Developing rirods
In rirods: R Client for 'iRODS'

knitr::opts_chunk$set(
  collapse = TRUE,
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)

Contributing to rirods development

To contribute to {rirods} fork the source files from: https://github.com/irods/irods_client_library_rirods, and make a Pull Request.

Prerequisites R

The following R packages are furthermore required for development: xml2, purrr, readr, testthat (>= 3.0.0), knitr, rmarkdown, spelling, kableExtra, and httptest2. For convenience, one can also use renv () and renv::restore() to install all dependencies. The usethis and the devtools packages are further suggestions to streamline development. See devtools and usethis for common development tasks and setups covered by these packages.

Development of rirods relies on the httptest2 which enables testing of the logic on the R side of the API without requiring access to the remote service. It does this by recording the API response as mock files. These mock files are stored in several directories under tests/testthat/.

Prerequisites iRODS

The unit test included in the source files can either be run against a local or remote iRODS C++ HTTP API service - https://github.com/irods/irods_client_http_api.

Local server

Launch a local demonstration iRODS service (including the HTTP API):

```{bash, eval=FALSE}

clone the repository (and submodule "irods_demo")

or use `git submodule update --init` when already cloned without submodules

git clone --recurse-submodules https://github.com/irods/irods_demo

start the REST API

cd irods_demo docker compose up -d nginx-reverse-proxy irods-client-http-api irods-client-icommands

Alternatively, one can use the R function `use_irods_demo()`.

Note, that both options can only be used if Docker and the Docker-compose plugin are installed.

This will result in the demonstration HTTP API running at `r rirods:::.irods_host` (or later version). 
No further configuration in R is needed for development (except for removing 
possible mock files). For example, to run the unit tests against this local 
server use: `devtools::test()`.

For miscellaneous development tasks one can, furthermore, use: `usethis::local_project`. 
This test fixture uses an alternative directory as the working directory thereby preventing 
cluttering of the package source files (defaults to a temporary directory). The working directory can be restored to the 
package directory by restarting the R session (possibly with `CTRL + SHIFT + F10`) or by running `withr::deferred_run()`. 

### Remote server

Testing against a remote server requires the specification of server 
information. This information needs to be entered in the `.Rprofile` file:

```r
# dependency management
options(renv.settings.snapshot.type = "explicit")
source("renv/activate.R")

# development key (create key with httr2::secret_make_key() and place in user
# level environment variables. One can use usethis::edit_r_environ() for this.
# Store the key under "DEV_KEY_IRODS")

# iRODS environment variables for development
Sys.setenv(DEV_HOST_IRODS = "nLO8T0IpHCT2kXklYE-IB0HjYpNkg5wN4ZKk7TPSvkwGf9FauDR-O5mVI-mmD2_zNFGLoaVcAgYl")
Sys.setenv(DEV_USER = "ZGlORquE2G6BIPS5JAcuPcngmBB6Wg")
Sys.setenv(DEV_PASS = "ZGlORquE2G6BIPS5JAcuPcngmBB6Wg")

The server information is stored in the environmental variables DEV_HOST_IRODS , DEV_USER, and DEV_PASS. Server information is provided in scrambled format to prevent leakage of sensitive information to GitHub.

The following step are needed to scramble this information.

1) Generate package development key:

httr2::secret_make_key()

2) Store the package development key as an environmental variable at the user level. For convenience one can use usethis::edit_r_environ() which opens the .Renviron file. Enter your key by replacing <key> as follows:

DEV_KEY_IRODS="<key>"

3) Scramble the iRODS server information with httr2::secret_encrypt(). For example, scramble the host name as follows:

httr2::secret_encrypt("http://localhost:9001/irods-http-api/0.1.0" ,"DEV_KEY_IRODS")

4) Store the scrambled information at the designated places in the project level .Rprofile: host name under DEV_HOST_IRODS, user name under DEV_USER, and password under DEV_PASS.

5) Restart the R sessions (possibly with CTRL + SHIFT + F10).

Note that the unit tests are built against a clean server with only one user (i.e., DEV_USER).