def get_annotations(self):
#-------------------------
"""
Return all Annotations about the recording.
:rtype: list of bsml:Annotations
"""
sparql = """PREFIX bsml: <%(bsml)s>
PREFIX rdfs: <%(rdfs)s>
PREFIX dct: <%(dct)s>
PREFIX prv: <%(prv)s>
PREFIX tl: <%(tl)s>
select ?ann ?about ?stype ?comment ?tag ?created
?source ?tm ?start ?duration ?timeline
where {
?ann a bsml:Annotation
minus { [] prv:precededBy ?ann }
{
?ann dct:subject ?about .
?about a ?stype .
optional { ?ann rdfs:comment ?comment }
optional { ?ann dct:created ?created }
optional { ?ann bsml:tag ?tag }
{ ?ann dct:subject <%(subject)s> }
union
{ ?about a bsml:Segment ;
dct:source <%(subject)s> ;
dct:source ?source ;
bsml:time ?tm .
?tm tl:timeline ?timeline .
{ ?tm a bsml:Interval ; tl:start ?start ; tl:duration ?duration }
union
{ ?tm a bsml:Instant ; tl:at ?start }
}
}
}""" % dict(subject=self._rec_uri,
bsml=BSML.prefix,
rdfs=RDFS.prefix,
dct=DCT.prefix,
prv=PRV.prefix,
tl=TL.prefix)
anns = [[
str(a[0].uri),
str(a[1].uri),
str(a[2]), a[3].value, a[5].value,
str(a[6].uri),
str(a[7].uri), a[8].value,
None if a[9] in ['', None] else a[9].value,
str(a[10].uri)
] for a in self.query(sparql)]
anns.sort(key=operator.itemgetter(7, 1, 0)) # start, about, uri
annotations = []
for a in anns:
ann = Annotation(a[0], about=a[1], comment=a[3], created=a[4])
if a[2] == str(BSML.Segment):
time = TemporalEntity.create(a[6], a[7], a[8], timeline=a[9])
ann.about = Segment(a[1], source=a[5], time=time)
annotations.append(ann)
return annotations
def get_annotations(self, subject, graph_uri=None):
#--------------------------------------------------
"""
Return all Annotations about a subject.
This is significantly faster (approx 15x) then getting a list of URIs
(fast) and then creating Annotations (slow).
Code could be used as a template for general abstract object creation
based on PropertyMap and bypassing internal use of RDF -- instead map
directly to and from SPARQL.
:param subject: The URI of the subject.
:param graph_uri: An optional URI of the graph to query.
:rtype: list of bsml:Annotations
"""
anns = self.get_resources(
BSML.Annotation,
rvars=
'?ann ?about ?stype ?comment ?tag ?created ?source ?tm ?start ?duration ?timeline',
condition='''minus { [] prv:precededBy ?ann }
{
?ann dct:subject ?about .
?about a ?stype .
optional { ?ann rdfs:comment ?comment }
optional { ?ann dct:created ?created }
optional { ?ann bsml:tag ?tag }
{ ?ann dct:subject <%(subject)s> }
union
{ ?about a bsml:Segment ;
dct:source <%(subject)s> ;
dct:source ?source ;
bsml:time ?tm .
?tm tl:timeline ?timeline .
{ ?tm a bsml:Interval ; tl:start ?start ; tl:duration ?duration }
union
{ ?tm a bsml:Instant ; tl:at ?start }
}
}''' % dict(subject=subject),
prefixes=dict(bsml=BSML.prefix,
dct=DCT.prefix,
prv=PRV.prefix,
tl=TL.prefix),
graph=graph_uri,
# order = '?start', ## Virtuoso doesn't correctly sort xsd:dayTimeDuration
)
anns.sort(key=operator.itemgetter(9, 2, 1)) # start, about, uri
annotations = []
for a in anns:
ann = Annotation(a[1], about=a[2], comment=a[4], created=a[6])
if str(a[3]) == str(BSML.Segment):
time = TemporalEntity.create(
a[8],
float(a[9]),
duration=None if a[10] in ['', None] else float(a[10]),
timeline=a[11])
ann.about = Segment(a[2], source=a[7], time=time)
annotations.append(ann)
return annotations
def get_annotations(self, subject, graph_uri=None):
# --------------------------------------------------
"""
Return all Annotations about a subject.
