diff --git a/nomad/metainfo/__init__.py b/nomad/metainfo/__init__.py
index e9a217aa25570b17a0e72576fa42eb2082a4366e..e27cf60e6009aa7ba83d8375543060f26f47f73b 100644
--- a/nomad/metainfo/__init__.py
+++ b/nomad/metainfo/__init__.py
@@ -1,2 +1,2 @@
from .metainfo import MSection, MCategory, Definition, Property, Quantity, SubSection, \
- Section, Category, Package, Enum, m_package, units
+ Section, Category, Package, Enum, Datetime, m_package, units
diff --git a/nomad/metainfo/example.py b/nomad/metainfo/example.py
index 14ac880dd2a37837d1ed89d652615698c50a87b3..9c30137dae6f1f8e3acad16d85671e0d148e41e0 100644
--- a/nomad/metainfo/example.py
+++ b/nomad/metainfo/example.py
@@ -1,8 +1,9 @@
""" An example metainfo package. """
import numpy as np
+from datetime import datetime
-from nomad.metainfo import MSection, MCategory, Section, Quantity, Package, SubSection, Enum, units
+from nomad.metainfo import MSection, MCategory, Section, Quantity, Package, SubSection, Enum, Datetime, units
m_package = Package(links=['http://metainfo.nomad-coe.eu'])
@@ -18,6 +19,7 @@ class Parsing(MSection):
parser_version = Quantity(type=str)
nomad_version = Quantity(type=str)
warnings = Quantity(type=str, shape=['0..*'])
+ parse_time = Quantity(type=Datetime)
class System(MSection):
@@ -93,6 +95,10 @@ if __name__ == '__main__':
run = Run()
run.code_name = 'VASP'
run.code_version = '1.0.0'
+
+ parsing = run.m_create(Parsing)
+ parsing.parse_time = datetime.now()
+
run.m_as(VaspRun).x_vasp_raw_format = 'outcar'
# The same as
run.x_vasp_raw_format = 'outcar' # type: ignore
@@ -117,4 +123,4 @@ if __name__ == '__main__':
run = Run.m_from_dict(serializable)
print(run.sccs[0].system)
- print(m_package.m_to_dict()) # type: ignore, pylint: disable=undefined-variable
+ # print(m_package.m_to_json(indent=2)) # type: ignore, pylint: disable=undefined-variable
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 227b751605c0db7576f28d8a34274936cd80deab..f85bd37df4a015f23088a360137ccafe1f4eaab5 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -134,7 +134,7 @@ See the reference of classes :class:`Section` and :class:`Quantities` for detail
.. autoclass:: Quantity
"""
-# TODO validation
+# TODO validation and constraints
from typing import Type, TypeVar, Union, Tuple, Iterable, List, Any, Dict, Set, \
Callable as TypingCallable, cast
@@ -148,6 +148,9 @@ import itertools
import numpy as np
from pint.unit import _Unit
from pint import UnitRegistry
+import aniso8601
+from datetime import datetime
+import pytz
m_package: 'Package' = None
@@ -384,13 +387,40 @@ class Reference(DataType):
return MProxy(value)
+class __Datetime(DataType):
+
+ def __parse(self, datetime_str: str) -> datetime:
+ try:
+ try:
+ return aniso8601.parse_datetime(datetime_str)
+ except ValueError:
+ date = aniso8601.parse_date(datetime_str)
+ return datetime(date.year, date.month, date.day)
+ except Exception:
+ raise TypeError('Invalid date literal "{0}"'.format(datetime_str))
+
+ def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
+ if isinstance(value, str):
+ value = self.__parse(value)
+
+ if not isinstance(value, datetime):
+ raise TypeError('%s is not a datetime.' % value)
+
+ return value
+
+ def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
+ value.replace(tzinfo=pytz.utc)
+ return value.isoformat()
+
+ def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
+ return self.__parse(value)
+
+
Dimension = __Dimension()
Unit = __Unit()
QuantityType = __QuantityType()
Callable = __Callable()
-
-
