def import_session(dsc, src, project, xnatSession, timezone='UTC'):
if project == None:
return
try:
attrs = xnatSession.attrs
dtype = xnat_api(xnatSession.datatype)
#print(dtype)
_log.info(' Importing session: ' + dtype)
dateString = xnat_api(attrs.get, dtype + '/date')
timeString = xnat_api(attrs.get, dtype + '/time')
purpose = xnat_api(attrs.get, dtype + '/note')
if not purpose: #None or len 0
purpose = 'XNAT experiment ' + xnatSession._uri
dateTimeString = dateString + ' ' + timeString
if timeString:
format = DATETIME_FORMAT if timeString.find('.') > 0 else DATETIMESHORT_FORMAT
else:
format = DATE_FORMAT
startTime = datetime.fromtimestamp(mktime(strptime(dateTimeString, format)))
exp = project.insertExperiment(purpose, to_joda_datetime(startTime, timezone))
_import_entity_common(exp, xnatSession)
scanIDs = xnat_api(xnatSession.scans().get)
for scanID in scanIDs:
import_scan(dsc, src, exp, xnat_api(xnatSession.scan, scanID), timezone=timezone)
return exp
except DatabaseError, e:
_log.exception("Unable to import session: " + e.message)
return None
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_with_one_epochgroup(self):
xnatProject,projectURI = self._import_first_project()
ctx = self.dsc.getContext()
project = ctx.objectdWithURI(projectURI)
for xnatSession in self.xnat.select('/projects/' + xnat_api(xnatProject.id) + '/subjects/*/experiments/*'):
attrs = xnatSession.attrs
dtype = xnat_api(xnatSession.datatype)
datestr = xnat_api(attrs.get, dtype + '/date') + ' ' + xnat_api(attrs.get, dtype + '/time')
startTime = to_joda_datetime(datestr, 'UTC')
exps = project.getExperiments(startTime)
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_import_session_from_subject_as_experiments_with_one_epochgroup(
self):
xnatProject, projectURI = self._import_first_project()
ctx = self.dsc.getContext()
project = ctx.objectdWithURI(projectURI)
for xnatSession in self.xnat.select('/projects/' +
xnat_api(xnatProject.id) +
'/subjects/*/experiments/*'):
attrs = xnatSession.attrs
dtype = xnat_api(xnatSession.datatype)
datestr = xnat_api(attrs.get, dtype + '/date') + ' ' + xnat_api(
attrs.get, dtype + '/time')
startTime = to_joda_datetime(datestr, 'UTC')
exps = project.getExperiments(startTime)
def import_session(dsc, src, project, xnatSession, timezone='UTC'):
if project == None:
return
try:
attrs = xnatSession.attrs
dtype = xnat_api(xnatSession.datatype)
#print(dtype)
_log.info(' Importing session: ' + dtype)
dateString = xnat_api(attrs.get, dtype + '/date')
timeString = xnat_api(attrs.get, dtype + '/time')
purpose = xnat_api(attrs.get, dtype + '/note')
if not purpose: #None or len 0
purpose = 'XNAT experiment ' + xnatSession._uri
dateTimeString = dateString + ' ' + timeString
if timeString:
format = DATETIME_FORMAT if timeString.find(
'.') > 0 else DATETIMESHORT_FORMAT
else:
format = DATE_FORMAT
startTime = datetime.fromtimestamp(
mktime(strptime(dateTimeString, format)))
exp = project.insertExperiment(purpose,
to_joda_datetime(startTime, timezone))
_import_entity_common(exp, xnatSession)
scanIDs = xnat_api(xnatSession.scans().get)
for scanID in scanIDs:
import_scan(dsc,
src,
exp,
xnat_api(xnatSession.scan, scanID),
timezone=timezone)
return exp
except DatabaseError, e:
_log.exception("Unable to import session: " + e.message)
return None
def should_set_project_start_date_from_earliest_session_date(self):
xnatProject, projectURI = self._import_first_project()
# Find the earliest session date in the project
projectID = xnat_api(xnatProject.id)
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(time_str['date'], DATE_FORMAT)))
for time_str in query if len(time_str['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, 'UTC')
else:
self.fail("Unable to find project sessions' start date")
ctx = self.dsc.getContext()
project = ctx.objectdWithURI(projectURI)
eq_(project.getStartTime(), startTime)
def should_set_project_start_date_from_earliest_session_date(self):
xnatProject,projectURI = self._import_first_project()
# Find the earliest session date in the project
projectID = xnat_api(xnatProject.id)
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(time_str['date'], DATE_FORMAT))) for
time_str in
query if len(time_str['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, 'UTC')
else:
self.fail("Unable to find project sessions' start date")
ctx = self.dsc.getContext()
project = ctx.objectdWithURI(projectURI)
eq_(project.getStartTime(), startTime)