def convert(self, value, param, ctx):
"""Attempt to interpret the value as a file first and if that fails try to load as a node."""
from aiida.orm import StructureData, QueryBuilder
try:
filepath = pathlib.Path(
__file__
).parent.parent / 'common' / 'data' / DEFAULT_STRUCTURES_MAPPING[
value]
except KeyError:
try:
return types.DataParamType(
sub_classes=('aiida.data:structure', )).convert(
value, param, ctx)
except click.BadParameter:
filepath = value
try:
import ase.io
except ImportError as exception:
raise click.BadParameter(
f'failed to load a structure with identifier `{value}`.\n'
'Cannot parse from file because `ase` is not installed.'
) from exception
try:
filepath = click.Path(exists=True,
dir_okay=False,
resolve_path=True).convert(
filepath, param, ctx)
except click.BadParameter as exception:
raise click.BadParameter(
f'failed to load a structure with identifier `{value}` and it can also not be resolved as a file.'
) from exception
try:
structure = StructureData(ase=ase.io.read(filepath))
except Exception as exception: # pylint: disable=broad-except
raise click.BadParameter(
f'file `{value}` could not be parsed into a `StructureData`: {exception}'
) from exception
duplicate = QueryBuilder().append(StructureData,
filters={
'extras._aiida_hash':
structure._get_hash()
}).first() # pylint: disable=protected-access
if duplicate:
return duplicate[0]
return structure
def convert(self, value, param, ctx):
is_path = False
# Alternative one could check if int or uuid
# aiida allows also for shorten uuids
from aiida.orm import StructureData, QueryBuilder
try:
structure = types.DataParamType(
sub_classes=('aiida.data:structure', )).convert(
value, param, ctx)
except (NotExistent, click.exceptions.BadParameter) as er:
echo.echo(f'Tried to load node, could not fine one for {value}. '
'I will further check if it is a filepath.')
is_path = True
if is_path:
# If it is a path to a file try to convert the structure
pathtype = click.Path(exists=True,
dir_okay=False,
resolve_path=True)
filename = pathtype.convert(value, param, ctx)
try:
import ase.io
except ImportError:
echo.echo_critical(
'You have not installed the package ase. \nYou can install it with: pip install ase'
)
try:
asecell = ase.io.read(filename)
structure = StructureData(ase=asecell)
except ValueError as err:
echo.echo_critical(str(err))
# do not store structure, since this option is for calculation and workflow
# input, which will store the structure anyway.
# do not store again if structure is already there.
duplicate = QueryBuilder().append(StructureData,
filters={
'extras._aiida_hash':
structure._get_hash()
}).first() # pylint: disable=protected-access
if duplicate:
return duplicate[0]
return structure
