osfr: R interface to OSF

[aaronwolen]

Submitting Author: Aaron Wolen (@aaronwolen)
Repository: https://github.com/CenterForOpenScience/osfr
Version submitted: 0.2.1
Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD

---

• Paste the full DESCRIPTION file inside a code block below:

Package: osfr
Title: R Interface to OSF
Version: 0.2.1
Authors@R: c(
    person("Aaron", "Wolen",, "aaron@wolen.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2542-2202")),
    person("Chris","Hartgerink",, "chjh@protonmail.com", role = "aut"),
    person("Timothy", "York",, "timothypyork@gmail.com", role = "ctb"),
    person("Richards", "Brian",, "brian.g.richards@gmail.com", role = "ctb"),
    person("Courtney", "Soderberg",, "courtney@cos.io", role = "ctb"))
Description: Manage your projects and access open research materials and data on OSF.
Depends: R (>= 3.1.0)
Imports:
    crul,
    jsonlite,
    stringi,
    purrr,
    tibble,
    rlang,
    fs
License: Apache License 2.0 | file LICENSE
URL: 
    http://centerforopenscience.github.io/osfr, 
    https://github.com/centerforopenscience/osfr
BugReports: https://github.com/centerforopenscience/osfr/issues
LazyData: true
Suggests:
    dplyr,
    testthat,
    knitr,
    rmarkdown,
    lintr,
    covr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
VignetteBuilder: knitr

Scope

• Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):

  • data retrieval
  • data extraction
  • database access
  • data munging
  • data deposition
  • reproducibility
  • geospatial data
  • text analysis

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences):

  osfr provides a suite of functions for interacting with OSF (https://osf.io), a project management repository that supports researchers across their entire project lifecycle. Using osfr and OSF, researchers can create and manage projects, upload and share materials, or explore publicly accessible projects and download the associated files.

• Who is the target audience and what are scientific applications of this package?

  Any R users who rely on OSF for managing their research or working with collaborators.

• Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?

  No.

• If you made a pre-submission enquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.

Technical checks

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:

JOSS Options

• The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

• Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

• The package is novel and will be of interest to the broad readership of the journal.
• The manuscript describing the package is no longer than 3000 words.
• You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see MEE's Policy on Publishing Code)
• (Scope: Do consider MEE's Aims and Scope for your manuscript. We make no guarantee that your manuscript will be within MEE scope.)
• (Although not required, we strongly recommend having a full manuscript prepared when you submit here.)
• (Please do not submit your package separately to Methods in Ecology and Evolution)

Code of conduct

• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

[sckott]

thanks for your submission @aaronwolen

@maelle has been assigned as editor

[maelle]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Thanks for your submission @aaronwolen! Here are a few questions/comments before I can start looking for reviewers.

• The installation instructions should include information about the authentication, and make it clear a token will be needed. Moreover, in a CONTRIBUTING.md file you could explain what scope a token needs for testing the package. I created one with scope for everything. 😁

• The repo also lacks a code of conduct see https://ropensci.github.io/dev_guide/collaboration.html#friendlyfiles

• Two tests fail

── Test failures ────────────────────────────────────────────────────────── testthat ────

> library(testthat)
> library(osfr)
Automatically registered OSF personal access token
> 
> test_check("osfr")
── 1. Error: (unknown) (@test-osf_ls.R#5)  ──────────────────────────────────────────────
Not found.
       HTTP status code 404.
1: osf_retrieve_node("brfza") at testthat/test-osf_ls.R:5
2: raise_error(out)
3: http_error(x$status_code, x$errors[[1]]$detail)
4: stop(args, msg, call. = FALSE)

── 2. Error: (unknown) (@test-osf_tbl.R#37)  ────────────────────────────────────────────
Not found.
       HTTP status code 404.
1: osf_retrieve_node("brfza") at testthat/test-osf_tbl.R:37
2: raise_error(out)
3: http_error(x$status_code, x$errors[[1]]$detail)
4: stop(args, msg, call. = FALSE)

══ testthat results  ════════════════════════════════════════════════════════════════════
OK: 90 SKIPPED: 1 FAILED: 2
1. Error: (unknown) (@test-osf_ls.R#5) 
2. Error: (unknown) (@test-osf_tbl.R#37) 

Error: testthat unit tests failed
Execution halted

1 error ✖ | 0 warnings ✔ | 0 notes ✔

I have not looked in detail, is it because this is a node that only exists in the account you use for testing? Couldn't the node be created before testing so that anyone can run the tests?

• goodpractice::gp() mentions a few too long code lines.

• I see there are a few open issues in your repo, labelled "feature requests". Are these features you plan to implement in the near future? In particular, before reviews?

---

Reviewers: @HeidiSeibold @cboettig
Due date: 2018-02-20

[aaronwolen]

Hi, @maelle! Thanks for checking out the package and I apologize for the delayed response—I’ve been out traveling most of this week and am still playing catchup.

I made the following changes based on your comments:

• added a code of conduct (ropensci/osfr@e6db814)

• added a note to the README explaining a PAT is necessary to manage projects and upload files, along with a link to the Authenticating osfr vignette (ropensci/osfr@68e29f3)

• indicated that contributors need to generate a PAT on the testing server with all scopes enabled (ropensci/osfr@1f601ca, ropensci/osfr@3f520fa)

• reformatted many of the overly long lines (ropensci/osfr@eb9a81b)

  (There are still a few places where I’m breaking the 80 line rule, primarily for errors, warnings, and other messages that aren’t as easily split up.)

Regarding the test failures you encountered, I believe the problem was the tests were run on the main OSF server (osf.io) and several of the required resources are located on OSF’s testing server (test.osf.io), which is where COS prefers development take place. The contributing guidelines mention you need to set OSF_SERVER=test to switch to the testing server, but it’s easy to miss.

This really underscored that the testing infrastructure was a little fragile, so I did some restructuring and added checks to skip certain tests if they’re being run on the production server or if no PAT is defined (ropensci/osfr@81cfe71). It was a big enough change that I bumped the version to 0.2.2.

Thanks again for looking it over and please let me know if you have any other questions or follow-up comments.

[maelle]

Thanks @aaronwolen, great work! Sorry for missing the contributing guidelines! Two small suggestions:

• "Create a .Renviron file in the root of your project directory" or one could edit the existing general .Renviron/create one (that's what I did :-) ). You could mention the handy usethis::edit_r_environ() function for that.

• Regarding the long lines, you could add # nolint at the end of the ones you do not want to split cf https://github.com/jimhester/lintr#project-configuration

I'll now look for reviewers! 😸

[aaronwolen]

Great suggestions! I did not know about edit_r_environ()—that package is just chock full of goodness—I’ll be sure to mention it.