def test_GetParticipantIDs():
kwargs = {
Constants.NIDM_PROJECT_NAME: "FBIRN_PhaseII",
Constants.NIDM_PROJECT_IDENTIFIER: 9610,
Constants.NIDM_PROJECT_DESCRIPTION: "Test investigation"
}
project = Project(uuid="_123456", attributes=kwargs)
session = Session(uuid="_13579", project=project)
acq = Acquisition(uuid="_15793", session=session)
acq2 = Acquisition(uuid="_15795", session=session)
person = acq.add_person(attributes=({Constants.NIDM_SUBJECTID: "9999"}))
acq.add_qualified_association(person=person,
role=Constants.NIDM_PARTICIPANT)
person2 = acq2.add_person(attributes=({Constants.NIDM_SUBJECTID: "8888"}))
acq2.add_qualified_association(person=person2,
role=Constants.NIDM_PARTICIPANT)
#save a turtle file
with open("test.ttl", 'w') as f:
f.write(project.serializeTurtle())
participant_list = Query.GetParticipantIDs(["test.ttl"])
remove("test.ttl")
assert (participant_list['ID'].str.contains('9999').any())
assert (participant_list['ID'].str.contains('8888').any())
def makeTestFile(filename, params):
global test_person_uuid, test_p2_subject_uuids
nidm_project_name = params.get('NIDM_PROJECT_NAME',
False) or "Project_name_sample"
nidm_project_identifier = params.get('NIDM_PROJECT_IDENTIFIER',
False) or 9610
nidm_project2_identifier = params.get('NIDM_PROJECT_IDENTIFIER',
False) or 550
nidm_project_description = params.get(
'NIDM_PROJECT_DESCRIPTION', False) or "1234356 Test investigation"
project_uuid = params.get('PROJECT_UUID', False) or "_proj1"
project_uuid2 = params.get('PROJECT2_UUID', False) or "_proj2"
session_uuid = params.get('SESSION_UUID', False) or "_ses1"
session_uuid2 = params.get('SESSION2_UUID', False) or "_ses2"
p1kwargs = {
Constants.NIDM_PROJECT_NAME: nidm_project_name,
Constants.NIDM_PROJECT_IDENTIFIER: nidm_project_identifier,
Constants.NIDM_PROJECT_DESCRIPTION: nidm_project_description
}
p2kwargs = {
Constants.NIDM_PROJECT_NAME: nidm_project_name,
Constants.NIDM_PROJECT_IDENTIFIER: nidm_project2_identifier,
Constants.NIDM_PROJECT_DESCRIPTION: nidm_project_description
}
project = Project(uuid=project_uuid, attributes=p1kwargs)
session = Session(uuid=session_uuid, project=project)
acq = Acquisition(uuid="_acq1", session=session)
acq2 = Acquisition(uuid="_acq2", session=session)
acq3 = Acquisition(uuid="_acq2", session=session)
person = acq.add_person(attributes=({Constants.NIDM_SUBJECTID: "a1_9999"}))
test_person_uuid = (str(person.identifier)).replace("niiri:", "")
acq.add_qualified_association(person=person,
role=Constants.NIDM_PARTICIPANT)
person2 = acq2.add_person(attributes=({
Constants.NIDM_SUBJECTID: "a1_8888"
}))
acq2.add_qualified_association(person=person2,
role=Constants.NIDM_PARTICIPANT)
person3 = acq3.add_person(attributes=({
Constants.NIDM_SUBJECTID: "a2_7777"
}))
acq2.add_qualified_association(person=person3,
role=Constants.NIDM_PARTICIPANT)
project2 = Project(uuid=project_uuid2, attributes=p2kwargs)
session2 = Session(uuid=session_uuid2, project=project2)
acq4 = Acquisition(uuid="_acq3", session=session2)
acq5 = Acquisition(uuid="_acq4", session=session2)
person4 = acq4.add_person(attributes=({
Constants.NIDM_SUBJECTID: "a3_6666"
}))
acq4.add_qualified_association(person=person4,
role=Constants.NIDM_PARTICIPANT)
person5 = acq5.add_person(attributes=({
Constants.NIDM_SUBJECTID: "a4_5555"
}))
acq5.add_qualified_association(person=person5,
role=Constants.NIDM_PARTICIPANT)
# now add some assessment instrument data
addData(
acq, {
Constants.NIDM_AGE: 9,
Constants.NIDM_HANDEDNESS: "R",
Constants.NIDM_DIAGNOSIS: "Anxiety"
})
addData(
acq2, {
Constants.NIDM_AGE: 8,
Constants.NIDM_HANDEDNESS: "L",
Constants.NIDM_DIAGNOSIS: "ADHD"
})
addData(
acq4, {
Constants.NIDM_AGE: 7,
Constants.NIDM_HANDEDNESS: "A",
Constants.NIDM_DIAGNOSIS: "Depression"
})
addData(
acq5, {
Constants.NIDM_AGE: 6,
Constants.NIDM_HANDEDNESS: "R",
Constants.NIDM_DIAGNOSIS: "Depression"
})
test_p2_subject_uuids.append(
(str(person4.identifier)).replace("niiri:", ""))
test_p2_subject_uuids.append(
(str(person5.identifier)).replace("niiri:", ""))
with open("a.ttl", 'w') as f:
f.write(project.graph.serialize(None, format='rdf', rdf_format='ttl'))
with open("b.ttl", 'w') as f:
f.write(project2.graph.serialize(None, format='rdf', rdf_format='ttl'))
#create empty graph
graph = Graph()
for nidm_file in ("a.ttl", "b.ttl"):
tmp = Graph()
graph = graph + tmp.parse(nidm_file,
format=util.guess_format(nidm_file))
graph.serialize(filename, format='turtle')
os.unlink("a.ttl")
os.unlink("b.ttl")
with open(filename, "r") as f:
x = f.read()
with open("./agent.ttl", "w") as f:
f.write(x)