[REVIEW]: SNIK Graph—Visualizing Knowledge about Management of Hospital Information Systems

[whedon]

Submitting author: @KonradHoeffner (Konrad Höffner)
Repository: https://github.com/snikproject/snik-graph
Branch with paper.md (empty if default branch):
Version: 3.0.0
Editor: @juanklopper
Reviewers: @behollister
Archive: Pending

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/789a3e340dadf910c4ac2e1b6e225f09"><img src="https://jose.theoj.org/papers/789a3e340dadf910c4ac2e1b6e225f09/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/789a3e340dadf910c4ac2e1b6e225f09/status.svg)](https://jose.theoj.org/papers/789a3e340dadf910c4ac2e1b6e225f09)

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

@behollister, 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/jose-reviews/invitations

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

Conflict of interest

• As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JOSE 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?
• Version: Does the release version given match the GitHub release (3.0.0)?
• Authorship: Has the submitting author (@KonradHoeffner) made substantial contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
• 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 the need for this software 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?
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Tests: Are there automated tests or manual steps described so that the function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state the need for this software and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

⚠️ JOSE reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-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/jose-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]

Wordcount for paper.md is 838

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (836.6 files/s, 82843.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TypeScript                      45            266            856           4234
HTML                             6             21             20            409
JSON                             5              0              0            250
CSS                              4             28              0            200
Markdown                         3             58              0            195
TeX                              1             13              0            125
JavaScript                       2              7              6             76
YAML                             1              9              0             40
Dockerfile                       1              1              0             15
Bourne Shell                     1              1              0              3
-------------------------------------------------------------------------------
SUM:                            69            404            882           5547
-------------------------------------------------------------------------------


Statistical information for the repository '39c1627625529e06909c50d2' was
gathered on 2022/07/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Konrad Hoeffner                 42          1189          27200           35.66
Konrad Höffner                 650         22149          20760           53.89
T-P-1                            3             7              6            0.02
Thomas Pause                    28           469            422            1.12
ThomasPause                    107          4148           3267            9.31

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
Konrad Höffner               23            0.1          4.2                0.00

[whedon]

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

[whedon]

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

OK DOIs

- 10.1093/bioinformatics/btv557 is OK
- 10.1145/75335.75352 is OK
- 10.3233/978-1-61499-678-1-349 is OK
- 10.1145/2362499.2362532 is OK
- 10.1109/jcsse.2018.8457325 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[labarba]

Hi @bwatson, @behollister 👋 — Thank you for agreeing to review for JOSE! I am the editor-in-chief, and @juanklopper is the handling editor for this submission.

This issue thread is where the action happens: work your way through the review checklist, feel free to ask questions or post comments here, and also open issues in the submission repository as needed. Godspeed!

[whedon]

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

[whedon]

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

[labarba]

I have sent an email to each reviewer (cc'ing the handling editor @juanklopper) reminding them of this pending review and asking if they will still be able to contribute, given the long delay. If they do not reply in a week or so, we may need to find alternative reviewers. Thank you for your patience.

[KonradHoeffner]

Thank you for contacting them!

[labarba]

@whedon remind @behollister in 3 weeks

[whedon]

Reminder set for @behollister in 3 weeks

[labarba]

We've heard back from both reviewers, @bwatson, @behollister, via email. We should see some activity in this review soon. Thank you for your patience!

[behollister]

Sorry for the delay. Was busy meeting manuscript deadlines. Should be able to finish my review by the middle of this week.

Still need to complete Functionality/Documentation checklist points.

[behollister]

Possible issue with instructions for using Node. See snikproject/graph#393 (comment)

[KonradHoeffner]

@behollister: Thanks for the correction! Fixed the documentation.

[behollister]

Issue with developer docs. See snikproject/graph#395 (comment)

[behollister]

finished review. only would make suggestions about usability, such as scaled labels for nodes hard to see at various zoom levels, and overlapping popup text for menu items.

otherwise, all claims have been met by project for jose.

[behollister]

one more note. was not able to reach service locally on windows after having completed all installation steps in docs. worked fine on linux however.

