def test_store_indirect():
"""Test the `BasisData.store` method when called indirectly because its is an input."""
basis = BasisData(io.BytesIO(b'basis'))
basis.element = 'Ar'
node = CalcJobNode()
node.add_incoming(basis, link_type=LinkType.INPUT_CALC, link_label='basis')
node.store_all()
def test_store_indirect():
"""Test the `PseudoPotentialData.store` method when called indirectly because its is an input."""
pseudo = PseudoPotentialData(io.BytesIO(b'pseudo'))
pseudo.element = 'Ar'
node = CalcJobNode()
node.add_incoming(pseudo,
link_type=LinkType.INPUT_CALC,
link_label='pseudo')
node.store_all()
def test_process_show(self):
"""Test verdi process show"""
workchain_one = WorkChainNode()
workchain_two = WorkChainNode()
workchains = [workchain_one, workchain_two]
workchain_two.set_attribute('process_label', 'workchain_one_caller')
workchain_two.store()
workchain_one.add_incoming(workchain_two, link_type=LinkType.CALL_WORK, link_label='called')
workchain_one.store()
calcjob_one = CalcJobNode()
calcjob_two = CalcJobNode()
calcjob_one.set_attribute('process_label', 'process_label_one')
calcjob_two.set_attribute('process_label', 'process_label_two')
calcjob_one.add_incoming(workchain_one, link_type=LinkType.CALL_CALC, link_label='one')
calcjob_two.add_incoming(workchain_one, link_type=LinkType.CALL_CALC, link_label='two')
calcjob_one.store()
calcjob_two.store()
# Running without identifiers should not except and not print anything
options = []
result = self.cli_runner.invoke(cmd_process.process_show, options)
self.assertIsNone(result.exception, result.output)
self.assertEqual(len(get_result_lines(result)), 0)
# Giving a single identifier should print a non empty string message
options = [str(workchain_one.pk)]
result = self.cli_runner.invoke(cmd_process.process_show, options)
lines = get_result_lines(result)
self.assertClickResultNoException(result)
self.assertTrue(len(lines) > 0)
self.assertIn('workchain_one_caller', result.output)
self.assertIn('process_label_one', lines[-2])
self.assertIn('process_label_two', lines[-1])
# Giving multiple identifiers should print a non empty string message
options = [str(node.pk) for node in workchains]
result = self.cli_runner.invoke(cmd_process.process_show, options)
self.assertIsNone(result.exception, result.output)
self.assertTrue(len(get_result_lines(result)) > 0)
def _inner(file_path, input_settings=None):
# Create a test computer
computer = localhost
process_type = 'aiida.calculations:{}'.format('vasp.vasp')
node = CalcJobNode(computer=computer, process_type=process_type)
node.set_attribute('input_filename', 'INCAR')
node.set_attribute('output_filename', 'OUTCAR')
#node.set_attribute('error_filename', 'aiida.err')
node.set_attribute('scheduler_stderr', '_scheduler-stderr.txt')
node.set_attribute('scheduler_stdout', '_scheduler-stdout.txt')
node.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
node.set_option('max_wallclock_seconds', 1800)
if input_settings is None:
input_settings = {}
settings = Dict(dict=input_settings)
node.add_incoming(settings,
link_type=LinkType.INPUT_CALC,
link_label='settings')
settings.store()
node.store()
# Create a `FolderData` that will represent the `retrieved` folder. Store the test
# output fixture in there and link it.
retrieved = FolderData()
retrieved.put_object_from_tree(file_path)
retrieved.add_incoming(node,
link_type=LinkType.CREATE,
link_label='retrieved')
retrieved.store()
return node
def _generate_remote_data(computer,
remote_path,
entry_point_name=None,
extras_root=[]):
"""Return a `KpointsData` with a mesh of npoints in each direction."""
from aiida.common.links import LinkType
from aiida.orm import CalcJobNode, RemoteData, Dict
from aiida.plugins.entry_point import format_entry_point_string
entry_point = format_entry_point_string('aiida.calculations',
entry_point_name)
remote = RemoteData(remote_path=remote_path)
remote.computer = computer
if entry_point_name is not None:
creator = CalcJobNode(computer=computer, process_type=entry_point)
creator.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
remote.add_incoming(creator,
link_type=LinkType.CREATE,
link_label='remote_folder')
for extra in extras_root:
to_link = extra[0]
if isinstance(to_link, dict):
to_link = Dict(dict=to_link)
to_link.store()
creator.add_incoming(to_link,
link_type=LinkType.INPUT_CALC,
link_label=extra[1])
creator.store()
return remote
def generate_calcjob_node(
self,
entry_point_name,
retrieved=None,
computer_name="localhost",
options=None,
mark_completed=False,
remote_path=None,
input_nodes=None,
):
"""Fixture to generate a mock `CalcJobNode` for testing parsers.
