def plot(png):
path = os.path.join(tmpdir, png)
if not os.path.isfile(path):
name, id = png[:-4].split('-')
dct = db[int(id)].data
dct2plot(dct, name, path, show=False)
return send_from_directory(tmpdir, png)
def plot(png):
path = os.path.join(tmpdir, png)
if not os.path.isfile(path):
name, id = png[:-4].split('-')
dct = db[int(id)].data
dct2plot(dct, name, path, show=False)
return send_from_directory(tmpdir, png)
def main(args):
verbosity = 1 - args.quiet + args.verbose
query = ','.join(args.query)
if args.sort.endswith('-'):
# Allow using "key-" instead of "-key" for reverse sorting
args.sort = '-' + args.sort[:-1]
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if args.add_key_value_pairs:
for pair in args.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_int_float_or_str(value)
if args.delete_keys:
delete_keys = args.delete_keys.split(',')
else:
delete_keys = []
db = connect(args.database, use_lock_file=not args.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if args.analyse:
db.analyse()
return
if args.show_keys:
keys = defaultdict(int)
for row in db.select(query):
for key in row._keys:
keys[key] += 1
n = max(len(key) for key in keys) + 1
for key, number in keys.items():
print('{:{}} {}'.format(key + ':', n, number))
return
if args.show_values:
keys = args.show_values.split(',')
values = {key: defaultdict(int) for key in keys}
numbers = set()
for row in db.select(query):
kvp = row.key_value_pairs
for key in keys:
value = kvp.get(key)
if value is not None:
values[key][value] += 1
if not isinstance(value, str):
numbers.add(key)
n = max(len(key) for key in keys) + 1
for key in keys:
vals = values[key]
if key in numbers:
print('{:{}} [{}..{}]'.format(key + ':', n, min(vals),
max(vals)))
else:
print('{:{}} {}'.format(
key + ':', n,
', '.join('{}({})'.format(v, n) for v, n in vals.items())))
return
if args.add_from_file:
filename = args.add_from_file
configs = ase.io.read(filename)
if not isinstance(configs, list):
configs = [configs]
for atoms in configs:
db.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added ' + plural(len(configs), 'row'))
return
if args.count:
n = db.count(query)
print('%s' % plural(n, 'row'))
return
if args.explain:
for row in db.select(query,
explain=True,
verbosity=verbosity,
limit=args.limit,
offset=args.offset):
print(row['explain'])
return
if args.show_metadata:
print(json.dumps(db.metadata, sort_keys=True, indent=4))
return
if args.set_metadata:
with open(args.set_metadata) as fd:
db.metadata = json.load(fd)
return
if args.insert_into:
nkvp = 0
nrows = 0
with connect(args.insert_into,
use_lock_file=not args.no_lock_file) as db2:
for row in db.select(query, sort=args.sort):
kvp = row.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if args.unique:
row['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
if args.strip_data:
db2.write(row.toatoms(), **kvp)
else:
db2.write(row, data=row.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [row['id'] for row in db.select(query)]
M = 0
N = 0
with db:
for id in ids:
m, n = db.update(id,
delete_keys=delete_keys,
**add_key_value_pairs)
M += m
N += n
out('Added %s (%s updated)' %
(plural(M, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - M, 'pair')))
out('Removed', plural(N, 'key-value pair'))
return
if args.delete:
ids = [row['id'] for row in db.select(query)]
if ids and not args.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
db.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if args.plot_data:
from ase.db.plot import dct2plot
dct2plot(db.get(query).data, args.plot_data)
return
if args.plot:
if ':' in args.plot:
tags, keys = args.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = args.plot
keys = keys.split(',')
plots = defaultdict(list)
X = {}
labels = []
for row in db.select(query, sort=args.sort, include_data=False):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if args.json:
row = db.get(query)
db2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = row.get('key_value_pairs', {})
db2.write(row, data=row.get('data'), **kvp)
return
db.python = args.metadata_from_python_script
if args.long:
db.meta = process_metadata(db, html=args.open_web_browser)
row = db.get(query)
summary = Summary(row, db.meta)
summary.write()
return
if args.open_web_browser:
try:
import ase.db.app as app
except ImportError:
print('Please install Flask: pip install flask')
return
app.databases['default'] = db
app.initialize_databases()
app.app.run(host='0.0.0.0', debug=True)
return
if args.write_summary_files:
prefix = args.write_summary_files
db.meta = process_metadata(db, html=args.open_web_browser)
ukey = db.meta.get('unique_key', 'id')
for row in db.select(query):
uid = row.get(ukey)
summary = Summary(row,
db.meta,
prefix='{}-{}-'.format(prefix, uid))
