def trajectory_list(raw, past_days, groups, all_users):
"""List TrajectoryData objects stored in the database."""
from aiida.orm import TrajectoryData
from tabulate import tabulate
elements = None
elements_only = False
formulamode = None
entry_list = data_list(TrajectoryData, LIST_PROJECT_HEADERS, elements,
elements_only, formulamode, past_days, groups,
all_users)
counter = 0
struct_list_data = list()
if not raw:
struct_list_data.append(LIST_PROJECT_HEADERS)
for entry in entry_list:
for i, value in enumerate(entry):
if isinstance(value, list):
entry[i] = ','.join(value)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
struct_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(struct_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(struct_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))
def cif_list(raw, formula_mode, past_days, groups, all_users):
"""List store CifData objects."""
from aiida.orm import CifData
from tabulate import tabulate
elements = None
elements_only = False
entry_list = data_list(CifData, LIST_PROJECT_HEADERS, elements,
elements_only, formula_mode, past_days, groups,
all_users)
counter = 0
cif_list_data = list()
if not raw:
cif_list_data.append(LIST_PROJECT_HEADERS)
for entry in entry_list:
for i, value in enumerate(entry):
if isinstance(value, list):
new_entry = list()
for elm in value:
if elm is None:
new_entry.append('')
else:
new_entry.append(elm)
entry[i] = ','.join(new_entry)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
cif_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(cif_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(cif_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))
def structure_list(elements, raw, formula_mode, past_days, groups, all_users):
"""List StructureData objects."""
from aiida.orm.nodes.data.structure import StructureData, get_formula, get_symbols_string
from tabulate import tabulate
elements_only = False
lst = data_list(StructureData, ['Id', 'Label', 'Kinds', 'Sites'], elements,
elements_only, formula_mode, past_days, groups, all_users)
entry_list = []
for [pid, label, akinds, asites] in lst:
# If symbols are defined there is a filtering of the structures
# based on the element
# When QueryBuilder will support this (attribute)s filtering,
# it will be pushed in the query.
if elements is not None:
all_symbols = [_['symbols'][0] for _ in akinds]
if not any([s in elements for s in all_symbols]):
continue
if elements_only:
echo.echo_critical('Not implemented elements-only search')
# We want only the StructureData that have attributes
if akinds is None or asites is None:
continue
symbol_dict = {}
for k in akinds:
symbols = k['symbols']
weights = k['weights']
symbol_dict[k['name']] = get_symbols_string(symbols, weights)
try:
symbol_list = []
for site in asites:
symbol_list.append(symbol_dict[site['kind_name']])
formula = get_formula(symbol_list, mode=formula_mode)
# If for some reason there is no kind with the name
# referenced by the site
except KeyError:
formula = '<<UNKNOWN>>'
entry_list.append([str(pid), label, str(formula)])
counter = 0
struct_list_data = list()
if not raw:
struct_list_data.append(LIST_PROJECT_HEADERS)
for entry in entry_list:
for i, value in enumerate(entry):
if isinstance(value, list):
entry[i] = ','.join(value)
for i in range(len(entry), len(LIST_PROJECT_HEADERS)):
entry.append(None)
counter += 1
struct_list_data.extend(entry_list)
if raw:
echo.echo(tabulate(struct_list_data, tablefmt='plain'))
else:
echo.echo(tabulate(struct_list_data, headers='firstrow'))
echo.echo('\nTotal results: {}\n'.format(counter))