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 __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 test_add_link(self):
'''Tests add_link method.'''
dna1 = _read('sbol.xml')
dna2 = _read('sbol2.xml')
ice_entry1 = ICEEntry(typ='PLASMID', dna=dna1)
self.__ice_client.set_ice_entry(ice_entry1)
ice_entry2 = ICEEntry(typ='PLASMID', dna=dna2)
self.__ice_client.set_ice_entry(ice_entry2)
self.__ice_client.add_link(
ice_entry1.get_ice_number(), ice_entry2.get_ice_number())
# "Refresh" (update metadata)
ice_entry1 = self.__ice_client.get_ice_entry(ice_entry1.get_ice_id())
ice_entry2 = self.__ice_client.get_ice_entry(ice_entry2.get_ice_id())
self.assertTrue(ice_entry1.get_ice_number() in
[par['id']
for par in ice_entry2.get_metadata()['parents']])
self.assertTrue(ice_entry2.get_ice_number() in
[link['id']
for link in ice_entry1.get_metadata()['linkedParts']])
def test_set_get_parameter(self):
'''Tests set/get_parameter method.'''
ice_entry = ICEEntry(typ='PLASMID')
ice_entry.set_parameter('Cheese', 'Brie')
self.__ice_client.set_ice_entry(ice_entry)
ice_entry = self.__ice_client.get_ice_entry(ice_entry.get_ice_id())
self.assertEqual(ice_entry.get_parameter('Cheese'), 'Brie')
def test_get_record_id(self):
'''Tests get_record_id method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.__ice_client.set_ice_entry(ice_entry1)
self.assertNotEqual(ice_entry1.get_record_id(), None)
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.__ice_client.set_ice_entry(ice_entry2)
self.assertNotEqual(ice_entry2.get_record_id(), None)
def test_get_seq(self):
'''Tests get_seq method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.__ice_client.set_ice_entry(ice_entry)
ice_entry = self.__ice_client.get_ice_entry(ice_entry.get_ice_id())
self.assertEqual(ice_entry.get_seq(), dna['seq'])
def test_get_seq(self):
'''Tests get_seq method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.__ice_client.set_ice_entry(ice_entry)
ice_entry = self.__ice_client.get_ice_entry(ice_entry.get_ice_id())
self.assertEqual(ice_entry.get_seq(), dna['seq'])
def test_get_ice_entry(self):
'''Tests get_ice_entry method.'''
dna = _read('sbol.xml')
ice_entry_in = ICEEntry(typ='PART', dna=dna)
self.__ice_client.set_ice_entry(ice_entry_in)
ice_entry_out = self.__ice_client.get_ice_entry(
ice_entry_in.get_ice_number())
self.assertEqual(ice_entry_out.get_seq(), dna['seq'])
def test_get_ice_entry(self):
'''Tests get_ice_entry method.'''
dna = _read('sbol.xml')
ice_entry_in = ICEEntry(typ='PART', dna=dna)
self.__ice_client.set_ice_entry(ice_entry_in)
ice_entry_out = self.__ice_client.get_ice_entry(
ice_entry_in.get_ice_number())
self.assertEqual(ice_entry_out.get_seq(), dna['seq'])
def test_set_ice_entry(self):
'''Tests set_ice_entry method.'''
dna_in = _read('sbol.xml')
ice_entry_in = ICEEntry(typ='PLASMID', dna=dna_in)
self.__ice_client.set_ice_entry(ice_entry_in)
ice_entry_out = self.__ice_client.get_ice_entry(
ice_entry_in.get_ice_number())
self.assertNotEqual(ice_entry_out, None)
def test_set_ice_entry(self):
'''Tests set_ice_entry method.'''
dna_in = _read('sbol.xml')
ice_entry_in = ICEEntry(typ='PLASMID', dna=dna_in)
self.__ice_client.set_ice_entry(ice_entry_in)
ice_entry_out = self.__ice_client.get_ice_entry(
ice_entry_in.get_ice_number())
self.assertNotEqual(ice_entry_out, None)
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 test_add_permission(self):
'''Tests add_permission method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.__ice_client.set_ice_entry(ice_entry)
groups = self.__ice_client.get_groups()
for group_num in groups.values():
self.__ice_client.add_permission(ice_entry.get_ice_id(), group_num)
# If test progresses to here, it has succeeded:
self.assertTrue(True)
def test_add_permission(self):
'''Tests add_permission method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.__ice_client.set_ice_entry(ice_entry)
groups = self.__ice_client.get_groups()
for group_num in groups.values():
self.__ice_client.add_permission(ice_entry.get_ice_id(), group_num)
# If test progresses to here, it has succeeded:
self.assertTrue(True)
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 test_get_ice_entries_by_seq(self):
'''Tests get_ice_entries_by_seq method.'''
dna = _read('sbol.xml')
# dna.set_seq(sequence_utils.get_random_dna(4096))
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.__ice_client.set_ice_entry(ice_entry)
self.__ice_client.reconnect()
result = self.__ice_client.get_ice_entries_by_seq(dna['seq'])
self.assertTrue(len(result) > 0)
def test_get_record_id(self):
'''Tests get_record_id method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.__ice_client.set_ice_entry(ice_entry1)
self.assertNotEqual(ice_entry1.get_record_id(), None)
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.__ice_client.set_ice_entry(ice_entry2)
self.assertNotEqual(ice_entry2.get_record_id(), None)
def test_set_get_parameter(self):
'''Tests set/get_parameter method.'''
