[REVIEW]: citesdb: A high-performance database of shipment-level CITES trade data #1483

whedon · 2019-05-30T22:12:55Z

Submitting author: @noamross (Noam Ross)
Repository: https://github.com/ropensci/citesdb
Version: 0.2.0
Editor: @kyleniemeyer
Reviewer: @kyleniemeyer
Archive: 10.5281/zenodo.3234871

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/819096e68b6d90011ac8485f07d95b94/status.svg)](http://joss.theoj.org/papers/819096e68b6d90011ac8485f07d95b94)

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

@kyleniemeyer, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @kyleniemeyer

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: Does the release version given match the GitHub release (0.2.0)?
Authorship: Has the submitting author (@noamross) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

The text was updated successfully, but these errors were encountered:

whedon · 2019-05-30T22:12:58Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @kyleniemeyer it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-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:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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@whedon commands

whedon · 2019-05-30T22:12:59Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-30T22:13:06Z

PDF failed to compile for issue #1483 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1483/inst/paper.md): did not find expected key while parsing a block mapping at line 2 column 1 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse_stream'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:in load'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in open'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:95:in load_yaml'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

kyleniemeyer · 2019-05-30T22:42:23Z

@noamross it looks like there is an issue with the YAML header in the paper preventing compilation

noamross · 2019-05-31T15:41:03Z

Thanks. Just pushed a fix - there was mis-indented line.

kyleniemeyer · 2019-05-31T16:57:55Z

@whedon generate pdf

whedon · 2019-05-31T16:57:57Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T16:58:12Z

PDF failed to compile for issue #1483 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Noam Ross, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/author.rb:57:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:141:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:141:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:138:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:138:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon.rb:84:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-379fcd917139/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

kyleniemeyer · 2019-05-31T17:06:43Z

@noamross ah, one more thing to fix. The affiliations need to be structured like this instead:

authors:
 - name: Noam Ross
   orcid: 0000-0002-2136-0000
   affiliation: 1
 - name: Evan A. Eskew
   orcid: 0000-0002-1153-5356
   affiliation: 1
 - name: Nicolas Ray
   affiliation: "2, 3"

(the quotes are needed for multiple affiliations)

noamross · 2019-05-31T17:17:43Z

Fixed and pushed

noamross · 2019-05-31T17:31:41Z

@whedon generate pdf

whedon · 2019-05-31T17:31:44Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T17:32:25Z

👉 Check article proof 📄 👈

eveskew · 2019-05-31T20:01:43Z

@whedon generate pdf

whedon · 2019-05-31T20:01:46Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T20:02:13Z

👉 Check article proof 📄 👈

noamross · 2019-05-31T20:16:58Z

@whedon generate pdf

whedon · 2019-05-31T20:17:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T20:17:36Z

👉 Check article proof 📄 👈

eveskew · 2019-05-31T20:55:38Z

@whedon generate pdf

whedon · 2019-05-31T20:55:40Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T20:56:09Z

👉 Check article proof 📄 👈

kyleniemeyer · 2019-05-31T21:46:14Z

@noamross can you archive the repo on Zenodo and provide the DOI? (or just the latter if the former has already been done)

kyleniemeyer · 2019-05-31T21:47:10Z

@noamross nvm, I found that in the README.

kyleniemeyer · 2019-05-31T21:47:25Z

@whedon set 10.5281/zenodo.3234871 as archive

whedon · 2019-05-31T21:47:28Z

OK. 10.5281/zenodo.3234871 is the archive.

kyleniemeyer · 2019-05-31T21:47:35Z

@whedon accept

whedon · 2019-05-31T21:47:38Z

Attempting dry run of processing paper acceptance...

