metainfo.py 41.3 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
# Copyright 2018 Markus Scheidgen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an"AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
14

15
16
17
18
"""
The NOMAD meta-info allows to define physics data quantities. These definitions are
necessary for all computer representations of respective data (e.g. in Python,
search engines, data-bases, and files).
19

20
This modules provides various Python interfaces for
21

22
23
24
- defining meta-info data
- to create and manipulate data that follows these definitions
- to (de-)serialize meta-info data in JSON (i.e. represent data in JSON formatted files)
25

26
27
28
29
Here is a simple example that demonstrates the definition of System related quantities:

.. code-block:: python

Markus Scheidgen's avatar
Markus Scheidgen committed
30
    class System(MSection):
31
32
33
34
35
        \"\"\"
        A system section includes all quantities that describe a single a simulated
        system (a.k.a. geometry).
        \"\"\"

36
37
38
39
        n_atoms = Quantity(
            type=int, description='''
            A Defines the number of atoms in the system.
            ''')
40

41
42
43
44
        atom_labels = Quantity(type=Enum(ase.data.chemical_symbols), shape['n_atoms'])
        atom_positions = Quantity(type=float, shape=['n_atoms', 3], unit=Units.m)
        simulation_cell = Quantity(type=float, shape=[3, 3], unit=Units.m)
        pbc = Quantity(type=bool, shape=[3])
45

46
47
48
    class Run(MSection):
        systems = SubSection(sub_section=System, repeats=True)

49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
Here, we define a `section` called ``System``. The section mechanism allows to organize
related data into, well, sections. Sections form containment hierarchies. Here
containment is a parent-child (whole-part) relationship. In this example many ``Systems``,
are part of one ``Run``. Each ``System`` can contain values for the defined quantities:
``n_atoms``, ``atom_labels``, ``atom_positions``, ``simulation_cell``, and ``pbc``.
Quantities allow to state type, shape, and physics unit to specify possible quantity
values.

Here is an example, were we use the above definition to create, read, and manipulate
data that follows these definitions:

.. code-bock:: python

    run = Run()
    system = run.m_create(System)
    system.n_atoms = 3
    system.atom_labels = ['H', 'H', 'O']

    print(system.atom_labels)
    print(run.m_to_json(ident=2))

This last statement, will produce the following JSON:

.. code-block:: JSON

    {
75
        "m_def" = "Run",
76
77
        "System": [
            {
78
                "m_def" = "System",
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
                "m_parent_index" = 0,
                "n_atoms" = 3,
                "atom_labels" = [
                    "H",
                    "H",
                    "O"
                ]
            }
        ]
    }

This is the JSON representation, a serialized version of the Python representation in
the example above.

Sections can be extended with new quantities outside the original section definition.
This provides the key mechanism to extend commonly defined parts with (code) specific
quantities:

.. code-block:: Python

    class Method(nomad.metainfo.common.Method):
        x_vasp_incar_ALGO=Quantity(
            type=Enum(['Normal', 'VeryFast', ...]),
            links=['https://cms.mpi.univie.ac.at/wiki/index.php/ALGO'])
        \"\"\"
        A convenient option to specify the electronic minimisation algorithm (as of VASP.4.5)
        and/or to select the type of GW calculations.
        \"\"\"


All meta-info definitions and classes for meta-info data objects (i.e. section instances)
110
inherit from :class:` MSection`. This base-class provides common functions and properties
111
112
113
114
115
116
for all meta-info data objects. Names of these common parts are prefixed with ``m_``
to distinguish them from user defined quantities. This also constitute's the `reflection`
interface (in addition to Python's build in ``getattr``, ``setattr``) that allows to
create and manipulate meta-info data, without prior program time knowledge of the underlying
definitions.

Markus Scheidgen's avatar
Markus Scheidgen committed
117
.. autoclass:: MSection
118
119
120

The following classes can be used to define and structure meta-info data:

Markus Scheidgen's avatar
Markus Scheidgen committed
121
- sections are defined by sub-classes :class:`MSection` and using :class:`Section` to
122
  populate the classattribute `m_def`
123
124
125
126
127
128
129
130
131
132
133
134
- quantities are defined by assigning classattributes of a section with :class:`Quantity`
  instances
- references (from one section to another) can be defined with quantities that use
  section definitions as type
- dimensions can use defined by simply using quantity names in shapes
- categories (former `abstract type definitions`) can be given in quantity definitions
  to assign quantities to additional specialization-generalization hierarchies

See the reference of classes :class:`Section` and :class:`Quantities` for details.

