[REVIEW]: Beiwe: A data collection platform for high-throughput digital phenotyping

[whedon]

Submitting author: @jponnela (Jukka-Pekka Onnela)
Repository: https://github.com/onnela-lab/beiwe-backend
Version: v1.0.0
Editor: @fboehm
Reviewer: @Tam-Pham, @erik-whiting
Archive: 10.5281/zenodo.5758811

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e7139705f3381770c3981adf7b438001"><img src="https://joss.theoj.org/papers/e7139705f3381770c3981adf7b438001/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e7139705f3381770c3981adf7b438001/status.svg)](https://joss.theoj.org/papers/e7139705f3381770c3981adf7b438001)

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

@Tam-Pham & @erik-whiting, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @Tam-Pham

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 repository url?
• 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 (@jponnela) 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

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 and who the target audience is?
• 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?

Review checklist for @erik-whiting

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 repository url?
• 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 (@jponnela) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Tam-Pham, @erik-whiting it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1177/2167702621993857 is OK
- 10.1002/mus.27110 is OK
- 10.1097/phm.0000000000001506 is OK
- 10.1097/SLA.0000000000004487 is OK
- 10.1245/s10434-020-09004-5 is OK
- 10.1001/jamasurg.2019.4702 is OK
- 10.1002/acn3.770 is OK
- 10.1016/j.wneu.2019.01.297 is OK
- 10.1038/s41746-018-0022-8 is OK
- 10.1200/cci.17.00149 is OK
- 10.1038/s41386-018-0030-z is OK
- 10.1038/s41537-017-0038-0 is OK
- 10.1038/npp.2016.7 is OK
- 10.2196/mental.5165 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.52 s (230.4 files/s, 48979.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      97           4837           6743          27061
Python                         184           3535           3412          14938
CSS                             11             98            221           8153
HTML                            41            371             57           3573
YAML                             2             11             33            393
SVG                              1              0              0            288
Bourne Shell                     4             71             72            272
Markdown                         4             53              0            182
TeX                              1             14              0            151
JSON                             6              0              0             83
-------------------------------------------------------------------------------
SUM:                           351           8990          10538          55094
-------------------------------------------------------------------------------


Statistical information for the repository 'eef02a8bf0564ffed26ceae7' was
gathered on 2021/06/25.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Aaron Klein                    161          7752           4993            9.23
Ali Abdullah                     3            29              7            0.03
Alvin Siu                       44          3181           1181            3.16
Caleb                           78          2853           1762            3.34
Caleb-Dixon                      3           331              9            0.25
Chris McCarthy                   9           290             98            0.28
Daniel Norton                    6             9              9            0.01
Dor Samet                      142         16833            494           12.55
Eli Jones                     1384         39004          25507           46.73
Erinn Looney-Triggs              8            77             17            0.07
Jake Klingensmith                3            13             12            0.02
Josh Zagorsky                    6            41             56            0.07
Keary Griffin                   17           147             38            0.13
Kevin Fan                        7           263             48            0.23
Leila                            1            10              5            0.01
Leila Minowada                  11          1071            509            1.14
Sean Esterkin                   35          1135            288            1.03
Teh Beebles                      1             1              1            0.00
kfan                            18           236            116            0.25
kfantastic                      24         10750            257            7.97
leila                            9           809            388            0.87
tjaeni01                        59          1609            626            1.62
zagorsky                       211         13426           1772           11.01

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Aaron Klein                1309           16.9         45.3                8.63
Ali Abdullah                  9           31.0         37.7                0.00
Alvin Siu                  2648           83.2         15.6               12.84
Caleb                       740           25.9          8.5                7.97
Caleb-Dixon                 267           80.7          9.0                6.74
Chris McCarthy                3            1.0         83.8                0.00
Daniel Norton                 1           11.1         17.0                0.00
Dor Samet                 16259           96.6         82.0               22.92
Eli Jones                 15573           39.9         26.6               14.49
Erinn Looney-Triggs          74           96.1         23.8                4.05
Jake Klingensmith             8           61.5         24.3                0.00
Josh Zagorsky                11           26.8          4.2               45.45
Keary Griffin                42           28.6         62.5                2.38
Kevin Fan                    12            4.6         49.6                0.00
Sean Esterkin               509           44.8         36.6                5.11
kfan                      10371         4394.5         82.2               16.58
leila                       949          117.3         24.2               12.96
tjaeni01                    693           43.1         15.5                9.09
zagorsky                  11048           82.3         70.5                8.08

