[REVIEW]: PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks

whedon commented 2 years ago

Submitting author: !--author-handle-->@ddeehere@danielskatz<!--end-editor-- Reviewers: @jhancock4d, @lrasmus Archive: 10.5281/zenodo.6325732

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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

@jhancock4d & @lrasmus, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @danielskatz 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 @jhancock4d

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@ddeehere) 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] #4119
[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 @lrasmus

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@ddeehere) 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?

editorialbot commented 2 years ago

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

OK DOIs

- 10.13063/2327-9214.1213 is OK
- 10.1097/MLR.0b013e3181d9919f is OK
- 10.17294/2330-0698.1149 is OK

MISSING DOIs

- 10.1371/journal.pone.0055811 may be a valid DOI for title: SHRINE: Enabling Nationally Scalable Multi-Site Disease Studies

INVALID DOIs

- None

danielskatz commented 2 years ago

@ddeehere - please add the DOI mentioned above to your bib file

editorialbot commented 2 years ago

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

ddeehere commented 2 years ago

@danielskatz doi added to paper.bib

danielskatz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.13063/2327-9214.1213 is OK
- 10.1097/MLR.0b013e3181d9919f is OK
- 10.17294/2330-0698.1149 is OK
- 10.1371/journal.pone.0055811 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 2 years ago

@ddeehere - proofreading the paper PDF, I found a couple of things that I suggest changing, as shown in https://github.com/PopMedNet-Team/popmednet/pull/44 Please merge this if you agree with these changes.

danielskatz commented 2 years ago

👋 @ddeehere - Thanks for merging. At this point could you:

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

I can then move forward with accepting the submission.

ddeehere commented 2 years ago

@danielskatz I release-tagged it PMN-2021.6-JOSS.

As for Zenodo, do you want me to zip the entire source tree and deposit it there?

danielskatz commented 2 years ago

See https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content for some advice on this

danielskatz commented 2 years ago

@ddeehere - Any news on this?

ddeehere commented 2 years ago

@ddeehere - Any news on this?

@danielskatz It processed for a long time and failed today. We are still investigating.

ddeehere commented 2 years ago

Zenodo appears to still be processing the last release.

danielskatz commented 2 years ago

You might want to contact their support - this should be very fast when it works, which it always has in my experience

ddeehere commented 2 years ago

You might want to contact their support - this should be very fast when it works, which it always has in my experience

@danielskatz Just want to let you know that we are still looking into this. We have sent a support request to Zenodo.

danielskatz commented 2 years ago

👋 @lnielsen - can you help us debug/solve this?

ddeehere commented 2 years ago

@danielskatz

DOI: 10.5281/zenodo.6325732](https://doi.org/10.5281/zenodo.6325732)

danielskatz commented 2 years ago

hmmm that DOI does not resolve for me right now. Does it for you?

ddeehere commented 2 years ago

@danielskatz It was just generated. Looks like it's resolving now.

danielskatz commented 2 years ago

@editorialbot set 10.5281/zenodo.6325732 as archive

editorialbot commented 2 years ago

Done! archive is now 10.5281/zenodo.6325732

danielskatz commented 2 years ago

@editorialbot set PMN-2021.6-JOSS as version

editorialbot commented 2 years ago

Done! version is now PMN-2021.6-JOSS

danielskatz commented 2 years ago

@ddeehere - Please check that the Zenodo item 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 - I should be removed). You may also add the authors' ORCID.

You can change metadata and then republish the zenodo item without getting or needing a new DOI, as long as you don't change the data itself (the zip file in this case)

ddeehere commented 2 years ago

@danielskatz Do I simply add a .zenodo.json file in our repository?

danielskatz commented 2 years ago

See "How can I edit the metadata of a published record?" on https://help.zenodo.org

ddeehere commented 2 years ago

See "How can I edit the metadata of a published record?" on https://help.zenodo.org

@danielskatz Thank you for all your help! Metadata is edited.

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

:warning: Error preparing acceptance. The generated XML metadata file is invalid.

danielskatz commented 2 years ago

👋 @xuanxu - Any ideas on this error?

xuanxu commented 2 years ago

It looks like both figures have the same id (fig:PopMedNet) in the paper.md file. Changing it in any of them should fix it.

danielskatz commented 2 years ago

Thanks @xuanxu

danielskatz commented 2 years ago

@ddeehere - can you update this? We don't need a new zenodo deposit, as we only require the software to be archived, not the final paper

ddeehere commented 2 years ago

@danielskatz Yes, just updated.

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3019

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3019, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.13063/2327-9214.1213 is OK
- 10.1097/MLR.0b013e3181d9919f is OK
- 10.17294/2330-0698.1149 is OK
- 10.1371/journal.pone.0055811 is OK

MISSING DOIs

- None

INVALID DOIs

- None

danielskatz commented 2 years ago

@ddeehere - there are a couple of things I'm not happy about in the metadata and pdf, but these are issues on the JOSS side, not on what you submitted. Until these are fixed, I'm not going to to ahead with the final acceptance and publishing, but hopefully this won't take long to resolve

ddeehere commented 2 years ago

@danielskatz I appreciate the status. Looking forward to having it approved in the near future. Thanks!

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3021

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3021, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@ddeehere - there are a couple of things I'm not happy about in the metadata and pdf, but these are issues on the JOSS side, not on what you submitted. Until these are fixed, I'm not going to to ahead with the final acceptance and publishing, but hopefully this won't take long to resolve

@danielskatz – these should be addressed now.

danielskatz commented 2 years ago

thanks @arfon

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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