This is significantly faster (approx 15x) then getting a list of URIs
(fast) and then creating Annotations (slow).
Code could be used as a template for general abstract object creation
based on PropertyMap and bypassing internal use of RDF -- instead map
directly to and from SPARQL.
:param subject: The URI of the subject.
:param graph_uri: An optional URI of the graph to query.
:rtype: list of bsml:Annotations
"""
anns = self.get_resources(
BSML.Annotation,
rvars="?ann ?about ?stype ?comment ?tag ?created ?source ?tm ?start ?duration ?timeline",
condition="""minus { [] prv:precededBy ?ann }
{
?ann dct:subject ?about .
?about a ?stype .
optional { ?ann rdfs:comment ?comment }
optional { ?ann dct:created ?created }
optional { ?ann bsml:tag ?tag }
{ ?ann dct:subject <%(subject)s> }
union
{ ?about a bsml:Segment ;
dct:source <%(subject)s> ;
dct:source ?source ;
bsml:time ?tm .
?tm tl:timeline ?timeline .
{ ?tm a bsml:Interval ; tl:start ?start ; tl:duration ?duration }
union
{ ?tm a bsml:Instant ; tl:at ?start }
}
}"""
% dict(subject=subject),
prefixes=dict(bsml=BSML.prefix, dct=DCT.prefix, prv=PRV.prefix, tl=TL.prefix),
graph=graph_uri,
# order = '?start', ## Virtuoso doesn't correctly sort xsd:dayTimeDuration
)
anns.sort(key=operator.itemgetter(9, 2, 1)) # start, about, uri
annotations = []
for a in anns:
ann = Annotation(a[1], about=a[2], comment=a[4], created=a[6])
if str(a[3]) == str(BSML.Segment):
time = TemporalEntity.create(
a[8], float(a[9]), duration=None if a[10] in ["", None] else float(a[10]), timeline=a[11]
)
ann.about = Segment(a[2], source=a[7], time=time)
annotations.append(ann)
return annotations
def get_annotation(self, uri, graph_uri=None):
#---------------------------------------------
"""
Get an Annotation from the repository.
:param uri: The URI of an Annotation.
:param graph_uri: An optional URI of the graph to query.
:rtype: :class:`~biosignalml.Annotation`
"""
# The following line works around a Virtuoso problem
if graph_uri is None:
graph_uri = self.get_graph_and_recording_uri(uri)[0]
graph = self.get_resource_as_graph(uri, BSML.Annotation, graph_uri)
##### Put into Annotation/Segment.load_from_graph() ????
for sg in graph.get_objects(uri,
DCT.subject): ## This could be improved...
graph.append_graph(
self.get_resource_as_graph(sg.uri, BSML.Segment, graph_uri))
for tm in graph.get_objects(
sg.uri, BSML.time): ## This could be improved...
graph.append_graph(
self.get_resource_as_graph(tm.uri, BSML.Instant,
graph_uri))
graph.append_graph(
self.get_resource_as_graph(tm.uri, BSML.Interval,
graph_uri))
return Annotation.create_from_graph(uri, graph)
def get_annotation(self, uri):
# -----------------------------
"""
Get an Annotation from its recording's graph.
:param uri: The URI of an Annotation.
:rtype: :class:`~biosignalml.Annotation`
"""
return Annotation.create_from_graph(uri, self)
def get_annotation(self, uri):
#-----------------------------
"""
Get an Annotation from its recording's graph.
:param uri: The URI of an Annotation.
:rtype: :class:`~biosignalml.Annotation`
"""
return Annotation.create_from_graph(uri, self)
def post(self):
#--------------
name = self.full_uri
text = self.get_argument('annotation', '').strip()
if self.get_argument('action') == 'Annotate' and text:
repo = options.repository
target = self.get_argument('target')
recording = repo.get_recording(target,
with_signals=False,
open_dataset=False)
ann = Annotation.Note(recording.make_uri(prefix='annotation'),
target,
text,
creator='%s/user/%s' %
(repo.uri, self.current_user)
if self.current_user is not None else None)
repo.extend_graph(recording.graph.uri, ann.metadata_as_string())
self._show_contents(name, False)
def get_annotation(self, uri, graph_uri=None):
# ---------------------------------------------
"""
Get an Annotation from the repository.
:param uri: The URI of an Annotation.
