def should_import_epoch_per_file(self):
"""
Should import files as URLResponses, not as Resources
"""
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for scanID in xnatSession.scans().get():
s = xnatSession.scan(scanID)
id = s.attrs.get('xnat:mrScanData/type')
g = exp.getEpochGroupsWithLabel(id).iterator().next()
for r in s.resources():
label = r.label()
typeGroup = g.getChildren(label)[0]
self.assertEqual(typeGroup.getEpochCount(), len(r.files()))
for epoch in typeGroup.getEpochs():
self.assertEqual(len(epoch.getResponseNames()), 1)
r = epoch.getResponse(sessionScanner)
self.assertIsNotNone(r)
def should_import_epoch_per_file(self):
"""
Should import files as URLResponses, not as Resources
"""
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for scanID in xnatSession.scans().get():
s = xnatSession.scan(scanID)
id = s.attrs.get('xnat:mrScanData/type')
g = exp.getEpochGroupsWithLabel(id).iterator().next()
for r in s.resources():
label = r.label()
typeGroup = g.getChildren(label)[0]
self.assertEqual(typeGroup.getEpochCount(), len(r.files()))
for epoch in typeGroup.getEpochs():
self.assertEqual(len(epoch.getResponseNames()), 1)
r = epoch.getResponse(sessionScanner)
self.assertIsNotNone(r)
def to_joda_datetime(date, timezone):
return api.datetime(date.year,
date.month,
date.day,
date.hour,
date.minute,
int(date.microsecond / 1000),
api.timezone_with_id(timezone))
def import_project(dsc, xnatProject, timezone='UTC', importProjectTree=True):
"""
Import a single XNAT project.
"""
projectID = xnat_api(xnatProject.id)
_log.info('Importing project: ' + projectID)
name = xnat_api(xnatProject.attrs.get,'xnat:projectData/name')
purpose = xnat_api(xnatProject.attrs.get, 'xnat:projectData/description')
if not purpose:
purpose = "<None>"
# Find the earliest session date in the project
xnat = xnatProject._intf
sessionTypes = xnat.inspect.experiment_types()
if len(sessionTypes) == 0:
sessionTypes = ('xnat:mrSessionData', 'xnat:ctSessionData')
#raise XnatImportError("No session types defined in database")
minSessionDate = None
for sessionType in sessionTypes:
columns = (sessionType + '/DATE', sessionType + '/PROJECT')
xnat_api_pause()
query = xnat.select(sessionType, columns=columns).where([(sessionType + '/Project', '=', projectID), 'AND'])
sessionDates = [ datetime.fromtimestamp(mktime(strptime(row['date'], DATE_FORMAT))) for
row in
query if len(row['date']) > 0]
if len(sessionDates) > 0:
for sd in sessionDates:
if minSessionDate is not None:
if sd < minSessionDate:
minSessionDate = sd
else:
minSessionDate = sd
if minSessionDate is not None:
startTime = to_joda_datetime(minSessionDate, timezone)
else:
startTime = api.datetime()
ctx = dsc.getContext()
project = ctx.insertProject(name,
purpose,
startTime)
_import_entity_common(project, xnatProject)
if importProjectTree:
_log.info(" Importing project tree...")
subjectIDs = xnat_api(xnatProject.subjects().get)
for subjectID in subjectIDs:
s = xnat_api(xnatProject.subject, subjectID)
import_subject(dsc, s, timezone=timezone, project=project)
return project
def import_project(dsc, xnatProject, timezone='UTC', importProjectTree=True):
"""
Import a single XNAT project.
