[REVIEW]: Carnival: JVM Property graph data unification toolkit

[editorialbot]

Submitting author: @hjwilli (Heather Williams)
Repository: https://github.com/carnival-data/carnival
Branch with paper.md (empty if default branch): joss2
Version: V2.1.5
Editor: @majensen
Reviewers: @kinow, @KonradHoeffner
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/77c829339608b3faaa92cc1baa7a012c"><img src="https://joss.theoj.org/papers/77c829339608b3faaa92cc1baa7a012c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/77c829339608b3faaa92cc1baa7a012c/status.svg)](https://joss.theoj.org/papers/77c829339608b3faaa92cc1baa7a012c)

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

@kinow & @KonradHoeffner, 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 @majensen 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 @KonradHoeffner

📝 Checklist for @kinow

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (990.7 files/s, 169519.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Groovy                         146           7463           5945          16706
Markdown                        35            912              0           2170
Gradle                           7            184            211            598
YAML                            10             18              8            139
XML                              2             49             25            120
Bourne Shell                     1             27            108             99
TeX                              1              5              0             82
DOS Batch                        1             21              2             66
RAML                             1             10              1             59
Dockerfile                       1             15             10             25
-------------------------------------------------------------------------------
SUM:                           205           8704           6310          20064
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1101

[editorialbot]

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

OK DOIs

- 10.1007/978-3-662-46641-4_40 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.3233/SHTI190178 is OK
- 10.1016/j.yjbinx.2020.100086 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[KonradHoeffner]

Review checklist for @KonradHoeffner

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/carnival-data/carnival?
• 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 (@hjwilli) 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?

[kinow]

Review checklist for @kinow

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/carnival-data/carnival?
• 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 (@hjwilli) 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?

[kinow]

Hi @majensen , @hjwilli

I've partially finished my review. I created issues in the Carnival source code repository, linking to this issue. I marked the items I've completed in my review as done, in my checklist ☝️ All the pending items are being mentioned in the issues I created.

@hjwilli feel free to ping me on any of those issues to discuss or suggest some fixes 👍 As we progress with those issues, I'll update my checklist and hopefully my review should be completed as soon as the issues are resolved.

Thanks!
-Bruno

[hjwilli]

Thanks @kinow, the team has started working on the issues you've raised and you should see some updates soon!

[KonradHoeffner]

The code has 13 commits by Hayden Freedman, who is not on the author list. On the other hand the author list includes Louis Lee, who does not seem to be a contributor to the codebase. Finally Christian Stoeckert only has a single commit where one word in the readme seems to have changed. Can you explain the choice of authors?

[majensen]

@hjwilli could you comment on the concern raised by @KonradHoeffner at #5117 (comment)?

[majensen]

Hello @hjwilli - can you give us a progress update in this thread? Thanks very much -

[hjwilli]

Hi @majensen, thank you for your patience. My team is still in the process of making updates to the paper and codebase based on feedback and hopes to address most of the issues in the next few weeks.

For the author list, Christian Stoeckert is an ontology expert who has been key collaborator in the development of Carnival for the lifetime of the project and has directly contributed to the paper and should be included as an author. Louis Lee is a newer member of the team who has participated software design process for carnival and the paper and has make significant contributions to the demo application for this submission and should be included as an author. Hayden is no longer an active member of the group but has make significant contributions to the codebase and we are reaching out to them for inclusion.

[KonradHoeffner]

@hjwilli: Yes, please definitely do include Hayden then, as required by the ethics guidelines:

all significant contributors should be included in the author list

[majensen]

@hjwilli - how are your responses coming along?

[KonradHoeffner]

@editorialbot generate pdf

[majensen]

Hi @hjwilli, how are your revisions coming along?

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

@hjwilli maybe you can give an overview of your progress so far on carnival-data/carnival#123. We may be able to negotiate a path forward; I think we all would love to set this paper free.

[hjwilli]

@hjwilli maybe you can give an overview of your progress so far on carnival-data/carnival#123. We may be able to negotiate a path forward; I think we all would love to set this paper free.

Thank you, I am working on a partial response and updates related to this that will be pushed next week, and would appreciate feedback at that point!

[hjwilli]

Hi @majensen, as an update, I've made extensive updates this week for carnival-data/carnival#123, a few small things left.

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

@hjwilli how is the work coming along? Thanks - @majensen

[majensen]

Hi @hjwilli, please let us know how things are progressing. I'm happy to discuss offline at maj -dot- fortinbras -at- gmail -dot- com. Thanks!

[majensen]

Hi @hjwilli - pinging you again on progress. Thank you!

[majensen]

Hello @hjwilli - have you been able to work on the revisions? @majensen

[hjwilli]

Hi @majensen, I've made changes and updates to respond to carnival-data/carnival#123.

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/978-3-662-46641-4_40 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.3233/SHTI190178 is OK
- 10.1016/j.yjbinx.2020.100086 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Cleaning Big Data: Most Time-Consuming, Least Enjo...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[majensen]

Thanks for this work @hjwilli. My opinion is that the additional documentation and example provided and described in the response to carnival-data/carnival#123 is very detailed and satisfies me. @KonradHoeffner, do you agree? (JOSS papers themselves are meant to be quite short, supplemented in documentation as in this instance.)

[KonradHoeffner]

@majensen: Of the two leftover major issues, carnival-data/carnival#123 has been sufficiently addressed but carnival-data/carnival#113 is still open and there seem to remain undocumented items in the API.

[majensen]

Thanks @KonradHoeffner - I've had a look at the documentation, my feeling is that major classes and "user facing" methods have a reasonable amount of explanation. The general documentation has also been expanded significantly. Just from my perspective, I think documentation also evolves and interaction with users will expose those components that are underdocumented. I'm inclined to recommend moving forward as-is, but it is up to you. If there are specific elements that you feel need docs, can you highlight these in the issue?

[KonradHoeffner]

@majensen: My general view is that all public items are "user facing" but I don't have any specific elements in mind, so if you want to move forward as-is I won't object.

[majensen]

@KonradHoeffner thanks for your comment. I do agree, and maybe the right direction would be to expose less. But I would like to move forward, since we are approaching 2 years in review, and I believe the functionality is established and the general documentation has been significantly improved. @hjwilli - I will review the paper itself and may have some minor updates to apply.

[majensen]

@hjwilli - just to note, in the online documentation there are some instances of "providence" which I believe should be "provenance"

[majensen]

The only minor proof comment I have on the paper is, can we make the 'Features' paragraph at l.50 into a sentence; keep the bullets but add "The main features of Carnival are:" before the list, and punctuate the bulleted sentences with comma, comma, period.

[hjwilli]

@majensen Thank you very much for all your feedback. I've updated the "providence" typos that I was able to find, and made the suggested changes to the "features" section of the paper. I will keep the notes on the API documentation in mind as the project evolves. Please let me know if there are other things I need to address to move the JOSS process forward!

[majensen]

@editorialbot generate pdf

[editorialbot]

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

[majensen]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/978-3-662-46641-4_40 is OK
- 10.1016/j.jbi.2019.103208 is OK
- 10.1016/j.jbi.2008.08.010 is OK
- 10.3233/SHTI190178 is OK
- 10.1016/j.yjbinx.2020.100086 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Cleaning Big Data: Most Time-Consuming, Least Enjo...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[majensen]

Thanks a lot @hjwilli - for some reason, the bullets didn't render right in lines 49-53, maybe check that. [I would also put a comma between "model" and "particularly" at line 43.]
For publication, we need an open archive of the code repo, using Zenodo or similar. There is a quick tutorial here if you need it. After you've made the repo, can you report the DOI and version number here?