def __init__(self, configuration):
#---------------------------------
"""
Reads and parses configuration information.
Configuration includes location of RDF store.
"""
self.rdfstore = Virtuoso('http://localhost:8890')
self._propdata = {
'Text':
PropertyValue('bif:contains', [Relation('contains', 'text_word')],
'text'),
'Tagged':
PropertyValue('bsml:tag', [
Relation('has tag', 'uri_match'),
Relation('not tagged', 'uri_nomatch')
], 'list'),
'Event':
PropertyValue('bsml:eventType', [
Relation('has type', 'uri_match'),
Relation('not type', 'uri_nomatch')
], 'list'),
'Duration':
PropertyValue(
'tl:duration', ['=', '!=', '<', '<=', '>', '>='],
'text'), ## Needs ?res bsml:time ?tm . ?tm tl:duration "value"
'Recording':
PropertyValue('bsml:recording',
[Relation('with URI', 'uri_match')], 'text'),
'Database':
PropertyValue('bsml:database', [Relation('with URI', 'uri_match')],
'text'),
}
self._propvalues = {}
for key, pv in self._propdata.iteritems():
if pv.valuetype == 'list':
values = []
for r in self.rdfstore.select(
'?value ?label',
'[] %(uri)s ?value . optional { ?value rdfs:label ?label }',
## prefixes=prefixes,
params=dict(uri=pv.uri)):
if r['value'].get('label'):
values.append(r['value']['label'])
else:
values.append(abbreviate_uri(r['value']['value']))
# values = [ 'Normal beat', 'Fusion beat', 'Paced beat', 'PVC beat' ] ###
self._propvalues[key] = sorted(values)
def __init__(self, configuration):
#---------------------------------
"""
Reads and parses configuration information.
Configuration includes location of RDF store.
"""
self.rdfstore = Virtuoso('http://localhost:8890')
self._propdata = {
'Text': PropertyValue('bif:contains',
[ Relation('contains', 'text_word') ],
'text'),
'Tagged': PropertyValue('bsml:tag',
[ Relation('has tag', 'uri_match'),
Relation('not tagged', 'uri_nomatch') ],
'list'),
'Event': PropertyValue('bsml:eventType',
[ Relation('has type', 'uri_match'),
Relation('not type', 'uri_nomatch') ],
'list'),
'Duration': PropertyValue('tl:duration',
['=', '!=', '<', '<=', '>', '>='],
'text'), ## Needs ?res bsml:time ?tm . ?tm tl:duration "value"
'Recording': PropertyValue('bsml:recording',
[ Relation('with URI', 'uri_match') ],
'text'),
'Database': PropertyValue('bsml:database',
[ Relation('with URI', 'uri_match') ],
'text'),
}
self._propvalues = { }
for key, pv in self._propdata.iteritems():
if pv.valuetype == 'list':
values = [ ]
for r in self.rdfstore.select('?value ?label',
'[] %(uri)s ?value . optional { ?value rdfs:label ?label }',
## prefixes=prefixes,
params=dict(uri=pv.uri)):
if r['value'].get('label'): values.append(r['value']['label'])
else: values.append(abbreviate_uri(r['value']['value']))
# values = [ 'Normal beat', 'Fusion beat', 'Paced beat', 'PVC beat' ] ###
self._propvalues[key] = sorted(values)
from biosignalml.rdf.sparqlstore import StoreException, Virtuoso
from biosignalml.repository import BSMLStore
if __name__ == '__main__':
#=========================
if len(sys.argv) < 2:
print "Usage: %s recording_uri" % sys.argv[0]
exit(1)
recording = sys.argv[1]
p = urlparse.urlparse(recording)
repo = p.scheme + '://' + p.netloc
store = Virtuoso('http://localhost:8890')
for g in [ r['g']['value'] for r in json.loads(
store.query("""select distinct ?g where {
graph <%s/provenance> {
?g a bsml:RecordingGraph ;
dct:subject <%s>
}
} order by ?g""" % (repo, recording),
format=Format.JSON,
prefixes={'bsml': BSML.prefix, 'dct': DCT.prefix})
).get('results', {}).get('bindings', [])
]:
try:
store.delete_graph(g)
except StoreException: ## Actual graph may not exist
[ 'db2', 1, 'db2', 'Database', '', '' ],
[ 'rec1', 2, 'rc1', 'Recording', 'duration', 1800 ],
[ 'Signal', 3, 'r2/sg1', '', 'rdfs:label', 'V5' ],
[ 'Signal', 3, 'sg2', '', 'rdfs:label', 'V1' ],
[ 'Event', 3, 'ev1', 'pvcBeat', 'count', 4 ],