"""
projectID = xnat_api(xnatProject.id)
_log.info('Importing project: ' + projectID)
name = xnat_api(xnatProject.attrs.get, 'xnat:projectData/name')
purpose = xnat_api(xnatProject.attrs.get, 'xnat:projectData/description')
if not purpose:
purpose = "<None>"
# Find the earliest session date in the project
xnat = xnatProject._intf
sessionTypes = xnat.inspect.experiment_types()
if len(sessionTypes) == 0:
sessionTypes = ('xnat:mrSessionData', 'xnat:ctSessionData')
#raise XnatImportError("No session types defined in database")
minSessionDate = None
for sessionType in sessionTypes:
columns = (sessionType + '/DATE', sessionType + '/PROJECT')
xnat_api_pause()
query = xnat.select(sessionType, columns=columns).where([
(sessionType + '/Project', '=', projectID), 'AND'
])
sessionDates = [
datetime.fromtimestamp(mktime(strptime(row['date'], DATE_FORMAT)))
for row in query if len(row['date']) > 0
]
if len(sessionDates) > 0:
for sd in sessionDates:
if minSessionDate is not None:
if sd < minSessionDate:
minSessionDate = sd
else:
minSessionDate = sd
if minSessionDate is not None:
startTime = to_joda_datetime(minSessionDate, timezone)
else:
startTime = api.datetime()
ctx = dsc.getContext()
project = ctx.insertProject(name, purpose, startTime)
_import_entity_common(project, xnatProject)
if importProjectTree:
_log.info(" Importing project tree...")
subjectIDs = xnat_api(xnatProject.subjects().get)
for subjectID in subjectIDs:
s = xnat_api(xnatProject.subject, subjectID)
import_subject(dsc, s, timezone=timezone, project=project)
return project
def should_import_session_from_subject_as_experiments(self):
xnatSubject = subject_mock("1", "PROJECT_NAME")
ctx = self.dsc.getContext()
project = ctx.insertProject("session_import", "session_import", api.datetime())
s = import_subject(self.dsc, xnatSubject, project=project)
# Assertions
self.assertGreaterEqual(len(xnatSubject.experiments().get()), 1)
self.assertEqual(len(project.getExperiments()), len(xnatSubject.experiments().get()))
def should_import_epochgroup_per_scan_with_scantype_as_label(self):
ctx = self.dsc.getContext()
project = ctx.insertProject('session_import', 'session_import', api.datetime())
src = ctx.insertSource('test')
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
self.assertGreaterEqual(xnatSession.scans().get(), 1)
self.assertEqual(len(exp.getEpochGroups()), len(xnatSession.scans().get()))
def should_import_session_from_subject_as_experiments(self):
xnatSubject = subject_mock("1", "PROJECT_NAME")
ctx = self.dsc.getContext()
project = ctx.insertProject('session_import', 'session_import',
api.datetime())
s = import_subject(self.dsc, xnatSubject, project=project)
# Assertions
self.assertGreaterEqual(len(xnatSubject.experiments().get()), 1)
self.assertEqual(len(project.getExperiments()),
len(xnatSubject.experiments().get()))
def should_set_scan_datatype(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for g in exp.getEpochGroups():
scanID = xnatSession.scans().get()[0]
dtype = xnatSession.scan(scanID).datatype()
self.assertEqual(g.getOwnerProperty(DATATYPE_PROPERTY), dtype)
def should_import_scan_parameters_as_epoch_parameters(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for epoch in exp.getEpochsIterable().iterator():
parameters = epoch.getProtocolParameters()
self.assertGreater(parameters.size(), 0)
def should_import_epochgroup_per_scan_with_scantype_as_label(self):
ctx = self.dsc.getContext()
project = ctx.insertProject('session_import', 'session_import',
api.datetime())
src = ctx.insertSource('test')
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
self.assertGreaterEqual(xnatSession.scans().get(), 1)
self.assertEqual(len(exp.getEpochGroups()),
len(xnatSession.scans().get()))
def should_set_scan_datatype(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for g in exp.getEpochGroups():
scanID = xnatSession.scans().get()[0]
dtype = xnatSession.scan(scanID).datatype()
self.assertEqual(g.getOwnerProperty(DATATYPE_PROPERTY), dtype)
def should_import_scan_parameters_as_epoch_parameters(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for epoch in exp.getEpochsIterable().iterator():
parameters = epoch.getProtocolParameters()
self.assertGreater(parameters.size(), 0)
def should_set_session_id_as_epochgroup_label(self):
ctx = self.dsc.getContext()
project = ctx.insertProject('session_import', 'session_import', api.datetime())
src = ctx.insertSource('test')
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for scanID in xnatSession.scans().get():
scan = xnatSession.scan(scanID)
id = scan.attrs.get('xnat:mrScanData/type')
self.assertEqual(len(list(exp.getEpochGroupsWithLabel(id).iterator())), 1)
def import_project(dsc, xnatProject, timezone="UTC"):
"""
Import a single XNAT project.
