[REVIEW]: 'Shinyscreen: Mass Spectrometry Data Inspection and Quality Checking Utility

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@MaliRemorker@dhhagan<!--end-editor-- Reviewers: @yguitton, @jspaezp Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/6c72d415b50149bc11729d43fc6bf702/status.svg)](https://joss.theoj.org/papers/6c72d415b50149bc11729d43fc6bf702)

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

@yguitton & @jspaezp, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @jspaezp

📝 Checklist for @yguitton

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (413.8 files/s, 60832.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             42              0            296
Markdown                         2             40              0            204
Bourne Shell                     1              0              0              6
-------------------------------------------------------------------------------
SUM:                             4             82              0            506
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1614

editorialbot commented 1 year ago

Failed to discover a valid open source license

editorialbot commented 1 year ago

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

OK DOIs

- 10.32614/RJ-2021-048 is OK
- 10.1038/nbt.2377 is OK
- 10.21105/joss.04029 is OK
- 10.1016/j.envint.2021.106885 is OK
- 10.1186/s12302-021-00475-1 is OK
- 10.1186/s13321-016-0115-9 is OK
- 10.1186/s13321-021-00489-0 is OK
- 10.1021/acsenvironau.1c00008 is OK
- 10.1021/ci00057a005 is OK

MISSING DOIs

- 10.1101/2020.04.29.067868 may be a valid DOI for title: MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data
- 10.1093/bioinformatics/btr645 may be a valid DOI for title: MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation
- 10.1021/acs.analchem.5b00941 may be a valid DOI for title: Accelerated Isotope Fine Structure Calculation Using Pruned Transition Trees
- 10.1002/jms.3131 may be a valid DOI for title: Automatic Recalibration and Processing of Tandem Mass Spectra using Formula Annotation.
- 10.1201/9781003097471 may be a valid DOI for title: R Markdown Cookbook

INVALID DOIs

- None

editorialbot 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:

jspaezp commented 1 year ago

Review checklist for @jspaezp (Work in progress)

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 https://gitlab.lcsb.uni.lu/eci/shinyscreen/?
[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 (@MaliRemorker) 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
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
- I fail to see a mention of the data used to generate figure 5.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
- Right now I do not have access to a system that would allow clean installation an removal, nontheless, the docker image build correctly (which entails that It should build as well in a debian machine). Unfortunately, forwarding port 3838 does not show the app in the host machine.
[ ] 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?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
- NOTE There is room to improve clarity on the documentation. Things like a a clear list that denotes the intended OS is or is tested in would be.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
- ASK I would like them to link testing/dummy data for the project. (both on the paper and the docs)
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
- OK There is extensive (not complete, but very good) coverage of roxygen2 comments that could generate api documentation. As well as fairly extensive in-line comments explaining the rationale and functioning of the package.
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
- Non-blocking note There are places (like here https://gitlab.lcsb.uni.lu/eci/shinyscreen/-/blob/master/tests/testthat/test-integration.R#L17) where unit testing is only verifying that the code runs without errors, but does not check the "correctness" of the output. I would encourage either testing correctness or adding comments explaining why it is not being tested.
[ ] 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
- In my opinion this is missing, I would like to see guidelines as a CONTRIBUTIONS.md or equivalent, in addition to a mention of the prefered method to start discussions on the usage/features of the project.

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, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
- NOTE there is a description, but my general perception is that there is not enough coverage of projects that are not within the R ecosystem (skyline for instance).
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
- Well written.
[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?

Technical recommendations (non-blocking).

Right now most of the data is stored in memory using a data.table, I would encourage the authors to use a database as a backend (sqlite)

dhhagan commented 1 year ago

Hi @yguitton let me know if you have any questions about getting started with the review and/or generating your checklist!

jspaezp commented 1 year ago

@MaliRemorker would you mind pointing me to the documentation on the usage of your docker image? I would highly appreciate that! (or is the intent of the image only to allow CICD ?)

Best Sebastian

MaliRemorker commented 1 year ago

@MaliRemorker would you mind pointing me to the documentation on the usage of your docker image? I would highly appreciate that! (or is the intent of the image only to allow CICD ?)

Best Sebastian

Hi @jspaezp, noted. Most docker images are for CICD purposes, but some can be easily used to demo the application. I should be able to get back to you during the next week. Thanks for giving this piece of software a look!

Cheers,

Todor

yguitton commented 1 year ago

Review checklist for @yguitton

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 https://gitlab.lcsb.uni.lu/eci/shinyscreen/?
[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 (@MaliRemorker) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
[ ] 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?

yguitton commented 1 year ago

Hi @MaliRemorker As @jspaezp I'm also interested by a functionnal docker version for your Shinyscreen. Where can I find it ? I found on docker hub kontrapunkt/shinyscreen and anjanae/shinyscreen one of these is from you?

Best Yann

dhhagan commented 1 year ago

Hi @MaliRemorker - just wanted to check in and see if you'd had a chance to respond to @yguitton and @jspaezp ?

dhhagan commented 1 year ago

Hi @MaliRemorker - just wanted to check in and see if you'd had a chance to respond to @yguitton and @jspaezp ?

Just wanted to bump this once more - Have you had time to address the comments from the reviewers, @MaliRemorker?

jspaezp commented 1 year ago

Hello @dhhagan Sorry for the late reply. I have updated my checklist, this version has more "actionable items" and reflects the extent that I can check right now (anything checked should be a "not at this time", not a "not gotten to it").

Overall I believe it is a well engineered project with some weaknesses in documentation that I would like to get published once those aspects have been polished.

(I assure that I will be more responsive in the future, sorry for the inconveniences).

dhhagan commented 1 year ago

Hi @jspaezp thanks for the response and no worries - I understand!

dhhagan commented 1 year ago

@MaliRemorker - have you had time to take a look at the above comments?

MaliRemorker commented 1 year ago

Dear David,

Terribly sorry for the delay in communication. I switched jobs away from academia recently which took me off the grid for the past months.

Will become responsive by the end of September again. Is this too late?

Thank you for all the patience.

Kind regards,

Todor

On 12 September 2023 15:02:02 CEST, David H Hagan @.***> wrote:

@MaliRemorker - have you had time to take a look at the above comments?

-- Reply to this email directly or view it on GitHub: https://github.com/openjournals/joss-reviews/issues/5520#issuecomment-1715682857 You are receiving this because you were mentioned.

Message ID: @.***> -- Sent from /e/ Mail.

dhhagan commented 1 year ago

Hi @MaliRemorker that sounds good - thanks for letting us know!

kthyng commented 10 months ago

Hi @MaliRemorker! Can you check in here? Will you be able to work on this submission again given your employment change or should we either pause it (to acknowledge you will work on it soon but not right away) or close it (if realistically you won't be able to work on it anytime soon, but we could subsequently restart a review in the future)?

kthyng commented 9 months ago

With apologies to @yguitton, @jspaezp for the time you've already invested in this review, I am going to close this issue since we have not heard from the author in a long time. Thank you very much for your time.

kthyng commented 9 months ago

@editorialbot reject

editorialbot commented 9 months ago

Paper rejected.

openjournals / joss-reviews