[REVIEW]: DataScribe: An Omeka S module for structured data transcription

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jmotis@arfon<!--end-editor-- Reviewers: @luxaritas, @koenedaele Archive: 10.5281/zenodo.10379756

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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

@luxaritas & @koenedaele, 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 @arfon 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 @luxaritas

📝 Checklist for @koenedaele

editorialbot commented 1 year ago

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:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (1540.0 files/s, 220803.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
PHP                            137           1923           2111          12447
PO File                          3           1080           1562           2413
JavaScript                      11             54            187           1147
CSS                              2            220             14           1022
TypeScript                      30             81            642            917
Markdown                         3            419              0            644
JSON                             1              0              0            183
YAML                             1              1              4             18
INI                              1              0              0             10
-------------------------------------------------------------------------------
SUM:                           189           3778           4520          18801
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 574

arfon commented 1 year ago

@luxaritas, @koenedaele – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing (in a new comment on this thread):

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5661 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

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:

luxaritas commented 1 year ago

Review checklist for @luxaritas

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://github.com/chnm/Datascribe-module?
[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 (@jmotis) 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
[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

[x] Installation: Does installation proceed as outlined in the documentation?
[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 what problems the software is designed to solve 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 (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality 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] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[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?

koenedaele commented 1 year ago

Review checklist for @koenedaele

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://github.com/chnm/Datascribe-module?
[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 (@jmotis) 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
[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

[x] Installation: Does installation proceed as outlined in the documentation?
[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 what problems the software is designed to solve 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 (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality 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] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] 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?

koenedaele commented 1 year ago

Hi @jmotis, I'm one of the reviewers having a look at your software. I'll conduct the review by creating issues in your repository to keep this thread clean as requested by JOSS.

koenedaele commented 1 year ago

I have reviewed the Software Paper and started on some of the documentation. I will be away for a bit. When I get back I'll have a further look at the documentation and the software itself.

luxaritas commented 1 year ago

Hi all, sorry for the delay on my end! Starting to work my way through this, and Koen has already filed some good issues.

@jmotis Since you do not appear to be a frequent committer to the codebase, can you describe your role as a contributor to the project? Additionally, I note Kim Nguyen as one of the larger committers to the project but is not a listed author, and I want to verify whether lack of authorship there is appropriate.

jmotis commented 1 year ago

This was a grant-funded project. I was the PI (along with Lincoln Mullen as co-PI) and did a lot of different things: project management and reporting, developing the required feature set, consulting and testing throughout the development of the module, documentation, and outreach. Kim was invited to be on the paper but didn't join us.

luxaritas commented 1 year ago

Just finished my first pass, and this looks really solid! Kudos on the thorough documentation especially. Only one additional thing came up in what I saw beyond what Koen already called out.

jmotis commented 1 year ago

Thanks both of you for your time and feedback. I've put a link in the readme.md to the external project website where we collected the concrete case studies and tutorials (vs. the abstracted documentation in the GitHub repository) and we'll tidy up the bibliography and add the CONTRIBUTING.md file.

arfon commented 1 year ago

Thanks for the update @jmotis.

@luxaritas, @koenedaele – could you take a look and see how much of your checklist can now be updated based on the recent changes from the authors?

koenedaele commented 1 year ago

Currently unable to continue review due to chnm/Datascribe-module#136. Could you handle this one first?

koenedaele commented 1 year ago

I have concluded my review. I have found the software to function as indicated. Being new to Omeka S, I had to learn about both Omeka S and Datascribe. I am especially pleased with the detailed documentation of the module. Congratulations on the authors, writing documentation is never an easy task.

I have created some minor issues that could be solved. I am aware the module only functions for the previous version of Omeka S, but I assume that's not an issue for JOSS (I have no information indicating it is). I do hope the module is updated to the newer version sooner or later.