return
columns = list(all_columns)
c = args.columns
if c and c.startswith('++'):
keys = set()
for row in db.select(query,
limit=args.limit,
offset=args.offset,
include_data=False):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(db, verbosity=verbosity, cut=args.cut)
table.select(query, columns, args.sort, args.limit, args.offset)
if args.csv:
table.write_csv()
else:
table.write(query)
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_int_float_or_str(value)
if opts.delete_keys:
delete_keys = opts.delete_keys.split(',')
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.analyse:
con.analyse()
return
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = con.count(query)
print('%s' % plural(n, 'row'))
return
if opts.explain:
for row in con.select(query, explain=True,
verbosity=verbosity,
limit=opts.limit, offset=opts.offset):
print(row['explain'])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into,
use_lock_file=not opts.no_lock_file) as con2:
for row in con.select(query):
kvp = row.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if opts.unique:
row['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
con2.write(row, data=row.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [row['id'] for row in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if opts.delete:
ids = [row['id'] for row in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if opts.plot_data:
from ase.db.plot import dct2plot
dct2plot(con.get(query).data, opts.plot_data)
return
if opts.plot:
if ':' in opts.plot:
tags, keys = opts.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = opts.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in con.select(query, sort=opts.sort):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if opts.long:
row = con.get(query)
summary = Summary(row)
summary.write()
elif opts.json:
row = con.get(query)
con2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = row.get('key_value_pairs', {})
con2.write(row, data=row.get('data'), **kvp)
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c and c.startswith('++'):
keys = set()
for row in con.select(query,
limit=opts.limit, offset=opts.offset):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write(query)
def run(opts, args, verbosity):
filename = args.pop(0)
query = ','.join(args)
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if opts.add_key_value_pairs:
for pair in opts.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_float_or_str(value)
if opts.delete_keys:
delete_keys = opts.delete_keys.split(',')
else:
delete_keys = []
con = connect(filename, use_lock_file=not opts.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if opts.analyse:
con.analyse()
return
if opts.add_from_file:
filename = opts.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
con.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if opts.count:
n = con.count(query)
print('%s' % plural(n, 'row'))
return
if opts.explain:
for dct in con.select(query,
explain=True,
verbosity=verbosity,
limit=opts.limit,
offset=opts.offset):
print(dct['explain'])
return
if opts.insert_into:
nkvp = 0
nrows = 0
with connect(opts.insert_into,
use_lock_file=not opts.no_lock_file) as con2:
for dct in con.select(query):
kvp = dct.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if opts.unique:
dct['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
con2.write(dct, data=dct.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [dct['id'] for dct in con.select(query)]
m, n = con.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if opts.delete:
ids = [dct['id'] for dct in con.select(query)]
if ids and not opts.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
con.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if opts.plot_data:
from ase.db.plot import dct2plot
dct2plot(con.get(query).data, opts.plot_data)
return
if opts.plot:
if ':' in opts.plot:
tags, keys = opts.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = opts.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in con.select(query, sort=opts.sort):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if opts.long:
dct = con.get(query)
summary = Summary(dct)
summary.write()
elif opts.json:
dct = con.get(query)
con2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = dct.get('key_value_pairs', {})
con2.write(dct, data=dct.get('data'), **kvp)
else:
if opts.open_web_browser:
import ase.db.app as app
app.db = con
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = opts.columns
if c and c.startswith('++'):
keys = set()
for row in con.select(query,
limit=opts.limit,
offset=opts.offset):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(con, verbosity, opts.cut)
table.select(query, columns, opts.sort, opts.limit, opts.offset)
