triplestore_access {avidaR}R Documentation

Class to manage triplestore access options

Description

Class to manage triplestore access options

Methods

Public methods

Method new()

Create and initialize the object.

Usage
triplestore_access$new()
Returns

Object of class triplestore_access.

Method get_access_options()

Get access options

Usage
triplestore_access$get_access_options()
Returns

list containing URL of the API server, user credentials, repository name, authentication status, and SPARQL protocol version

Method set_access_options()

Set authentication access options for graphdb triplestore

Usage
triplestore_access$set_access_options(
  url = NULL,
  user = NULL,
  password = NULL,
  repository = NULL,
  timeout = 100
)
Arguments
url

String containing the URL of the triplestore server

user

String containing the username if authentication is needed

password

String containing the password if authentication is needed

repository

String containing the ID of the repository to which you want to connect to

timeout

Connection timeout limit in seconds used for queries

Method submit_query()

Submit a SPARQL query to the triplestore to obtain data

Usage
triplestore_access$submit_query(query)
Arguments
query

String containing the SPARQL query to retrieve data

Method ontology()

Show ontology information

Usage
triplestore_access$ontology()
Returns

List containing title, description and versionIRI of the ontology

Method clone()

The objects of this class are cloneable with this method.

Usage
triplestore_access$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples


# Create object triplestore

triplestore <- triplestore_access$new()


# Set options to access a specific triple-store implemented in GraphDB

triplestore$set_access_options(
  url = "https://graphdb.fortunalab.org",
  user = "public_avida",
  password = "public_avida",
  repository = "avidaDB_test"
)


# Show current access options

triplestore$get_access_options()


# Querying data with SPARQL

triplestore$submit_query('PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
                          PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
                          select ?tandem_id where { 
                            ?digital_tandem_repeat rdfs:label "digital tandem repeat"@en .
                            ?tandem_id a ?digital_tandem_repeat .
                          } limit 10')


# Show ontology info

triplestore$ontology()
[Package avidaR version 1.2.0 Index]