[REVIEW]: rdataretriever: An R package for downloading, cleaning, and installing publicly available datasets

[whedon]

Submitting author: @henrykironde (henry senyondo) Repository: https://github.com/ropensci/rdataretriever Version: v3.0.1 Editor: @fboehm Reviewer: @rmhogervorst, @jsgalan Archive: 10.5281/zenodo.4314115

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Reviewer instructions & questions

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

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Review checklist for @rmhogervorst

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
• [x] Contribution and authorship: Has the submitting author (@henrykironde) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @jsgalan

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
• [x] Contribution and authorship: Has the submitting author (@henrykironde) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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

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[whedon]

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

OK DOIs

- 10.1371/journal.pone.0065848 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[fboehm]

@jsgalan and @RMHogervorst - please check boxes above as you complete your review. For any boxes that you can't check right now, due to needed edits or fixes, please discuss the issues here or open issues in the submission repository. And please let me know if you have any questions. Thank you again!

[RMHogervorst]

@henrykironde some notes about the JOSS paper:

The description in Statement of need is really beautiful and only after reading that part I finally understood what the problem is that this package is solving. I really really wish you'd include something like that in the Readme (and maybe Description) too.

REQUIRED:

• Add citations so that the references work in the text.
• I am asked to review a State of the field: Do the authors describe how this software compares to other commonly-used packages? However I don't see that in the paper at this moment. Could you add something about the state of the field? I don't know what the state of the art is at this moment for the field, but I imagine workflow tools like Drake are used? What is the current state of automation/datapreparation? Is everyone using home brewed scripts? I am genuinely curious.

OPTIONAL / SUGGESTIONS:

• I am not very knowledgeable of the world of ecology or environmental sciences but the concept of frictionless data was new for me. Maybe add one sentence about what that entails?

[RMHogervorst]

Required Issues opened:

• [x] https://github.com/ropensci/rdataretriever/issues/261 "make value more clear"
• [x] https://github.com/ropensci/rdataretriever/issues/260 "vignette incomplete"
• [x] https://github.com/ropensci/rdataretriever/issues/257 "clarify OSI licence"

Optional issues opened:

• [x] https://github.com/ropensci/rdataretriever/issues/259 "suggestion for remotes in stead of devtools::install_github"
• [x] https://github.com/ropensci/rdataretriever/issues/262 "is it necessary to download all the scripts"
• [x] https://github.com/ropensci/rdataretriever/issues/263 "vignette of more examples"
• [x] https://github.com/ropensci/rdataretriever/issues/264 "consider more explanation about commit"

[whedon]

:wave: @rmhogervorst, please update us on how your review is going.

[whedon]

:wave: @jsgalan, please update us on how your review is going.

[fboehm]

@jsgalan - I hope that the review is going well. As you work through the checklist above, please check the boxes to reflect your approval of the checklist items. Please let me know if there's something that I might do to assist you. Thanks again!

[henrykironde]

Just an update, @RMHogervorst made some great suggestions and I am working to resolve those. Thanks to the issues btw, I guess @jsgalan is inline with the issues raised.

[fboehm]

Thank you for the update, @henrykironde ! Please let me know how the resolution of issues goes, and don't hesitate to contact me when I might help with something.

[RMHogervorst]

Just an update: I feel @henrykironde and others are doing great work. I really look forward to the finished version!

[henrykironde]

Thanks folks. We have covered all the issues, I am happy to get more recommendations to consider.

[jsgalan]

Hi all, is there any confirmation I might be missing?

I am unable to check the ticks for the revision (Just checked in two distinct browsers to discard a software issue).

Thanks

Ps. has the invitation link expired? Attn: @fboehm

[jsgalan]

Hi all,

No problem in the Conda installation

But a problem was found in the R installation.

Did not found any description on the repository, are there any set requirements for the R installation?

Best

EDIT: I installed version 3.6.3 and everything installed correctly.

[jsgalan]

Hi all, It seems I was not in a top level repository.

All datasets are visible from Python

Had a bit of trouble to finally set up the Reticulate package but everything was set at the end (Extra information that helped https://docs.ropensci.org/rdataretriever/ , https://rstudio.github.io/reticulate/articles/versions.html and https://stackoverflow.com/questions/40788645/how-to-create-renviron-file)

All the tabular datasets and updates were collected correctly

[jsgalan]

Hi all,

I had problems installing the spatial datasets

Even though I have everything set up in Postgres

Any ideas?

