def getFieldInfoForSubject(self, project, subject):
'''
Returns a dictionary of activities where the subject has matching field data
The result[activity] is the full data_element so to get the value you would use result[activity].value
Note that a subject could match the same field in multiple activities.
:param project:
:param subject:
:return:
'''
result = {}
# if we got fields, drill into each subject and pull out the field data
# subject details -> derivitives / instrument -> values -> element
if 'fields' in self.query and len(self.query['fields']) > 0:
# get all the synonyms for all the fields - we can seach for them all at once
field_synonyms = functools.reduce(operator.iconcat, [
Query.GetDatatypeSynonyms(self.nidm_files, project, x)
for x in self.query['fields']
], [])
# print (field_synonyms)
for activity in Navigate.getActivities(self.nidm_files, subject):
activity_data = Navigate.getActivityData(
self.nidm_files, activity)
# print ([ x.label for x in activity.data])
for data_element in activity_data.data:
if not set([
data_element.dataElement, data_element.label,
data_element.isAbout
]).isdisjoint(set(field_synonyms)):
result[Query.URITail(activity)] = data_element
return result
def projects(self):
result = []
field_values = []
self.restLog("Returning all projects", 2)
projects = Query.GetProjectsUUID(self.nidm_files)
for uuid in projects:
result.append(str(uuid).replace(Constants.NIIRI, ""))
# if we got fields, drill into each subject and pull out the field data
# subject details -> derivitives / instrument -> values -> element
if 'fields' in self.query and len(self.query['fields']) > 0:
subjects_set = set()
dataelements_set = set()
self.restLog("Using fields {}".format(self.query['fields']), 2)
# result['field_values'] = []
for proj in projects:
# get all the synonyms for all the fields
field_synonyms = functools.reduce(operator.iconcat, [
Query.GetDatatypeSynonyms(self.nidm_files, proj, x)
for x in self.query['fields']
], [])
files = self.nidm_files
all_subjects = Query.GetParticipantUUIDsForProject(
self.nidm_files, proj, self.query['filter']
) # nidm_file_list= files, project_id=proj['uuid'], filter=self.query['filter']):
for sub in all_subjects['uuid']:
for activity in Navigate.getActivities(
self.nidm_files, sub):
activity = Navigate.getActivityData(
self.nidm_files, activity)
for data_element in activity.data:
if data_element.dataElement in field_synonyms:
field_values.append(
data_element._replace(subject=sub))
subjects_set.add(sub)
dataelements_set.add((data_element.datumType,
data_element.label))
if len(field_values) == 0:
raise ValueError("Supplied field not found. (" +
", ".join(self.query['fields']) + ")")
else:
summary_result = {}
summary_result['subjects'] = {"uuid": [], "subject id": []}
for sub in subjects_set:
summary_result["subjects"]["uuid"].append(sub)
summary_result["subjects"]["subject id"].append("")
summary_result['data_elements'] = {"uuid": [], "lable": []}
for de in dataelements_set:
summary_result['data_elements']["uuid"] = de[0]
summary_result['data_elements']["label"] = de[1]
summary_result['field_values'] = field_values
return self.projectSummaryFormat(summary_result)
return self.format(result, ["UUID"])
def test_Filter_Flexibility():
restParser = RestParser(output_format=RestParser.OBJECT_FORMAT)
if cmu_test_project_uuid:
project = cmu_test_project_uuid
else:
projects = restParser.run(BRAIN_VOL_FILES, '/projects')
project = projects[0]
synonyms = Query.GetDatatypeSynonyms(tuple(BRAIN_VOL_FILES),project, 'ADOS_MODULE')
real_synonyms = [x for x in synonyms if len(x) > 1]
assert len(real_synonyms) > 1
for syn in real_synonyms:
if ' ' in syn:
continue
details = restParser.run(BRAIN_VOL_FILES, '/projects/{}?filter=instruments.{} gt 2'.format(project, syn))
assert len(details['subjects']['uuid']) > 0
assert len(details['data_elements']['uuid']) > 0
def projectSummary(self):
match = re.match(r"^/?projects/([^/]+)$", self.command)
id = parse.unquote(str(match.group(1)))
self.restLog("Returing project {} summary".format(id), 2)
result = nidm.experiment.Navigate.GetProjectAttributes(self.nidm_files,
project_id=id)
result['subjects'] = Query.GetParticipantUUIDsForProject(
self.nidm_files, project_id=id, filter=self.query['filter'])
result['data_elements'] = Query.GetProjectDataElements(self.nidm_files,
project_id=id)
# if we got fields, drill into each subject and pull out the field data
# subject details -> derivitives / instrument -> values -> element
if 'fields' in self.query and len(self.query['fields']) > 0:
self.restLog("Using fields {}".format(self.query['fields']), 2)
result['field_values'] = []
# get all the synonyms for all the fields
field_synonyms = functools.reduce(operator.iconcat, [
Query.GetDatatypeSynonyms(self.nidm_files, id, x)
for x in self.query['fields']
], [])
for sub in result['subjects']['uuid']:
for activity in Navigate.getActivities(self.nidm_files, sub):
activity = Navigate.getActivityData(
self.nidm_files, activity)
for data_element in activity.data:
if data_element.dataElement in field_synonyms:
result['field_values'].append(
data_element._replace(subject=sub))
if len(result['field_values']) == 0:
raise ValueError("Supplied field not found. (" +
", ".join(self.query['fields']) + ")")
return self.projectSummaryFormat(result)