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[REVIEW]: Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data. #6704

Open editorialbot opened 5 months ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@CedricMidoux<!--end-author-handle-- (Cédric Midoux) Repository: https://forgemia.inra.fr/migale/easy16s Branch with paper.md (empty if default branch): Version: v24.07 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @adrientaudiere, @tmaklin Archive: 10.57745/ZN1HXQ

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e"><img src="https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e/status.svg)](https://joss.theoj.org/papers/e03bb9530fd2e1c0621e35352b71691e)

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

@adrientaudiere & @tmaklin, 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 @fboehm 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 @adrientaudiere

📝 Checklist for @tmaklin

fboehm commented 1 week ago

@CedricMidoux - we also need the authors' affiliations listed in both the archive and manuscript pdf (on github, ie, here) to match each other.

fboehm commented 1 week ago

Here is what I currently see when I access the archive: screencapture-entrepot-recherche-data-gouv-fr-dataset-xhtml-2024-09-26-17_05_57-edit

CedricMidoux commented 6 days ago

I just fixed it

MIDOUX, CEDRIC; RUÉ, OLIVIER; CHAPLEUR, OLIVIER; BIZE, ARIANE; LOUX, VALENTIN; MARIADASSOU, MAHENDRA, 2024, "Easy16S", https://doi.org/10.57745/ZN1HXQ, Recherche Data Gouv, V1

MIDOUX, CEDRIC (INRAE) - idHAL: cedric-midoux RUÉ, OLIVIER (INRAE) - idHAL: olivier-rue CHAPLEUR, OLIVIER (INRAE) - idHAL: olivier-chapleur BIZE, ARIANE (INRAE) - idHAL: ariane-bize LOUX, VALENTIN (INRAE) - idHAL: valentin-loux MARIADASSOU, MAHENDRA (INRAE) - idHAL: mahendra-mariadassou

Is everything good with RechercheDataGouv ?

fboehm commented 4 days ago

@CedricMidoux - I should have seen this last time, but we actually need the titles of the archive and the joss submission to match exactly. Right now, i see the joss submission title to be "Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data" while it looks like the archive title is: "Easy 16S", ie, the archive is missing the colon and the text that follows. Can you fix this?

thanks again!

CedricMidoux commented 4 days ago

I just fixed the archive name

fboehm commented 3 days ago

I just fixed the archive name

thank you, @CedricMidoux ! The archive title looks good

fboehm commented 3 days ago

Comparing github repo with archive

version number:

archive version: Release v24.07 github submission version: v24.07

license info:

github submission license: from "license.md" file: GNU Affero General Public License Version 3, 19 November 2007 Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/

Archive license info: License/Data Use Agreement Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

Terms of Use GNU Affero General Public License version 3

these two criteria - license & version number matching for github submission & archive - are met

fboehm commented 3 days ago

@editorialbot check references

fboehm commented 3 days ago

@editorialbot generate pdf

editorialbot commented 3 days ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1186/s40168-021-01013-0 is OK
- 10.1038/ismej.2014.202 is OK
- 10.1038/nmeth.3869 is OK
- 10.1186/s13059-014-0550-8 is OK
- 10.32614/CRAN.package.esquisse is OK
- 10.1093/bioinformatics/btx791 is OK
- 10.1111/1755-0998.13847 is OK
- 10.1111/geb.13118 is OK
- 10.1038/nature12506 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.18129/b9.bioc.microbiome is OK
- 10.15454/1.5572390655343293E12 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.watres.2016.05.041 is OK
- 10.1038/nmeth.f.303 is OK
- 10.12688/f1000research.16680.1 is OK
- 10.1186/s12859-020-03666-4 is OK
- 10.32614/CRAN.package.shiny is OK
- 10.1093/bioinformatics/btu616 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
fboehm commented 3 days ago

references look good; no updates needed

fboehm commented 3 days ago

@editorialbot generate pdf

editorialbot commented 3 days ago

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

editorialbot commented 3 days ago

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

fboehm commented 3 days ago

In reading the generated pdf, I didn't find typos or other errors that need fixing.

fboehm commented 3 days ago

@editorialbot recommend-accept

editorialbot commented 3 days ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 3 days ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1186/s40168-021-01013-0 is OK
- 10.1038/ismej.2014.202 is OK
- 10.1038/nmeth.3869 is OK
- 10.1186/s13059-014-0550-8 is OK
- 10.32614/CRAN.package.esquisse is OK
- 10.1093/bioinformatics/btx791 is OK
- 10.1111/1755-0998.13847 is OK
- 10.1111/geb.13118 is OK
- 10.1038/nature12506 is OK
- 10.1371/journal.pcbi.1005404 is OK
- 10.18129/b9.bioc.microbiome is OK
- 10.15454/1.5572390655343293E12 is OK
- 10.1371/journal.pone.0061217 is OK
- 10.1016/j.watres.2016.05.041 is OK
- 10.1038/nmeth.f.303 is OK
- 10.12688/f1000research.16680.1 is OK
- 10.1186/s12859-020-03666-4 is OK
- 10.32614/CRAN.package.shiny is OK
- 10.1093/bioinformatics/btu616 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 3 days ago

:wave: @openjournals/bcm-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/5961, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept