def test_GetProjectsComputedMetadata():
p1 = makeProjectTestFile("testfile.ttl")
p2 = makeProjectTestFile2("testfile2.ttl")
if not Path('./cmu_a.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl",
"cmu_a.nidm.ttl")
#DBK: this is a bit unsafe as the TTL files in the github repo above can change and the UUID will change since they are randomly
#generated at this point. It's probably more robust to explicitly create these files for the time being and explicitly set the
#UUID in the test file:
# For example: kwargs={Constants.NIDM_PROJECT_NAME:"FBIRN_PhaseIII",Constants.NIDM_PROJECT_IDENTIFIER:1200,Constants.NIDM_PROJECT_DESCRIPTION:"Test investigation2"}
# project = Project(uuid="_654321",attributes=kwargs)
#
p3 = "nidm:_504a60b0-7e86-11e9-ae20-003ee1ce9545" # from the cmu_a ttl file
json_response = Query.GetProjectsComputedMetadata(
["testfile.ttl", "testfile2.ttl", "cmu_a.nidm.ttl"])
parsed = json.loads(json_response)
assert parsed['projects'][p1][str(
Constants.NIDM_PROJECT_DESCRIPTION)] == "Test investigation"
assert parsed['projects'][p2][str(
Constants.NIDM_PROJECT_DESCRIPTION)] == "More Scans"
assert parsed['projects'][p3][str(
Constants.NIDM_PROJECT_NAME)] == "ABIDE CMU_a Site"
assert parsed['projects'][p2][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 0
#DBK - this isn't working
#assert parsed['projects'][p3][Query.matchPrefix(str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 14
assert parsed['projects'][p1][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 0
def test_CMU_GetProjectsComputedMetadata():
'''
This will run the getProjectsComputedMetadata on a downloaded ttl file from the ABIDE dataset
This is for dev purposes only and should be skipped during a normal test
'''
if not Path('./cmu_a.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl",
"cmu_a.nidm.ttl")
json_response = Query.GetProjectsComputedMetadata(["cmu_a.nidm.ttl"])
parsed = json.loads(json_response)
print(parsed)
# should be only one
p1 = list(parsed['projects'].keys())[0]
assert parsed['projects'][p1][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 14
assert parsed['projects'][p1]["age_min"] == 21
assert parsed['projects'][p1]["age_max"] == 33
assert parsed['projects'][p1][str(Constants.NIDM_GENDER)] == ['1', '2']
assert parsed['projects'][p1][str(
Constants.NIDM_HANDEDNESS)] == ['R', 'L', 'Ambi']
def test_GetProjectsComputedMetadata():
p1 = makeProjectTestFile("testfile.ttl")
p2 = makeProjectTestFile2("testfile2.ttl")
files = ["testfile.ttl", "testfile2.ttl"]
if USE_GITHUB_DATA:
if not Path('./cmu_a.nidm.ttl').is_file():
urllib.request.urlretrieve(
"https://raw.githubusercontent.com/dbkeator/simple2_NIDM_examples/master/datasets.datalad.org/abide/RawDataBIDS/CMU_a/nidm.ttl",
"cmu_a.nidm.ttl")
files.append("cmu_a.nidm.ttl")
parsed = Query.GetProjectsComputedMetadata(files)
if USE_GITHUB_DATA:
for project_id in parsed['projects']:
print("looking at {}".format(project_id))
if project_id != p1 and project_id != p2:
p3 = project_id
print("got p3 of {}".format(p3))
assert parsed['projects'][p3][str(
Constants.NIDM_PROJECT_NAME)] == "ABIDE CMU_a Site"
assert parsed['projects'][p3][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 14
assert parsed['projects'][p3]["age_min"] == 21
assert parsed['projects'][p3]["age_max"] == 33
assert parsed['projects'][p3][str(Constants.NIDM_GENDER)] == ['1', '2']
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)
text = ('On', 'Disable',
'unsetting') if os.getenv('PYNIDM_GRAPH_CACHE') != None else (
'Off', 'Enable', 'setting')
restLog("Graph cache is {}".format(text[0]), 1, verbosity_level)
restLog(
"{} graph cache by {} the PYNIDM_GRAPH_CACHE environment variable".