-# TODO class Datetime(DataType)
+Datetime = __Datetime()
class MObjectMeta(type):
@@ -737,10 +767,6 @@ class MSection(metaclass=MObjectMeta):
'The value %s is not an enum value for quantity %s.' %
(value, quantity_def))
- elif quantity_def in [Quantity.type, Quantity.derived]:
- # TODO check these special cases for Quantity quantities
- pass
-
elif quantity_def.type == Any:
pass
@@ -999,45 +1025,43 @@ class MSection(metaclass=MObjectMeta):
dct.pop('m_parent_index', None)
dct.pop('m_parent_sub_section', None)
- def items():
- for name, sub_section_def in section_def.all_sub_sections.items():
- if name in dct:
- sub_section_value = dct.pop(name)
- if sub_section_def.repeats:
- yield name, [
- sub_section_def.sub_section.section_cls.m_from_dict(sub_section_dct)
- for sub_section_dct in sub_section_value]
+ section = cls()
+
+ for name, sub_section_def in section_def.all_sub_sections.items():
+ if name in dct:
+ sub_section_value = dct.pop(name)
+ if sub_section_def.repeats:
+ for sub_section_dct in sub_section_value:
+ sub_section = sub_section_def.sub_section.section_cls.m_from_dict(sub_section_dct)
+ section.m_add_sub_section(sub_section_def, sub_section)
+
+ else:
+ sub_section = sub_section_def.sub_section.section_cls.m_from_dict(sub_section_value)
+ section.m_add_sub_section(sub_section_def, sub_section)
+
+ for name, quantity_def in section_def.all_quantities.items():
+ if name in dct:
+ quantity_value = dct[name]
+
+ if type(quantity_def.type) == np.dtype:
+ quantity_value = np.asarray(quantity_value)
+
+ if isinstance(quantity_def.type, DataType):
+ dimensions = len(quantity_def.shape)
+ if dimensions == 0:
+ quantity_value = quantity_def.type.deserialize(
+ section, quantity_def, quantity_value)
+ elif dimensions == 1:
+ quantity_value = list(
+ quantity_def.type.deserialize(section, quantity_def, item)
+ for item in quantity_value)
else:
- yield name, sub_section_def.sub_section.section_cls.m_from_dict(sub_section_value)
-
- for name, quantity_def in section_def.all_quantities.items():
- if name in dct:
- quantity_value = dct[name]
-
- if type(quantity_def.type) == np.dtype:
- quantity_value = np.asarray(quantity_value)
-
- if isinstance(quantity_def.type, DataType):
- dimensions = len(quantity_def.shape)
- # TODO hand in the context, which is currently create after!
- if dimensions == 0:
- quantity_value = quantity_def.type.deserialize(
- None, quantity_def, quantity_value)
- elif dimensions == 1:
- quantity_value = list(
- quantity_def.type.deserialize(None, quantity_def, item)
- for item in quantity_value)
- else:
- raise MetainfoError(
- 'Only numpy quantities can have more than 1 dimension.')
+ raise MetainfoError(
+ 'Only numpy quantities can have more than 1 dimension.')
- yield name, quantity_value
+ section.m_data.dct[name] = quantity_value # type: ignore
- dct = {key: value for key, value in items()}
- section_instance = cast(MSectionBound, section_def.section_cls())
- # TODO !do not update, but set directly!
- section_instance.m_update(**dct)
- return section_instance
+ return section
def m_to_json(self, **kwargs):
"""Returns the data of this section as a json string. """
@@ -1271,9 +1295,6 @@ class Quantity(Property):
virtual: 'Quantity' = None
# TODO derived_from = Quantity(type=Quantity, shape=['0..*'])
- # TODO categories = Quantity(type=Category, shape=['0..*'])
- # TODO converter = Quantity(type=Converter), a class with set of functions for
- # normalizing, (de-)serializing values.
def __get__(self, obj, cls):
if obj is None: