virtuoso

:package: Interact with Virtuoso Open Source database instances from R

https://github.com/ropensci/virtuoso

Science Score: 26.0%

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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Scientific vocabulary similarity
Low similarity (19.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

:package: Interact with Virtuoso Open Source database instances from R

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/virtuoso
Size: 640 KB

Statistics

Stars: 9
Watchers: 2
Forks: 5
Open Issues: 2
Releases: 2

Created over 7 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

README.Rmd

---
output: github_document
---


# virtuoso 

[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
[![Travis build status](https://travis-ci.org/ropensci/virtuoso.svg?branch=master)](https://travis-ci.org/ropensci/virtuoso)
[![Build status](https://ci.appveyor.com/api/projects/status/x5r18x1cvu6khksd/branch/master?svg=true)](https://ci.appveyor.com/project/cboettig/virtuoso/branch/master)
[![Coverage status](https://codecov.io/gh/ropensci/virtuoso/branch/master/graph/badge.svg)](https://codecov.io/github/ropensci/virtuoso?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/virtuoso)](https://cran.r-project.org/package=virtuoso) 
[![Peer review](http://badges.ropensci.org/271_status.svg)](https://github.com/ropensci/software-review/issues/271)

 


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


The goal of virtuoso is to provide an easy interface to Virtuoso RDF database from R. 

## Installation

You can install the development version of virtuoso from GitHub with:

``` r
remotes::install_github("ropensci/virtuoso")
```

## Getting Started

```{r}
library(virtuoso)
```

For Mac users, `virtuoso` package includes a utility function to install and configure a local Virtuoso Open Source instance using Homebrew.  Otherwise, simply install the Virtuoso Open Source edition for your operating system. 


```{r install}
vos_install()
```

We can now start our Virtuoso server from R:

```{r}
vos_start()
```



 Once the server is running, we can connect to the database.

```{r}
con <- vos_connect()
```

Our connection is now live, and accepts SPARQL queries directly.  

```{r}
DBI::dbGetQuery(con, "SPARQL SELECT * WHERE { ?s ?p ?o } LIMIT 4")
```

## DSL

`virtuoso` also provides wrappers around some common queries to make it easier to work with Virtuoso and RDF.

The bulk loader can be used to quickly import existing sets of triples. 

```{r}
example <- system.file("extdata", "person.nq", package = "virtuoso")
vos_import(con, example)
```

Can also read in compressed formats as well.  Remember to set the pattern match appropriately.  This is convenient because N-Quads compress particularly well, often by a factor of 20 (or rather, can be particularly large when uncompressed, owing to the repeated property and subject URIs).  

```{r}
ex <- system.file("extdata", "library.nq.gz", package = "virtuoso")
vos_import(con, ex)
```

`vos_import` invisibly returns a table of the loaded files, with error message and loading times.  If a file cannot be imported, an error message is returned:

```{r error = TRUE}
bad_file <- system.file("extdata", "bad_quads.nq", package = "virtuoso")
vos_import(con, bad_file)
```

 
We can now query the imported data using SPARQL.  

```{r}
df <- vos_query(con, 
"SELECT ?p ?o 
 WHERE { ?s ?p ?o .
        ?s a 
       }")
head(df)
```

```{r}
vos_query(con, 
"SELECT ?p ?o 
 WHERE { ?s ?p ?o .
        ?s a 
       }")
```


## Server controls

We can control any `virtuoso` server started with `vos_start()` using a series of helper commands.  

```{r}
vos_status()
```

Advanced usage note: `vos_start()` invisibly returns a `processx` object which we can pass to other server control functions, or access the embedded `processx` control methods directly.  The `virtuoso` package also caches this object in an environment so that it can be accessed directly without having to keep track of an object in the global environment. Use `vos_process()` to return the `processx` object.  For example:

```{r}
library(ps)
p <- vos_process()
ps_is_running(p)
ps_cpu_times(p)
ps_suspend(p)
ps_resume(p)
```

```{r include = FALSE}
vos_kill()
```

## Going further

Please see the package vignettes for more information:

- [details on Virtuoso Installation & configuration](https://docs.ropensci.org/virtuoso/articles/installation.html)
- [The Data Lake: richer examples of RDF use](https://docs.ropensci.org/virtuoso/articles/articles/datalake.html)

---

Please note that the `virtuoso` R package is released with a [Contributor Code of Conduct](https://docs.ropensci.org/virtuoso/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.


```{r include=FALSE}
if(require(codemetar)) codemetar::write_codemeta()
```


[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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GitHub Events

Total

Issue comment event: 1
Push event: 2
Pull request event: 1
Create event: 1

Last Year

Issue comment event: 1
Push event: 2
Pull request event: 1
Create event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 167
Total Committers: 2
Avg Commits per committer: 83.5
Development Distribution Score (DDS): 0.012

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Carl Boettiger	c**g@g**m	165
Jeroen Ooms	j**s@g**m	2

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 15
Total pull requests: 28
Average time to close issues: about 2 months
Average time to close pull requests: 1 day
Total issue authors: 5
Total pull request authors: 4
Average comments per issue: 2.27
Average comments per pull request: 0.18
Merged pull requests: 27
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 5 minutes
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

cboettig (9)
maelle (3)
lddurbin (1)
allenbaron (1)
jeroen (1)

Pull Request Authors

cboettig (25)
Rekyt (2)
maelle (1)
amoeba (1)

Top Labels

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Packages

Total packages: 1
Total downloads:
- cran 163 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

cran.r-project.org: virtuoso

Interface to 'Virtuoso' using 'ODBC'

Homepage: https://github.com/ropensci/virtuoso
Documentation: http://cran.r-project.org/web/packages/virtuoso/virtuoso.pdf
License: MIT + file LICENSE
Latest release: 0.1.8
published over 4 years ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 163 Last month

Rankings

Forks count: 14.9%

Stargazers count: 17.9%

Dependent packages count: 29.8%

Average: 33.2%

Dependent repos count: 35.5%

Downloads: 68.0%

Maintainers (1)

cboettig@gmail.com

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

DBI * imports
curl * imports
digest * imports
fs * imports
ini * imports
odbc * imports
processx * imports
ps * imports
rappdirs * imports
utils * imports
covr * suggests
dplyr * suggests
jsonld * suggests
knitr * suggests
nycflights13 * suggests
rmarkdown * suggests
spelling * suggests
testthat * suggests

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/check-r-package v1 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite
r-lib/actions/setup-r-dependencies v1 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

virtuoso

Science Score: 26.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

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cran.r-project.org: virtuoso

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Maintainers (1)

Dependencies