Parameters
----------
entry_point_name : str
entry point name of the calculation class
retrieved : aiida.orm.FolderData
containing the file(s) to be parsed
computer_name : str
used to get or create a ``Computer``, by default 'localhost'
options : None or dict
any additional metadata options to set on the node
remote_path : str
path to a folder on the computer
mark_completed : bool
if True, set the process state to finished, and the exit_status = 0
input_nodes: dict
mapping of link label to node
Returns
-------
aiida.orm.CalcJobNode
instance with the `retrieved` node linked as outgoing
"""
from aiida.common.links import LinkType
from aiida.engine import ExitCode, ProcessState
from aiida.orm import CalcJobNode, Node, RemoteData
from aiida.plugins.entry_point import format_entry_point_string
process = self.get_calc_cls(entry_point_name)
computer = self.get_or_create_computer(computer_name)
entry_point = format_entry_point_string("aiida.calculations",
entry_point_name)
calc_node = CalcJobNode(computer=computer, process_type=entry_point)
calc_node.set_options({
k: v.default() if callable(v.default) else v.default
for k, v in process.spec_options.items() if v.has_default()
})
calc_node.set_option("resources", {
"num_machines": 1,
"num_mpiprocs_per_machine": 1
})
calc_node.set_option("max_wallclock_seconds", 1800)
if options:
calc_node.set_options(options)
if mark_completed:
calc_node.set_process_state(ProcessState.FINISHED)
calc_node.set_exit_status(ExitCode().status)
if input_nodes is not None:
for label, in_node in input_nodes.items():
in_node_map = in_node
if isinstance(in_node, Node):
in_node_map = {None: in_node_map}
for sublabel, in_node in in_node_map.items():
in_node.store()
link_label = (label if sublabel is None else
"{}__{}".format(label, sublabel))
calc_node.add_incoming(in_node,
link_type=LinkType.INPUT_CALC,
link_label=link_label)
calc_node.store()
if retrieved is not None:
retrieved.add_incoming(calc_node,
link_type=LinkType.CREATE,
link_label="retrieved")
retrieved.store()
if remote_path is not None:
remote = RemoteData(remote_path=remote_path, computer=computer)
remote.add_incoming(calc_node,
link_type=LinkType.CREATE,
link_label="remote_folder")
remote.store()
return calc_node
def _generate_calc_job_node(
entry_point_name,
results_folder,
inputs=None,
computer=None,
outputs=None,
outfile_override=None,
):
"""
Generate a CalcJob node with fake retrieved node in the
tests/data
"""
calc_class = CalculationFactory(entry_point_name)
entry_point = format_entry_point_string('aiida.calculations',
entry_point_name)
builder = calc_class.get_builder()
if not computer:
computer = db_test_app.localhost
node = CalcJobNode(computer=computer, process_type=entry_point)
# Monkypatch the inputs
if inputs is not None:
inputs = AttributeDict(inputs)
node.__dict__['inputs'] = inputs
# Add direct inputs, pseudos are omitted
for k, v in inputs.items():
if isinstance(v, Node):
if not v.is_stored:
v.store()
node.add_incoming(v,
link_type=LinkType.INPUT_CALC,
link_label=k)
options = builder.metadata.options
options.update(inputs.metadata.options)
node.set_attribute('input_filename', options.input_filename)
node.set_attribute('seedname', options.seedname)
node.set_attribute('output_filename', options.output_filename)
node.set_attribute('error_filename', 'aiida.err')
node.set_option('resources', {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
})
node.set_option('max_wallclock_seconds', 1800)
node.store()
filepath = this_folder.parent / 'data' / results_folder
retrieved = FolderData()
retrieved.put_object_from_tree(str(filepath.resolve()))
# Apply overriding output files
if outfile_override is not None:
for key, content in outfile_override.items():
if content is None:
retrieved.delete_object(key)
continue
buf = BytesIO(content.encode())
retrieved.put_object_from_filelike(buf, key)
retrieved.add_incoming(node,
link_type=LinkType.CREATE,
link_label='retrieved')
retrieved.store()
if outputs is not None:
for label, out_node in outputs.items():
out_node.add_incoming(node,
link_type=LinkType.CREATE,
link_label=label)
if not out_node.is_stored:
out_node.store()
return node