"""
projectID = xnat_api(xnatProject.id)
name = xnat_api(xnatProject.attrs.get, "xnat:projectData/name")
purpose = xnat_api(xnatProject.attrs.get, "xnat:projectData/description")
# Find the earliest session date in the project
xnat = xnatProject._intf
sessionTypes = xnat.inspect.experiment_types()
if len(sessionTypes) == 0:
sessionTypes = ("xnat:mrSessionData", "xnat:ctSessionData")
# raise XnatImportError("No session types defined in database")
minSessionDate = None
for sessionType in sessionTypes:
columns = (sessionType + "/DATE", sessionType + "/PROJECT")
xnat_api_pause()
query = xnat.select(sessionType, columns=columns).where([(sessionType + "/Project", "=", projectID), "AND"])
sessionDates = [
datetime.fromtimestamp(mktime(strptime(row["date"], DATE_FORMAT))) for row in query if len(row["date"]) > 0
]
if len(sessionDates) > 0:
for sd in sessionDates:
if minSessionDate is not None:
if sd < minSessionDate:
minSessionDate = sd
else:
minSessionDate = sd
if minSessionDate is not None:
startTime = to_joda_datetime(minSessionDate, timezone)
else:
startTime = api.datetime()
ctx = dsc.getContext()
project = ctx.insertProject(name, purpose, startTime)
_import_entity_common(project, xnatProject)
for s in iterate_entity_collection(xnatProject.subjects):
src = import_source(dsc, s)
for session in iterate_entity_collection(s.sessions):
import_session(dsc, src, project, session)
return project
def should_set_session_id_as_epochgroup_label(self):
ctx = self.dsc.getContext()
project = ctx.insertProject('session_import', 'session_import',
api.datetime())
src = ctx.insertSource('test')
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for scanID in xnatSession.scans().get():
scan = xnatSession.scan(scanID)
id = scan.attrs.get('xnat:mrScanData/type')
self.assertEqual(
len(list(exp.getEpochGroupsWithLabel(id).iterator())), 1)
def should_import_scanner_perameters_as_device_parameters(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for epoch in exp.getEpochsIterable().iterator():
r = epoch.getResponse(sessionScanner)
self.assertIsNotNone(r)
parameters = r.getDeviceParameters()
self.assertIsNotNone(parameters)
self.assertGreater(parameters.size(), 0)
def should_import_scanner_perameters_as_device_parameters(self):
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
sessionType = xnatSession.datatype()
sessionScanner = xnatSession.attrs.get(sessionType + '/scanner')
for epoch in exp.getEpochsIterable().iterator():
r = epoch.getResponse(sessionScanner)
self.assertIsNotNone(r)
parameters = r.getDeviceParameters()
self.assertIsNotNone(parameters)
self.assertGreater(parameters.size(), 0)
def should_insert_epochgroup_per_resource_group(self):
"""
Should import files as URLResponses, not as Resources
"""
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for scanID in xnatSession.scans().get():
s = xnatSession.scan(scanID)
id = s.attrs.get('xnat:mrScanData/type')
g = exp.getEpochGroupsWithLabel(id).iterator().next()
for r in s.resources():
label = r.label()
self.assertEqual(len(g.getChildren(label)), 1)
def should_insert_epochgroup_per_resource_group(self):
"""
Should import files as URLResponses, not as Resources
"""
ctx = self.dsc.getContext()
src = ctx.insertSource('test')
project = ctx.insertProject('test', 'test', api.datetime())
xnatSession = session_mock()
exp = import_session(self.dsc, src, project, xnatSession)
for scanID in xnatSession.scans().get():
s = xnatSession.scan(scanID)
id = s.attrs.get('xnat:mrScanData/type')
g = exp.getEpochGroupsWithLabel(id).iterator().next()
for r in s.resources():
label = r.label()
self.assertEqual(len(g.getChildren(label)), 1)
def to_joda_datetime(date, timezone):
return api.datetime(date.year, date.month, date.day, date.hour,
date.minute, date.second, int(date.microsecond / 1000),
api.timezone_with_id(timezone))