[ 'db', 1, 'db1', 'Database', '', '' ],
[ 'rec1', 2, 'rc1', 'Recording', 'duration', 1800 ],
[ 'sig1', 3, 'sg1', 'Signal', 'label', 'V5' ],
[ 'sig2', 3, 'sg2', 'Signal', 'label', 'V1' ],
[ 'evt1', 3, 'ev1', 'Event', 'pvsBeat', 4 ],
[ 'rec2', 2, 'rc2', 'Recording', 'duration', 1600 ],
]
rdfstore = Virtuoso('http://localhost:8890')
bsmlstore = BSMLStore('http://devel.biosignalml.org', rdfstore)
PREFIXES = {
'bsml': 'http://www.biosignalml.org/ontologies/2011/04/biosignalml#',
'dct': 'http://purl.org/dc/terms/',
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'pbank': 'http://www.biosignalml.org/ontologies/examples/physiobank#',
'repo': 'http://devel.biosignalml.org/resource/',
}
def abbreviate(v):
#-----------------
for pfx, ns in PREFIXES.iteritems():
import sys
import biosignalml.rdf as rdf
from biosignalml.rdf.sparqlstore import StoreException, Virtuoso
if __name__ == "__main__":
#=========================
if len(sys.argv) < 3:
print "Usage: %s store graph_uri" % sys.argv[0]
exit(1)
store = Virtuoso(sys.argv[1])
try:
store.delete_graph(sys.argv[2])
except StoreException: ## Actual graph may not exist
pass
if __name__ == "__main__":
#=========================
import biosignalml.rdf as rdf
from biosignalml.repository import BSMLStore
from biosignalml.rdf.sparqlstore import Virtuoso
from biosignalml.rdf.sparqlstore import get_result_value
logging.basicConfig(format='%(asctime)s: %(message)s')
logging.getLogger().setLevel('DEBUG')
app = QtGui.QApplication(sys.argv)
rdfstore = Virtuoso('http://localhost:8890')
bsmlstore = BSMLStore('http://devel.biosignalml.org', rdfstore)
PREFIXES = {
'bsml': 'http://www.biosignalml.org/ontologies/2011/04/biosignalml#',
'dct': 'http://purl.org/dc/terms/',
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'pbank': 'http://www.biosignalml.org/ontologies/examples/physiobank#',
'repo': 'http://devel.biosignalml.org/resource/',
}
def abbreviate(v):
#-----------------
for pfx, ns in PREFIXES.iteritems():
import sys
import biosignalml.rdf as rdf
from biosignalml.rdf.sparqlstore import Virtuoso
if __name__ == "__main__":
#=========================
if len(sys.argv) < 4:
print "Usage: %s store graph_uri graph_source [format]" % sys.argv[0]
exit(1)
if len(sys.argv) == 5: format = rdf.Format.format(sys.argv[4])
else: format = rdf.Format.RDFXML
store = Virtuoso(sys.argv[1])
graph = rdf.Graph.create_from_resource(rdf.Uri(sys.argv[3]), format, base=rdf.Uri(sys.argv[3]))
##print graph.serialise(format=rdf.Format.TURTLE)
store.extend_graph(sys.argv[2], graph.serialise(format=rdf.Format.RDFXML), format=rdf.Format.RDFXML)
import sys
import biosignalml.rdf as rdf
from biosignalml.rdf.sparqlstore import StoreException, Virtuoso
if __name__ == "__main__":
#=========================
if len(sys.argv) < 3:
print "Usage: %s store graph_uri" % sys.argv[0]
exit(1)
store = Virtuoso(sys.argv[1])
try:
store.delete_graph(sys.argv[2])
except StoreException: ## Actual graph may not exist
pass
if __name__ == "__main__":
#=========================
import biosignalml.rdf as rdf
from biosignalml.repository import BSMLStore
from biosignalml.rdf.sparqlstore import Virtuoso
from biosignalml.rdf.sparqlstore import get_result_value
logging.basicConfig(format='%(asctime)s: %(message)s')
logging.getLogger().setLevel('DEBUG')
app = QtGui.QApplication(sys.argv)
rdfstore = Virtuoso('http://localhost:8890')
bsmlstore = BSMLStore('http://devel.biosignalml.org', rdfstore)
PREFIXES = {
'bsml': 'http://www.biosignalml.org/ontologies/2011/04/biosignalml#',
'dct': 'http://purl.org/dc/terms/',
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'pbank': 'http://www.biosignalml.org/ontologies/examples/physiobank#',
'repo': 'http://devel.biosignalml.org/resource/',
}
def abbreviate(v):
