def execute(self, args):
"""Run select query, output table."""
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()
c = db.cursor()
self.columns = ['molecule.inchikey']
self.joins = set()
self.wheres = ['1=1']
if args.query:
try:
c.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:
c.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 or args.property_value == 0):
# self.joins.add(('JOIN molecule_method_property '
# 'ON molecule_method_property.inchikey = '
# 'molecule.inchikey'))
# self.add_condition(args.property_name, args.property_operator)
# c.execute(self.generate_query), (args.property_name,
# args.property_value))
else:
c.execute(self.generate_query())
# check that sql returns inchikey in first column
if not c.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 c.description))
for r in c:
if args.regex_subset and not re.match(args.regex_subset, r[0],
re.IGNORECASE):
continue
if args.part and args.of:
if not any(r[0].startswith(a) for a in subset):
continue
writer.writerow(list(xstr(v).decode('utf-8') for v in r))
db.close() # must be closed manually to prevent db locking during pipe
def execute(self, args):
"""Remove specified elements."""
db = MessDB()
c = db.cursor()
for row in args.inchikeys:
inchikey = row.split()[0].strip()
try:
inchikey_dir = self.get_inchikey_dir(inchikey)
shutil.rmtree(inchikey_dir)
print('%s dir removed\n' % inchikey, file=sys.stderr)
except OSError:
print('%s did not have a directory\n' % inchikey,
file=sys.stderr)
try:
parent = os.path.relpath(os.path.join(inchikey_dir, '../'))
os.removedirs(parent)
except OSError:
pass
records = 0
q = 'DELETE from molecule WHERE inchikey=?'
c.execute(q, (inchikey,))
records += c.rowcount
q = 'DELETE from molecule_synonym WHERE inchikey=?'
c.execute(q, (inchikey,))
records += c.rowcount
q = 'DELETE from molecule_source WHERE inchikey=?'
c.execute(q, (inchikey,))
records += c.rowcount
q = 'DELETE from molecule_state_method_property WHERE inchikey=?'
c.execute(q, (inchikey,))
records += c.rowcount
db.commit()
print('%i %s records removed from db\n\n' % (records, inchikey),
file=sys.stderr)
def execute(self, args):
"""Run self checks."""
db = MessDB()
self.c = db.cursor()
self.c.execute('SELECT inchikey FROM molecule')
self.db_inchikeys = set()
# check that inchikeys are all valid
for r in self.c:
if is_inchikey(r.inchikey, enforce_standard=True):
self.db_inchikeys.add(r.inchikey)
else:
print('%s is not a valid standard InChiKey!' % r.inchikey)
self.check_dir_structure()
self.check_db_structure()
self.check_db_dir_inchikey_concordance()
self.summary()
