[REVIEW]: DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@RoryChenXY@crvernon<!--end-editor-- Reviewers: @elimillera, @pydemull, @ZekeMarshall Archive: 10.5281/zenodo.13777122

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb"><img src="https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb/status.svg)](https://joss.theoj.org/papers/08ca6a54216bb27b7ec37ead6bf951cb)

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

@elimillera & @pydemull & @ZekeMarshall, 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 @crvernon 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 @pydemull

📝 Checklist for @ZekeMarshall

📝 Checklist for @elimillera

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1371/journal.pcbi.1006038 is OK
- 10.1371/journal.pcbi.1009768 is OK
- 10.1007/s10654-023-00997-3 is OK
- 10.1007/s10654-022-00916-y is OK
- 10.1007/s10654-020-00633-4 is OK
- 10.32614/CRAN.package.dplyr is OK
- 10.32614/CRAN.package.DT is OK
- 10.32614/CRAN.package.fontawesome is OK
- 10.32614/CRAN.package.forcats is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.32614/CRAN.package.htmltools is OK
- 10.18637/jss.v040.i03 is OK
- 10.32614/CRAN.package.magrittr is OK
- 10.1201/9780429447273 is OK
- 10.32614/CRAN.package.purrr is OK
- 10.32614/CRAN.package.readr is OK
- 10.32614/CRAN.package.scales is OK
- 10.32614/CRAN.package.shiny is OK
- 10.32614/CRAN.package.shinydashboard is OK
- 10.32614/CRAN.package.shinyjs is OK
- 10.32614/CRAN.package.shinyWidgets is OK
- 10.32614/CRAN.package.stringr is OK
- 10.32614/CRAN.package.tibble is OK
- 10.32614/CRAN.package.tidyr is OK
- 10.21105/joss.01686 is OK
- 10.32614/CRAN.package.useful is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.18637/jss.v040.i03 is OK
- 10.1201/9780429447273 is OK
- 10.21105/joss.01686 is OK
- 10.32614/CRAN.package.golem is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dementias Platform Australia
- No DOI given, and none found for title: Alzheimer’s Disease Data Initiative
- No DOI given, and none found for title: Dementias Platform Australia Data Portal
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

RoryChenXY commented 2 months ago

Hi @crvernon, I hope you are well.

Our centre has a media office, they would like to prepare a media release and have enquired if any update to the publication date could be advised in advance.

Thank you so much!

Best, Rory

RoryChenXY commented 2 months ago

Hi @crvernon,

Apologies for the ignorance. I have now made a tagged release (v1.0.0) and deposited it into Zenodo and hope we are ready to do:

Chen, R. (2024). DataRepExp. In Journal of Open Source Software (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.13777122

Please let me know if any further information is required.

Best wishes, Rory

crvernon commented 2 months ago

Hi @RoryChenXY - I will provide a full response tomorrow morning for you! Thank you!

crvernon commented 2 months ago

@editorialbot set v1.0.0 as version

editorialbot commented 2 months ago

Done! version is now v1.0.0

crvernon commented 2 months ago

@editorialbot set 10.5281/zenodo.13777122 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.13777122

crvernon commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

crvernon commented 2 months ago

:wave: @RoryChenXY - thanks for setting up the archive and version! Here are a few things I need you to address:

In the Zenodo archive:

[x] The 1) tile of the archive and 2) the authors and the order in which they appear need to match what is in your paper exactly. Also, the license you specify in the Zenodo archive should match the one you use in your GitHub repository for the code base. Could you edit the metadata in the Zenodo archive to fix these three things? No need to create another release.

In your paper:

[x] LINES 21-26: I would cut these lines from the paper...so, ending after your CHeBA citation. All of this information can be found in your repository which will be available alongside your paper when it gets published.
[x] Throughout the paper, you only need to cite the Wilkinson et al. paper after the FAIR acronym on the first occurrence. The same goes for the CHeBA citation for DPAU.
[x] LINES 66-68: I would remove the statement: "R programming skill is required for reproducibility, detailed documentation and syntax is open-source and publicly available." as it should be assumed by the reader.
[x] LINE 88: Missing period at the end of the line.
[x] LINE 103: Should "integrative" be "interactive" here?
[x] Please fix references that have characters that need to be capitalized. For example, in LINE 121, "r" should be capitalized. There are others as well so take a look at these and fix them where necessary. You can maintain formatting of particular characters in your bib file by using curly brackets around the characters you wish to maintain the formatting of.

There is no need to create another release after you make these changes. Once you have done these, let me know and I will accept this for publication.

Thanks!

RoryChenXY commented 2 months ago

@crvernon Hi Chris! Thank you for the feedback. I have updated the Zenodo and the paper - except: 'LINE 103: Should "integrative" be "interactive" here?' - It is interactive - meant for the functions enabled with Plotly and DT.

Really appreciate your support!

