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[REVIEW]: GRLC - the Git Repository Linked data api Constructor #2731

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: @c-martinez (Carlos Martinez-Ortiz) Repository: https://github.com/CLARIAH/grlc Version: v1.3.7 Editor: @arfon Reviewer: @essepuntato, @alexdma Archive: 10.5281/zenodo.5644276

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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

@essepuntato & @alexdma, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @lorenanicole 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 ✨

Review checklist for @essepuntato

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @alexdma

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @essepuntato, @alexdma it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 4 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18174/505685 is OK

MISSING DOIs

- 10.1007/978-3-030-30796-7_28 may be a valid DOI for title: Easy Web API Development with SPARQL Transformer
- 10.1007/978-3-319-47602-5_48 may be a valid DOI for title: grlc Makes GitHub Taste Like Linked Data APIs
- 10.1007/978-3-319-70407-4_27 may be a valid DOI for title: SPARQL2Git: Transparent SPARQL and Linked Data API Curation via Git
- 10.1007/978-3-319-68204-4_30 may be a valid DOI for title: Automatic Query-Centric API for Routine Access to Linked Data

INVALID DOIs

- None
whedon commented 4 years ago

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

arfon commented 3 years ago

:wave: @essepuntato, @alexdma - happy new year! From the looks of things, neither of you have made any progress on your reviews here. Do you think you might be able to complete your initial review in the next two weeks?

alexdma commented 3 years ago

My apologies @arfon - it is certainly no justification that I have moved to a new job and country in the meantime.

I'm trying to work through it but I can't seem to be able to tick any of the checkboxes on my list (code of conduct etc.) - how do I do that? The issue does not seem to be editable.

arfon commented 3 years ago

@whedon re-invite @alexdma as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@alexdma please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

arfon commented 3 years ago

I'm trying to work through it but I can't seem to be able to tick any of the checkboxes on my list (code of conduct etc.) - how do I do that? The issue does not seem to be editable.

Thanks for the update @alexdma. Please accept the invite from @whedon above and then you should be able to update the checklist.

alexdma commented 3 years ago

Hi - Does the Software paper section of the review checklist refer to the article as found here: https://github.com/openjournals/joss-papers/blob/joss.02731/joss.02731/10.21105.joss.02731.pdf ?

Thanks

arfon commented 3 years ago

Yes, that's correct @alexdma

alexdma commented 3 years ago

Thank you @arfon - if I have any recommendation regarding that paper, should the issue be filed with the GRLC code repository or somewhere else?

arfon commented 3 years ago

@alexdma - please open issues on the associated repository (https://github.com/CLARIAH/grlc) and mention this issue when doing so (https://github.com/openjournals/joss-reviews/issues/2731), that way they will be cross-linked.

arfon commented 3 years ago

:wave: @essepuntato - just checking in here - do you need any assistance with your review?

lorenanicole commented 3 years ago

@essepuntato just bumping the below to see if you needed anything additional:

https://github.com/openjournals/joss-reviews/issues/2731#issuecomment-774939456

essepuntato commented 3 years ago

Hi @arfon and @lorenanicole,

I really apologies for my silence - strangely, all your messages went to my SPAM folder and I did not notice them until now. Of course, this is not a justification, since I am tremendously late with the review that, honestly, I totally forgot about it. Thus, please accept my sincere apologies for it.

Back to the topic: I won't be able to address it this week due to prior commitments, but you can expect the review by the end of the next week. Apologies again and have a nice day :-)

lorenanicole commented 3 years ago

No worries, thank you @essepuntato for the update! Just ping us back on this channel in a week to let us know if you need anything (e.g. more time).

arfon commented 3 years ago

:wave: @essepuntato – just checking in here. Do you think you might be able to provide your review in the next couple of weeks?

c-martinez commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

arfon commented 3 years ago

I just emailed @essepuntato directly to see when they might be able to complete their review by.

essepuntato commented 3 years ago

Hi @arfon,

Apologies again, and thanks for writing directly to me to remind the review - as before, all the GitHub messages went to the SPAM folder. I've completed my review, and wrote an issue to the authors of the tool with some comments about how to improve some aspects (mainly the accompanying paper).

Have a nice day :-)

arfon commented 3 years ago

Apologies again, and thanks for writing directly to me to remind the review - as before, all the GitHub messages went to the SPAM folder. I've completed my review, and wrote an issue to the authors of the tool with some comments about how to improve some aspects (mainly the accompanying paper).

Wonderful, thank you so much @essepuntato!

arfon commented 3 years ago

@c-martinez – how are you getting along here? Have you had a chance to incorporate the feedback from our reviewers?

c-martinez commented 3 years ago

Hi @arfon -- we are working on it, but still have a couple of points to address. I think we should be done in the next couple of weeks.

arfon commented 3 years ago

@whedon assign me as editor

Unfortunately @lorenanicole is no longer able to edit this submission so I'll be taking over from here.

c-martinez commented 3 years ago

Hi @arfon -- it took a bit longer than expected, but we've now addressed the last of @essepuntato 's comments in https://github.com/CLARIAH/grlc/issues/356. Thanks for all the useful feedback!

arfon commented 3 years ago

Got it. Thanks @c-martinez. It looks like there are still a couple of issues open on your repo related to the review (e.g., https://github.com/CLARIAH/grlc/issues/311 and https://github.com/CLARIAH/grlc/issues/327). Could you share what your intent here is?