if opts.csv:
table.write_csv()
else:
table.write(query)
def main(args):
verbosity = 1 - args.quiet + args.verbose
query = ','.join(args.query)
if args.sort.endswith('-'):
args.sort = '-' + args.sort[:-1]
if query.isdigit():
query = int(query)
add_key_value_pairs = {}
if args.add_key_value_pairs:
for pair in args.add_key_value_pairs.split(','):
key, value = pair.split('=')
add_key_value_pairs[key] = convert_str_to_int_float_or_str(value)
if args.delete_keys:
delete_keys = args.delete_keys.split(',')
else:
delete_keys = []
db = connect(args.database, use_lock_file=not args.no_lock_file)
def out(*args):
if verbosity > 0:
print(*args)
if args.analyse:
db.analyse()
return
if args.add_from_file:
filename = args.add_from_file
if ':' in filename:
calculator_name, filename = filename.split(':')
atoms = get_calculator(calculator_name)(filename).get_atoms()
else:
atoms = ase.io.read(filename)
db.write(atoms, key_value_pairs=add_key_value_pairs)
out('Added {0} from {1}'.format(atoms.get_chemical_formula(),
filename))
return
if args.count:
n = db.count(query)
print('%s' % plural(n, 'row'))
return
if args.explain:
for row in db.select(query,
explain=True,
verbosity=verbosity,
limit=args.limit,
offset=args.offset):
print(row['explain'])
return
if args.show_metadata:
print(json.dumps(db.metadata, sort_keys=True, indent=4))
return
if args.set_metadata:
with open(args.set_metadata) as fd:
db.metadata = json.load(fd)
return
if args.insert_into:
nkvp = 0
nrows = 0
with connect(args.insert_into,
use_lock_file=not args.no_lock_file) as db2:
for row in db.select(query, sort=args.sort):
kvp = row.get('key_value_pairs', {})
nkvp -= len(kvp)
kvp.update(add_key_value_pairs)
nkvp += len(kvp)
if args.unique:
row['unique_id'] = '%x' % randint(16**31, 16**32 - 1)
db2.write(row, data=row.get('data'), **kvp)
nrows += 1
out('Added %s (%s updated)' %
(plural(nkvp, 'key-value pair'),
plural(len(add_key_value_pairs) * nrows - nkvp, 'pair')))
out('Inserted %s' % plural(nrows, 'row'))
return
if add_key_value_pairs or delete_keys:
ids = [row['id'] for row in db.select(query)]
m, n = db.update(ids, delete_keys, **add_key_value_pairs)
out('Added %s (%s updated)' %
(plural(m, 'key-value pair'),
plural(len(add_key_value_pairs) * len(ids) - m, 'pair')))
out('Removed', plural(n, 'key-value pair'))
return
if args.delete:
ids = [row['id'] for row in db.select(query)]
if ids and not args.yes:
msg = 'Delete %s? (yes/No): ' % plural(len(ids), 'row')
if input(msg).lower() != 'yes':
return
db.delete(ids)
out('Deleted %s' % plural(len(ids), 'row'))
return
if args.plot_data:
from ase.db.plot import dct2plot
dct2plot(db.get(query).data, args.plot_data)
return
if args.plot:
if ':' in args.plot:
tags, keys = args.plot.split(':')
tags = tags.split(',')
else:
tags = []
keys = args.plot
keys = keys.split(',')
plots = collections.defaultdict(list)
X = {}
labels = []
for row in db.select(query, sort=args.sort, include_data=False):
name = ','.join(str(row[tag]) for tag in tags)
x = row.get(keys[0])
if x is not None:
if isinstance(x, basestring):
if x not in X:
X[x] = len(X)
labels.append(x)
x = X[x]
plots[name].append([x] + [row.get(key) for key in keys[1:]])
import matplotlib.pyplot as plt
for name, plot in plots.items():
xyy = zip(*plot)
x = xyy[0]
for y, key in zip(xyy[1:], keys[1:]):
plt.plot(x, y, label=name + ':' + key)
if X:
plt.xticks(range(len(labels)), labels, rotation=90)
plt.legend()
plt.show()
return
if args.json:
row = db.get(query)
db2 = connect(sys.stdout, 'json', use_lock_file=False)
kvp = row.get('key_value_pairs', {})
db2.write(row, data=row.get('data'), **kvp)
return
db.python = args.metadata_from_python_script
db.meta = process_metadata(db, html=args.open_web_browser)
if args.long:
# Remove .png files so that new ones will be created.
for func, filenames in db.meta.get('functions', []):
for filename in filenames:
try:
os.remove(filename)
except OSError: # Python 3 only: FileNotFoundError
pass
row = db.get(query)
summary = Summary(row, db.meta)
summary.write()
else:
if args.open_web_browser:
import ase.db.app as app
app.databases['default'] = db
app.app.run(host='0.0.0.0', debug=True)
else:
columns = list(all_columns)
c = args.columns
if c and c.startswith('++'):
keys = set()
for row in db.select(query,
limit=args.limit,
offset=args.offset,
include_data=False):
keys.update(row._keys)
columns.extend(keys)
if c[2:3] == ',':
c = c[3:]
else:
c = ''
if c:
if c[0] == '+':
c = c[1:]
elif c[0] != '-':
columns = []
for col in c.split(','):
if col[0] == '-':
columns.remove(col[1:])
else:
columns.append(col.lstrip('+'))
table = Table(db, verbosity, args.cut)
table.select(query, columns, args.sort, args.limit, args.offset)
if args.csv:
table.write_csv()
else:
table.write(query)