[REVIEW]: Rosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling about joss-reviews HOT 14 OPEN

Hi @suragnair and @JDRomano2

Do you think you'll have a chance to begin your reviews soon?

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (1674.9 files/s, 208634.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            31              0              0           8342
JavaScript                      73            973            275           5144
Vuejs Component                 40            491             69           4500
Python                          43           1207            719           3446
Markdown                        10            418              0           1012
SVG                              6              0              2            737
YAML                            12             46              1            495
Bourne Shell                    10            102             54            403
CSS                              3             63             45            295
TeX                              1             13              0            218
Dockerfile                       3              6              6             47
HTML                             1              0              1             18
INI                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           234           3319           1172          24658
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1093/genetics/iyac022 is OK
- 10.1093/bioinformatics/btu613 is OK
- 10.1093/nar/gkx1098 is OK
- 10.1186/s13059-016-0974-4 is OK
- 10.1093/nar/gkaa1043 is OK
- 10.1093/nar/gkl993 is OK
- 10.1093/nar/gkac888 is OK
- 10.1093/nar/gkx1153 is OK
- 10.1093/nar/gku1205 is OK
- 10.1101/gr.176601 is OK
- 10.1038/nmeth0410-248 is OK
- 10.1093/nar/gkv1189 is OK
- 10.1186/s13073-021-00835-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 1653

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

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Howdy @suragnair and @JDRomano2!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

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Review checklist for @suragnair

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/uab-cgds-worthey/rosalution?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SeriousHorncat) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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?

from joss-reviews.

@SeriousHorncat would it be possible to include either a link to a demo website (pre-populated with a few examples) or a video covering basic usage in the GitHub README? This would allow potential users to get a quick overview of the functionality and how to use Rosalution.

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@JDRomano2 can we get an update on your progress?

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@jmschrei I'll have the review completed tomorrow. Thanks for your patience!

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Review checklist for @JDRomano2

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/uab-cgds-worthey/rosalution?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@SeriousHorncat) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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?

from joss-reviews.

@SeriousHorncat I agree with @suragnair - I've been struggling to get the software running on my local computer. I think two things would significantly help:

1. Provide troubleshooting details for deployment
2. Stand up a public demo server that will allow users to quickly explore the core functionality of the software.

To provide a bit more information about the issue I'm experiencing, after following all of the deployment instructions I'm seeing a 404 page not found message when I navigate to localhost:80 in my browser.

Nothing in the logs suggests the cause of the issue. E.g., for rosalution-frontend-1:

2023-07-01 09:11:07 yarn run v1.22.5
2023-07-01 09:11:07 $ vite --host 0.0.0.0 --port 80
2023-07-01 09:11:07 
2023-07-01 09:11:07   VITE v4.0.4  ready in 241 ms
2023-07-01 09:11:07 
2023-07-01 09:11:07   ➜  Local:   http://localhost:80/
2023-07-01 09:11:07   ➜  Network: http://172.18.0.2:80/

and for rosalution-backend-1:

2023-07-01 09:11:08 INFO:     Will watch for changes in these directories: ['/app']
2023-07-01 09:11:08 INFO:     Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
2023-07-01 09:11:08 INFO:     Started reloader process [11] using WatchFiles
2023-07-01 09:11:08 INFO:     Started server process [13]
2023-07-01 09:11:08 INFO:     Waiting for application startup.
2023-07-01 09:11:08 INFO:     Application startup complete.

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Please note that I am satisfied with all other aspects of the study. If the authors are able to provide a usable example and improve documentation such that I can get everything running locally I should be able to assess the outstanding items in the checklist.

I do feel that this is within the scope of JOSS and is a valuable contribution to the field.

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