format(text[1], text[2]), 1, verbosity_level)
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/?$", command)
project = match.group((1))
restLog("Returning all agents for project {}".format(project), 2,
verbosity_level)
agents = Query.GetParticipantUUIDsForProject(nidm_files, project)
result = []
vals = agents.values
for x in vals:
result.append(str(x[0]).replace("http://iri.nidash.org/", ""))
elif re.match(r"^/?projects/[^/]+/subjects/[^/]+/?$", command):
match = re.match(r"^/?projects/([^/]+)/subjects/([^/]+)/?$", command)
restLog("Returning info about subject {}".format(match.group(2)), 2,
verbosity_level)
result = Query.GetParticipantDetails(nidm_files, match.group(1),
match.group(2))
else:
restLog("NO MATCH!", 2, verbosity_level)
return result
def test_GetProjectsComputedMetadata():
p1 = makeProjectTestFile("testfile.ttl")
p2 = makeProjectTestFile2("testfile2.ttl")
json_response = Query.GetProjectsComputedMetadata(
["testfile.ttl", "testfile2.ttl"])
parsed = json.loads(json_response)
assert parsed['projects'][p1][str(
Constants.NIDM_PROJECT_DESCRIPTION)] == "Test investigation"
assert parsed['projects'][p2][str(
Constants.NIDM_PROJECT_DESCRIPTION)] == "More Scans"
assert parsed['projects'][p2][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 0
assert parsed['projects'][p1][Query.matchPrefix(
str(Constants.NIDM_NUMBER_OF_SUBJECTS))] == 0
def projectStats(self):
result = dict()
subjects = None
path = (urlparse(self.command)).path
match = re.match(r"^/?statistics/projects/([^/]+)\??$", path)
id = parse.unquote(str(match.group(1)))
self.restLog("Returing project {} stats metadata".format(id), 2)
projects = Query.GetProjectsComputedMetadata(self.nidm_files)
for pid in projects['projects'].keys():
self.restLog("comparng " + str(pid) + " with " + str(id), 5)
self.restLog(
"comparng " + str(pid) + " with " + Constants.NIIRI + id, 5)
self.restLog("comparng " + str(pid) + " with niiri:" + id, 5)
if pid == id or pid == Constants.NIIRI + id or pid == "niiri:" + id:
# stip off prefixes to make it more human readable
for key in projects['projects'][pid]:
short_key = key
possible_prefix = re.sub(':.*', '', short_key)
if possible_prefix in Constants.namespaces:
short_key = re.sub('^.*:', '', short_key)
result[short_key] = projects['projects'][pid][key]
# now get any fields they reqested
for field in self.query['fields']:
if subjects == None:
subjects = Query.GetParticipantUUIDsForProject(
tuple(self.nidm_files),
project_id=id,
filter=self.query['filter'])
result['subjects'] = subjects
bits = field.split('.')
if len(bits) > 1:
stat_type = self.getStatType(
bits[0]
) # should be either instruments or derivatives for now.
self.addFieldStats(result, id, subjects, bits[1],
stat_type) # bits[1] will be the ID
return self.dictFormat(result)
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)
result = []
if re.match(r"^/?projects/?$", command):
restLog("Returning all projects", 2, verbosity_level)
projects = Query.GetProjectsUUID(nidm_files)
for uuid in projects:
result.append(Query.matchPrefix(str(uuid)))
elif re.match(r"^/?projects/[^/]+$", command):
restLog("Returing metadata ", 2, verbosity_level)
match = re.match(r"^/?projects/([^/]+)$", command)
id = parse.unquote(str(match.group(1)))
restLog("computing metadata", 5, verbosity_level)
projects = Query.GetProjectsComputedMetadata(nidm_files)
for pid in projects['projects'].keys():
restLog("comparng " + str(pid) + " with " + str(id), 5,
verbosity_level)
if pid == id:
result = projects['projects'][pid]
return result
def restParser(nidm_files, command, verbosity_level=0):
restLog("parsing command " + command, 1, verbosity_level)
restLog("Files to read:" + str(nidm_files), 1, verbosity_level)
restLog("Using {} as the graph cache directory".format(gettempdir()), 1,
verbosity_level)
filter = ""
if str(command).find('?') != -1:
(command, query) = str(command).split('?')
for q in query.split('&'):
if len(q.split('=')) == 2:
left, right = q.split('=')[0], q.split('=')[1]
if left == 'filter':
filter = right
result = []
if re.match(r"^/?projects/?$", 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