:wave: @essepuntato, @alexdma – could you take a look at the changes that @c-martinez has made and see if you are able to update the remaining checkboxes for the review?

c-martinez commented 3 years ago

I see those two (particularly https://github.com/CLARIAH/grlc/issues/327) as future improvements -- we will leave the issues open and implement them in the future, but that might take a while.

Is that acceptable? Or is it preferable to close them before moving forward?

arfon commented 3 years ago

Is that acceptable? Or is it preferable to close them before moving forward?

I think it's fine to leave them as potential future improvements. I would still like to hear back from @essepuntato & @alexdma that they have completed their reviews and are happy with the state of the submission at this point before moving forward. What do you think @essepuntato & @alexdma? Are you still waiting on changes by the authors at this point?

essepuntato commented 3 years ago

That's fine with me: considering them as future development is appropriate.

alexdma commented 3 years ago

I'm fine to consider CLARIAH/grlc#327 for the future.

However, I would still urge the authors to add a couple of guidelines on using linked data fragments on their quicktutorial Wiki: that would be enough for a quick fulfilment of CLARIAH/grlc#311 since the feature is advertised.

arfon commented 3 years ago

However, I would still urge the authors to add a couple of guidelines on using linked data fragments on their quicktutorial Wiki: that would be enough for a quick fulfilment of CLARIAH/grlc#311 since the feature is advertised.

That sounds like a good idea.

alexdma commented 3 years ago

I have updated the reviewer checklist following core issues now solved. Everything checks. Thanks to the authors for all the work done to onboard the advice!

arfon commented 3 years ago

@c-martinez – At this point 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:

I can then move forward with accepting the submission.

c-martinez commented 3 years ago

Great, thanks @arfon !

I've just made a release in Zenodo

I hope everything is as expected?

arfon commented 3 years ago

@whedon set 10.5281/zenodo.5644276 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5644276 is the archive.

arfon commented 3 years ago

@whedon set v1.3.7 as version

whedon commented 3 years ago

OK. v1.3.7 is the version.

arfon commented 3 years ago

@whedon check references

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

OK DOIs

- 10.18174/505685 is OK
- 10.1016/j.websem.2016.03.003 is OK

MISSING DOIs

- 10.1007/978-3-030-30796-7_28 may be a valid DOI for title: Easy Web API Development with SPARQL Transformer
- 10.1007/978-3-319-47602-5_48 may be a valid DOI for title: grlc Makes GitHub Taste Like Linked Data APIs
- 10.1007/978-3-319-70407-4_27 may be a valid DOI for title: SPARQL2Git: Transparent SPARQL and Linked Data API Curation via Git
- 10.1007/978-3-319-68204-4_30 may be a valid DOI for title: Automatic Query-Centric API for Routine Access to Linked Data

INVALID DOIs

- https://doi.org/10.1016/j.websem.2021.100655 is INVALID because of 'https://doi.org/' prefix
arfon commented 3 years ago

@c-martinez - could you please check if those DOIs recommended by Whedon are correct, and if so, add them to your BibTeX file? Also, this one https://doi.org/10.1016/j.websem.2021.100655 should be written as 10.1016/j.websem.2021.100655 in your BibTeX file please.

c-martinez commented 3 years ago

Sure no problem -- is a new release necessary after fixing those?

arfon commented 3 years ago

Sure no problem -- is a new release necessary after fixing those?

No, we can just stick with the same release number and Zenodo archive.

c-martinez commented 3 years ago

Great -- I've added the DOI's recommended by Wheadon.

arfon commented 3 years ago

@whedon check references

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

OK DOIs

- 10.1016/j.websem.2021.100655 is OK
- 10.1007/978-3-030-30796-7_28 is OK
- 10.18174/505685 is OK
- 10.1007/978-3-319-47602-5_48 is OK
- 10.1007/978-3-319-70407-4_27 is OK
- 10.1007/978-3-319-68204-4_30 is OK
- 10.1016/j.websem.2016.03.003 is OK

MISSING DOIs

- None

INVALID DOIs

- None
arfon commented 3 years ago

@whedon recommend-accept

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

OK DOIs

- 10.1016/j.websem.2021.100655 is OK
- 10.1007/978-3-030-30796-7_28 is OK
- 10.18174/505685 is OK
- 10.1007/978-3-319-47602-5_48 is OK
- 10.1007/978-3-319-70407-4_27 is OK
- 10.1007/978-3-319-68204-4_30 is OK
- 10.1016/j.websem.2016.03.003 is OK

MISSING DOIs

- None

INVALID DOIs

- None