def test_brain_vols():
projects = restParser(BRAIN_VOL_FILES, '/projects')
subjects = restParser(BRAIN_VOL_FILES, '/projects/{}/subjects'.format(projects[0]))
subject = subjects[0]
data = Query.getStatsDataForSubject(BRAIN_VOL_FILES, subject)
assert(len(data) > 0)
assert('StatCollectionType' in data[0])
assert('URI' in data[0])
assert('values' in data[0])
def test_uri_project_id():
kwargs = {
Constants.NIDM_PROJECT_NAME: "FBIRN_PhaseII",
Constants.NIDM_PROJECT_IDENTIFIER: 9610,
Constants.NIDM_PROJECT_DESCRIPTION: "1234356 Test investigation"
}
project = Project(uuid="_123456", attributes=kwargs)
#save a turtle file
with open("uri2test.ttl", 'w') as f:
f.write(project.serializeTurtle())
kwargs = {
Constants.NIDM_PROJECT_NAME: "FBIRN_PhaseIII",
Constants.NIDM_PROJECT_IDENTIFIER: 1200,
Constants.NIDM_PROJECT_DESCRIPTION: "Test investigation2"
}
project = Project(uuid="_654321", attributes=kwargs)
#save a turtle file
with open("uri2test2.ttl", 'w') as f:
f.write(project.serializeTurtle())
result = restParser(['uri2test.ttl', 'uri2test2.ttl'],
'/projects/nidm:_123456')
pp = pprint.PrettyPrinter()
pp.pprint(result)
assert type(result) == dict
assert result["dct:description"] == "1234356 Test investigation"
def test_uri_project_list():
kwargs={Constants.NIDM_PROJECT_NAME:"FBIRN_PhaseII",Constants.NIDM_PROJECT_IDENTIFIER:9610,Constants.NIDM_PROJECT_DESCRIPTION:"Test investigation"}
project = Project(uuid="_123456",attributes=kwargs)
#save a turtle file
with open("uritest.ttl",'w') as f:
f.write(project.serializeTurtle())
kwargs={Constants.NIDM_PROJECT_NAME:"FBIRN_PhaseIII",Constants.NIDM_PROJECT_IDENTIFIER:1200,Constants.NIDM_PROJECT_DESCRIPTION:"Test investigation2"}
project = Project(uuid="_654321",attributes=kwargs)
#save a turtle file
with open("uritest2.ttl",'w') as f:
f.write(project.serializeTurtle())
result = restParser(['uritest.ttl', 'uritest2.ttl'], '/projects')
project_uuids = []
for uuid in result:
project_uuids.append(uuid)
assert type(result) == list
assert len(project_uuids) == 2
assert "_123456" in project_uuids
assert "_654321" in project_uuids
os.remove("uritest.ttl")
os.remove("uritest2.ttl")
def get(self, all):
files = getTTLFiles()
if len(files) == 0:
return ({
'error':
'No NIDM files found. You may need to add NIDM ttl files to ~/PyNIDM/ttl'
})
return restParser(files, all, 5)
def test_uri_projects_subjects_1():
global test_p2_subject_uuids
proj_uuid = 'p2'
result = restParser([REST_TEST_FILE], '/projects/{}/subjects'.format(proj_uuid), 0)
assert type(result) == list
assert len(result) == 2
assert test_p2_subject_uuids[0] in result
assert test_p2_subject_uuids[1] in result
def test_GetParticipantDetails():
projects = restParser(BRAIN_VOL_FILES, '/projects')
project = projects[0]
subjects = restParser(BRAIN_VOL_FILES, '/projects/{}/subjects'.format(projects[0]))
subject = subjects[0]
import time
start = time.time()
Query.GetParticipantInstrumentData( BRAIN_VOL_FILES, project, subject )
end = time.time()
runtime = end - start
# assert (runtime < 12)
details = Query.GetParticipantDetails( BRAIN_VOL_FILES, project, subject )
assert ('uuid' in details)
assert ('id' in details)
assert ('activity' in details)
assert ('instruments' in details)
assert ('stats' in details)
def test_uri_projects_subjects_id():
global test_person_uuid
result = restParser(['./cmu_a.nidm.ttl'], '/projects')
project = result[0]
result = restParser(['./cmu_a.nidm.ttl'], '/projects/{}/subjects'.format(project))
subject = result[0]
uri = '/projects/{}/subjects/{}'.format(project,subject)
result = restParser(['./cmu_a.nidm.ttl'], uri, 0)
assert type(result) == dict
assert result['uuid'] == subject
assert len(result['instruments']) == 1
for i in result['instruments']:
assert 'AGE_AT_SCAN' in result['instruments'][i]
age = float(result['instruments'][i]['AGE_AT_SCAN'])