whedon · 2019-05-31T21:47:54Z


OK DOIs

- 10.1017/S0030605302000637 is OK
- 10.1038/nature11145 is OK
- 10.1111/cobi.12240 is OK
- 10.1111/cobi.12448 is OK
- 10.1126/science.aaf3565 is OK
- 10.3897/natureconservation.21.13071 is OK
- 10.1126/science.aan5158 is OK
- 10.1016/j.biocon.2018.05.025 is OK
- 10.1016/j.biocon.2018.04.017 is OK
- 10.1111/cobi.13095 is OK
- 10.1016/j.gecco.2019.e00631 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.475/123_4 is INVALID

whedon · 2019-05-31T21:48:14Z

Check final proof 👉 openjournals/joss-papers#725

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#725, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer · 2019-05-31T21:54:51Z

@noamross @eveskew it looks like the DOI for the Raasveldt and Muhleisen 2018 reference is not correct. Could you fix this and let me know when you have?

noamross · 2019-05-31T23:02:49Z

Just fixed, thanks.

noamross · 2019-05-31T23:03:29Z

@whedon generate pdf

whedon · 2019-05-31T23:03:31Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-31T23:04:11Z

👉 Check article proof 📄 👈

kyleniemeyer · 2019-05-31T23:06:53Z

@whedon accept

whedon · 2019-05-31T23:06:56Z

Attempting dry run of processing paper acceptance...

whedon · 2019-05-31T23:07:13Z


OK DOIs

- 10.1145/3183713.3183722 is OK
- 10.1017/S0030605302000637 is OK
- 10.1038/nature11145 is OK
- 10.1111/cobi.12240 is OK
- 10.1111/cobi.12448 is OK
- 10.1126/science.aaf3565 is OK
- 10.3897/natureconservation.21.13071 is OK
- 10.1126/science.aan5158 is OK
- 10.1016/j.biocon.2018.05.025 is OK
- 10.1016/j.biocon.2018.04.017 is OK
- 10.1111/cobi.13095 is OK
- 10.1016/j.gecco.2019.e00631 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-05-31T23:07:26Z

Check final proof 👉 openjournals/joss-papers#728

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#728, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer · 2019-05-31T23:08:48Z

@whedon accept deposit=true

whedon · 2019-05-31T23:08:51Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2019-05-31T23:09:28Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-05-31T23:09:28Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01483 joss-papers#729
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01483
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

noamross · 2019-05-31T23:58:58Z

Review of the source code can be found at ropensci/software-review#292

kyleniemeyer · 2019-06-02T00:14:39Z

@noamross congrats on your submission's publication in JOSS, and thanks for sharing that link in here for future reference.

whedon · 2019-06-02T00:14:43Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01483/status.svg)](https://doi.org/10.21105/joss.01483)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01483">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01483/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01483/status.svg
   :target: https://doi.org/10.21105/joss.01483

This is how it will look in your documentation:

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noamross · 2019-06-03T21:34:08Z

@arfon @kyleniemeyer We noticed after acceptance in the two authors have same initials so the initial used in our Acknowledgements section are ambiguous. We've pushed a change to use our full names to clear this up. Is it possible to re-build to fix at this stage?

arfon · 2019-06-03T21:42:36Z

Sure thing. Fixing...

arfon · 2019-06-03T21:47:29Z

OK, the PDF is fixed here: https://github.com/openjournals/joss-papers/blob/master/joss.01483/10.21105.joss.01483.pdf

It can take a few hours before the caching of the PDFs expires so you might not see this change reflected on the JOSS site immediately.

whedon assigned kyleniemeyer May 30, 2019

whedon added the review label May 30, 2019

whedon mentioned this issue May 30, 2019

[PRE REVIEW]: citesdb: A high-performance database of shipment-level CITES trade data #1482

Closed

whedon added the accepted label May 31, 2019

kyleniemeyer closed this as completed Jun 2, 2019

arfon added the rOpenSci Submissions associated with rOpenSci label Feb 6, 2020

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

editorialbot mentioned this issue Jan 29, 2024

[PRE REVIEW]: whalestrike: An R package for simulating ship strikes on whales #6303

Closed

[REVIEW]: citesdb: A high-performance database of shipment-level CITES trade data #1483

[REVIEW]: citesdb: A high-performance database of shipment-level CITES trade data #1483

Comments

whedon commented May 30, 2019 • edited Loading

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