[KonradHoeffner]

Issue with developer docs. See snikproject/graph#395 (comment)

The issue has been fixed, thanks for notifying us!

[KonradHoeffner]

one more note. was not able to reach service locally on windows after having completed all installation steps in docs. worked fine on Linux however.

We usually develop under Linux but would like to enable development under Windows as well.
Can you share what happened exactly so we can extend our Windows workaround section in the docs?

[KonradHoeffner]

@bwatson: As behollister has completed the review, it would be really nice if you could find the time to review the paper soon.

[labarba]

@KonradHoeffner — thanks for your patience! We have heard from Bruce via email and he is aware and will be working on it these days.

[KonradHoeffner]

@bwatson @labarba : I would really appreciate it if the review could start soon, because it is now going on since July 12, which is nearly 5 months.

[labarba]

@KonradHoeffner — I request your patience in this, with a gentle reminder to leave the task of following up with reviewers to the editor. You are welcome to tag me or @juanklopper, but try not to ping the reviewer directly with reminders. This is just to respect editorial roles (remembering that everyone is a volunteer!). Of course, you can address the reviewers directly when responding to their review comments. Thanks!

[KonradHoeffner]

@labarba: Sorry, I will not ping the reviewers with reminders again.

[labarba]

Just a quick update that we have been in email contact with reviewer @bwatson, and he is looking into this!

[juanklopper]

Thank you @labarba for reminders. Thank you for taking the time @bwatson.

[KonradHoeffner]

@behollister: The overlapping mouseover text was adressed in snikproject/graph#379 and is now fixed in snikproject/graph@974580a.
These changes are now also deployed on https://www.snik.eu/graph/.

[juanklopper]

@bwatson good to have caught up with you via email. How are you doing for time?

[labarba]

@whedon generate pdf

[whedon]

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

[juanklopper]

@whedon remove @bwatson as reviewer

[whedon]

OK, @bwatson is no longer a reviewer

[KonradHoeffner]

I just went through my notes from one year ago and remembered that this paper still exists, is there anything I can do to get this moving again?

[bwatson]

Hi there, TBH, I thought that it was moved off my plate, but was moved ahead in any case. Is it somehow stuck, and action needed from me? Best regards to you, Bruce On 19 Jun 2023, at 12:04, Konrad Höffner ***@***.******@***.***>> wrote: I just went through my notes from one year ago and remembered that this paper still exists, is there anything I can do to get this moving again? — Reply to this email directly, view it on GitHub<#180 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAGAYTNXL3YZZQ3DXQU6KL3XMAP2ZANCNFSM53KJ74RA>. You are receiving this because you were mentioned.Message ID: ***@***.***> The integrity and confidentiality of this email are governed by these terms. Disclaimer<https://www.sun.ac.za/emaildisclaimer/default.aspx> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<https://www.sun.ac.za/emaildisclaimer/default.aspx>

[KonradHoeffner]

@bwatson It has indeed been moved off your plate, no worries!
@juanklopper: Can I help find another reviewer somehow? I was looking for the reviewer list but didn't find it.

[KonradHoeffner]

@juanklopper: Is there anything I can do to get this going again?

[KonradHoeffner]

@labarba, @juanklopper: This paper is now in the review queue for almost 1.5 years, is there anything I can do to get this to continue?

[KonradHoeffner]

@labarba @juanklopper once again nearly a month has passed with no visible change, should I retract this paper and submit it elsewhere or is there anything I can do to get this review going again?

[KonradHoeffner]

@labarba @juanklopper new year, new try :-) Is there any way I can help moving this process forward?

[juanklopper]

@Lorena After our previous discussions regarding the reviewer, can we move ahead and accept this for publication?

[KonradHoeffner]

@whedon generate pdf

[editorialbot]

My name is now @editorialbot

[KonradHoeffner]

@editorialbot generate pdf

[editorialbot]

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

[KonradHoeffner]

@juanklopper @labarba: Another three months later, I hope it is OK to ask again if I can do anything to move this forward :-)