.. autoclass:: Section
.. autoclass:: Quantity
135
136
"""

137
138
# TODO validation

139
from typing import Type, TypeVar, Union, Tuple, Iterable, List, Any, Dict, Set, cast
140
import sys
141
import inspect
142
import re
143
import json
144
import itertools
145

146
import numpy as np
147
148
from pint.unit import _Unit
from pint import UnitRegistry
149

Markus Scheidgen's avatar
Markus Scheidgen committed
150
151
is_bootstrapping = True
MSectionBound = TypeVar('MSectionBound', bound='MSection')
152
T = TypeVar('T')
153

154

155
# Reflection
156

157
class Enum(list):
158
    """ Allows to define str types with values limited to a pre-set list of possible values. """
159
160
161
    pass


162
163
164
165
166
167
168
169
class DataType:
    """
    Allows to define custom data types that can be used in the meta-info.

    The metainfo supports most types out of the box. These includes the python build-in
    primitive types (int, bool, str, float, ...), references to sections, and enums.
    However, in some occasions you need to add custom data types.
    """
Markus Scheidgen's avatar
Markus Scheidgen committed
170
    def type_check(self, section, value):
171
172
        return value

Markus Scheidgen's avatar
Markus Scheidgen committed
173
    def to_json_serializable(self, section, value):
174
175
        return value

Markus Scheidgen's avatar
Markus Scheidgen committed
176
    def from_json_serializable(self, section, value):
177
178
179
180
        return value


class Dimension(DataType):
181
    def type_check(self, section, value):
182
        if isinstance(value, int):
Markus Scheidgen's avatar
Markus Scheidgen committed
183
            return value
184
185
186

        if isinstance(value, str):
            if value.isidentifier():
Markus Scheidgen's avatar
Markus Scheidgen committed
187
                return value
188
            if re.match(r'(\d)\.\.(\d|\*)', value):
Markus Scheidgen's avatar
Markus Scheidgen committed
189
                return value
190
191

        if isinstance(value, Section):
Markus Scheidgen's avatar
Markus Scheidgen committed
192
            return value
193

194
        if isinstance(value, type) and hasattr(value, 'm_def'):
Markus Scheidgen's avatar
Markus Scheidgen committed
195
            return value
196
197
198
199

        raise TypeError('%s is not a valid dimension' % str(value))


Markus Scheidgen's avatar
Markus Scheidgen committed
200
201
202
203
204
205
206
207
208
209
210
211
class Reference(DataType):
    """ A datatype class that can be used to define reference types based on section definitions.

    A quantity can be used to define possible references between sections. Instantiate
    this class to create a reference type that specified that a quantity with this type
    is actually a reference (or references, depending on shape) to a section of the
    given definition.
    """
    def __init__(self, section: 'Section'):
        self.section = section


212
213
214
215
# TODO class Unit(DataType)
# TODO class Datetime(DataType)


216
class MObjectMeta(type):
217

218
219
    def __new__(self, cls_name, bases, dct):
        cls = super().__new__(self, cls_name, bases, dct)
Markus Scheidgen's avatar
Markus Scheidgen committed
220

Markus Scheidgen's avatar
Markus Scheidgen committed
221
222
        init = getattr(cls, '__init_cls__')
        if init is not None and not is_bootstrapping:
223
224
            init()
        return cls
225
226


Markus Scheidgen's avatar
Markus Scheidgen committed
227
Content = Tuple[MSectionBound, Union[List[MSectionBound], MSectionBound], str, MSectionBound]
228
229
230
231
232
233
234
235
236
237
238

SectionDef = Union[str, 'Section', 'SubSection', Type[MSectionBound]]
""" Type for section definition references.

This can either be :

- the name of the section
- the section definition itself
- the definition of a sub section
- or the section definition Python class
"""
239
240


Markus Scheidgen's avatar
Markus Scheidgen committed
241
242
class MSection(metaclass=MObjectMeta):
    """Base class for all section instances on all meta-info levels.
243

Markus Scheidgen's avatar
Markus Scheidgen committed
244
245
246
    All metainfo objects instantiate classes that inherit from ``MSection``. Each
    section or quantity definition is an ``MSection``, each actual (meta-)data carrying
    section is an ``MSection``. This class consitutes the reflection interface of the
247
248
249
250
251
252
253
254
255
256
257
258
259
    meta-info, since it allows to manipulate sections (and therefore all meta-info data)
    without having to know the specific sub-class.