# WIP commented out by DBK to get tests to pass for the moment. Needs updating?
# assert age > 0
assert len(result['stats']) > 0
def test_uri_project_id():
kwargs={Constants.NIDM_PROJECT_NAME:"FBIRN_PhaseII",Constants.NIDM_PROJECT_IDENTIFIER:9610,Constants.NIDM_PROJECT_DESCRIPTION:"1234356 Test investigation"}
project = Project(uuid="_123456",attributes=kwargs)
#save a turtle file
with open("uri2test.ttl",'w') as f:
f.write(project.serializeTurtle())
kwargs={Constants.NIDM_PROJECT_NAME:"FBIRN_PhaseIII",Constants.NIDM_PROJECT_IDENTIFIER:1200,Constants.NIDM_PROJECT_DESCRIPTION:"Test investigation2"}
project = Project(uuid="_654321",attributes=kwargs)
#save a turtle file
with open("uri2test2.ttl",'w') as f:
f.write(project.serializeTurtle())
result = restParser(['uri2test.ttl', 'uri2test2.ttl'], '/projects/{}_123456'.format(Query.matchPrefix(Constants.NIIRI)) )
assert type(result) == dict
assert result["dct:description"] == "1234356 Test investigation"
os.remove("uri2test.ttl")
os.remove("uri2test2.ttl")
def query(nidm_file_list, query_file, output_file, get_participants,
get_instruments, get_instrument_vars, uri, j, verbosity):
#query result list
results = []
if get_participants:
df = GetParticipantIDs(nidm_file_list.split(','),
output_file=output_file)
elif get_instruments:
#first get all project UUIDs then iterate and get instruments adding to output dataframe
project_list = GetProjectsUUID(nidm_file_list.split(','))
count = 1
for project in project_list:
if count == 1:
df = GetProjectInstruments(nidm_file_list.split(','),
project_id=project)
count += 1
else:
df = df.append(
GetProjectInstruments(nidm_file_list.split(','),
project_id=project))
#write dataframe
#if output file parameter specified
if (output_file is not None):
df.to_csv(output_file)
#with open(output_file,'w') as myfile:
# wr=csv.writer(myfile,quoting=csv.QUOTE_ALL)
# wr.writerow(df)
#pd.DataFrame.from_records(df,columns=["Instruments"]).to_csv(output_file)
else:
print(df)
elif get_instrument_vars:
#first get all project UUIDs then iterate and get instruments adding to output dataframe
project_list = GetProjectsUUID(nidm_file_list.split(','))
count = 1
for project in project_list:
if count == 1:
df = GetInstrumentVariables(nidm_file_list.split(','),
project_id=project)
count += 1
else:
df = df.append(
GetInstrumentVariables(nidm_file_list.split(','),
project_id=project))
#write dataframe
#if output file parameter specified
if (output_file is not None):
df.to_csv(output_file)
else:
print(df)
elif uri:
df = restParser(nidm_file_list.split(','), uri, int(verbosity))
if j:
print(dumps(df))
else:
if type(df) == list:
for x in df:
print(x)
elif type(df) == dict:
for k in df.keys():
print(str(k) + ' ' + str(df[k]))
else:
print(df)
else:
#read query from text fiile
with open(query_file, 'r') as fp:
query = fp.read()
df = sparql_query_nidm(nidm_file_list.split(','), query, output_file)
return df
