def write_ice_entry(ice_client, ice_id1, ice_id2, typ, write_seq, group_names):
'''Write a composite ICE entry (part in plasmid, or plasmid in strain).'''
comp1 = ice_client.get_ice_entry(ice_id1)
comp2 = ice_client.get_ice_entry(ice_id2)
name = comp1.get_metadata()['name'] + \
' (' + comp2.get_metadata()['name'] + ')'
product = ICEEntry(typ=typ)
product.set_values({'name': name[:127], 'shortDescription': name})
taxonomy = comp1.get_parameter('Taxonomy')
if taxonomy:
product.set_parameter('Taxonomy', taxonomy)
ice_client.set_ice_entry(product)
ice_client.add_link(product.get_ice_id(), comp1.get_ice_id())
ice_client.add_link(product.get_ice_id(), comp2.get_ice_id())
if write_seq:
product.set_dna(dna_utils.concat(
[comp1.get_dna(), comp2.get_dna()]))
ice_client.set_ice_entry(product)
if group_names:
groups = ice_client.get_groups()
for group_name in group_names:
ice_client.add_permission(product.get_ice_id(),
groups[group_name])
return product, comp1, comp2
def test_set_dna(self):
'''Tests set_dna method.'''
dna1 = _read('sbol.xml')
dna2 = _read('sbol2.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna1)
self.__ice_client.set_ice_entry(ice_entry)
ice_entry.set_dna(dna2)
self.__ice_client.set_ice_entry(ice_entry)
self.assertEqual(ice_entry.get_seq(), dna2['seq'])
def test_set_dna(self):
'''Tests set_dna method.'''
dna1 = _read('sbol.xml')
dna2 = _read('sbol2.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna1)
self.__ice_client.set_ice_entry(ice_entry)
ice_entry.set_dna(dna2)
self.__ice_client.set_ice_entry(ice_entry)
self.assertEqual(ice_entry.get_seq(), dna2['seq'])
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)