    It also carries all the data for each section. All sub-classes only define specific
    sections in terms of possible sub-sections and quantities. The data is managed here.

    The reflection insterface for reading and manipulating quantity values consists of
    Pythons build in ``getattr``, ``setattr``, and ``del``, as well as member functions
    :func:`m_add_value`, and :func:`m_add_values`.

    Sub-sections and parent sections can be read and manipulated with :data:`m_parent`,
    :func:`m_sub_section`, :func:`m_create`.

260
261
262
263
264
    .. code-block:: python

        system = run.m_create(System)
        assert system.m_parent == run
        assert run.m_sub_section(System, system.m_parent_index) == system
265
266

    Attributes:
267
        m_def: The section definition that defines this sections, its possible
268
269
270
271
272
273
274
275
276
277
278
            sub-sections and quantities.
        m_parent: The parent section instance that this section is a sub-section of.
        m_parent_index: For repeatable sections, parent keep a list of sub-sections for
            each section definition. This is the index of this section in the respective
            parent sub-section list.
        m_data: The dictionary that holds all data of this section. It keeps the quantity
            values and sub-section. It should only be read directly (and never manipulated)
            if you are know what you are doing. You should always use the reflection interface
            if possible.
    """

279
    m_def: 'Section' = None
280

Markus Scheidgen's avatar
Markus Scheidgen committed
281
    def __init__(self, m_def: 'Section' = None, m_parent: 'MSection' = None, **kwargs):
282
        self.m_def: 'Section' = m_def
Markus Scheidgen's avatar
Markus Scheidgen committed
283
        self.m_parent: 'MSection' = m_parent
284
        self.m_parent_index = -1
285

286
        cls = self.__class__
287
288
        if self.m_def is None:
            self.m_def = cls.m_def
289

290
291
        if cls.m_def is not None:
            assert self.m_def == cls.m_def, \
292
293
                'Section class and section definition must match'

294
        self.m_annotations: Dict[str, Any] = {}
Markus Scheidgen's avatar
Markus Scheidgen committed
295
        rest = {}
296
297
298
299
        for key, value in kwargs.items():
            if key.startswith('a_'):
                self.m_annotations[key[2:]] = value
            else:
Markus Scheidgen's avatar
Markus Scheidgen committed
300
301
302
303
304
                rest[key] = value

        if is_bootstrapping:
            self.m_data: Dict[str, Any] = {}
            for key, value in rest.items():
305
306
                self.m_data[key] = value

Markus Scheidgen's avatar
Markus Scheidgen committed
307
308
        else:
            self.m_data = {}
309
310
311
312
            self.m_update(**rest)
            # self.m_data = {}
            # for key, value in rest.items():
            #     self.m_data[key] = value
313

314
    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
315
    def __init_cls__(cls):
316
317
        # ensure that the m_def is defined
        m_def = cls.m_def
Markus Scheidgen's avatar
Markus Scheidgen committed
318
        if m_def is None:
319
320
            m_def = Section()
            setattr(cls, 'm_def', m_def)
321

322
323
        # transfer name and description to m_def
        m_def.name = cls.__name__
324
        if cls.__doc__ is not None:
325
            m_def.description = inspect.cleandoc(cls.__doc__).strip()
326
        m_def.section_cls = cls
327

328
        for name, attr in cls.__dict__.items():
329
330
            # transfer names and descriptions for properties
            if isinstance(attr, Property):
331
                attr.name = name
332
                if attr.description is not None:
333
                    attr.description = inspect.cleandoc(attr.description).strip()
334
                    attr.__doc__ = attr.description
335

Markus Scheidgen's avatar
Markus Scheidgen committed
336
                # manual manipulation of m_data due to bootstrapping
337
338
339
340
341
342
343
344
345
                if isinstance(attr, Quantity):
                    properties = m_def.m_data.setdefault('quantities', [])
                elif isinstance(attr, SubSection):
                    properties = m_def.m_data.setdefault('sub_sections', [])
                else:
                    raise NotImplementedError('Unknown property kind.')
                properties.append(attr)
                attr.m_parent = m_def
                attr.m_parent_index = len(properties) - 1
346

Markus Scheidgen's avatar
Markus Scheidgen committed
347
348
349
350
351
352
353
354
355
356
357
358
        # add base sections
        for base_cls in cls.__bases__:
            if base_cls != MSection:
                section = getattr(base_cls, 'm_def')
                if section is None:
                    raise TypeError(
                        'Section defining classes must have MSection or a decendant as '
                        'base classes.')

