def map(self, mol, source):
"""Import molecule into MESS.DB."""
# setup local variables
self.inchikey = mol.write('inchikey').rstrip()
inchikey_dir = get_inchikey_dir(self.inchikey)
inchikey_basename = os.path.join(inchikey_dir, self.inchikey)
identifier = unicode(mol.title, 'utf-8', 'replace')
# setup directory
setup_dir(inchikey_dir)
if not self.check():
mol.title = b''
mol.write('inchi',
(inchikey_basename + '.inchi'),
overwrite=True)
if not os.path.exists(inchikey_basename + '.png'):
mol.write('_png2',
(inchikey_basename + '.png'))
touch(inchikey_basename + '.log')
touch(inchikey_basename + '.notes')
touch(os.path.join(inchikey_dir,
'%s.sources.tsv' % inchikey_basename))
self.log_all.info('%s molecule directory initialized',
self.inchikey)
source.update_source_tsv(self.inchikey, identifier)
yield source.update_molecule_source_query(self.inchikey, identifier)
yield self.insert_molecule_query(self.inchikey, mol)
for query, values in self.get_insert_moldata_queries(
self.inchikey,
mol,
description='molecule data from %s input' % source.dirname):
yield query, values
for query, values in self.get_openbabel_property_queries(self.inchikey,
mol):
yield query, values
def test_touch(self):
test_file = os.path.join(self.tmp_dir, 'temp.txt')
utils.touch(test_file)
self.assertTrue(os.path.exists(test_file))
