def get_organization(self, pattern):
organization = None
if pattern is not None:
if "HBP-SP" in pattern:
address = Address(locality='HBP', country='Europe')
organization = Organization(pattern, address, None)
elif pattern == "Blue Brain Project":
address = Address(locality='Geneva', country='Switzerland')
organization = Organization("Blue Brain Project", address,
None)
elif pattern == "Allen Institute":
address = Address(locality='Seattle', country='United States')
organization = Organization("Allen Institute", address, None)
elif pattern in ("KTH-UNIC", "KOKI-UNIC"):
address = Address(locality='HBP', country='Europe')
organization = Organization("HBP-SP6", address, None)
elif pattern == "Destexhe Lab":
address = Address(locality='Gif-sur-Yvette', country='France')
organization = Organization("CNRS", address, None)
elif pattern in ("<<empty>>", "Other"):
organization = None
else:
raise ValueError(
"Can't handle this pattern: {}".format(pattern))
return organization
def test_round_trip(self, kg_client):
obj1 = Organization(name="NeuroPSI",
address=Address(locality="Saclay", country="France"),
parent=KGProxy(Organization, "http://fake_uuid_00481be7a1"))
instance = Instance(Organization.path, obj1._build_data(kg_client), Instance.path)
instance.data["@id"] = "http://fake_uuid_7bb3c1e78b"
instance.data["@type"] = Organization.type
obj2 = Organization.from_kg_instance(instance, kg_client)
for field in ("name", "address", "parent"):
assert getattr(obj1, field) == getattr(obj2, field)
def test_build_data(self, kg_client):
obj1 = Organization(name="NeuroPSI",
address=Address(locality="Saclay", country="France"),
parent=KGProxy(Organization, "http://fake_uuid_00481be7a1"))
expected = {
"name": "NeuroPSI",
"address": {
"@type": "schema:PostalAddress",
"addressLocality": "Saclay",
"addressCountry": "France"
},
"parentOrganization": {
"@type": "nsg:Organization",
"@id": "http://fake_uuid_00481be7a1"
}
}
assert obj1._build_data(kg_client) == expected
def add_organizations_in_KG_database(self):
address = Address(locality='HBP', country='Europe')
for sp_num in range(1, 13):
org = Organization("HBP-SP{}".format(sp_num), address, None)
org.save(NAR_client)
addressBBP = Address(locality='Geneva', country='Switzerland')
BBP = Organization("Blue Brain Project", addressBBP, None)
BBP.save(NAR_client)
addressAllen = Address(locality='Seattle', country='United States')
spAllen = Organization("Allen Institute", addressAllen, None)
spAllen.save(NAR_client)
return ''
def save(self, allow_update=True):
if self.obj is None: # create
for key in ("author", "owner"):
if isinstance(self.data[key], dict):
self.data[key] = [self.data[key]]
self.obj = ModelProject(
self.data["name"],
[
Person(p["family_name"], p["given_name"],
p.get("email", None))
for p in as_list(self.data["owner"])
],
[
Person(p["family_name"], p["given_name"],
p.get("email", None))
for p in as_list(self.data["author"])
], # need to update person representation in clients,
self.data.get("description"),
datetime.now(),
self.data.get("private", True),
self.context["collab_id"],
self.data.get("alias"),
Organization(self.data["organization"]) if self.data.get(
"organization", False) else None,
pla_components=None,
brain_region=self._get_ontology_obj(BrainRegion,
"brain_region"),
species=self._get_ontology_obj(Species, "species"),
celltype=self._get_ontology_obj(CellType, "cell_type"),
abstraction_level=self._get_ontology_obj(
AbstractionLevel, "abstraction_level"),
model_of=self._get_ontology_obj(ModelScope, "model_scope"),
old_uuid=self.data.get("old_uuid"),
images=self.data.get("images"))
else: # update
if "name" in self.data:
self.obj.name = self.data["name"]
if "alias" in self.data:
self.obj.alias = self.data["alias"]
if "author" in self.data:
self.obj.authors = [
Person(p["family_name"], p["given_name"],
p.get("email", None))
for p in as_list(self.data["author"])
] # need to update person representation in clients
if "owner" in self.data:
self.obj.owners = [
Person(p["family_name"], p["given_name"],
p.get("email", None))
for p in as_list(self.data["owner"])
] # need to update person representation in clients
if "app" in self.data:
self.obj.collab_id = self.data["app"]["collab_id"]
if "organization" in self.data and self.data[
"organization"] is not None:
self.obj.organization = Organization(self.data["organization"])
if "private" in self.data:
self.obj.private = self.data["private"]
if "cell_type" in self.data:
self.obj.celltype = self._get_ontology_obj(
CellType, "cell_type")
if "model_scope" in self.data:
self.obj.model_of = self._get_ontology_obj(
ModelScope, "model_scope")
if "abstraction_level" in self.data:
self.obj.abstraction_level = self._get_ontology_obj(
AbstractionLevel, "abstraction_level")
if "brain_region" in self.data:
self.obj.brain_region = self._get_ontology_obj(
BrainRegion, "brain_region")
if "species" in self.data:
self.obj.species = self._get_ontology_obj(Species, "species")
if "description" in self.data:
self.obj.description = self.data["description"]
if "old_uuid" in self.data:
self.obj.old_uuid = self.data["old_uuid"]
if "images" in self.data:
self.obj.images = self.data["images"]