Currently I'm awaiting a newer version of the paper with proper references, before I sign off on that last aspect. Once the citations are properly formatted, I'm ok with this paper.

luxaritas commented 1 year ago

Just did one more pass and agree, references is the only remaining thing to be resolved

arfon commented 1 year ago

Great, thanks for the updates @luxaritas & @koenedaele. @jmotis – please let us know when you've had a change to address the last outstanding items here.

arfon commented 11 months ago

Friendly reminder to check back in here @jmotis and update us on your progress making changes.

jmotis commented 10 months ago

I'd hoped to have a coauthor pitch in here, but it looks like that's not going to be possible. I'm moving the last action item onto my to-do list and will try to finish it up soon.

editorialbot commented 10 months ago

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

jmotis commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

jmotis commented 10 months ago

@arfon @luxaritas @koenedaele I've addressed and closed the two outstanding issues (a documentation tweak and reformatting the paper's bibliography properly) and regenerated the PDF (please look at the second article proof not the one I did an hour ago). I think that's everything.

luxaritas commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

luxaritas commented 10 months ago

I'm noticing that a number of the references are showing up with just a date or even multiple non-disambiguated instances of n.d.. Looking at prior JOSS papers, it is very rare that no author is listed on a reference, even for websites (in which case you'd typically use some variation on the copyright holder, site owner, responsible organization, etc). I don't know what JOSS preferences/standards on this are

Also for Tesseract, it may be preferable to use one of the citations listed in https://github.com/tesseract-ocr/tesseract/blob/main/CITATIONS.bib? Also not sure here what typical convention is since you're not referring to one of the papers specifically and they don't appear to list a specific preference

jmotis commented 10 months ago

@luxaritas The multiple (n.d.)s are because the citation is referenced in line and you're just getting the date parenthetically after it. E.g. a "Smith (2018) talks about" style reference. I agree, though, it looks a little odd all coming in a row in the same sentence.

The goal of the software citations was to point readers to existing software websites/downloads, so people reading the article can go look at other software options we comped against. I didn't want to clutter up the text with non-hyperlinked URLs in parentheses. If there's some other way JOSS would like those displayed, I'm happy to add additional information/formatting. I could also remove those references if people think that's better, as they're not quite references in the traditional sense.

luxaritas commented 10 months ago

Right - what Im wondering is if you can add reasonable authors to those citations. Other JOSS papers appear to do this, even when there aren't specific named authors like there are for papers or articles

jmotis commented 10 months ago

I can try to add some corporate authorships in and see if that works better.

jmotis commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

arfon commented 10 months ago

@jmotis – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

The title of the archive is the same as the JOSS paper title
That the authors of the archive are the same as the JOSS paper authors
I can then move forward with accepting the submission.

koenedaele commented 10 months ago

Looks good to me. Haven't found any typos in the final paper.

luxaritas commented 10 months ago

Looks good to me as well

jmotis commented 10 months ago

DOI: 10.5281/zenodo.10379756

jmotis commented 10 months ago

The PDF looks good to me and I don't see any typos either. Thank you @koenedaele & @luxaritas for reviewing this for us!

arfon commented 9 months ago

@editorialbot set 10.5281/zenodo.10379756 as archive

editorialbot commented 9 months ago

Done! archive is now 10.5281/zenodo.10379756

arfon commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- None

MISSING DOIs

- 10.1093/jahist/jaad098 may be a valid DOI for title: American Religious Ecologies

INVALID DOIs

- None

editorialbot commented 9 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element cYear: This element is not expected.
Element cYear: This element is not expected.
Element cYear: This element is not expected.

arfon commented 9 months ago

@jmotis – I don't think the BibTeX entries with multiple year values are valid (e.g., https://github.com/chnm/Datascribe-module/blob/JOSS/paper.bib#L82). Please could you correct those three entries to only have a single year value?

jmotis commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 months ago

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

arfon commented 9 months ago

@editorialbot recommend-accept

editorialbot commented 9 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 9 months ago

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

OK DOIs

- None

MISSING DOIs

- 10.1093/jahist/jaad098 may be a valid DOI for title: American Religious Ecologies

INVALID DOIs

- None

editorialbot commented 9 months ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4883, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

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