def export(self, nidm_version, export_dir):
"""
Create prov entities and activities.
"""
if nidm_version['num'] in ["1.0.0", "1.1.0"]:
self.label = self.label.replace("Supra-Threshold", "Significant")
# FIXME deal with multiple contrasts
atts = ((PROV['type'], NIDM_SIGNIFICANT_CLUSTER),
(PROV['label'], self.label), (NIDM_CLUSTER_LABEL_ID, self.num),
(NIDM_CLUSTER_SIZE_IN_VOXELS, self.size))
if self.clust_size_resels is not None:
atts = atts + (
(NIDM_CLUSTER_SIZE_IN_RESELS, self.clust_size_resels), )
if self.punc is not None:
atts = atts + ((NIDM_P_VALUE_UNCORRECTED,
Literal(self.punc, datatype=XSD_FLOAT)), )
if self.pFDR is not None:
atts = atts + (
(NIDM_Q_VALUE_FDR, Literal(self.pFDR, datatype=XSD_FLOAT)), )
if self.pFWER is not None:
atts = atts + (
(NIDM_P_VALUE_FWER, Literal(self.pFWER, datatype=XSD_FLOAT)), )
self.add_attributes(atts)
def export(self, nidm_version, export_dir):
"""
Create prov entities and activities.
"""
if self.p_unc is None:
norm_cdf_z = (1.0 + erf(self.equiv_z / sqrt(2.0))) / 2.0
self.p_unc = 1 - norm_cdf_z
atts = ((PROV['type'], self.type), (PROV['label'], self.label),
(PROV['location'], self.coordinate.id))
if self.value is not None:
atts = atts + ((PROV['value'], self.value), )
if self.p_unc is not None:
atts = atts + ((NIDM_P_VALUE_UNCORRECTED,
Literal(self.p_unc, datatype=XSD_FLOAT)), )
if self.equiv_z is not None:
atts = atts + ((NIDM_EQUIVALENT_ZSTATISTIC,
Literal(self.equiv_z, datatype=XSD_FLOAT)), )
if self.p_fdr is not None:
atts = atts + (
(NIDM_Q_VALUE_FDR, Literal(self.p_fdr, datatype=XSD_FLOAT)), )
if self.p_fwer is not None:
atts = atts + ((NIDM_P_VALUE_FWER,
Literal(self.p_fwer, datatype=XSD_FLOAT)), )
self.add_attributes(atts)
def datatypes():
g = ProvDocument()
ex = Namespace("ex", "http://example.org/")
g.add_namespace(ex)
attributes = {
"ex:int":
100,
"ex:float":
100.123456,
"ex:long":
123456789000,
"ex:bool":
True,
"ex:str":
"Some string",
"ex:unicode":
"Some unicode string with accents: Huỳnh Trung Đông",
"ex:timedate":
datetime.datetime(2012, 12, 12, 14, 7, 48),
"ex:intstr":
Literal("PROV Internationalized string",
PROV["InternationalizedString"], "en"),
}
multiline = """Line1
Line2
Line3"""
attributes["ex:multi-line"] = multiline
g.entity("ex:e1", attributes)
return g
def decode_rdf_representation(self, literal, graph):
if isinstance(literal, RDFLiteral):
value = literal.value if literal.value is not None else literal
datatype = literal.datatype if hasattr(literal,
'datatype') else None
langtag = literal.language if hasattr(literal,
'language') else None
if datatype and 'XMLLiteral' in datatype:
value = literal
if datatype and 'base64Binary' in datatype:
value = base64.standard_b64encode(value)
if datatype == XSD['QName']:
return pm.Literal(literal, datatype=XSD_QNAME)
if datatype == XSD['dateTime']:
return dateutil.parser.parse(literal)
else:
# The literal of standard Python types is not converted here
# It will be automatically converted when added to a record by _auto_literal_conversion()
return Literal(value, self.valid_identifier(datatype), langtag)
elif isinstance(literal, URIRef):
rval = self.valid_identifier(literal)
if rval is None:
prefix, iri, _ = graph.namespace_manager.compute_qname(literal)
ns = self.document.add_namespace(prefix, iri)
