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 create_from_graph(cls, uri, graph, **kwds):
#----------------------------------------------
from biosignalml.data.time import TemporalEntity # Prevent a circular import
self = cls(uri, None, **kwds)
self.add_metadata(graph)
if self.time is not None:
self.time = TemporalEntity.create_from_graph(self.time, graph)
return self
def create_from_graph(cls, uri, graph, **kwds):
#----------------------------------------------
from biosignalml.data.time import TemporalEntity # Prevent a circular import
self = cls(uri, None, **kwds)
self.add_metadata(graph)
if self.time is not None:
self.time = TemporalEntity.create_from_graph(self.time, graph)
return self
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 create_from_graph(cls, uri, graph, **kwds):
#----------------------------------------------
'''
Create a new instance of a Segment, setting attributes from RDF triples in a graph.
:param uri: The URI of the Segment.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
:rtype: :class:`Segment`
'''
from biosignalml.data.time import TemporalEntity # Prevent a circular import
self = super(Segment, cls).create_from_graph(cls, uri, graph, **kwds)
if self.time is not None: ## Could add_metadata automatically do this for sub-elements??
## PropertyMap would need to know class (TemporalEntity)
self.time = TemporalEntity.create_from_graph(self.time, graph)
return self
def create_from_graph(cls, uri, graph, **kwds):
#----------------------------------------------
'''
Create a new instance of a Segment, setting attributes from RDF triples in a graph.
:param uri: The URI of the Segment.
:param graph: A RDF graph.
:type graph: :class:`~biosignalml.rdf.Graph`
:rtype: :class:`Segment`
'''
from biosignalml.data.time import TemporalEntity # Prevent a circular import
self = super(Segment, cls).create_from_graph(cls, uri, graph, **kwds)
if self.time is not None: ## Could add_metadata automatically do this for sub-elements??
## PropertyMap would need to know class (TemporalEntity)
self.time = TemporalEntity.create_from_graph(self.time, graph)
return self
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
