def test_GetParticipantDetails():
import time
start = time.time()
restParser = RestParser()
if cmu_test_project_uuid:
project = cmu_test_project_uuid
else:
projects = restParser.run(BRAIN_VOL_FILES, '/projects')
project = projects[0]
import time
start = time.time()
subjects = restParser.run(BRAIN_VOL_FILES,
'/projects/{}/subjects'.format(project))
subject = subjects['uuid'][0]
Query.GetParticipantInstrumentData(BRAIN_VOL_FILES, project, subject)
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 ('derivatives' in details)
end = time.time()
runtime = end - start
def test_CheckSubjectMatchesFilter():
restParser = RestParser()
if cmu_test_project_uuid:
project = cmu_test_project_uuid
else:
projects = restParser.run(BRAIN_VOL_FILES, '/projects')
project = projects[0]
subjects = restParser.run(BRAIN_VOL_FILES,
'/projects/{}/subjects'.format(project))
subject = subjects['uuid'][0]
derivatives = Query.GetDerivativesDataForSubject(BRAIN_VOL_FILES, project,
subject)
for skey in derivatives:
for vkey in derivatives[skey]['values']:
dt = vkey
val = derivatives[skey]['values'][vkey]['value']
if (dt and val):
break
# find an actual stat and build a matching filter to make sure our matcher passes it
filter = "derivatives.{} eq {}".format(dt, val)
assert Query.CheckSubjectMatchesFilter(BRAIN_VOL_FILES, project, subject,
filter)
instruments = Query.GetParticipantInstrumentData(BRAIN_VOL_FILES, project,
subject)
for (i, inst) in instruments.items():
if 'AGE_AT_SCAN' in inst:
age = inst['AGE_AT_SCAN']
older = str(float(age) + 1)
younger = str(float(age) - 1)
assert Query.CheckSubjectMatchesFilter(
BRAIN_VOL_FILES, project, subject,
"instruments.AGE_AT_SCAN eq {}".format(str(age)))
assert (Query.CheckSubjectMatchesFilter(
BRAIN_VOL_FILES, project, subject,
"instruments.AGE_AT_SCAN lt {}".format(younger)) == False)
assert (Query.CheckSubjectMatchesFilter(
BRAIN_VOL_FILES, project, subject,
"instruments.AGE_AT_SCAN gt {}".format(younger)) == True)
assert Query.CheckSubjectMatchesFilter(
BRAIN_VOL_FILES, project, subject,
"instruments.AGE_AT_SCAN lt {}".format(older))
assert (Query.CheckSubjectMatchesFilter(
BRAIN_VOL_FILES, project, subject,
"instruments.AGE_AT_SCAN gt {}".format(older)) == False)
eq__format = "instruments.{} eq '{}'".format('WISC_IV_VOCAB_SCALED', 'nan')
assert Query.CheckSubjectMatchesFilter(BRAIN_VOL_FILES, project, subject,
eq__format)
eq__format = "instruments.{} eq '{}'".format('WISC_IV_VOCAB_SCALED',
'not a match')
assert (Query.CheckSubjectMatchesFilter(BRAIN_VOL_FILES, project, subject,
eq__format) == False)
def instrumentSummary(self):
match = re.match(
r"^/?projects/([^/]+)/subjects/([^/]+)/instruments/([^/]+)$",
self.command)
self.restLog(
"Returning instrument {} in subject {}".format(
match.group(3), match.group(2)), 2)
instruments = Query.GetParticipantInstrumentData(
self.nidm_files, match.group(1), match.group(2))
return self.format(instruments[match.group(3)],
headers=["Category", "Value"])
def instrumentsList(self):
result = []
match = re.match(r"^/?projects/([^/]+)/subjects/([^/]+)$",
self.command)
self.restLog(
"Returning instruments in subject {}".format(match.group(2)), 2)
instruments = Query.GetParticipantInstrumentData(
self.nidm_files, match.group(1), match.group(2))
for i in instruments:
result.append(i)
return self.format(result)
def addFieldStats(self, result, project, subjects, field, type):
'''
Geneerates basic stats on a group of subjects and adds it to the result
:param result:
:param subjects:
:param field:
:return:
'''
values = []
for s in subjects:
if type == self.STAT_TYPE_INSTRUMENTS:
data = Query.GetParticipantInstrumentData(
tuple(self.nidm_files), project, s)
for i in data:
if field in data[i]:
values.append(float(data[i][field]))
# derivatives are of the form [UUID]['values'][URI]{datumType, label, values, units}
if type == self.STAT_TYPE_DERIVATIVES:
data = Query.GetDerivativesDataForSubject(
tuple(self.nidm_files), project, s)
for deriv in data:
for URI in data[deriv]['values']:
measures = data[deriv]['values'][URI]
if field == measures[
'label'] or field == self.getTailOfURI(URI):
values.append(float(measures['value']))
if len(values) > 0:
med = median(values)
avg = mean(values)
st = std(values)
mn = min(values)
mx = max(values)
else:
med = avg = st = mn = mx = None
result[field] = {
"max": mx,
"min": mn,
"median": med,
"mean": avg,
"standard_deviation": st
}
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 restParser(nidm_files, command, verbosity_level=0):
restLog("parsing command " + command, 1, verbosity_level)
restLog("Files to read:" + str(nidm_files), 1, verbosity_level)
restLog("Using {} as the graph cache directory".format(gettempdir()), 1,
verbosity_level)
filter = ""
if str(command).find('?') != -1:
(command, query) = str(command).split('?')