#-----------------
for pfx, ns in PREFIXES.iteritems():
if v.startswith(ns): return '%s:%s' % (pfx, v[len(ns):])
query_results = [
# Each row has [ reslabel, reslevel, resuri, type, prop, value ]
['db2', 1, 'db2', 'Database', '', ''],
['rec1', 2, 'rc1', 'Recording', 'duration', 1800],
['Signal', 3, 'r2/sg1', '', 'rdfs:label', 'V5'],
['Signal', 3, 'sg2', '', 'rdfs:label', 'V1'],
['Event', 3, 'ev1', 'pvcBeat', 'count', 4],
['db', 1, 'db1', 'Database', '', ''],
['rec1', 2, 'rc1', 'Recording', 'duration', 1800],
['sig1', 3, 'sg1', 'Signal', 'label', 'V5'],
['sig2', 3, 'sg2', 'Signal', 'label', 'V1'],
['evt1', 3, 'ev1', 'Event', 'pvsBeat', 4],
['rec2', 2, 'rc2', 'Recording', 'duration', 1600],
]
rdfstore = Virtuoso('http://localhost:8890')
bsmlstore = BSMLStore('http://devel.biosignalml.org', rdfstore)
PREFIXES = {
'bsml': 'http://www.biosignalml.org/ontologies/2011/04/biosignalml#',
'dct': 'http://purl.org/dc/terms/',
'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
'xsd': 'http://www.w3.org/2001/XMLSchema#',
'pbank': 'http://www.biosignalml.org/ontologies/examples/physiobank#',
'repo': 'http://devel.biosignalml.org/resource/',
}
def abbreviate(v):
#-----------------
for pfx, ns in PREFIXES.iteritems():
if v.startswith(ns): return '%s:%s' % (pfx, v[len(ns):])
from biosignalml.rdf import Format, DCT, PRV
from biosignalml.rdf.sparqlstore import StoreException, Virtuoso
from biosignalml.repository import BSMLStore
if __name__ == '__main__':
#=========================
if len(sys.argv) < 2:
print "Usage: %s recording_uri" % sys.argv[0]
exit(1)
recording = sys.argv[1]
p = urlparse.urlparse(recording)
repo = p.scheme + '://' + p.netloc
store = Virtuoso('http://localhost:8890')
for g in [
r['g']['value'] for r in json.loads(
store.query("""select distinct ?g where {
graph <%s/provenance> {
?g a bsml:RecordingGraph ;
dct:subject <%s>
}
} order by ?g""" % (repo, recording),
format=Format.JSON,
prefixes={
'bsml': BSML.prefix,
'dct': DCT.prefix
})).get('results', {}).get('bindings', [])
]:
from biosignalml.repository import BSMLUpdateStore
if __name__ == '__main__':
#=========================
logging.basicConfig(format='%(asctime)s: %(message)s')
logging.getLogger().setLevel('DEBUG')
if len(sys.argv) < 3:
print "Usage: %s REPOSITORY_URI BIOSIGNALML_HDF5_FILE" % sys.argv[0]
sys.exit(1)
store = BSMLUpdateStore(
sys.argv[1],
# FourStore('http://localhost:8083'))
Virtuoso('http://localhost:8890'))
rec = H5Recording.open(sys.argv[2])
statements, format = rec.get_metadata()
if statements is None: raise ValueError("No metadata in source file")
# rec.dataset = .... From repo? Parameter?? Default to filename's full path??
# Move/rename/copy file ??
dataset = rdf.Uri('file://' + os.path.abspath(sys.argv[2]))
graph = rdf.Graph.create_from_string(rec.uri, statements, format)
graph.set_subject_property(rec.uri, BSML.dataset, dataset)
graph_uri = store.add_recording_graph(
rec.uri, graph.serialise(), 'file://' + os.path.abspath(__file__))
if len(sys.argv) < 2:
print "Usage: %s repository" % sys.argv[0]
exit(1)
repo = sys.argv[1]
print "***"
print "*** This utility will remove all BioSignalML content from the repository at %s ***" % repo
print "***"
print "*** Are your sure? [NO/yes]"
if sys.stdin.readline() != "yes\n": sys.exit(1)
print "***"
print "*** Are your *really* sure? [NO/yes]"
if sys.stdin.readline() != "yes\n": sys.exit(1)
store = Virtuoso('http://localhost:8890')
for g in [ r['g']['value'] for r in json.loads(
store.query("""select distinct ?g where {
graph <%s/provenance> {
?g a bsml:RecordingGraph
}
} order by ?g""" % repo,
format=Format.JSON,
prefixes={'bsml': BSML.prefix})
).get('results', {}).get('bindings', [])
]:
try:
store.delete_graph(g)
except StoreException: ## Actual graph may not exist
pass