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another round of review fixes
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jrudz committed Dec 15, 2023
1 parent c616845 commit 1040c59
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Showing 3 changed files with 36 additions and 19 deletions.
2 changes: 1 addition & 1 deletion atomisticparsers/h5md/metainfo/h5md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -187,4 +187,4 @@ class Run(simulation.run.Run):

x_h5md_author = SubSection(sub_section=Author.m_def)

x_h5md_creator = SubSection(sub_section=simulation.run.Program.m_def)
x_h5md_creator = SubSection(sub_section=simulation.run.Program.m_def)
5 changes: 3 additions & 2 deletions atomisticparsers/h5md/nomad_plugin.yaml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
code_category: Atomistic code
code_homepage: http://www.??.org/
# code_homepage: http://www.??.org/
# TODO is this the correct category
code_name: H5MD
metadata:
codeCategory: Atomistic code
codeLabel: H5MD
codeLabelStyle: All in capitals
codeName: h5md
codeUrl: http://www.??.org/
# codeUrl: http://www.??.org/
parserDirName: dependencies/parsers/atomistic/atomisticparsers/h5md/
parserGitUrl: https://github.com/nomad-coe/atomistic-parsers.git
parserSpecific: ''
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48 changes: 32 additions & 16 deletions atomisticparsers/h5md/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,9 @@
import logging
import h5py

from typing import List, Dict, Tuple, Any, Union, Iterable, cast, Callable, TYPE_CHECKING
from h5py import Group

from nomad.datamodel import EntryArchive
from nomad.metainfo.util import MEnum
from nomad.parsing.file_parser import FileParser
Expand Down Expand Up @@ -124,6 +127,18 @@ def get_value(self, group, path: str, default=None):
def parse(self, quantity_key: str = None, **kwargs):
pass

# def parse(self, key, **kwargs):
# source = kwargs.get('source', self.filehdf5)
# path = kwargs.get('path')
# attribute = kwargs.get('attribute')
# if attribute is not None:
# value = self.hdf5_attr_getter(source, path, attribute)
# else:
# value = self.hdf5_getter(source, path)
# # i do not know how to construct the full path here relative to root
# full_path = f'...{path}.{attribute}'
# self._results[full_path] = value


class H5MDParser(MDParser):
def __init__(self):
Expand Down Expand Up @@ -326,25 +341,26 @@ def observable_info(self):
if observables_group is None:
return self._observable_info

def get_observable_paths(observable_group, current_path, paths):
def get_observable_paths(observable_group: Dict, current_path: str) -> List:
paths = []
for obs_key in observable_group.keys():
path = obs_key + '.'
observable = self._data_parser.get_value(observable_group, obs_key)
observable_type = self._data_parser.get_value(observable_group, obs_key).attrs.get('type')
if not observable_type:
paths = get_observable_paths(observable, current_path + path, paths)
paths.extend(get_observable_paths(observable, f'{current_path}{path}'))
else:
paths.append(current_path + path[:-1])

return paths

observable_paths = get_observable_paths(observables_group, current_path='', paths=[])
observable_paths = get_observable_paths(observables_group, current_path='')

for path in observable_paths:
observable = self._data_parser.get_value(observables_group, path)
observable_type = self._data_parser.get_value(observables_group, path).attrs.get('type')
observable_name = path.split('.')[0]
observable_label = '-'.join(path.split('.')[1:]) if len(path.split('.')) > 1 else ''
observable_label = '-'.join(path.split('.')[1:])
if observable_name not in self._observable_info[observable_type].keys():
self._observable_info[observable_type][observable_name] = {}
self._observable_info[observable_type][observable_name][observable_label] = {}
Expand All @@ -356,10 +372,11 @@ def get_observable_paths(observable_group, current_path, paths):
self._observable_info[observable_type][observable_name][observable_label][key] = observable_attribute
return self._observable_info

