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

whedon commented 2 years ago

Submitting author: !--author-handle-->@KonradHoeffner@juanklopper@behollister<!--end-reviewers-list-- Archive: 10.5281/zenodo.12094738

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

@behollister, 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/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

[x] 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

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

Functionality

[x] Installation: Does installation proceed as outlined in the documentation? (and documentation is sufficient?)
[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 the need for this software 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?
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Tests: Are there automated tests or manual steps described so that the function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state the need for this software and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 2 years ago

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 :tada:.

:warning: JOSE reduced service mode :warning:

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

:star: Important :star:

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:

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whedon commented 2 years ago

Wordcount for paper.md is 838

whedon commented 2 years ago

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 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:

whedon commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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

whedon commented 2 years ago

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

labarba commented 1 year ago

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 commented 1 year ago

Thank you for contacting them!

labarba commented 1 year ago

@whedon remind @behollister in 3 weeks

whedon commented 1 year ago

Reminder set for @behollister in 3 weeks

labarba commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Possible issue with instructions for using Node. See https://github.com/snikproject/graph/issues/393#issue-1429074319

KonradHoeffner commented 1 year ago

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

behollister commented 1 year ago

Issue with developer docs. See https://github.com/snikproject/graph/issues/395#issue-1431896646

behollister commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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

The issue has been fixed, thanks for notifying us!

KonradHoeffner commented 1 year ago

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 commented 1 year ago

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

labarba commented 1 year ago

@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 commented 1 year ago

@labarba, @bwatson is there an estimated timeframe when the review will begin?

bwatson commented 1 year ago

I’m still on this, but only from later this week

On 21 Nov 2022, at 10:32, Konrad Höffner @.**@.>> wrote:

@labarbahttps://github.com/labarba, @bwatsonhttps://github.com/bwatson is there an estimated timeframe when the review will begin?

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/jose-reviews/issues/180#issuecomment-1321688599, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAGAYTKYMYUD72YC2AWPSDTWJMXR7ANCNFSM53KJ74RA. You are receiving this because you were mentioned.Message ID: @.***>

The integrity and confidentiality of this email are governed by these terms. Disclaimerhttps://www.sun.ac.za/emaildisclaimer/default.aspx Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousulehttps://www.sun.ac.za/emaildisclaimer/default.aspx

KonradHoeffner commented 1 year ago

@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 commented 1 year ago

@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 commented 1 year ago

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

labarba commented 1 year ago

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

juanklopper commented 1 year ago

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

KonradHoeffner commented 1 year ago

@behollister: The overlapping mouseover text was adressed in https://github.com/snikproject/graph/issues/379 and is now fixed in https://github.com/snikproject/graph/commit/974580af526186c33fead46447d3908e5b7ab5d9. These changes are now also deployed on https://www.snik.eu/graph/.

juanklopper commented 1 year ago

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

labarba commented 1 year ago

@whedon generate pdf

whedon commented 1 year ago

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

juanklopper commented 1 year ago

@whedon remove @bwatson as reviewer

whedon commented 1 year ago

OK, @bwatson is no longer a reviewer

KonradHoeffner commented 1 year ago

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 commented 1 year ago

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 GitHubhttps://github.com/openjournals/jose-reviews/issues/180#issuecomment-1596891895, or unsubscribehttps://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. Disclaimerhttps://www.sun.ac.za/emaildisclaimer/default.aspx Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousulehttps://www.sun.ac.za/emaildisclaimer/default.aspx

KonradHoeffner commented 1 year ago

@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 commented 1 year ago

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

KonradHoeffner commented 11 months ago

@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 commented 10 months ago

@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 commented 8 months ago

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

juanklopper commented 8 months ago

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

KonradHoeffner commented 8 months ago

@whedon generate pdf

editorialbot commented 8 months ago

My name is now @editorialbot

KonradHoeffner commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

KonradHoeffner commented 5 months ago

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

labarba commented 3 months ago

Hi @KonradHoeffner — thank you ever so much for your kind patience. I've read the paper and found two tiny typos: repetitions on page 3 ("of of") and on page 4 ("the the"). Do make these little fixes, then please make a tagged release for the publication and report the version number here. Finally, you should make an archive deposit on Zenodo and report the DOI here.

openjournals / jose-reviews