def test_full_round_robin():
pif = System(properties=[
Property(
name="foo",
scalars=[Scalar(value=np.float32(2.4)),
Scalar(value=np.int64(2))]),
Property(name="bar", scalars=[Scalar(value=2.4),
Scalar(value=2)]),
Property(name="spam", files=[FileReference(relative_path="/tmp/file")])
],
preparation=[
ProcessStep(name="processed",
details=[
Value(name="temp",
scalars=[Scalar(value=1.0)])
])
],
contacts=[Person(name=Name(family="Einstein"))])
pif2 = loads(dumps(pif))
assert pif2.as_dictionary() == pif.as_dictionary(
), "PIF contents are not the same"
assert pif.properties[0].scalars[0].value == pif2.properties[0].scalars[
0].value
assert pif.properties[1].scalars[0].value == pif2.properties[1].scalars[
0].value
assert pif.properties[2].files[0].relative_path == pif2.properties[
2].files[0].relative_path
assert pif.preparation[0].details[0].scalars[0].value == pif2.preparation[
0].details[0].scalars[0].value
assert pif.contacts[0].name.family == pif2.contacts[0].name.family
def test_upload_pif():
"""
Tests that a PIF can be created, serialized, uploaded
then downloaded and deserialized
"""
pif = System()
pif.id = 0
uid = random_string()
pif.uid = uid
with open("tmp.json", "w") as fp:
dump(pif, fp)
assert client.upload(dataset_id, "tmp.json").successful()
tries = 0
while True:
try:
pif = client.get_pif(dataset_id, uid)
break
except ResourceNotFoundException:
if tries < 10:
tries += 1
time.sleep(1)
else:
raise
status = client.get_ingest_status(dataset_id)
assert status == "Finished"
with open("tmp.json", "r") as fp:
assert json.loads(fp.read())["uid"] == pif.uid
def test_update_pif_append():
pif1 = System(
properties=[Property(name="foo", scalars=[Scalar(value="bar")])])
pif2 = System(
properties=[Property(name="spam", scalars=[Scalar(value="eggs")])])
new = update_pif(pif1, pif2)
assert len(new.properties) == 2
assert set(x.name for x in new.properties) == set(["foo", "spam"])
def test_upload_pif():
client = CitrinationClient(environ['CITRINATION_API_KEY'], environ['CITRINATION_SITE'])
dataset = loads(client.create_data_set(name="Tutorial dataset", description="Dataset for tutorial", share=0).content.decode('utf-8'))['id']
pif = System()
pif.id = 0
with open("tmp.json", "w") as fp:
dump(pif, fp)
response = loads(client.upload_file("tmp.json", dataset))
assert response["message"] == "Upload is complete."
def test_update_pif_set():
pif1 = System(contacts=[
Person(name=Name(given="Steve", family="Holt"), email="*****@*****.**")
])
pif2 = System(
properties=[Property(name="spam", scalars=[Scalar(value="eggs")])])
new = update_pif(pif1, pif2)
assert new.contacts[0].name.given == "Steve"
assert new.contacts[0].email == "*****@*****.**"
assert new.properties[0].scalars[0].value == "eggs"
def test_upload_pif():
client = CitrinationClient(environ['CITRINATION_API_KEY'], 'https://stage.citrination.com')
dataset = loads(client.create_data_set(name="Tutorial dataset", description="Dataset for tutorial", share=0).content.decode('utf-8'))['id']
pif = System()
pif.id = 0
with TemporaryDirectory() as tmpdir:
tempname = join(tmpdir, "pif.json")
with open(tempname, "w") as fp:
dump(pif, fp)
response = loads(client.upload_file(tempname, dataset))
assert response["message"] == "Upload is complete."
def test_upload_pif():
client = CitrinationClient(environ['CITRINATION_API_KEY'],
environ['CITRINATION_SITE'])
dataset = loads(
client.create_data_set(name="Tutorial dataset",
description="Dataset for tutorial",
share=0).content.decode('utf-8'))['id']
pif = System()
pif.id = 0
with open("tmp.json", "w") as fp:
dump(pif, fp)
response = loads(client.upload_file("tmp.json", dataset))
assert response["message"] == "Upload is complete."
def test_condition():
"""Test that conditions are flattened and added"""
condition = Value(name="spam", scalars=[Scalar(value="eggs")])
sys = System(properties=[
Property(name="foo", scalars=[Scalar(value="bar")], conditions=[condition])
])
user_data = _to_user_defined(sys)
assert user_data["spam"] == "eggs"
def test_property_list():
"""Test that a property with a list of scalars gets pulled out"""
sys = System(properties=[
Property(name="foo",
scalars=[Scalar(
value="spam"), Scalar(value="eggs")])
])
user_data = _to_user_defined(sys)
assert user_data["foo"] == ["spam", "eggs"]
def test_property_vector():
"""Test that a vector gets pulled out"""
sys = System(properties=[
Property(name="foo",
units="bar",
vectors=[[Scalar(
value="spam"), Scalar(value="eggs")]])
])
user_data = _to_user_defined(sys)
assert user_data["foo_bar"] == ["spam", "eggs"]
def test_add_datacite():
data_pif = System(
properties=[Property(name="Foo", scalars=[Scalar(value="bar")])])
dc = {
"identifier": {
"identifier": "000.000",
"identifierType": "DOI"
},
"title":
"The joy of the PIF",
"publisher":
"Ether",
"publicationYear":
"2014",
"creators": [{
"creatorName": "Kyle Michel",
"affiliations": ["Berklee", "NW"]
}]
}
res = add_datacite(data_pif, dc)
assert res.properties[0].scalars[0].value == "bar"
assert res.references[0].doi == "000.000"
data_pif2 = System(
properties=[Property(name="Foo", scalars=[Scalar(value="bar")])])
dc2 = {
"title":
"The joy of the PIF",
"publisher":
"Ether",
"publicationYear":
"2014",
"creators": [{
"creatorName": "Kyle Michel",
"affiliations": ["Berklee", "NW"]
}]
}
res2 = add_datacite(data_pif2, dc2)
assert res2.properties[0].scalars[0].value == "bar"
assert res2.references[0].doi is None
def test_basic_round_robin():
pif = System()
pif.uid = "foo"
pif2 = loads(dumps(pif))
assert pif2.uid == pif.uid
def test_dup_pifs():
pifs = [System(names=["foo"]), System(names=["foo"])]
set_uids(pifs)
assert len({p.uid for p in pifs}) == 1
def test_get_url():
pif = System(uid="foobar")
url = get_url(pif, version=2, dataset=8)
assert url == "https://citrination.com/datasets/8/version/2/pif/foobar"
def test_property_value():
"""Test that a simple property gets pulled out"""
sys = System(
properties=[Property(name="foo", scalars=[Scalar(value="bar")])])
user_data = _to_user_defined(sys)
assert user_data["foo"] == "bar"
def test_explicit_uids():
pifs = [System(names=["foo"]), System(names=["bar"])]
uids = ["spam", "eggs"]
set_uids(pifs, ["spam", "eggs"])
assert [p.uid for p in pifs] == uids
def test_set_uids():
pifs = [System(names=["foo"]), System(names=["bar"])]
set_uids(pifs)
for pif in pifs:
assert pif.uid
assert len({p.uid for p in pifs}) == 2
def test_update_pif_replace():
pif1 = System(uid="0")
pif2 = System(uid="1")
new = update_pif(pif1, pif2)
assert new.uid == "1"