# now save people, organization, model. No easy way to make this atomic, I don't think.
for person in chain(as_list(self.obj.authors),
as_list(self.obj.owners)):
if not isinstance(person, KGProxy):
# no need to save if we have a proxy object, as
# that means the person hasn't been updated
person.save(self.client)
if self.obj.organization and not isinstance(self.obj.organization,
KGProxy):
self.obj.organization.save(self.client)
self.obj.save(self.client)
return self.obj
def test__build_data(self):
input_data = dict(
name="PyNN v0.9.4",
version="0.9.4",
summary=
"A Python package for simulator-independent specification of neuronal network models",
description=
"PyNN (pronounced 'pine') is a simulator-independent language for building neuronal network models.",
#identifier=Identifier("RRID:SCR_002715"),
citation=
("Davison AP, Brüderle D, Eppler JM, Kremkow J, Muller E, Pecevski DA, Perrinet L and Yger P (2009) "
"PyNN: a common interface for neuronal network simulators. "
"Front. Neuroinform. 2:11 doi:10.3389/neuro.11.011.2008"),
license=License("CeCILL v2"),
release_date=date(2019, 3, 22),
previous_version=None,
contributors=[
Person("Davison", "Andrew", "*****@*****.**")
],
project=None,
image="https://neuralensemble.org/static/photos/pynn_logo.png",
download_url=
"https://files.pythonhosted.org/packages/a2/1c/78b5d476900254c2c638a29a343ea12985ea16b12c7aed8cec252215c848/PyNN-0.9.4.tar.gz",
access_url="https://pypi.org/project/PyNN/0.9.4/",
categories=None,
subcategories=None,
operating_system=[
OperatingSystem("Linux"),
OperatingSystem("MacOS"),
OperatingSystem("Windows")
],
release_notes=
"http://neuralensemble.org/docs/PyNN/releases/0.9.4.html",
requirements="neo, lazyarray",
copyright=Organization("The PyNN community"),
components=None,
part_of=None,
funding=[
Organization("CNRS"),
Organization("Human Brain Project")
],
languages=ProgrammingLanguage("Python"),
features=None,
#keywords="simulation, neuroscience",
is_free=True,
homepage="https://neuralensemble.org/PyNN/",
documentation="http://neuralensemble.org/docs/PyNN/",
help="https://groups.google.com/forum/#!forum/neuralensemble")
software_release = Software(**input_data)
kg_data = software_release._build_data(client=None)
assert kg_data == {
'name':
input_data["name"],
'version':
input_data["version"],
'headline':
input_data["summary"],
'description':
input_data["description"],
'citation':
input_data["citation"],
'license': {
'@id': input_data["license"].iri,
'label': input_data["license"].label
},
'dateCreated':
'2019-03-22',
#'copyrightYear': input_data["release_date"].year,
'author': {
'@id': None,
'@type': ['nsg:Person', 'prov:Agent']
},
#'image': {'@id': input_data["image"]},
#'distribution': {
# 'downloadURL': {"@id": input_data["download_url"]},
# 'accessURL': {"@id": input_data["access_url"]}
#},
'operatingSystem': [{
'@id': os.iri,
'label': os.label
} for os in input_data["operating_system"]],
'releaseNotes': {
'@id': input_data["release_notes"]
},
'softwareRequirements':
input_data["requirements"],
'copyrightHolder': {
'@id': None,
'@type': ['nsg:Organization']
},
'funder': [{
'@id': None,
'@type': ['nsg:Organization']
}, {
'@id': None,
'@type': ['nsg:Organization']
}],
#'programmingLanguage': [{'@id': input_data["languages"].iri, 'label': input_data["languages"].label}],
#'keywords': input_data["keywords"],
'isAccessibleForFree':
input_data["is_free"],
'url': {
'@id': input_data["homepage"]
},
'documentation': {
'@id': input_data["documentation"]
},
'softwareHelp': {
'@id': input_data["help"]
}
}