def test_assessor_full_object(self):
with SanityChecks.__get_connection() as intf:
assrobj1 = intf.select_assessor(proj_id, subj_id, sess_id, assr_id)
csess = XnatUtils.CachedImageSession(intf, proj_id, subj_id, sess_id)
cassr = filter(lambda x: x.label() == assr_id, csess.assessors())[0]
assrobj2 = cassr.full_object()
self.assertEqual(assrobj1.label(), assrobj2.label())
def test_scan_full_object(self):
with SanityChecks.__get_connection() as intf:
scanobj1 = intf.select_scan(proj_id, subj_id, sess_id, scan_id)
csess = XnatUtils.CachedImageSession(intf, proj_id, subj_id, sess_id)
cscan = filter(lambda x: x.label() == scan_id, csess.scans())[0]
scanobj2 = cscan.full_object()
self.assertEqual(scanobj1.label(), scanobj2.label())
def test_assessor_out_resources(self):
with XnatUtils.get_interface(host=host) as intf:
cisess = XnatUtils.CachedImageSession(intf, proj_id, subj_id,
sess_id)
for asr in cisess.assessors():
asrobj = intf.select_assessor(proj_id, subj_id, sess_id,
asr.label())
print((asrobj.out_resources()))
def test_xnat_parse_session(self):
with XnatUtils.get_interface(host=host) as intf:
intf.connect()
SanityChecks.__prep_project(intf)
yamldoc = YamlDoc().from_string(yamls.proc_a)
csess = XnatUtils.CachedImageSession(intf, proj_id, subj_id,
sess_id)
ap = AutoProcessor(XnatUtils, yamldoc)
ap.parse_session(ap)
def test_xnat_has_inputs(self):
with XnatUtils.get_interface(host=host) as intf:
intf.connect()
print((yamls.proc_a))
SanityChecks.__prep_project(intf)
yamldoc = YamlDoc().from_string(yamls.proc_a)
ap = AutoProcessor(XnatUtils, yamldoc)
csess = XnatUtils.CachedImageSession(intf, proj_id, subj_id,
sess_id)
results = []
for cassr in csess.assessors():
has, errors = ap.has_inputs(cassr)
results.append((has, errors))
print(results)
def test_xnat_get_cached_image_session(self):
with XnatUtils.get_interface(host=host) as intf:
cisess = XnatUtils.CachedImageSession(intf, proj_id, subj_id,
sess_id)
print(cisess)
print((cisess.info()))
for ciscan in cisess.scans():
print((ciscan.info()))
scanobj = ciscan.full_object()
print(scanobj)
for ciassr in cisess.assessors():
print((ciassr.info()))
for cirsrc in ciassr.out_resources():
print((cirsrc.info()))
asrinfo = ciassr.info()
rsrcobj = intf.select_assessor_resource(
asrinfo['project_id'], asrinfo['subject_id'],
asrinfo['session_id'], asrinfo['assessor_label'],
cirsrc.info()['label'])
print(rsrcobj)
sessobj = cisess.full_object()
print(sessobj)
def get_cmds(self, assessor, job_dir_path):
"""
This function generates the spider command for the cluster job
"""
project = assessor.parent().parent().parent().label()
subject = assessor.parent().parent().label()
session = assessor.parent().label()
csess = XnatUtils.CachedImageSession(assessor._intf, project, subject,
session)
xnat = XnatUtils.get_interface()
scan = csess.scans()[0].label()
scan_data = get_scan_resource_uri(xnat, project, subject, session,
scan)
cmd = csai_CMD.format(spider_path=self.spider_path,
job_dir_path=job_dir_path,
assessor_label=assessor.label(),
project=project,
subject=subject,
session=session,
scan_data=scan_data,
suffix_proc=self.suffix_proc,
matlab_utils=self.matlab_utils,
matlab_bin=self.matlab_path)
return [cmd]
def test_session_full_object(self):
with SanityChecks.__get_connection() as intf:
sessobj1 = intf.select_experiment(proj_id, subj_id, sess_id)
sessobj2 = XnatUtils.CachedImageSession(intf, proj_id, subj_id,
sess_id).full_object()
self.assertEqual(sessobj1.label(), sessobj2.label())
"""
Remove the flagfile to unlock the process
:param lock_file: flag file use to lock the process
:return: None
"""
if os.path.exists(lock_file):
os.remove(lock_file)
def check_dir(dir_path):
try:
os.makedirs(dir_path)
except OSError:
if not os.path.isdir(dir_path):
raise
if __name__ == '__main__':
d = Module_baxter_redcap_sync(directory='/Users/yuqian',
mod_name=DEFAULT_MODULE_NAME,
text_report=DEFAULT_TEXT_REPORT,
resources='STATS',
proctypes='naleg-roi_v1')
xnat = XnatUtils.get_interface("http://xnat.vanderbilt.edu:8080/xnat",
"masispider", "xnatisawesome!!")
csess = XnatUtils.CachedImageSession(xnat, 'IKIZLER', '133511', '133511')
d.prerun()
d.needs_run(csess, xnat)
d.run(csess.info(), csess.full_object())