def execute(self, args):
"""Remove specified elements."""
db = MessDB()
cur = db.cursor()
for row in args.inchikeys:
inchikey = row.split()[0].strip()
try:
inchikey_dir = get_inchikey_dir(inchikey)
shutil.rmtree(inchikey_dir)
self.log_all.info('%s dir removed', inchikey)
except OSError:
self.log_console.info('%s did not have a directory', inchikey)
try:
parent = os.path.relpath(os.path.join(inchikey_dir, '../'))
os.removedirs(parent)
except OSError:
pass
records = 0
query = 'DELETE from molecule WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = 'DELETE from molecule_synonym WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = 'DELETE from molecule_source WHERE inchikey=?'
cur.execute(query, (inchikey,))
records += cur.rowcount
query = ('DELETE from molecule_state_method_property '
'WHERE inchikey=?')
cur.execute(query, (inchikey,))
records += cur.rowcount
db.commit()
self.log_all.info('%i %s records removed from db',
records, inchikey)
def execute(self, args):
"""Run select query, output table."""
if args.inchikeys.name == '<stdin>' and args.inchikeys.isatty():
filter_from = None
else:
try:
filter_from = set(row.split()[0].strip()
for row in args.inchikeys)
except IndexError:
filter_from = set([])
return
if args.query and (args.property_name
or args.property_operator
or args.property_value):
sys.exit(('Custom SQL queries are mutually exclusive with '
'property filtering.'))
if (args.part or args.of) and not (args.part and args.of):
sys.exit(('If you specify a --part n, you must also specify --of '
'N (e.g. something like --part 1 --of 5).'))
if args.part and args.of:
if args.part > args.of:
sys.exit('--part must be smaller than --of.')
if args.part < 1:
sys.exit('--part must be >=1.')
alpha = string.ascii_uppercase
alpha3 = [''.join([a, b, c]) for a in alpha
for b in alpha
for c in alpha] # AAA to ZZZ
if args.of > len(alpha3):
sys.exit(('MESS.DB does not support subsetting into more than '
'%i parts.' % len(alpha3)))
subsets = [alpha3[i::args.of] for i in xrange(args.of)]
subset = subsets[args.part - 1]
db = MessDB()
cur = db.cursor()
if args.query:
try:
cur.execute(codecs.open(args.query, encoding='utf-8').read())
except sqlite3.OperationalError:
sys.exit("'%s' does not contain valid sql." % args.query)
except IOError:
try:
cur.execute(args.query)
except sqlite3.OperationalError:
sys.exit(("'%s' is neither valid sql nor a path "
'to a file containing valid sql.') % args.query)
elif (args.property_name and args.property_operator and
args.property_value is not None):
query, values = self.property_query(args.property_name,
args.property_operator,
args.property_value,
args.path)
cur.execute(query, values)
else:
cur.execute('SELECT inchikey FROM molecule')
# check that sql returns inchikey in first column
if not cur.description[0][0].lower() == 'inchikey':
sys.exit('Query must return inchikey in first column.')
# print table
writer = csv.writer(sys.stdout, delimiter=args.delimiter)
if args.headers:
writer.writerow(list(h[0] for h in cur.description))
for result in cur:
if filter_from is not None and result[0] not in filter_from:
continue
if args.regex_subset and not re.match(args.regex_subset, result[0],
re.IGNORECASE):
continue
if args.part and args.of:
if not any(result[0].startswith(a) for a in subset):
continue
if args.smarts:
matches = 0
query = 'SELECT inchi FROM molecule WHERE inchikey = ?'
inchi = db.execute(query, (result[0],)).fetchone()[0]
mol = pybel.readstring('inchi', 'InChI=%s' % inchi)
for (smarts_obj,
smarts_str) in Match.smarts_generator(args.smarts):
matches += len(smarts_obj.findall(mol))
if not matches:
continue
writer.writerow(list(xstr(v).decode('utf-8') for v in result))
db.close() # must be closed manually to prevent db locking during pipe