vivo-rdflib-sparqlstore

A RDFLib SPARQLStore implementation for the VIVO SPARQL query and update APIs.

This library supports Python 2.7 and 3.5+.

The VIVO SPARQL APIs require a user email and password for authentication.

See RDFLib's docs for detailed documentation on the SPARQLStore implementation.

Install

pip install vivo-rdflib-sparqlstore

For the latest development version, install directly from Github.

pip install git+https://github.com/lawlesst/rdflib-vivo-sparqlstore.git

API Usage

See example.py for example usage.

basic usage

from vstore import VIVOUpdateStore, VIVOStore
from rdflib.namespace import SKOS, RDF
from rdflib.graph import Dataset

#Define the VIVO store
query_endpoint = 'http://localhost:8983/vivo/api/sparqlQuery'
update_endpoint = 'http://localhost:8983/vivo/api/sparqlUpdate'

#Setup the VIVO store
store = VIVOUpdateStore('vivo_root@school.edu', 'passwd')
store.open((query_endpoint, update_endpoint))

ds = Dataset(store=store)

#All skos:Concepts in the store.
for subj in ds.subjects(predicate=RDF.type, object=SKOS.Concept):
    print 'Concept: ', subj

With a default VIVO installation, several URIS for skos:Concepts should be included, e.g.:

Concept:  http://vivoweb.org/ontology/core#yearMonthPrecision
Concept:  http://vivoweb.org/ontology/core#yearPrecision
Concept:  http://vivoweb.org/ontology/core#yearMonthDayTimePrecision
Concept:  http://vivoweb.org/ontology/core#yearMonthDayPrecision

Command line tool

A command line tool is included for adding or removing files of triples to/from VIVO. This can be a quick way to insert data into VIVO.

$ vivoUpdate --help
Usage: vivoUpdate [OPTIONS] TRIPLE_FILE ACTION

  Pass in the file to add or remove and the action 'add' or 'remove'.

Options:
  --email TEXT        [required]
  --password TEXT     [required]
  --url TEXT          [required]
  --named_graph TEXT
  --help              Show this message and exit.

The email, password, and url options will be read from environment variables if set.

$ export VIVO_EMAIL=you@example.org
$ export VIVO_PASSWORD=xxxx
$ export VIVO_URL=http://vivo.example.org/