Joss-reviews: [REVIEW]: secuTrialR: Seamless interaction with clinical trial databases in R

[whedon]

Submitting author: @PatrickRWright (Patrick R. Wright)
Repository: https://github.com/SwissClinicalTrialOrganisation/secuTrialR
Version: 1.0.6
Editor: @csoneson
Reviewer: @pacoramon, @sachsmc
Archive: 10.5281/zenodo.4280767

:warning: JOSS reduced service mode :warning:

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/42515acce06c46e43dbb236e00682dcf"><img src="https://joss.theoj.org/papers/42515acce06c46e43dbb236e00682dcf/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/42515acce06c46e43dbb236e00682dcf/status.svg)](https://joss.theoj.org/papers/42515acce06c46e43dbb236e00682dcf)

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

@pacoramon & @sachsmc, 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 @csoneson 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 @pacoramon

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 (@PatrickRWright) 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: Do the authors clearly state 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 @sachsmc

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 (@PatrickRWright) 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: Do the authors clearly state 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]

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

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

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

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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

- 10.1017/CBO9781107256644 is OK
- 10.1186/1745-6215-11-79 is OK
- 10.1038/d41586-020-00758-2 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[csoneson]

@pacoramon, @sachsmc - thanks for agreeing to review this submissions. This is where the review happens. You can find some instructions above, as well as your individual checklists. Don't hesitate to ping me if you have any questions (I will also be checking in regularly).

[PatrickRWright]

Thank you for taking this on from my side too :thumbsup:

[sachsmc]

Hi @PatrickRWright ,

I noted a few small issues with the documentation and the software paper in issues 225 and 226 on your repo:

https://github.com/SwissClinicalTrialOrganisation/secuTrialR/issues/225
https://github.com/SwissClinicalTrialOrganisation/secuTrialR/issues/226

Otherwise the package looks and works great!

Best wishes,

Michael

[PatrickRWright]

Thank you @sachsmc for the taking the time and your comments. I'll try and get on to them asap.

[PatrickRWright]

Note to myself: Add the reviewers and editor to the acknowledgements.

[whedon]

:wave: @sachsmc, please update us on how your review is going.

[whedon]

:wave: @pacoramon, please update us on how your review is going.

[PatrickRWright]

@whedon generate pdf

[whedon]

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

[PatrickRWright]

@csoneson we have addressed all points brought up by @sachsmc

We are, however, not sure how to solve the issue with one of the links in the references moving out of the page. Any idea?

[PatrickRWright]

@pacoramon can you tell us your legal name so we can adjust it in the acknowledgements?

[csoneson]

We are, however, not sure how to solve the issue with one of the links in the references moving out of the page. Any idea?

Good question. I'm not sure why that link is not wrapped like the others. Perhaps someone from the @openjournals/dev team has an idea.

[sachsmc]

@csoneson One way to solve it requires modifying the latex template (not sure how onerous that would be). If you add the code

\usepackage[hyphens]{url}

to the header before the hyperref package is loaded, it will break the url at hyphens. By default, it will only break at slashes.

https://tex.stackexchange.com/questions/175399/line-breaking-of-urls-at

[pacoramon]

@pacoramon, please update us on how your review is going.
I am progressing, although not very fast. Sorry!

@pacoramon can you tell us your legal name so we can adjust it in the acknowledgements?
My legal name is Francisco Estupiñán-Romero. Thanks for the acknowledgement, although I am not going very fast with my review just now. I will try to catch up.

[whedon]

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

[PatrickRWright]

@whedon generate pdf

[whedon]

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

[PatrickRWright]

@whedon generate pdf

[whedon]

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

[xuanxu]

We are, however, not sure how to solve the issue with one of the links in the references moving out of the page. Any idea?

A quick fix would be to use the shorter-form url for the same article:
https://www.spiegel.de/a-13bd06d7-22a1-4b3d-af23-ff43e5e8abd6

[PatrickRWright]

@whedon generate pdf

[whedon]

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

[sachsmc]

I've completed my review. Thanks @PatrickRWright for addressing my comments

[pacoramon]

I've also finished mine. Thanks, @PatrickRWright for the work done, and @csoneson for inviting me to review.
I feel I have not contributed much, but this review process has been swift, and all just worked out right away or was already done accordingly to guidelines, so congrats!

[csoneson]

@sachsmc, @pacoramon - thanks a lot for your reviews!

@PatrickRWright - I will give a quick look at the submission too and come back to you with the next steps shortly.

[csoneson]

@whedon check references

[whedon]

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

OK DOIs

- 10.1017/CBO9781107256644 is OK
- 10.1186/1745-6215-11-79 is OK
- 10.1038/d41586-020-00758-2 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.jbi.2019.103208 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jbi.2008.08.010 is INVALID because of 'https://doi.org/' prefix

[csoneson]

@whedon generate pdf

[whedon]

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

[PatrickRWright]

@whedon check references

[whedon]

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

OK DOIs

- 10.1017/CBO9781107256644 is OK
- 10.1186/1745-6215-11-79 is OK
- 10.1038/d41586-020-00758-2 is OK
- 10.21105/joss.01686 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[PatrickRWright]

@csoneson the dois should be fixed.

