rirods

rirods R Package

https://github.com/irods/irods_client_library_rirods

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rirods R Package

README.Rmd

---
output: 
  github_document:
    md_extensions: [ 
      "-autolink_bare_uris" 
    ]
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
knitr::opts_knit$set(
  root.dir = tempdir()
)
```

# rirods 


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The rirods package is an R client for iRODS.

## Installation

You can install the latest CRAN version of rirods like so:

```r
install.packages("rirods")
```

Or, the development version from GitHub, like so:

``` r
# install.packages("devtools")
devtools::install_github("irods/irods_client_library_rirods")
```

## Prerequisites

This package connects to the iRODS C++ HTTP API - https://github.com/irods/irods_client_http_api.

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

```{r echo=FALSE}
library(rirods)
```

```{r setup, eval=FALSE}
# load
library(rirods)
# setup a mock iRODS server (https://github.com/irods/irods_demo)
use_irods_demo("alice", "passWORD")
```

```{r rmirods, echo=FALSE}
unlink(rirods:::path_to_irods_conf())
```

This will result in the demonstration HTTP API running at `r URLencode(rirods:::.irods_host)`.

These Docker containers are designed to easily stand up a **DEMONSTRATION** of the iRODS server. It is intended for education and exploration. (See also `vignette("demo")`.)

**DO NOT USE IN PRODUCTION**

## Example Usage

To connect to the HTTP API endpoint of your choice, load `rirods`, connect with `create_irods()`, and authenticate with your iRODS credentials:

```{r project_mock, echo=FALSE, comment=""}
substitute(create_irods(x), list(x = rirods:::.irods_host))
```

```{r project, eval=is_irods_demo_running(), echo=FALSE}
eval(substitute(create_irods(x), list(x = rirods:::.irods_host)))
```

### Authentication

In this example Alice is a user of iRODS and she can authenticate herself with `iauth("alice")`. This prompts a dialog where you can enter your password without hardcoding this information in your scripts.

```{r, Alice, eval=FALSE}
# login as alice with password "passWORD"
iauth("alice") # or iauth("alice", "passWORD")
```

```{r, secret, include=FALSE, eval=is_irods_demo_running()}
# login as alice
iauth("alice", "passWORD")
```

### Save R objects

Suppose Alice would like to upload an R object from her current R session to an iRODS collection. For this, use the `isaveRDS()` command:

```{r put, eval=is_irods_demo_running()}
# some data
foo <- data.frame(x = c(1, 8, 9), y = c("x", "y", "z"))

# check where we are in the iRODS namespace
ipwd()

# store data in iRODS
isaveRDS(foo, "foo.rds")
```

### Metadata

To truly appreciate the strength of iRODS, we can add some metadata that describes the data object "foo":

```{r meta, eval=is_irods_demo_running()}
# add some metadata
imeta(
  "foo.rds", 
  operations = 
    data.frame(operation = "add", attribute = "foo", value = "bar", units = "baz")
)

# check if file is stored with associated metadata
ils(metadata = TRUE)
```

For more on using metadata, check out `vignette("metadata")`.

### Read R objects

If Alice wanted to copy the foo R object from an iRODS collection to her current R session, she would use `ireadRDS()`:

```{r get, eval=is_irods_demo_running()}
# retrieve in native R format
ireadRDS("foo.rds")
```

### Other file formats

Possibly Alice does not want a native R object to be stored on iRODS but a file type that can be accessed by other programs. For this, use the `iput()` command:

```{r filetypes, eval=requireNamespace("readr") & is_irods_demo_running()}
library(readr)

# creates a csv file of foo
write_csv(foo, "foo.csv")

# send file
iput("foo.csv", "foo.csv")

# check whether it is stored
ils()
```

```{r rmfile, include=FALSE, eval=requireNamespace("readr") & is_irods_demo_running()}
unlink("foo.csv")
```

Later on somebody else might want to download this file again and store it locally:

```{r csv, eval=requireNamespace("readr") & is_irods_demo_running()}
# retrieve it again later
iget("foo.csv", "foo.csv")
read_csv("foo.csv")
```

### Query

By adding metadata you and others can more easily discover data in future projects. Objects can be searched with General Queries and `iquery()`:

```{r query, eval=is_irods_demo_running()}
# look for objects in the home collection with a wildcard `%`
iquery("SELECT COLL_NAME, DATA_NAME WHERE COLL_NAME LIKE '/tempZone/home/%'")
```

```{r query2, eval=is_irods_demo_running()}
# or for data objects with a name that starts with "foo"
iquery("SELECT COLL_NAME, DATA_NAME WHERE DATA_NAME LIKE 'foo%'")
```

For more on querying, check out `vignette("metadata")`.

### Cleanup

Finally, we can clean up Alice's home collection:

```{r clean, eval=requireNamespace("readr") & is_irods_demo_running()}
# delete object
irm("foo.rds", force = TRUE)
irm("foo.csv", force = TRUE)

# check if objects are removed
ils()
```

```{r down, eval=is_irods_demo_running()}
# close the server
stop_irods_demo()
# optionally remove the Docker images
# irods:::remove_docker_images()
```

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