Best

[henrykironde]

Thanks @jsgalan for testing this. Make sure you are creating the extensions in the same database that you want to install the data. The default is postgres. In case you, are using a different database, please try to provide the database name in the function call. Let me know if that works

[jsgalan]

@whedon assign @jsgalan

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[jsgalan]

@whedon commands

[whedon]

Here are some things you can ask me to do:

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EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
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# Ask Whedon to check the references for missing DOIs
@whedon check references

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@whedon check repository

[jsgalan]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[jsgalan]

Thanks @jsgalan for testing this. Make sure you are creating the extensions in the same database that you want to install the data. The default is postgres. In case you, are using a different database, please try to provide the database name in the function call. Let me know if that works

Hi all, the extensions are created in all databases. Now I got a problem with finding shp2pgsql

even thought the bin is listed in the $PATH

Plus the binaries are accesible throughout the command line

Any way this can be overridden?

[jsgalan]

@fboehm I am unable to click any of the ticks, and I somehow managed to exclude myself from the reviewers :(

Any way this could change?

[jsgalan]

Hi @henrykironde

Why are there no references in the article proof?

Am I reading the latest version?

Best

[henrykironde]

even thought the bin is listed in the $PATH

Can you try to run psql and or shp2pgsql from command line

About the citation, I will update that to render correctly

[jsgalan]

even thought the bin is listed in the $PATH

Can you try to run psql and or shp2pgsql from command line

They are accesible from the command line

[fboehm]

@fboehm I am unable to click any of the ticks, and I somehow managed to exclude myself from the reviewers :(

Any way this could change?

Yes, Let me fix that @jsgalan.

[fboehm]

@whedon reinvite @jsgalan as reviewer

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[fboehm]

@whedon commands

[whedon]

Here are some things you can ask me to do:

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[fboehm]

@whedon re-invite @jsgalan as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[fboehm]

@jsgalan - sorry for the difficulty. Please click on the link in the previous comment to confirm your addition as a reviewer. After doing that, you should be able to check the boxes for the review, once you're comfortable doing so.

[jsgalan]

@jsgalan - sorry for the difficulty. Please click on the link in the previous comment to confirm your addition as a reviewer. After doing that, you should be able to check the boxes for the review, once you're comfortable doing so.

Thanks @fboehm we will be done with the revision soon

[henrykironde]

@jsgalan, I see you are using a Conda environment, make sure that R has access to the same Python paths as well. Usually, changing to a virtual environment may change the paths. R may be communicating with another python rather that where the programs are installed.

Check the paths in R

library(reticulate)
sys <- import("sys")
sys$path
#Or  
reticulate::py_config()

Compare to the ones when python is used from the terminal

import sys
sys.path

[henrykironde]

@whedon generate pdf

[whedon]

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

[jsgalan]

@jsgalan, I see you are using a Conda environment, make sure that R has access to the same Python paths as well. Usually, changing to a virtual environment may change the paths. R may be communicating with another python rather that where the programs are installed.

Check the paths in R

library(reticulate)
sys <- import("sys")
sys$path
#Or  
reticulate::py_config()

Compare to the ones when python is used from the terminal

import sys
sys.path

Hi that is pointing to the same place

and

[henrykironde]

reticulate::py_config() can we try this too

[jsgalan]

reticulate::py_config() can we try this too

[henrykironde]

Could you please try this in the terminal

import subprocess
subprocess.call('shp2pgsql -d ', shell=True)

This must be a path problem but it is hard for me to replicate on my side. Could you try running it on another machine or in a virtual environment.

[jsgalan]

Could you please try this in the terminal

import subprocess
subprocess.call('shp2pgsql -d ', shell=True)

This must be a path problem but it is hard for me to replicate on my side. Could you try running it on another machine or in a virtual environment.

Hi,

I think it is doing exactly what I am telling it to do .. 👍

I am finding a way to change it from /sh to /bash where everything is set up. That will probably solve it

Best

[RMHogervorst]

@fboehm All my concerns where addressed and the article proof seems in order too (I would advise another read through before publishing, because I think some words are missing, but I'm no native speaker). For me the review is done. It looks great, and you have my approval.

Anything else I need to do?

[fboehm]

@RMHogervorst - Thank you so much for your work on this review! There is nothing left for you to do. I'll proofread the article before publishing.

[fboehm]

@jsgalan - Thanks for your work on this review! Do you have any remaining concerns? or have they all been resolved satisfactorily?

[fboehm]

@whedon generate pdf