def from_mrfile(cls, mrfile, nims_path, archived=True):
series_uid = nimsutil.pack_dicom_uid(mrfile.series_uid)
dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.filetype == mrfile.filetype)
.first())
if not dataset:
alt_dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.kind == u'primary')
.first())
if not alt_dataset:
kind = u'primary'
elif alt_dataset.priority < mrfile.priority:
kind = u'primary'
alt_dataset.kind = u'secondary'
else:
kind = u'secondary'
epoch = Epoch.from_mrfile(mrfile)
dataset = cls(
container=epoch,
priority = mrfile.priority,
filetype=mrfile.filetype,
compressed=mrfile.compressed,
kind=kind,
label=cls.default_labels[mrfile.filetype],
archived=archived,
)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
def from_metadata(cls, md):
dataset = (
cls.query.join(Epoch)
.filter(Epoch.uid == md.series_uid)
.filter(Epoch.acq == md.acq_no)
.with_lockmode("update")
.first()
)
if not dataset:
epoch = Epoch.from_metadata(md)
dataset = cls(container=epoch, datatype=md.datatype, kind=u"primary", archived=True)
transaction.commit()
DBSession.add(dataset)
return dataset
def latest_exp_session(self, min_access_level=u'Anon-Read'):
query = DBSession.query(Experiment, Session).join(Subject, Experiment.subjects).join(Session, Subject.sessions)
if not self.is_superuser:
query = self._filter_access(query, min_access_level)
if self.trash_flag == 0:
query = query.filter(Session.trashtime == None)
elif self.trash_flag == 2:
query = query.filter(Session.trashtime != None)
return query.order_by(Session.timestamp.desc()).first() or (None, None)
def dataset_cnt(self):
query = DBSession.query(Session)
if not self.is_superuser:
query = (
query.join(Subject, Session.subject)
.join(Experiment, Subject.experiment)
.join(Access)
.filter(Access.user == self)
)
return query.count()
def from_mrfile(cls, mrfile, nims_path, archived=True):
series_uid = nimsutil.pack_dicom_uid(mrfile.series_uid)
dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.filetype == mrfile.filetype)
.first())
if not dataset:
alt_dataset = (cls.query.join(Epoch)
.filter(Epoch.uid == series_uid)
.filter(Epoch.acq == mrfile.acq_no)
.filter(cls.kind == u'primary')
.first())
if not alt_dataset:
kind = u'primary'
elif alt_dataset.priority < mrfile.priority:
kind = u'primary'
alt_dataset.kind = u'secondary'
alt_dataset.container.qa_status = u'rerun'
else:
kind = u'secondary'
epoch = Epoch.from_mrfile(mrfile)
dataset = cls(
container=epoch,
priority = mrfile.priority,
filetype=mrfile.filetype,
compressed=mrfile.compressed,
kind=kind,
label=cls.default_labels[mrfile.filetype],
archived=archived,
qa_status=u'pending',
)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
def setUp(self):
"""Prepare model test fixture."""
try:
new_attrs = {}
new_attrs.update(self.attrs)
new_attrs.update(self.do_get_dependencies())
self.obj = self.klass(**new_attrs)
DBSession.add(self.obj)
DBSession.flush()
return self.obj
except:
DBSession.rollback()
raise
def setUp(self):
"""Prepare model test fixture."""
try:
new_attrs = {}
new_attrs.update(self.attrs)
new_attrs.update(self.do_get_dependencies())
self.obj = self.klass(**new_attrs)
DBSession.add(self.obj)
DBSession.flush()
return self.obj
except:
DBSession.rollback()
raise
def at_path(cls, nims_path, filetype, label=None, archived=False):
dataset = cls(filetype=filetype, label=(label if label else cls.default_labels[filetype]), archived=archived)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
def experiment(self):
return DBSession.query(Session, Experiment).join(Subject, Session.subject).join(Experiment, Subject.experiment).filter(Session.id == self.id).one().Experiment
def dataset_cnt(self):
query = DBSession.query(Session)
if not self.is_superuser:
query = query.join(Subject, Session.subject).join(Experiment, Subject.experiment).join(Access).filter(Access.user==self)
return query.count()
def test_query_obj(self):
"""Model objects can be queried"""
obj = DBSession.query(self.klass).one()
for key, value in self.attrs.iteritems():
assert_equals(getattr(obj, key), value)
def tearDown(self):
"""Finish model test fixture."""
DBSession.rollback()
def test_query_obj(self):
"""Model objects can be queried"""
obj = DBSession.query(self.klass).one()
for key, value in self.attrs.iteritems():
assert_equals(getattr(obj, key), value)
def tearDown(self):
"""Finish model test fixture."""
DBSession.rollback()
def at_path(cls, nims_path, filename=None, datatype=None, archived=False):
dataset = cls(datatype=datatype, archived=archived)
transaction.commit()
DBSession.add(dataset)
nimsutil.make_joined_path(nims_path, dataset.relpath)
return dataset
