def getActivities(nidm_file_tuples, subject_id):
activities = set([])
subject_uri = expandID(subject_id, Constants.NIIRI)
for file in nidm_file_tuples:
rdf_graph = OpenGraph(file)
for blank_node in rdf_graph.subjects(predicate=Constants.PROV['agent'],
object=subject_uri):
for activity in rdf_graph.subjects(
predicate=Constants.PROV['qualifiedAssociation'],
object=blank_node):
if (activity, isa, Constants.PROV['Activity']) in rdf_graph:
activities.add(activity)
return activities
def GetDataelements(nidm_files_tuple):
result = {"data_elements": {"uuid": [], "label": [], "data_type_info": []}}
found_uris = set()
for file in nidm_files_tuple:
rdf_graph = OpenGraph(file)
#find all the datatypes
for de_uri in rdf_graph.subjects(predicate=isa,
object=Constants.NIDM['DataElement']):
if de_uri not in found_uris: # don't add duplicates
dti = getDataTypeInfo(rdf_graph, de_uri)
result['data_elements']['uuid'].append(
str(dti['dataElementURI']))
result['data_elements']['label'].append(str(dti['label']))
result['data_elements']['data_type_info'].append(dti)
found_uris.add(de_uri)
# find all the datatypes
for de_uri in rdf_graph.subjects(
predicate=isa, object=Constants.NIDM['PersonalDataElement']):
if de_uri not in found_uris: # don't add duplicates
dti = getDataTypeInfo(rdf_graph, de_uri)
result['data_elements']['uuid'].append(
str(dti['dataElementURI']))
result['data_elements']['label'].append(str(dti['label']))
result['data_elements']['data_type_info'].append(dti)
found_uris.add(de_uri)
# now look for any of the CDEs
all_predicates = GetAllPredicates(nidm_files_tuple)
cde_graph = nidm.experiment.CDE.getCDEs()
cde_types = cde_graph.subjects(predicate=Constants.RDFS['subClassOf'],
object=Constants.NIDM['DataElement'])
cde_type_set = set() # i.e. fs:DataElement
known_cde_types = set() # i.e. fs_003579
for t in cde_types:
cde_type_set.add(t)
for s in cde_graph.subjects(predicate=isa, object=t):
known_cde_types.add(s)
for predicate in all_predicates:
if predicate in known_cde_types:
dti = getDataTypeInfo(cde_graph, predicate)
result['data_elements']['uuid'].append(str(dti['dataElementURI']))
result['data_elements']['label'].append(str(dti['label']))
result['data_elements']['data_type_info'].append(dti)
return result
def getActivities(nidm_file_tuples, subject_id):
activities = set([])
# if we were passed in a sub_id rather than a UUID, lookup the associated UUID. (we might get multiple!)
if validate_uuid(URITail(subject_id)):
sub_uris = [subject_id]
else:
sub_uris = getSubjectUUIDsfromID(nidm_file_tuples, subject_id)
for file in nidm_file_tuples:
rdf_graph = OpenGraph(file)
for subject_uri in sub_uris:
subject_uri = expandID(subject_uri, Constants.NIIRI)
for blank_node in rdf_graph.subjects(
predicate=Constants.PROV['agent'], object=subject_uri):
for activity in rdf_graph.subjects(
predicate=Constants.PROV['qualifiedAssociation'],
object=blank_node):
if (activity, isa,
Constants.PROV['Activity']) in rdf_graph:
activities.add(activity)
return activities
def GetDataelementDetails(nidm_files_tuple, dataelement):
result = {}
for file in nidm_files_tuple:
rdf_graph = OpenGraph(file)
for de_uri in rdf_graph.subjects(predicate=isa,
object=Constants.NIDM['DataElement']):
dti = getDataTypeInfo(rdf_graph, de_uri)
# check if this is the correct one
if not (dataelement in [
str(dti['label']),
str(dti['dataElement']),
str(dti['dataElementURI'])
]):
continue
for key in dti.keys():
result[key] = dti[key]
result['inProjects'] = set()
# figure out what project the dataelement was used in
uri = dti["dataElementURI"]
a_list = rdf_graph.subjects(predicate=uri)
for a in a_list: # a is an assessment / AcquisitionObject
b_list = rdf_graph.objects(
subject=a, predicate=Constants.PROV['wasGeneratedBy'])
for b in b_list: # b is an Acquisition / Activity
c_list = rdf_graph.objects(
subject=b, predicate=Constants.DCT['isPartOf'])
for c in c_list: # c is a session
d_list = rdf_graph.objects(
subject=c, predicate=Constants.DCT['isPartOf'])
for d in d_list: # d is most likely a project
if d in rdf_graph.subjects(
predicate=isa,
object=Constants.NIDM['Project']):
result['inProjects'].add("{} ({})".format(
str(d), file))
return result # found it, we are done
if result == {}: # didn't find it yet, check the CDEs
cde_graph = nidm.experiment.CDE.getCDEs()
for de_uri in cde_graph.subjects(predicate=isa):
dti = getDataTypeInfo(cde_graph, de_uri)
# check if this is the correct one
if not (dataelement in [
str(dti['label']),
str(dti['dataElement']),
str(dti['dataElementURI'])
]):
continue
for key in dti.keys():
result[key] = dti[key]
result['inProjects'] = set()
result['inProjects'].add("Common Data Element")
for file in nidm_files_tuple:
rdf_graph = OpenGraph(file)
if result['dataElementURI'] in rdf_graph.predicates():
result['inProjects'].add(file)
return result # found it, we are done
return result
