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Use iRODS demo

Mariana Montes

2024-03-16

Source: vignettes/demo.Rmd
demo.Rmd

If you don’t have access to an iRODS server with the iRODS C++ HTTP API installed, you can still try it out with a local demo on Linux or WSL2 (using Linux inside Windows).

As initial requirements, you need bash, docker and the docker-compose plugin in your Linux distribution. You can check if they are installed like so (the command should provide the path to where your version is installed):

which bash
which docker
which docker-compose

You should also start a Docker daemon in your Linux session, for example:

sudo dockerd

Make sure you don’t need sudo for docker, though, by adding yourself to the docker group. You can check that this is the case by running docker run hello-world on the command line.

If you use WSL, you can start RStudio Server with sudo rstudio-server start and run it from your browser (http://localhost:8787). The Posit site has installation instructions for R and RStudio Server in Linux.

Then, in your script or console, load rirods and run use_irods_demo():

The first time you run it it may ask you questions to guiding through generating the first docker image. Once you get the message shown above, you can create the configuration file (if it doesn’t exist yet) and authenticate. Here we authenticate with the default “rods” account, but you could have another account as well; remember that running iauth() will open an interactive dialog to provide a username and password.

create_irods("http://localhost:9001/irods-http-api/0.2.0")
iauth("rods", "rods")
ils()
#> This collection does not contain any objects or collections.

If you have any issues running the demo, check:

  • that you are working from Linux (or WSL2)
  • that you have docker, and docker-compose installed
  • that you don’t need sudo permissions to run docker
  • that you have (re-)installed the package locally after checking all these to be true (and restarted R)
  • that you use the same username and password in use_irods_demo() and in iauth().

If you still have problems, please report them in the Issues of the repository and we’ll try to help you.

Using the development version

If instead of installing rirods with install.packages() you want to use a development version, you need to make sure you have the appropriate submodules to run the demo. Instead of installing with devtools::install_github(), clone the repository (or a fork thereof) and update all submodules:

git clone git@github.com:irods/irods_client_library_rirods.git # clone your fork instead
cd irods_client_library_rirods.git # go to the repository
git submodule update --init inst/irods_demo # update the demo submodule
cd inst/irods_demo # update the sub-submodule
git submodule update --init irods_client_zone_management_tool

Only then, from R, install the package with devtools::install() (either from the project of the package or providing the path to the package).

If you have any issues running the demo, check:

  • that you are working from Linux (or WSL2)
  • that you have docker, and docker-compose installed
  • that you don’t need sudo permissions to run docker
  • that “inst/irods_demo” inside the package repository contains files
  • that “irods_client_zone_management_tool” in “inst/irods_demo” also contains files
  • that you have installed the package locally after checking all these to be true (and restarted R)

If you still have problems, please report them in the Issues of the repository and we’ll try to help you.