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# fmt: off
from typing import List, Optional
import numpy as np
from ase.db.core import float_to_time_string, now
all_columns = ('id', 'age', 'user', 'formula', 'calculator',
'energy', 'natoms', 'fmax', 'pbc', 'volume',
'charge', 'mass', 'smax', 'magmom')
def get_sql_columns(columns):
""" Map the names of table columns to names of columns in
the SQL tables"""
sql_columns = list(columns)
if 'age' in columns:
sql_columns.remove('age')
sql_columns += ['mtime', 'ctime']
if 'user' in columns:
sql_columns[sql_columns.index('user')] = 'username'
if 'formula' in columns:
sql_columns[sql_columns.index('formula')] = 'numbers'
if 'fmax' in columns:
sql_columns[sql_columns.index('fmax')] = 'forces'
if 'smax' in columns:
sql_columns[sql_columns.index('smax')] = 'stress'
if 'volume' in columns:
sql_columns[sql_columns.index('volume')] = 'cell'
if 'mass' in columns:
sql_columns[sql_columns.index('mass')] = 'masses'
if 'charge' in columns:
sql_columns[sql_columns.index('charge')] = 'charges'
sql_columns.append('key_value_pairs')
sql_columns.append('constraints')
if 'id' not in sql_columns:
sql_columns.append('id')
return sql_columns
def plural(n, word):
if n == 1:
return '1 ' + word
return '%d %ss' % (n, word)
def cut(txt, length):
if len(txt) <= length or length == 0:
return txt
return txt[:length - 3] + '...'
def cutlist(lst, length):
if len(lst) <= length or length == 0:
return lst
return lst[:9] + [f'... ({len(lst) - 9} more)']
class Table:
def __init__(
self,
connection,
unique_key: str = 'id',
verbosity: int = 1,
cut: int = 35,
):
self.connection = connection
self.verbosity = verbosity
self.cut = cut
self.rows: list[Row] = []
self.columns = None
self.id = None
self.right = None
self.keys = None
self.unique_key = unique_key
self.addcolumns: Optional[List[str]] = None
def select(self, query, columns, sort, limit, offset,
show_empty_columns=False):
"""Query datatbase and create rows."""
sql_columns = get_sql_columns(columns)
self.limit = limit
self.offset = offset
self.rows = [Row(row, columns, self.unique_key)
for row in self.connection.select(
query, verbosity=self.verbosity,
limit=limit, offset=offset, sort=sort,
include_data=False, columns=sql_columns)]
self.columns = list(columns)
if not show_empty_columns:
delete = set(range(len(columns)))
for row in self.rows:
for n in delete.copy():
if row.values[n] is not None:
delete.remove(n)
delete = sorted(delete, reverse=True)
for row in self.rows:
for n in delete:
del row.values[n]
for n in delete:
del self.columns[n]
def format(self, subscript=None):
right = set() # right-adjust numbers
allkeys = set()
for row in self.rows:
numbers = row.format(self.columns, subscript)
right.update(numbers)
allkeys.update(row.dct.get('key_value_pairs', {}))
right.add('age')
self.right = [column in right for column in self.columns]
self.keys = sorted(allkeys)
def write(self, query=None):
self.format()
L = [[len(s) for s in row.strings]
for row in self.rows]
L.append([len(c) for c in self.columns])
N = np.max(L, axis=0)
fmt = '{:{align}{width}}'
if self.verbosity > 0:
print('|'.join(fmt.format(c, align='<>'[a], width=w)
for c, a, w in zip(self.columns, self.right, N)))
for row in self.rows:
print('|'.join(fmt.format(c, align='<>'[a], width=w)
for c, a, w in
zip(row.strings, self.right, N)))
if self.verbosity == 0:
return
nrows = len(self.rows)
if self.limit and nrows == self.limit:
n = self.connection.count(query)
print('Rows:', n, f'(showing first {self.limit})')
else:
print('Rows:', nrows)
if self.keys:
print('Keys:', ', '.join(cutlist(self.keys, self.cut)))
def write_csv(self):
if self.verbosity > 0:
print(', '.join(self.columns))
for row in self.rows:
print(', '.join(str(val) for val in row.values))
class Row:
def __init__(self, dct, columns, unique_key='id'):
self.dct = dct
self.values = None
self.strings = None
self.set_columns(columns)
self.uid = getattr(dct, unique_key)
def set_columns(self, columns):
self.values = []
for c in columns:
if c == 'age':
value = float_to_time_string(now() - self.dct.ctime)
elif c == 'pbc':
value = ''.join('FT'[int(p)] for p in self.dct.pbc)
else:
value = getattr(self.dct, c, None)
self.values.append(value)
def format(self, columns, subscript=None):
self.strings = []
numbers = set()
for value, column in zip(self.values, columns):
if column == 'formula' and subscript:
value = subscript.sub(r'<sub>\1</sub>', value)
elif isinstance(value, dict):
value = str(value)
elif isinstance(value, list):
value = str(value)
elif isinstance(value, np.ndarray):
value = str(value.tolist())
elif isinstance(value, int):
value = str(value)
numbers.add(column)
elif isinstance(value, float):
numbers.add(column)
value = f'{value:.3f}'
elif value is None:
value = ''
self.strings.append(value)
return numbers
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