jspijker/ricmd

R package for iRODS icommands

ricmd

R package for iRODS icommands. This R package is an interface between R and iRODS the integrated Rule Oriented Data System.

Features

This package tries to implement the core functionality to work with iRODS collections from within R.

With this package you can:

• Connect to an iRODS Zone
• Create and remove collections
• store and retrieve data from a collection
• add and remove meta data from data objects

prerequisites

For this package to run you need Python3. This package is based on the python irodsclient and it uses reticulate to interact with this library.

You also need access to an iRODS zone and make sure that your iRODS environment is set up properly.

This package is developed and tested on Linux systems. If you want to use it on MacOS or Windows, you're on your own.

Release

The current release is version 1.0.0. Version numbers follow the major.minor.patch versioning system. Please, see the [NEWS] (https://github.com/jspijker/ricmd/blob/master/NEWS.md) file for the release info.

Development version

This package is still under development and new features will be added in the future. For example meta data management for collections and search queries on meta data are anticipated.

latest features can be found in the development branches of this package.

This package contains tests. However, for these tests to run successfully a speficic testing environment with an iRODS install is needed.

Install

This package is not (yet) available on CRAN, you can install it directly from GitHub:

remotes::install_github("jspijker/ricmd",build_vignettes=TRUE)

To read the vignette:

vignette("ricmd")

Licence

This package is publicly available under the GPL 3.0 licence, please see accompanying LICENCE file.

ricmd's Issues

Update vignette

Build vignette against irods_demo cluster

ri_getCollection gives cryptic error when no collection is set

ri_getCollection without ri_setCollection gives an error:

Error in get("collection", envir = .ricmdEnv) :            
object 'collection' not found

Explain to user that it should run setCollection first

ri_rm is silent when object doesn't exists

If I use ri_rm to remove an non-existing object, ri_rm is silent. I expect a warning (or error)

Tests ri_metaGet, avuhelpers fails due to extra meta data

When testing against local instance, data objects get object_id by default. Meta data tests count meta data records, which is +1 due to object_id. Make test explicit, don't count but check contents of meta record.

ichmod function

Create function that acts like the ichmod command

create function to return avu list

ri_getMeta returns data.frame with meta data. But sometimes you want the original avu list. create ri_getMetaList function.

be more verbose when no irods session exists

make more verbose error when no session exists. E.g. when using ri_put without calling ri_session()

Error in getSession() : session does not exists 

ri_session fails when irods session needs password authentication

When starting a session with

 session <- irods$iRODSSession(irods_env_file=env)

the password file irodsA is ignored, so user authentication fails.

Update tests to irods_demo

Testing frame uses a custom Docker environment. Update this so it can use the irods_demo environment, see https://github.com/irods/irods_demo.

Skip test if no iRODS cluster is available

If no iRODS is available, tests fail. Detect presence of iRODS. Skip tests if not

ri_getDatadir is not exported in NAMESPACE