:param graph_uri: An optional URI of the graph to query.
:rtype: :class:`~biosignalml.Annotation`
"""
# The following line works around a Virtuoso problem
if graph_uri is None:
graph_uri = self.get_graph_and_recording_uri(uri)[0]
graph = self.get_resource_as_graph(uri, BSML.Annotation, graph_uri)
##### Put into Annotation/Segment.load_from_graph() ????
for sg in graph.get_objects(uri, DCT.subject): ## This could be improved...
graph.append_graph(self.get_resource_as_graph(sg.uri, BSML.Segment, graph_uri))
for tm in graph.get_objects(sg.uri, BSML.time): ## This could be improved...
graph.append_graph(self.get_resource_as_graph(tm.uri, BSML.Instant, graph_uri))
graph.append_graph(self.get_resource_as_graph(tm.uri, BSML.Interval, graph_uri))
return Annotation.create_from_graph(uri, graph)
def get_annotations(self):
# -------------------------
"""
Return all Annotations about the recording.
:rtype: list of bsml:Annotations
"""
sparql = """PREFIX bsml: <%(bsml)s>
PREFIX rdfs: <%(rdfs)s>
PREFIX dct: <%(dct)s>
PREFIX prv: <%(prv)s>
PREFIX tl: <%(tl)s>
select ?ann ?about ?stype ?comment ?tag ?created
?source ?tm ?start ?duration ?timeline
where {
?ann a bsml:Annotation
minus { [] prv:precededBy ?ann }
{
?ann dct:subject ?about .
?about a ?stype .
optional { ?ann rdfs:comment ?comment }
optional { ?ann dct:created ?created }
optional { ?ann bsml:tag ?tag }
{ ?ann dct:subject <%(subject)s> }
union
{ ?about a bsml:Segment ;
dct:source <%(subject)s> ;
dct:source ?source ;
bsml:time ?tm .
?tm tl:timeline ?timeline .
{ ?tm a bsml:Interval ; tl:start ?start ; tl:duration ?duration }
union
{ ?tm a bsml:Instant ; tl:at ?start }
}
}
}""" % dict(
subject=self._rec_uri, bsml=BSML.prefix, rdfs=RDFS.prefix, dct=DCT.prefix, prv=PRV.prefix, tl=TL.prefix
)
anns = [
[
str(a[0].uri),
str(a[1].uri),
str(a[2]),
a[3].value,
a[5].value,
str(a[6].uri),
str(a[7].uri),
a[8].value,
None if a[9] in ["", None] else a[9].value,
str(a[10].uri),
]
for a in self.query(sparql)
]
anns.sort(key=operator.itemgetter(7, 1, 0)) # start, about, uri
annotations = []
for a in anns:
ann = Annotation(a[0], about=a[1], comment=a[3], created=a[4])
if a[2] == str(BSML.Segment):
time = TemporalEntity.create(a[6], a[7], a[8], timeline=a[9])
ann.about = Segment(a[1], source=a[5], time=time)
annotations.append(ann)
return annotations
r.save_metadata_to_graph(g)
s = MyRecording.create_from_graph('http://example.org/uri1', g)
assert(r.metadata_as_string(rdf.Format.TURTLE) == s.metadata_as_string(rdf.Format.TURTLE))
s.comment='From graph'
user = '******'
a1 = 'http://example.org/annotation/1'
a2 = 'http://example.org/annotation/2'
a3 = 'http://example.org/annotation/3'
t1 = 'http://example.org/onto#tag1'
t2 = 'http://example.org/onto#tag2'
t3 = 'http://example.org/onto#tag3'
a = Annotation.Note(a1, s.uri, user, 'A test recording...')
b = Annotation.Tag(a2, s.uri, user, t1)
c = Annotation(a3, s.uri, user, tags=[t2, t3], text='Multiple tags')
#print a.metadata_as_string(rdf.Format.TURTLE)
#print b.metadata_as_string(rdf.Format.TURTLE)
#print c.metadata_as_string(rdf.Format.TURTLE)
c.save_metadata_to_graph(g)
d = Annotation.create_from_graph(a3, g)
assert(c.metadata_as_string(rdf.Format.TURTLE) == d.metadata_as_string(rdf.Format.TURTLE))
s.metadata['zz'] = [ a, b, c ]
print s.metadata_as_string(rdf.Format.TURTLE)