def get_w3c(self, bundle=None):
"""get this element in the prov version which is an implementation of the W3C PROV-DM standard"""
if bundle is None:
bundle = ProvBundle()
w3c_record = ProvEntity(bundle, self.identifier, self.attributes)
w3c_record.add_asserted_type(self._prov_type) # self.__class__.__name__)
return bundle.add_record(w3c_record)
def get_w3c(self, bundle=None):
if bundle is None:
bundle = ProvBundle()
w3c_record = ProvEntity(bundle, self.identifier, self.attributes)
w3c_record.add_asserted_type(
self._prov_type) # self.__class__.__name__)
return bundle.add_record(w3c_record)
def decode_json_document(content, document):
bundles = dict()
if 'bundle' in content:
bundles = content['bundle']
del content['bundle']
decode_json_container(content, document)
for bundle_id, bundle_content in bundles.items():
bundle = ProvBundle(document=document)
decode_json_container(bundle_content, bundle)
document.add_bundle(bundle, bundle.valid_qualified_name(bundle_id))
def _create_bundle(self, version):
"""
Initialise NIDM-Results bundle.
"""
# *** Bundle entity
if not hasattr(self, 'bundle_ent'):
self.bundle_ent = NIDMResultsBundle(nidm_version=version['num'])
self.bundle = ProvBundle(identifier=self.bundle_ent.id)
self.bundle_ent.export(self.version, self.export_dir)
# # provn export
# self.bundle = ProvBundle(identifier=bundle_id)
self.doc.entity(self.bundle_ent.id,
other_attributes=self.bundle_ent.attributes)
# *** NIDM-Results Export Activity
if version['num'] not in ["1.0.0", "1.1.0"]:
if not hasattr(self, 'export_act'):
self.export_act = NIDMResultsExport()
self.export_act.export(self.version, self.export_dir)
# self.doc.update(self.export_act.p)
self.doc.activity(self.export_act.id,
other_attributes=self.export_act.attributes)
# *** bundle was Generated by NIDM-Results Export Activity
if not hasattr(self, 'export_time'):
self.export_time = str(datetime.datetime.now().time())
if version['num'] in ["1.0.0", "1.1.0"]:
self.doc.wasGeneratedBy(entity=self.bundle_ent.id,
time=self.export_time)
else:
# provn
self.doc.wasGeneratedBy(entity=self.bundle_ent.id,
activity=self.export_act.id,
time=self.export_time)
# *** NIDM-Results Exporter (Software Agent)
if version['num'] not in ["1.0.0", "1.1.0"]:
if not hasattr(self, 'exporter'):
self.exporter = self._get_exporter()
self.exporter.export(self.version, self.export_dir)
# self.doc.update(self.exporter.p)
self.doc.agent(self.exporter.id,
other_attributes=self.exporter.attributes)
self.doc.wasAssociatedWith(self.export_act.id, self.exporter.id)
def get_w3c(self, bundle=None):
"""get this relation in the prov version which is an implementation of the W3C PROV-DM standard"""
if bundle is None:
bundle = ProvBundle()
attribute = self.extra_attributes
relation_formal_attribute = self.formal_attributes[0:2]
w3c_record = ProvInfluence(bundle, self.identifier, attribute)
namespaces = [list(i) for i in w3c_record.formal_attributes]
for i in range(0, 2):
namespaces[i][1] = relation_formal_attribute[i][1]
w3c_record.add_attributes(namespaces)
w3c_record.add_asserted_type(
self._prov_type) # self.__class__.__name__)
return bundle.add_record(w3c_record)
def test_add_bundle_document(self):
d1 = self.document_1()
d2 = self.document_2()
def sub_test_1():
d1.add_bundle(d2)
self.assertRaises(ProvException, sub_test_1)
ex2_b2 = d2.valid_qualified_name('ex:b2')
d1.add_bundle(d2, 'ex:b2')
self.assertEqual(ex2_b2, first(d1.bundles).identifier)
self.assertNotIn(d2, d1.bundles)
b2 = ProvBundle()
b2.update(d2)
self.assertIn(b2, d1.bundles)
def _create_bundle(self, version):
"""
Initialise NIDM-Results bundle.
"""
software_lc = self.software.name.lower()
software_uc = self.software.name.upper()
bundle_id = NIIRI[str(uuid.uuid4())]
self.bundle = ProvBundle(identifier=bundle_id)
self.doc.entity(bundle_id,
other_attributes=((
PROV['type'],
PROV['Bundle'],
), (PROV['label'], software_uc + " Results"),
(NIDM['objectModel'],
NIDM[software_uc + 'Results']),
(NIDM['version'], version)))
self.doc.wasGeneratedBy(NIIRI[software_lc + '_results_id'],
time=str(datetime.datetime.now().time()))
def test_add_bundle_simple(self):
d1 = self.document_1()
b0 = self.bundle_0()
def sub_test_1():
d1.add_bundle(b0)
self.assertRaises(ProvException, sub_test_1)
self.assertFalse(d1.has_bundles())
d1.add_bundle(b0, 'ex:b0')
self.assertTrue(d1.has_bundles())
self.assertIn(b0, d1.bundles)
def sub_test_2():
ex2_b0 = b0.identifier
d1.add_bundle(ProvBundle(identifier=ex2_b0))
self.assertRaises(ProvException, sub_test_2)
d1.add_bundle(ProvBundle(), 'ex:b0')
self.assertEqual(len(d1.bundles), 2)
def sub_test_2():
ex2_b0 = b0.identifier
d1.add_bundle(ProvBundle(identifier=ex2_b0))
def bundle_0(self):
b = ProvBundle(namespaces={'ex': EX2_URI})
return b
def __init__(self, export_dir=None, coordinate_space_id=None):
self.export_dir = export_dir
self.coordinate_space_id = coordinate_space_id
self.p = ProvBundle()
self.id = None