def retrieve_dataset(self):
connection = Connection(get_bamboo_url(self.project))
self.dataset = CachedDataset(get_option(self.project, 'ests_dataset'),
connection=connection)
self.data = self.dataset.get_data(query={u'barcode': self.sample_id},
cache=True)[0]
self.siblings = {}
for position in self.POSITIONS:
if position == self.position:
self.siblings[position] = self.sample_id
continue
try:
data = self.dataset.get_data(query={u'position': position,
u'block': self.data['block'],
u'quadrant': self.data['quadrant'],
u'cluster': self.data['cluster'],
u'plot': self.data['plot'],
},
select=['barcode'],
cache=True)[-1]
if isinstance(data, dict):
data = data.get(u'barcode', u'')
except:
# raise
data = None
self.siblings[position] = data
def options(request):
if not request.method == "POST":
return ms_options(request)
response = ms_options(request)
# try to update bamboo datasets
for key_prefix in ('ests1', 'ests2', 'ests3', 'ests4', 'ests5', 'ests6'):
form = get_option(request.user.project, '%s_form' % key_prefix)
key = '%s_dataset' % key_prefix
if raw_getset_bamboo_dataset(request.user.project, form, key):
messages.success(request, u"%s bamboo dataset "
u"retrieved successfuly." % key_prefix)
else:
messages.warning(request, u"Unable to retrieve %s bamboo dataset."
% key_prefix)
return response
def get_bamboo_url(project):
return get_option(project, 'bamboo_uri')
def get_bamboo_ids_dataset(project):
return get_option(project, 'bamboo_ids_dataset')
def get_formhub_ids_form(project):
return get_option(project, 'formhub_ids_form')
def get_formhub_ids_user(project):
return get_option(project, 'formhub_ids_user')
def get_formhub_url(project):
return get_option(project, 'formhub_uri')
def get_ests_dataset(project):
connection = Connection(get_bamboo_url(project))
return CachedDataset(get_option(project, 'ests_dataset'),
connection=connection)
