def __init__(self, query):
JobThread.__init__(self)
self._query = query
self._ice_client = ICEClient(query['ice']['url'],
query['ice']['username'],
query['ice']['password'],
group_names=query['ice'].get(
'groups', None))
self._ice_ids = query['ice_ids']
self._data = {}
def __init__(self, url, username, psswrd, group_names=None):
self.__ice_client = ICEClient(url, username, psswrd)
if group_names is None:
group_names = []
self.__group_ids = [group_id
for name, group_id
in self.__ice_client.get_groups().iteritems()
if name in group_names]
def setUpClass(cls):
try:
std_input = raw_input
except NameError:
std_input = input
ice_url = std_input('ICE url: ')
username = std_input('ICE username: '******'ICE password: ')
cls.__ice_client = ICEClient(ice_url, username, password)
class BuildGenieBase(JobThread):
'''Base class for build applications.'''
def __init__(self, query):
JobThread.__init__(self)
self._query = query
self._ice_client = ICEClient(query['ice']['url'],
query['ice']['username'],
query['ice']['password'],
group_names=query['ice'].get(
'groups', None))
self._ice_ids = query['ice_ids']
self._data = {}
def get_order(self):
'''Gets a plasmids constituent parts list for ordering.'''
entries = {}
for ice_id in self._ice_ids:
data = self._get_data(ice_id)
for part in data[0].get_metadata()['linkedParts']:
data = self._get_data(part['partId'])
entries[data[1]] = list(data[2:])
# Format into list of lists:
return [[key] + entries[key] for key in sorted(entries)]
def _get_data(self, ice_id):
'''Gets data from ICE entry.'''
if ice_id in self._data:
return self._data[ice_id]
ice_entry = self._ice_client.get_ice_entry(ice_id)
metadata = ice_entry.get_metadata()
data = ice_entry, \
metadata['partId'], \
metadata['name'], \
metadata['type'], \
ice_entry.get_parameter('Type'), \
re.sub('\\s*\\[[^\\]]*\\]\\s*', ' ',
metadata['shortDescription']).replace(' - ', '_'), \
ice_entry.get_seq()
self._data[ice_id] = data
return data
class ICEInterface(object):
'''Class to inferface with ICE.'''
def __init__(self, url, username, psswrd, group_names=None):
self.__ice_client = ICEClient(url, username, psswrd)
if group_names is None:
group_names = []
self.__group_ids = [group_id
for name, group_id
in self.__ice_client.get_groups().iteritems()
if name in group_names]
def get_dna(self, ice_id):
'''Gets DNA object from ICE.'''
return self.__ice_client.get_ice_entry(ice_id).get_dna()
def submit(self, designs):
'''Writes plasmids and dominoes to ICE.'''
for design in designs:
self.__write_plasmid(design)
self.__write_dominoes(design)
def __write_plasmid(self, design):
'''Writes plasmids to ICE.'''
ice_entry = ICEEntry(typ='PLASMID')
self.__ice_client.set_ice_entry(ice_entry)
self.__add_permissions(ice_entry)
design['ice_id'] = ice_entry.get_ice_id()
_set_metadata(ice_entry, design['name'], ' '.join(design['design']),
'PLASMID')
ice_entry.set_dna(design['plasmid'])
self.__ice_client.set_ice_entry(ice_entry)
# Add link from plasmid -> parts:
for part_id in design['design']:
self.__ice_client.add_link(design['ice_id'], part_id)
def __write_dominoes(self, design):
'''Writes dominoes to ICE, or retrieves them if pre-existing.'''
seq_entries = {}
for domino in design['dominoes']:
seq = domino[1][0][0] + domino[1][1][0]
if seq in seq_entries:
ice_entry = seq_entries[seq]
else:
ice_entries = self.__ice_client.get_ice_entries_by_seq(seq)
if len(ice_entries) == 0:
dna = _get_domino_dna('name', seq, domino[1][0][0],
domino[1][1][0])
ice_entry = ICEEntry(dna, 'PART')
else:
ice_entry = ice_entries[0]
name, description = self.__get_metadata(ice_entry, domino[0])
_set_metadata(ice_entry, name, description, 'DOMINO')
self.__ice_client.set_ice_entry(ice_entry)
self.__add_permissions(ice_entry)
# Add link from plasmid -> domino:
self.__ice_client.add_link(
design['ice_id'], ice_entry.get_ice_id())
seq_entries[seq] = ice_entry
def __get_metadata(self, ice_entry, part_ids):
'''Gets metadata for a domino.'''
metadata = ice_entry.get_metadata()
# Set name if necessary:
name = metadata['name'] if 'name' in metadata \
else ' - '.join([self.__ice_client.get_ice_entry(prt_id).get_name()
for prt_id in part_ids])
# Update Designs and Pairs in description:
pairs = metadata['shortDescription'].split(', ') \
if 'shortDescription' in metadata else []
pairs.append('_'.join(part_ids))
description = ', '.join(list(set(pairs)))
return name, description
def __add_permissions(self, ice_entry):
'''Adds permissions for all default groups.'''
for group_id in self.__group_ids:
self.__ice_client.add_permission(ice_entry.get_ice_id(), group_id)