for q in query.split('&'):
if len(q.split('=')) == 2:
left, right = q.split('=')[0], q.split('=')[1]
if left == 'filter':
filter = right
result = []
if re.match(r"^/?projects/?$", command):
restLog("Returning all projects", 2, verbosity_level)
projects = Query.GetProjectsUUID(nidm_files)
for uuid in projects:
result.append(str(uuid).replace(Constants.NIIRI, ""))
elif re.match(r"^/?projects/[^/]+$", command):
restLog("Returing metadata ", 2, verbosity_level)
match = re.match(r"^/?projects/([^/]+)$", command)
id = parse.unquote(str(match.group(1)))
restLog("computing metadata", 5, verbosity_level)
projects = Query.GetProjectsComputedMetadata(nidm_files)
for pid in projects['projects'].keys():
restLog("comparng " + str(pid) + " with " + str(id), 5,
verbosity_level)
restLog("comparng " + str(pid) + " with " + Constants.NIIRI + id,
5, verbosity_level)
restLog("comparng " + str(pid) + " with niiri:" + id, 5,
verbosity_level)
if pid == id or pid == Constants.NIIRI + id or pid == "niiri:" + id:
result = projects['projects'][pid]
elif re.match(r"^/?projects/[^/]+/subjects/?$", command):
match = re.match(r"^/?projects/([^/]+)/subjects/?$", command)
project = match.group((1))
restLog(
"Returning all agents matching filter '{}' for project {}".format(
filter, project), 2, verbosity_level)
result = Query.GetParticipantUUIDsForProject(nidm_files, project,
filter, None)
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/?$", command):
match = re.match(r"^/?projects/([^/]+)/subjects/([^/]+)/?$", command)
restLog("Returning info about subject {}".format(match.group(2)), 2,
verbosity_level)
result = Query.GetParticipantDetails(nidm_files, match.group(1),
match.group(2))
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/instruments/?$", command):
match = re.match(r"^/?projects/([^/]+)/subjects/([^/]+)", command)
restLog("Returning instruments in subject {}".format(match.group(2)),
2, verbosity_level)
instruments = Query.GetParticipantInstrumentData(
nidm_files, match.group(1), match.group(2))
for i in instruments:
result.append(i)
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/instruments/[^/]+/?$",
command):
match = re.match(
r"^/?projects/([^/]+)/subjects/([^/]+)/instruments/([^/]+)",
command)
restLog(
"Returning instrument {} in subject {}".format(
match.group(3), match.group(2)), 2, verbosity_level)
instruments = Query.GetParticipantInstrumentData(
nidm_files, match.group(1), match.group(2))
result = instruments[match.group(3)]
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/derivatives/?$", command):
match = re.match(r"^/?projects/([^/]+)/subjects/([^/]+)", command)
restLog("Returning derivatives in subject {}".format(match.group(2)),
2, verbosity_level)
derivatives = Query.GetDerivativesDataForSubject(
nidm_files, match.group(1), match.group(2))
for s in derivatives:
result.append(s)
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/derivatives/[^/]+/?$",
command):
match = re.match(
r"^/?projects/([^/]+)/subjects/([^/]+)/derivatives/([^/]+)",
command)
restLog(
"Returning stat {} in subject {}".format(match.group(3),
match.group(2)), 2,
verbosity_level)
derivatives = Query.GetDerivativesDataForSubject(
nidm_files, match.group(1), match.group(2))
result = derivatives[match.group(3)]
else:
restLog("NO MATCH!", 2, verbosity_level)
return result