rval = pm.QualifiedName(ns, literal.replace(ns.uri, ''))
return rval
else:
# simple type, just return it
return literal
def datatypes():
g = ProvDocument()
ex = Namespace('ex', 'http://example.org/')
g.add_namespace(ex)
attributes = {
'ex:int':
100,
'ex:float':
100.123456,
'ex:long':
123456789000,
'ex:bool':
True,
'ex:str':
'Some string',
'ex:unicode':
u'Some unicode string with accents: Huỳnh Trung Đông',
'ex:timedate':
datetime.datetime(2012, 12, 12, 14, 7, 48),
'ex:intstr':
Literal("PROV Internationalized string",
PROV["InternationalizedString"], "en"),
}
multiline = """Line1
Line2
Line3"""
attributes['ex:multi-line'] = multiline
g.entity('ex:e1', attributes)
return g
def decode_json_representation(value, type, bundle):
"""
Return the value based on the type see also encode_json_representation
:param value:
:param type:
:param bundle:
:return:
"""
if isinstance(type, dict):
# complex type
datatype = type['type'] if 'type' in type else None
datatype = bundle.valid_qualified_name(datatype)
langtag = type['lang'] if 'lang' in type else None
if datatype == XSD_ANYURI:
return Identifier(value)
elif datatype == PROV_QUALIFIEDNAME:
return bundle.valid_qualified_name(value)
else:
# The literal of standard Python types is not converted here
# It will be automatically converted when added to a record by
# _auto_literal_conversion()
return Literal(value, datatype, langtag)
else:
# simple type, just return it
return value
def export(self, nidm_version, export_dir):
"""
Create prov entities and activities.
"""
if nidm_version['major'] < 1 or \
(nidm_version['major'] == 1 and nidm_version['minor'] < 3):
self.type = NLX_OLD_FSL
atts = ((PROV['type'], self.type), (PROV['type'],
PROV['SoftwareAgent']),
(PROV['label'], Literal(self.label, datatype=XSD_STRING)),
(NIDM_SOFTWARE_VERSION, self.version))
if self.feat_version:
atts = atts + ((FSL_FEAT_VERSION, self.feat_version), )
self.add_attributes(atts)
def decode_json_representation(literal, bundle):
if isinstance(literal, dict):
# complex type
value = literal['$']
datatype = literal['type'] if 'type' in literal else None
datatype = valid_qualified_name(bundle, datatype)
langtag = literal['lang'] if 'lang' in literal else None
if datatype == XSD_ANYURI:
return Identifier(value)
elif datatype == PROV_QUALIFIEDNAME:
return valid_qualified_name(bundle, value)
else:
# The literal of standard Python types is not converted here
# It will be automatically converted when added to a record by
# _auto_literal_conversion()
return Literal(value, datatype, langtag)
else:
# simple type, just return it
return literal
def test_literal_provn_with_triple_quotes(self):
l = Literal('"""foo\\nbar"""')
string_rep = l.provn_representation()
self.assertTrue('\\"\\"\\"f' in string_rep)
def test_literal_provn_with_single_quotes(self):
l = Literal('{"foo": "bar"}')
string_rep = l.provn_representation()
self.assertTrue('{\\"f' in string_rep)
VOPROV_ATTR_REFERRER,
})
VOPROV_ATTR_TIME = VOPROV['time']
VOPROV_ATTR_STARTTIME = VOPROV['startTime']
VOPROV_ATTR_ENDTIME = VOPROV['endTime']
# adding the voprov identifier for the literals attribute
PROV_ATTRIBUTE_LITERALS.update({
# update of prov literals to voprov literals
VOPROV_ATTR_TIME,
VOPROV_ATTR_STARTTIME,
VOPROV_ATTR_ENDTIME,
# voprov description
Literal(VOPROV_ATTR_NAME),