[whedon]

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

[fboehm]

@Tam-Pham and @erik-whiting - this is the review thread. Please conduct your reviews with a focus on the checklist items above. Please use the checklists to record which items are satisfied. For those items that you can't check right away, please specify in this thread what the authors must do to satisfy the criteria. Thanks again!

[erik-whiting]

hi @fboehm , quick question for you. Do I just start making issues/comments on their repo as I go through review or should I make all issues at one time? Also, do I need to introduce myself to them or anything? I've never done a none-blind review before so just want to make sure I'm up-to-date on procedure and etiquette.

[fboehm]

hi, @erik-whiting - thank you for the questions. I suggest that you make comments and open issues as you proceed through the review checklist. There's no need to wait for everything at once. I also suggest that you link from this "review" thread to any issues that you open on the submission repository, ie, the beiwe repo. As long as you do that, I think that no introduction is needed. Thanks again for asking these questions. I know that the JOSS review format can feel a little foreign at first.

[erik-whiting]

I opened this issue as my review to their paper

[erik-whiting]

I opened this issue as my review to their documentation and installation.

I cannot review the functionality portion of the checklist until the installation issues are fixed or someone offers a workaround. Otherwise, I'm done with my first round of reviewing.

[fboehm]

Thanks so much, @erik-whiting!

[whedon]

👋 @Tam-Pham, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @erik-whiting, please update us on how your review is going (this is an automated reminder).

[erik-whiting]

@erik-whiting, please update us on how your review is going (this is an automated reminder).

I opened two issues, one for documentation and one for the paper. I cannot review the functionality section until the documentation issues are addressed

[Tam-Pham]

@Tam-Pham, please update us on how your review is going (this is an automated reminder).

I'm currently following the issue opened by @erik-whiting regarding the development setup (onnela-lab/beiwe-backend#210). I too ran into the same problem that @erik-whiting faced. Erik has cleverly summarized those in the issue that was opened and hence I will wait till those are addressed before continuing with my review.

[fboehm]

@jponnela - Do you have a sense of when your team will implement the suggested fixes? Thanks!

[fboehm]

I sent the following email message to the submitting author's email address today:

Hi, Professor Onnela,

I'm writing as a JOSS editor to update you on the status of your submission (Beiwe: A data collection platform for high-throughput digital phenotyping) to Journal of Open Source Software.

It seems that there have been no responses from you and your team in more than a month. Please begin to address the issues raised by the reviewers and indicate progress on them before September 30, 2021.

You and your team should feel free to discuss the issues raised by reviewers in the review thread: #3417

If this timeline seems unreasonable, please indicate what would be a reasonable timeline.

Thank you,
fred

[fboehm]

I followed up with this email message:

Professor Onnela, 
I need to amend the earlier statement to say that, if no progress is noted by September 30, we'll need to reject the submission. 
Thanks for your attention to this. 
fred

[fboehm]

Today I sent this email to Eli Jones, a collaborator of the submitting author. I copied the submitting author, too.

Hi, Eli,

Thanks so much! I really appreciate your enthusiasm and look forward to guiding you through the review process.

The only deadline is for, at a minimum, demonstration of further discussion - on the Github issue #3417 and on the issues that the reviewers have opened on your repository. If this process can begin as soon as possible, and no later than Sept 30, then we can continue with the review and ultimately publish the submission.