[csoneson]

@whedon generate pdf

[whedon]

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

[csoneson]

Thanks @PatrickRWright, looks good. I had a look through the submission, and I just noted one other thing: I think there is at least one place where secuTrialdata should be in fixed-width font, could you double-check this?

The next steps are as follows:

• [ ] Make a tagged release of the current state of your software, and list the version tag of the archived version here.
• [ ] Archive the reviewed software in Zenodo or a similar service
• [ ] Check that the archival deposit has the correct metadata. This includes the title (should match the paper title) and author list (should match the paper author list). You may also add the authors' ORCID.
• [ ] Please list the DOI of the archived version here.

[PatrickRWright]

Thank you @csoneson
The version tag would be: 1.0.6
Zenodo link: https://zenodo.org/record/4278979#.X7TdUq4o-EL
DOI: seems to be the one I entered for this publication. i.e. 10.21105/joss.02816

[csoneson]

Ah, I see. The Zenodo archive should have its own DOI, something like 10.5281/zenodo.XXXXXX (i.e., not the one of the JOSS paper).

[PatrickRWright]

Hm... I'm a bit confused now. since the DOI tooltip for zenodo said:

Optional. Did your publisher already assign a DOI to your upload? If not, leave
the field empty and we will register a new DOI for you. A DOI allows others to
easily and unambiguously cite your upload. Please note that it is NOT possible
to edit a Zenodo DOI once it has been registered by us, while it is always
possible to edit a custom DOI.

For me this indicated to use a preexisting DOI (i.e. JOSS) if available. I tried to remove the JOSS DOI now, but saving on zenodo doesn't actually remove it. Any suggestions?

[danielskatz]

Zenodo will issue its own DOI for the deposit (which you will see once it is published "Cite as" on the lower right). In addition, you can put other DOIs into the page where you submit to zenodo, such as references and links. These DOIs are stored in the metadata of the published article under the published DOI.

When you manually upload to Zenodo, there's a place for a DOI, which says "Optional. Did your publisher already assign a DOI to your upload? If not, leave the field empty and we will register a new DOI for you. A DOI allows others to easily and unambiguously cite your upload. Please note that it is NOT possible to edit a Zenodo DOI once it has been registered by us, while it is always possible to edit a custom DOI." In the case of JOSS, we do not assign a DOI to the software upload, so you should leave this empty. We will assign a DOI to the paper, which will refer to the DOI of the software upload (which is why we need you to tell us what it at this stage of the acceptance process).

[csoneson]

Thanks @danielskatz for the more extensive explanation.

@PatrickRWright - I think you may need to email Zenodo to resolve this and replace the JOSS DOI with a Zenodo-assigned one.

[PatrickRWright]

@csoneson I have gotten in touch with Zenodo and hope they can resolve this.

Thank you for the guidance.

[PatrickRWright]

@csoneson Zenodo suggested to reupload the package leaving the DOI field empty. They will then delete the old submission.

I have done this: https://zenodo.org/record/4280767#.X7Zbqa4o_MU
DOI: http://doi.org/10.5281/zenodo.4280767
Version: 1.0.6

[csoneson]

@whedon set 10.5281/zenodo.4280767 as archive

[whedon]

OK. 10.5281/zenodo.4280767 is the archive.

[csoneson]

@whedon set 1.0.6 as version

[whedon]

OK. 1.0.6 is the version.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[csoneson]

Thanks @PatrickRWright - the associate editor in chief on rotation will take over from here.

[whedon]

: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/1928

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1928, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1017/CBO9781107256644 is OK
- 10.1186/1745-6215-11-79 is OK
- 10.1038/d41586-020-00758-2 is OK
- 10.21105/joss.01686 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[PatrickRWright]

Thank you a lot @csoneson this has been such a great process.

@aghaynes @markomi looks like its accepted. Thanks to both of you too for all your efforts in the project :rocket:

[PatrickRWright]

Should I run this @whedon accept deposit=true or is the something the associate editor needs to do?

Also I saw that the XML omits the middle names. i.e. Alan Haynes should be Alan G. Haynes and Patrick Wright should be Patrick R. Wright. Is that possible?

[danielskatz]

I'll take over from here, with a final proofreading and then the acceptance. I'll also look at the name issue in the XML - thanks for catching it as a potential issue.

[danielskatz]

Please merge the changes in https://github.com/SwissClinicalTrialOrganisation/secuTrialR/pull/229 or let me know what you don't agree with.

[PatrickRWright]

It is merged.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

: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/1929

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1929, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1017/CBO9781107256644 is OK
- 10.1186/1745-6215-11-79 is OK
- 10.1038/d41586-020-00758-2 is OK
- 10.21105/joss.01686 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@PatrickRWright - It turns out that Crossref only wants the given name (e.g. Alan). We omit the middle initial deliberately. But since we add the ORCID, the authors should still be uniquely identified.

[danielskatz]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1930
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02816
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @PatrickRWright (Patrick R. Wright) and co-authors!!

And thanks to @pacoramon & @sachsmc for reviewing and @csoneson for editing!

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02816/status.svg)](https://doi.org/10.21105/joss.02816)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02816">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02816/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02816/status.svg
   :target: https://doi.org/10.21105/joss.02816

This is how it will look in your documentation:

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