Literal(VOPROV_ATTR_ROLE),
Literal(VOPROV_ATTR_VALUE_TYPE),
Literal(VOPROV_ATTR_CONTENT_TYPE),
# voprov configuration
Literal(VOPROV_ATTR_LOCATION),
Literal(VOPROV_ATTR_VALUE),
Literal(VOPROV_ATTR_ARTEFACT_TYPE),
})
# Extra definition for convenience
VOPROV_TYPE = VOPROV['type']
VOPROV_LABEL = VOPROV['label']
VOPROV_VALUE = VOPROV['value']
VOPROV_LOCATION = VOPROV['location']
def test_literal_provn_with_triple_quotes(self):
l = Literal('"""foo\\nbar"""')
string_rep = l.provn_representation()
self.assertTrue('\\"\\"\\"f' in string_rep)
def test_literal_provn_with_single_quotes(self):
l = Literal('{"foo": "bar"}')
string_rep = l.provn_representation()
self.assertTrue('{\\"f' in string_rep)
def prov_api_record_example():
doc = ProvDocument()
doc.add_namespace("ex", "http://example.com")
doc.add_namespace("custom", "http://custom.com")
attributes = attributes_dict_example()
del attributes[
"ex:dict value"] # remove dict value because it is not allowed in a prov_record, but for low level adapter tests necessary
del attributes[
"ex:list value"] # remove dict value because it is not allowed in a prov_record, but for low level adapter tests necessary
attributes.update({
"ex:Qualified name ":
doc.valid_qualified_name("custom:qualified name")
})
attributes.update({"ex:Qualified name 2": "ex:unqualified_name"})
attributes.update({"ex:Literal": Literal("test literal", langtag="en")})
attributes.update({
"ex:Literal 2":
Literal("test literal with datatype",
langtag="en",
datatype=PROV["InternationalizedString"])
})
attributes.update(
{"ex:identifier type": Identifier("http://example.com/#test")})
expected_attributes = dict()
for key, value in attributes.items():
new_key = doc.valid_qualified_name(key)
expected_attributes.update({new_key: value})
# The prov lib don't require to auto convert string values into qualified names
# valid_name = doc.valid_qualified_name("ex:Qualified name 2")
# expected_attributes[valid_name] = doc.valid_qualified_name("ex:unqualified_name")
namespaces = dict()
namespaces.update({"ex": "http://example.com"})
namespaces.update({"custom": "http://custom.com"})
namespaces.update({"prov": "http://www.w3.org/ns/prov#"})
type_map = dict()
type_map.update({"ex:date value": {"type": "xsd:dateTime"}})
type_map.update({"ex:double value": {"type": "xsd:double"}})
type_map.update({"ex:int value": {"type": "xsd:int"}})
type_map.update({"ex:Qualified name ": {'type': 'prov:QUALIFIED_NAME'}})
# type_map.update({"ex:Qualified name 2":{'type': 'prov:QUALIFIED_NAME'}}) #The prov lib don't require to auto convert strings into qualified names
type_map.update({"ex:Literal": {'lang': 'en'}})
type_map.update({"ex:Literal 2": {'lang': 'en'}})
type_map.update({"ex:identifier type": {'type': 'xsd:anyURI'}})
metadata = dict()
metadata.update({METADATA_KEY_PROV_TYPE: PROV_RECORD_IDS_MAP["activity"]})
metadata.update(
{METADATA_KEY_IDENTIFIER: doc.valid_qualified_name("ex:record")})
metadata.update({METADATA_KEY_NAMESPACES: namespaces})
metadata.update({METADATA_KEY_TYPE_MAP: type_map})
record = ProvActivity(doc, "ex:record", attributes)
Example = namedtuple(
"prov_api_metadata_record_example",
"metadata, attributes, prov_record, expected_attributes")
return Example(metadata, attributes, record, expected_attributes)