Ideally, we'd like to see the review completed within about 6 to 8 weeks. We do have some flexibility on the duration of the review so that, as long as continuous progress is made, there won't be additional deadlines that could lead to rejection of the submission. The only reason for imposing the Sept 30 deadline was the apparent inactivity on the review and a desire to not unnecessarily prolong the involvement of our reviewers.

Additionally, I encourage both you and our reviewers to avoid email communications in favor of posting communications on the "review" issue on Github. This way, we can have a more transparent record of what is said. We'll also then have a record that's more accessible. In keeping with that spirit, I'll post the text of this email to the review thread right away.

Thanks again!

fred

PS - please feel free to ask me any questions along the way. My github username is fboehm, so mentioning me with an at sign (eg, @fboehm) in the issue will get my attention.

[fboehm]

@biblicabeebli @jponnela - we should try to wrap up the final steps soon. Please let me know if you have any questions.

[jponnela]

Hi @fboehm, I completed the remaining steps, i.e., made a GitHub release and created an archive of the repo using Zenodo. I also added the Zenodo badge to the jp/paper branch. @biblicabeebli if you're ok to merge jp/paper to main, we should be all set!

[fboehm]

Thank you, @jponnela and @biblicabeebli ! Please report here two pieces of information: 1. the doi for the zenodo archive and 2. the version number for the release. Thanks again!

[jponnela]

Hi @fboehm and @biblicabeebli! The DOI is 10.5281/zenodo.5758811. I called the version number of the release v1.0.0.

[fboehm]

@whedon set 10.5281/zenodo.5758811 as archive

[whedon]

OK. 10.5281/zenodo.5758811 is the archive.

[fboehm]

@whedon generate pdf

[whedon]

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

[fboehm]

@jponnela @biblicabeebli - would you please edit the title of the archive so that it matches exactly the title of the paper, Beiwe: A data collection platform for high-throughput digital phenotyping?

[fboehm]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[fboehm]

@jponnela @biblicabeebli - once the archive title is updated, the submission will then be handed off to an associate editor in chief. They'll do the final checks before publication.

[jponnela]

Hi @fboehm and @biblicabeebli, I've now updated the title, let me know if it looks ok!

10.5281/zenodo.5758811

[fboehm]

Thanks, @jponnela ! It looks good now.

[fboehm]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1177/2167702621993857 is OK
- 10.1002/mus.27110 is OK
- 10.1097/phm.0000000000001506 is OK
- 10.1097/SLA.0000000000004487 is OK
- 10.1245/s10434-020-09004-5 is OK
- 10.1001/jamasurg.2019.4702 is OK
- 10.1002/acn3.770 is OK
- 10.1016/j.wneu.2019.01.297 is OK
- 10.1038/s41746-018-0022-8 is OK
- 10.1200/cci.17.00149 is OK
- 10.1038/s41386-018-0030-z is OK
- 10.1038/s41537-017-0038-0 is OK
- 10.1038/npp.2016.7 is OK
- 10.2196/mental.5165 is OK
- 10.1038/nrg2897 is OK
- 10.1038/527S14a is OK
- 10.1016/j.neuroscience.2009.01.027 is OK
- 10.1002/humu.22080 is OK
- 10.1016/S1474-4422(17)30289-2 is OK
- 10.1002/acn3.770 is OK
- 10.1038/s41746-021-00514-4 is OK
- 10.1038/s41386-020-0771-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2821

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2821, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03417 joss-papers#2824
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03417
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...

[kyleniemeyer]

Congratulations @jponnela on your article's publication in JOSS!

Many thanks to @Tam-Pham and @erik-whiting for reviewing this, and @fboehm for editing.

[whedon]

🎉🎉🎉 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.03417/status.svg)](https://doi.org/10.21105/joss.03417)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03417">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03417/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03417/status.svg
   :target: https://doi.org/10.21105/joss.03417

This is how it will look in your documentation:

We need your help!

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://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[jponnela]

Thank you so much everyone, my first time publishing in JOSS and I'm very impressed!

@Tam-Pham @erik-whiting @fboehm @kyleniemeyer @biblicabeebli