Cheers, Rory

crvernon commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

crvernon commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.1038/sdata.2016.18 is OK
- 10.1371/journal.pcbi.1006038 is OK
- 10.1371/journal.pcbi.1009768 is OK
- 10.1007/s10654-023-00997-3 is OK
- 10.1007/s10654-022-00916-y is OK
- 10.1007/s10654-020-00633-4 is OK
- 10.32614/CRAN.package.dplyr is OK
- 10.32614/CRAN.package.DT is OK
- 10.32614/CRAN.package.fontawesome is OK
- 10.32614/CRAN.package.forcats is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.32614/CRAN.package.htmltools is OK
- 10.18637/jss.v040.i03 is OK
- 10.32614/CRAN.package.magrittr is OK
- 10.32614/CRAN.package.purrr is OK
- 10.32614/CRAN.package.readr is OK
- 10.32614/CRAN.package.scales is OK
- 10.32614/CRAN.package.shiny is OK
- 10.32614/CRAN.package.shinydashboard is OK
- 10.32614/CRAN.package.shinyjs is OK
- 10.32614/CRAN.package.shinyWidgets is OK
- 10.32614/CRAN.package.stringr is OK
- 10.32614/CRAN.package.tibble is OK
- 10.32614/CRAN.package.tidyr is OK
- 10.21105/joss.01686 is OK
- 10.32614/CRAN.package.useful is OK
- 10.1007/978-3-319-24277-4 is OK
- 10.18637/jss.v040.i03 is OK
- 10.1201/9780429447273 is OK
- 10.21105/joss.01686 is OK
- 10.32614/CRAN.package.golem is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dementias Platform Australia
- No DOI given, and none found for title: Alzheimer’s Disease Data Initiative
- No DOI given, and none found for title: Dementias Platform Australia Data Portal
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 2 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/5941, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Chen given-names: Rory orcid: "https://orcid.org/0000-0002-2094-2682" - family-names: Catts given-names: Vibeke S orcid: "https://orcid.org/0000-0002-9892-0547" - family-names: Vella given-names: Ashleigh orcid: "https://orcid.org/0000-0002-5653-5077" - family-names: Jose given-names: Juan Carlo San orcid: "https://orcid.org/0000-0002-2365-9153" - family-names: Bauermeister given-names: Sarah orcid: "https://orcid.org/0000-0001-9463-6971" - family-names: Bauermeister given-names: Joshua orcid: "https://orcid.org/0000-0002-9154-1392" - family-names: Squires given-names: Emma orcid: "https://orcid.org/0000-0003-0693-5846" - family-names: Thompson given-names: Simon orcid: "https://orcid.org/0000-0001-6799-0705" - family-names: Gallacher given-names: John orcid: "https://orcid.org/0000-0002-2394-5299" - family-names: Sachdev given-names: Perminder S. orcid: "https://orcid.org/0000-0002-9595-3220" doi: 10.5281/zenodo.13777122 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Chen given-names: Rory orcid: "https://orcid.org/0000-0002-2094-2682" - family-names: Catts given-names: Vibeke S orcid: "https://orcid.org/0000-0002-9892-0547" - family-names: Vella given-names: Ashleigh orcid: "https://orcid.org/0000-0002-5653-5077" - family-names: Jose given-names: Juan Carlo San orcid: "https://orcid.org/0000-0002-2365-9153" - family-names: Bauermeister given-names: Sarah orcid: "https://orcid.org/0000-0001-9463-6971" - family-names: Bauermeister given-names: Joshua orcid: "https://orcid.org/0000-0002-9154-1392" - family-names: Squires given-names: Emma orcid: "https://orcid.org/0000-0003-0693-5846" - family-names: Thompson given-names: Simon orcid: "https://orcid.org/0000-0001-6799-0705" - family-names: Gallacher given-names: John orcid: "https://orcid.org/0000-0002-2394-5299" - family-names: Sachdev given-names: Perminder S. orcid: "https://orcid.org/0000-0002-9595-3220" date-published: 2024-09-30 doi: 10.21105/joss.06693 issn: 2475-9066 issue: 101 journal: Journal of Open Source Software publisher: name: Open Journals start: 6693 title: "DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06693" volume: 9 title: "DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 2 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 2 months ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5943
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06693
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

RoryChenXY commented 2 months ago

@crvernon, @elimillera @ZekeMarshall @pydemull - Dear all, huge thanks! I have learned so much through the process. Really appreciate your feedback and help.

crvernon commented 2 months ago

🥳 Congratulations on your new publication @RoryChenXY! Many thanks to @elimillera, @pydemull and @ZekeMarshall for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot commented 2 months ago

: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: [![DOI](https://joss.theoj.org/papers/10.21105/joss.06693/status.svg)](https://doi.org/10.21105/joss.06693) HTML: reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.06693/status.svg :target: https://doi.org/10.21105/joss.06693 ```

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews