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import os
import sys
from contextlib import ExitStack
import numpy as np
from ase.db.core import Database, ops, lock, now
from ase.db.row import AtomsRow
from ase.io.jsonio import encode, decode
from ase.parallel import world, parallel_function
class JSONDatabase(Database):
def __enter__(self):
return self
def __exit__(self, exc_type, exc_value, tb):
pass
def _write(self, atoms, key_value_pairs, data, id):
Database._write(self, atoms, key_value_pairs, data)
bigdct = {}
ids = []
nextid = 1
if (isinstance(self.filename, str) and
os.path.isfile(self.filename)):
try:
bigdct, ids, nextid = self._read_json()
except (SyntaxError, ValueError):
pass
mtime = now()
if isinstance(atoms, AtomsRow):
row = atoms
else:
row = AtomsRow(atoms)
row.ctime = mtime
row.user = os.getenv('USER')
dct = {}
for key in row.__dict__:
if key[0] == '_' or key in row._keys or key == 'id':
continue
dct[key] = row[key]
dct['mtime'] = mtime
if key_value_pairs:
dct['key_value_pairs'] = key_value_pairs
if data:
dct['data'] = data
constraints = row.get('constraints')
if constraints:
dct['constraints'] = constraints
if id is None:
id = nextid
ids.append(id)
nextid += 1
else:
assert id in bigdct
bigdct[id] = dct
self._write_json(bigdct, ids, nextid)
return id
def _read_json(self):
if isinstance(self.filename, str):
with open(self.filename) as fd:
bigdct = decode(fd.read())
else:
bigdct = decode(self.filename.read())
if self.filename is not sys.stdin:
self.filename.seek(0)
if not isinstance(bigdct, dict) or not ('ids' in bigdct
or 1 in bigdct):
from ase.io.formats import UnknownFileTypeError
raise UnknownFileTypeError('Does not resemble ASE JSON database')
ids = bigdct.get('ids')
if ids is None:
# Allow for missing "ids" and "nextid":
assert 1 in bigdct
return bigdct, [1], 2
if not isinstance(ids, list):
ids = ids.tolist()
return bigdct, ids, bigdct['nextid']
def _write_json(self, bigdct, ids, nextid):
if world.rank > 0:
return
with ExitStack() as stack:
if isinstance(self.filename, str):
fd = stack.enter_context(open(self.filename, 'w'))
else:
fd = self.filename
print('{', end='', file=fd)
for id in ids:
dct = bigdct[id]
txt = ',\n '.join('"{0}": {1}'.format(key, encode(dct[key]))
for key in sorted(dct.keys()))
print('"{0}": {{\n {1}}},'.format(id, txt), file=fd)
if self._metadata is not None:
print('"metadata": {0},'.format(encode(self.metadata)), file=fd)
print('"ids": {0},'.format(ids), file=fd)
print('"nextid": {0}}}'.format(nextid), file=fd)
@parallel_function
@lock
def delete(self, ids):
bigdct, myids, nextid = self._read_json()
for id in ids:
del bigdct[id]
myids.remove(id)
self._write_json(bigdct, myids, nextid)
def _get_row(self, id):
bigdct, ids, nextid = self._read_json()
if id is None:
assert len(ids) == 1
id = ids[0]
dct = bigdct[id]
dct['id'] = id
return AtomsRow(dct)
def _select(self, keys, cmps, explain=False, verbosity=0,
limit=None, offset=0, sort=None, include_data=True,
columns='all'):
if explain:
yield {'explain': (0, 0, 0, 'scan table')}
return
if sort:
if sort[0] == '-':
reverse = True
sort = sort[1:]
else:
reverse = False
def f(row):
return row.get(sort, missing)
rows = []
missing = []
for row in self._select(keys, cmps):
key = row.get(sort)
if key is None:
missing.append((0, row))
else:
rows.append((key, row))
rows.sort(reverse=reverse, key=lambda x: x[0])
rows += missing
if limit:
rows = rows[offset:offset + limit]
for key, row in rows:
yield row
return
try:
bigdct, ids, nextid = self._read_json()
except IOError:
return
if not limit:
limit = -offset - 1
cmps = [(key, ops[op], val) for key, op, val in cmps]
n = 0
for id in ids:
if n - offset == limit:
return
dct = bigdct[id]
if not include_data:
dct.pop('data', None)
row = AtomsRow(dct)
row.id = id
for key in keys:
if key not in row:
break
else:
for key, op, val in cmps:
if isinstance(key, int):
value = np.equal(row.numbers, key).sum()
else:
value = row.get(key)
if key == 'pbc':
assert op in [ops['='], ops['!=']]
value = ''.join('FT'[x] for x in value)
if value is None or not op(value, val):
break
else:
if n >= offset:
yield row
n += 1
@property
def metadata(self):
if self._metadata is None:
bigdct, myids, nextid = self._read_json()
self._metadata = bigdct.get('metadata', {})
return self._metadata.copy()
@metadata.setter
def metadata(self, dct):
bigdct, ids, nextid = self._read_json()
self._metadata = dct
self._write_json(bigdct, ids, nextid)
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