards, Dominic

[tmickleydoyle]

@doumdi, do you mind sending over a version of the paper I can edit? Thank you

[doumdi]

@tmickleydoyle You can download the files by clicking here: https://github.com/introlab/opentera/tree/joss-paper-review/joss-paper, paper.md, paper.bib. Is this working for you ?

[tmickleydoyle]

Works on my phone! Thank you 😌

[tmickleydoyle]

I will prioritize this work 🙇