def get_atomsgroup_fromh5md(self, nomad_sec, h5md_sec_particlesgroup):
def parse_atomsgroup(self, nomad_sec, h5md_sec_particlesgroup: Group):
for i_key, key in enumerate(h5md_sec_particlesgroup.keys()):
particles_group = {group_key: self._data_parser.get_value(h5md_sec_particlesgroup[key], group_key) for group_key in h5md_sec_particlesgroup[key].keys()}
sec_atomsgroup = nomad_sec.m_create(AtomsGroup)
sec_atomsgroup = AtomsGroup()
nomad_sec.atoms_group.append(sec_atomsgroup)
sec_atomsgroup.type = particles_group.pop('type', None)
sec_atomsgroup.index = i_key
sec_atomsgroup.atom_indices = particles_group.pop('indices', None)
Expand All @@ -376,9 +393,9 @@ def get_atomsgroup_fromh5md(self, nomad_sec, h5md_sec_particlesgroup):
sec_atomsgroup.x_h5md_parameters.append(ParamEntry(kind=particles_group_key, value=val, unit=units))
# get the next atomsgroup
if particles_subgroup:
self.get_atomsgroup_fromh5md(sec_atomsgroup, particles_subgroup)
self.parse_atomsgroup(sec_atomsgroup, particles_subgroup)

def is_valid_key_val(self, metainfo_class, key, val):
def is_valid_key_val(self, metainfo_class, key: str, val) -> bool:
if hasattr(metainfo_class, key):
quant_type = getattr(metainfo_class, key).get('type')
is_MEnum = isinstance(quant_type, MEnum) if quant_type else False
Expand All @@ -397,7 +414,7 @@ def parameter_info(self):
if parameters_group is None:
return self._parameter_info

def get_parameters(parameter_group):
def get_parameters(parameter_group: Group) -> Dict:
param_dict = {}
for key, val in parameter_group.items():
if isinstance(val, h5py.Group):
Expand Down Expand Up @@ -500,7 +517,7 @@ def format_times(times):
if key == 'forces':
data[key] = dict(total=dict(value=val[system_index]))
else:
if key in BaseCalculation.__dict__.keys():
if hasattr(BaseCalculation, key):
data[key] = val[system_index]
else:
unit = None
Expand All @@ -516,7 +533,7 @@ def format_times(times):
if obs_index:
val = observable.get('value', [None] * (obs_index + 1))[obs_index]
if 'energ' in observable_type: # TODO check for energies or energy when matching name
if key in Energy.__dict__.keys():
if hasattr(Energy, key):
data['energy'][key] = dict(value=val)
else:
data_h5md['x_h5md_energy_contributions'].append(EnergyEntry(kind=map_key, value=val))
Expand All @@ -526,7 +543,7 @@ def format_times(times):
else:
key = map_key

if key in BaseCalculation.__dict__.keys():
if hasattr(BaseCalculation, key):
data[key] = val
else:
unit = None
Expand Down Expand Up @@ -559,6 +576,7 @@ def parse_system(self):
n_frames = len(system_info.get('times', []))
self._system_time_map = {}
self._system_step_map = {}

for frame in range(n_frames):
# if (n % self.frame_rate) > 0:
# continue
Expand Down Expand Up @@ -588,7 +606,7 @@ def parse_system(self):
if frame == 0: # TODO extend to time-dependent topologies
topology = self._data_parser.get_value(connectivity, 'particles_group', None)
if topology:
self.get_atomsgroup_fromh5md(sec_run.system[frame], topology)
self.parse_atomsgroup(sec_run.system[frame], topology)

def parse_method(self):

Expand Down Expand Up @@ -639,7 +657,6 @@ def parse_method(self):

for key, val in force_calculation_parameters.items():
if not isinstance(val, dict):
# key = self.resolve_key(ForceCalculations, key, val)
if self.is_valid_key_val(ForceCalculations, key, val):
sec_force_calculations.m_set(sec_force_calculations.m_get_quantity_definition(key), val)
else:
Expand All @@ -649,7 +666,6 @@ def parse_method(self):
else:
if key == 'neighbor_searching':
for neigh_key, neigh_val in val.items():
# neigh_key = self.resolve_key(NeighborSearching, neigh_key, neigh_val)
if self.is_valid_key_val(NeighborSearching, neigh_key, neigh_val):
sec_neighbor_searching.m_set(sec_neighbor_searching.m_get_quantity_definition(neigh_key), neigh_val)
else:
Expand All @@ -660,7 +676,7 @@ def parse_method(self):
self.logger.warning('Unknown parameters in force calculations section. These will not be stored.')

def get_workflow_properties_dict(
self, observables: dict, property_type_key=None, property_type_value_key=None,
self, observables: Dict, property_type_key=None, property_type_value_key=None,
properties_known={}, property_keys_list=[], property_value_keys_list=[]):

def populate_property_dict(property_dict, val_name, val, flag_known_property=False):
Expand Down

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