In ices-tools-prod/icesDevops: Functions to link to the ICES Devops webservices

library(knitr)
library(icesDevops)

icesDevops

icesDevops functions to link to the ICES Devops webservices to allow users to interact with ICES TAF git repositoroes, and download summaries and data products from ICES TAF repositories.

icesDevops is implemented as an R package and available on GitHub

Installation

icesVMS can be installed from GitHub using the install_github command from the remotes package:

library(remotes)
install_github("ices-tools-prod/icesDevops")

Usage

For a summary of the package:

library(icesDevops)
?icesDevops

Examples

getting and saving your Personal Access Token (PAT)

To create a PAT login to https://devops.ices.dk and follow the instructions in this link

once you have created the token you need to save it somewhere that is accessible only to you. You must store this token somewhere because you'll never be able to see it again, once you leave that page or close the windows. If you somehow goof this up, just generate a new PAT and, so you don't confuse yourself, delete the lost token.

It is customary to save the PAT as an environment variable in your .Renviron, with the name ICESDEVOPS_PAT.

library(usethis)
edit_r_environ()

usethis::edit_r_environ() will open .Renviron for editing. Add a line like this, but substitute your PAT:

```{sh, eval = FALSE} ICESDEVOPS_PAT=8c70fd8419398999c9ac5bacf3192882193cadf2

Make sure this file ends in a newline! Lack of a newline can lead to
silent failure to load this environment variable, which can be tricky
to debug.

Restart R and confirm your PAT is now available:

```r
Sys.getenv("ICESDEVOPS_PAT")
# or
devops_pat()

list repositories you have access to

To get a list of the repositories you have access to use the following conveinience function, what it does in more detail is listed below.

devops_repos()

At the lowest level, this is how this is done. First form the url, then perform the GET request. Note you will need to have created a Personal Access Token (PAT) and saved this in a variable called pat for this line to work.

res <-
  devops_get(
    devops_url(
      "repositories",
      area = "git"
    )
  )
res

once you have the response, you can extract the content, and parse into a simplyfied structure (where possible, lists are converted to data.frames)

cont <- httr::content(res, simplifyVector = TRUE)

# only show some of the content, for simplicity
repos <- cont$value
repos[c("name", "webUrl")]

clone a repository

test_dir <- file.path(tempdir(), "test")
if (dir.exists(test_dir)) unlink(test_dir, recursive = TRUE, force = TRUE)

# get repository list
repos <- devops_repos()
# get remote url
remote_url <- repos$remoteUrl[repos$name == "test"]
# clone (into a temporary directory)
repo <-
  devops_clone(
    remote_url,
    local_dir = file.path(tempdir(), "test")
  )
repo

make a change to a repo, commit and push

# move into repo and make changes
old_dir <- setwd(workdir(repo))
# run taf.skeleton to ensure all taf files exist
icesTAF::taf.skeleton()
# as a test add some comments to the end of data.R
cat("# some more comments on", date(), "\n", file = "data.R", append = TRUE)
setwd(old_dir)

git2r::status(repo)
# add all files
git2r::add(repo, path = "*")
# commit
git2r::commit(repo, all = TRUE, message = "test changes")
# push!
devops_push(repo)