Joss-reviews: [REVIEW]: TraitDB: Web application database of phenotypic trait data

[whedon]

Submitting author: @dleehr (Dan Leehr)
Repository: https://github.com/NESCent/TraitDB
Version: v1.0.1
Editor: @pjotrp
Reviewer: @amoeba
Archive: 10.5281/zenodo.2609163

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/94404e364d0cc8e5b7a025743133212c"><img src="http://joss.theoj.org/papers/94404e364d0cc8e5b7a025743133212c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/94404e364d0cc8e5b7a025743133212c/status.svg)](http://joss.theoj.org/papers/94404e364d0cc8e5b7a025743133212c)

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) 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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @pjotrp know.

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

Review checklist for @amoeba

Conflict of interest

• [x] 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

• [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 repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [ ] Version: v1.0.1
• [x] Authorship: Has the submitting author (@dleehr) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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

:star: Important :star:

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:

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

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

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[pjotrp]

@dleehr, we are starting review in this issue tracker. To expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.

[dleehr]

Thanks @pjotrp ! I need to get the tests and installation in order. I'll reply again when that's done.

[dleehr]

OK, ready for the next steps and the PDF looks good to me.

[pjotrp]

Thanks @dleehr. @amoeba you can start review.

[amoeba]

Hi @pjotrp I started my review but encountered some issues I didn't expect (documented on https://github.com/NESCent/TraitDB/issues/222) so I'll need some more time for my review.

[pjotrp]

No worries.

[pjotrp]

@dleehr is this really a blocker?

[amoeba]

Hi @pjotrp, @dleehr has addresses all of my outstanding issues with the review over on https://github.com/NESCent/TraitDB/issues/222 and I've updated the checklist above to reflect that. Everything is in order for your final stamp except

Version: Does the release version given match the GitHub release (v0.9.1)?

which should be updated to 1.0.0 (See: https://github.com/NESCent/TraitDB/releases/tag/v1.0.0).

My review is: Accept (conditional upon the above)

[pjotrp]

Thank you @amoeba! @dleehr to finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI in the bibliography (if one exists).

Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service.

To do so:

1. Create a GitHub release of the current version of your software repository
2. Deposit that release with Zenodo, figshare, or a similar DOI issuer.
3. Post a comment here with the DOI for the release.

[dleehr]

Thanks @pjotrp

First, can you confirm that all references in your bibliography have a DOI in the bibliography

Yes

Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service.

https://doi.org/10.5281/zenodo.2583988

[pjotrp]

@whedon set 10.5281/zenodo.2583988 as archive

[whedon]

OK. 10.5281/zenodo.2583988 is the archive.

[pjotrp]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1038/sdata.2014.15 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[pjotrp]

ping eic @openjournals/joss-eics

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/546

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/546, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[labarba]

Hi @dleehr — Please edit the metadata of the Zenodo deposit (note: no need for a new DOI or version) so the title and author list match the paper.

The paper proof has a References section, but no references listed. Can you check that?

Editorial suggestions/fixes:

• you could merge your first four mini-paragraphs into one paragraph.
• "While these software are technically proficient can facilitate robust operations…" >> something is wrong with this phrase
• "TraitDB aids the ingest of datasets">> grammar? if "ingest" is a verb, why the article?

To be honest, after reading the paper, it's hard to visualize wha the software does. I remind you that the JOSS paper should be understandable to non-specialists. Can you try to improve the readability, overall, and state more clearly what the software _does_?

[pjotrp]

@labarba some valid comment. Except for the last one. I checked the paper for having a topical introduction for laymen. It says that it stores data from different formats using templates. What else do you want to add?

[labarba]

Since the author is requested to make some edits, seems like a final effort to make it read easier is not too much to ask.

[pjotrp]

@dleehr feel free to share your thoughts.

[dleehr]

Appreciate the feedback. I'll take another pass at the paper and make the requested specific changes. Thank you all for your time.

[pjotrp]

@dleehr are you OK?

[dleehr]

Yes. In the middle of an edit today. Will be updating tomorrow.

[dleehr]

Hey @pjotrp, I revised the intro paragraph to move some information up and state the case more clearly to a general audience.

I registered a new DOI at Zenodo: 10.5281/zenodo.2609163, since the auto-generated github submission did not allow any edits (e.g. to correct the author list)

[pjotrp]

@labarba happy?

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[labarba]

@whedon set 10.5281/zenodo.2609163 as archive

[whedon]

OK. 10.5281/zenodo.2609163 is the archive.

[labarba]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[labarba]

@dleehr — Please check your proof, and if you are happy with it, we can proceed to publish your paper. Cheers!

[dleehr]

Looks good to me, thanks!

[labarba]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1038/sdata.2014.15 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/581

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/581, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[labarba]

The XML deposit includes one citation, whereas the paper has no references.

@arfon : Why does whedon find a citation when there are none? Is it picking it up from a .bib file? In that case, should the .bib file be deleted? Is the citation included in the XML going to cause a false citation entry with Crossref?

[arfon]

@arfon : Why does whedon find a citation when there are none? Is it picking it up from a .bib file? In that case, should the .bib file be deleted? Is the citation included in the XML going to cause a false citation entry with Crossref?

Yes please remove the entry from the bibtex file (but don't delete it).

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• https://doi.org/10.1038/sdata.2014.15 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/596

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/596, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/597
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01201
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

@amoeba - many thanks for your review here and to @pjotrp for editing this submission ✨

@dleehr - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01201/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01201/status.svg
   :target: https://doi.org/10.21105/joss.01201

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