ice_entry = ICEEntry(typ='PLASMID')
ice_entry.set_parameter('Cheese', 'Brie')
self.__ice_client.set_ice_entry(ice_entry)
ice_entry = self.__ice_client.get_ice_entry(ice_entry.get_ice_id())
self.assertEqual(ice_entry.get_parameter('Cheese'), 'Brie')
def test_set_value(self):
'''Tests set_value method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
ice_entry1.set_value('creator', 'God')
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry1.get_metadata()['creator'], 'God')
self.__ice_client.set_ice_entry(ice_entry1)
ice_entry2 = self.__ice_client.get_ice_entry(
ice_entry1.get_ice_number())
ice_entry2.set_value('creator', 'Aitor Karanka')
self.__ice_client.set_ice_entry(ice_entry2)
ice_entry3 = self.__ice_client.get_ice_entry(
ice_entry1.get_ice_number())
self.assertEqual(ice_entry3.get_metadata()['creator'], 'Aitor Karanka')
ice_entry4 = ICEEntry(metadata={'type': 'PLASMID'})
ice_entry4.set_value('creator', 'God')
self.assertEqual(ice_entry4.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry4.get_metadata()['creator'], 'God')
def test_get_sbol_doc(self):
'''Tests get_sbol_doc method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.assertEqual(ice_entry.get_dna(), dna)
def test_get_metadata(self):
'''Tests get_metadata method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.assertEqual(ice_entry2.get_metadata()['type'], 'PLASMID')
def test_get_ice_number_none(self):
'''Tests get_ice_number method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.assertEqual(ice_entry1.get_ice_number(), None)
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.assertEqual(ice_entry2.get_ice_number(), None)
def test_add_link(self):
'''Tests add_link method.'''
dna1 = _read('sbol.xml')
dna2 = _read('sbol2.xml')
ice_entry1 = ICEEntry(typ='PLASMID', dna=dna1)
self.__ice_client.set_ice_entry(ice_entry1)
ice_entry2 = ICEEntry(typ='PLASMID', dna=dna2)
self.__ice_client.set_ice_entry(ice_entry2)
self.__ice_client.add_link(ice_entry1.get_ice_number(),
ice_entry2.get_ice_number())
# "Refresh" (update metadata)
ice_entry1 = self.__ice_client.get_ice_entry(ice_entry1.get_ice_id())
ice_entry2 = self.__ice_client.get_ice_entry(ice_entry2.get_ice_id())
self.assertTrue(ice_entry1.get_ice_number(
) in [par['id'] for par in ice_entry2.get_metadata()['parents']])
self.assertTrue(ice_entry2.get_ice_number(
) in [link['id'] for link in ice_entry1.get_metadata()['linkedParts']])
def test_get_ice_number_none(self):
'''Tests get_ice_number method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.assertEqual(ice_entry1.get_ice_number(), None)
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.assertEqual(ice_entry2.get_ice_number(), None)
def test_get_metadata(self):
'''Tests get_metadata method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
self.assertEqual(ice_entry2.get_metadata()['type'], 'PLASMID')
def test_set_value(self):
'''Tests set_value method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
ice_entry1.set_value('creator', 'God')
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry1.get_metadata()['creator'], 'God')
self.__ice_client.set_ice_entry(ice_entry1)
ice_entry2 = self.__ice_client.get_ice_entry(
ice_entry1.get_ice_number())
ice_entry2.set_value('creator', 'Aitor Karanka')
self.__ice_client.set_ice_entry(ice_entry2)
ice_entry3 = self.__ice_client.get_ice_entry(
ice_entry1.get_ice_number())
self.assertEqual(ice_entry3.get_metadata()['creator'], 'Aitor Karanka')
ice_entry4 = ICEEntry(metadata={'type': 'PLASMID'})
ice_entry4.set_value('creator', 'God')
self.assertEqual(ice_entry4.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry4.get_metadata()['creator'], 'God')
def test_get_sbol_doc(self):
'''Tests get_sbol_doc method.'''
dna = _read('sbol.xml')
ice_entry = ICEEntry(typ='PLASMID', dna=dna)
self.assertEqual(ice_entry.get_dna(), dna)
def test_set_values(self):
'''Tests set_values method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
ice_entry1.set_values({'creator': 'God', 'name': 'Test'})
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry1.get_metadata()['creator'], 'God')
self.assertEqual(ice_entry1.get_metadata()['name'], 'Test')
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
ice_entry2.set_values({'creator': 'God', 'name': 'Test'})
self.assertEqual(ice_entry2.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry2.get_metadata()['creator'], 'God')
self.assertEqual(ice_entry2.get_metadata()['name'], 'Test')
def test_set_values(self):
'''Tests set_values method.'''
ice_entry1 = ICEEntry(typ='PLASMID')
ice_entry1.set_values({'creator': 'God', 'name': 'Test'})
self.assertEqual(ice_entry1.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry1.get_metadata()['creator'], 'God')
self.assertEqual(ice_entry1.get_metadata()['name'], 'Test')
ice_entry2 = ICEEntry(metadata={'type': 'PLASMID'})
ice_entry2.set_values({'creator': 'God', 'name': 'Test'})
self.assertEqual(ice_entry2.get_metadata()['type'], 'PLASMID')
self.assertEqual(ice_entry2.get_metadata()['creator'], 'God')
self.assertEqual(ice_entry2.get_metadata()['name'], 'Test')