                # manual manipulation of m_data due to bootstrapping
                m_def.m_data.setdefault('base_sections', []).append(section)

359
360
361
        # add section cls' section to the module's package
        module_name = cls.__module__
        pkg = Package.from_module(module_name)
362
        pkg.m_add_sub_section(cls.m_def)
363

Markus Scheidgen's avatar
Markus Scheidgen committed
364
365
    def m_type_check(self, definition: 'Quantity', value: Any, check_item: bool = False):
        """ Checks and normalized the given value according to the quantity type. """
366
367
368

        if value is None and not check_item and definition.default is None:
            # Allow the default None value even if it would violate the type
369
            return value
370
371
372
373

        def check_value(value):
            if isinstance(definition.type, Enum):
                if value not in definition.type:
374
                    raise TypeError('Not one of the enum values.')
375
376
377

            elif isinstance(definition.type, type):
                if not isinstance(value, definition.type):
378
379
380
                    raise TypeError(
                        'Value %s is not of type %s, required by quantity %s.' %
                        (value, definition.type, definition))
381
382

            elif isinstance(definition.type, Section):
383
384
385
386
                if not isinstance(value, MSection) or not value.m_follows(definition.type):
                    raise TypeError(
                        'The section %s is not of section definition %s, required by quantity %s.' %
                        (value, definition.type, definition))
387

Markus Scheidgen's avatar
Markus Scheidgen committed
388
389
390
            elif isinstance(definition.type, DataType):
                value = definition.type.type_check(self, value)

391
            else:
392
393
394
                # TODO
                # raise Exception('Invalid quantity type: %s' % str(definition.type))
                pass
395

Markus Scheidgen's avatar
Markus Scheidgen committed
396
397
            return value

398
399
400
401
402
403
404
        shape = None
        try:
            shape = definition.shape
        except KeyError:
            pass

        if shape is None or len(shape) == 0 or check_item:
Markus Scheidgen's avatar
Markus Scheidgen committed
405
            value = check_value(value)
406

407
408
409
410
411
412
413
414
        else:
            if type(definition.type) == np.dtype:
                if len(shape) != len(value.shape):
                    raise TypeError('Wrong shape')
            else:
                if len(shape) == 1:
                    if not isinstance(value, list):
                        raise TypeError('Wrong shape')
415

Markus Scheidgen's avatar
Markus Scheidgen committed
416
                    value = [check_value(item) for item in value]
417

418
                else:
Markus Scheidgen's avatar
Markus Scheidgen committed
419
                    raise NotImplementedError('Checking types is not available for complex shapes.')
420
421
422

        # TODO check dimension

Markus Scheidgen's avatar
Markus Scheidgen committed
423
424
        return value

425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
    def _resolve_sub_section(self, definition: SectionDef) -> 'SubSection':
        """ Resolves and checks the given section definition. """

        if isinstance(definition, type):
            definition = getattr(definition, 'm_def', None)
            if definition is None:
                raise TypeError(
                    'The type/class %s is not definining a section, i.e. not derived from '
                    'MSection.' % str(definition))

        if isinstance(definition, Section):
            sub_section = self.m_def.all_sub_sections_by_section.get(definition, None)
            if sub_section is None:
                raise KeyError(
                    'The section %s is not a sub section of %s.' %
                    (definition.name, self.m_def.name))

        elif isinstance(definition, str):
            sub_section = self.m_def.all_sub_sections[definition]

        elif isinstance(definition, SubSection):
            sub_section = definition
447
448

        else:
449
450
451
452
            raise TypeError(
                '%s does not refer to a section definition. Either use the section '
                'definition, sub section definition, section class, or name.' %
                str(definition))
453

454
455
456
457
458
459
460
461
462
463
464
        if sub_section is None:
            raise KeyError(
                'The section %s is not a sub section of %s.' %
                (cast(Definition, definition).name, self.m_def.name))

        if sub_section.m_parent is not self.m_def:
            raise KeyError(
                'The section %s is not a sub section of %s.' %
                (cast(Definition, definition).name, self.m_def.name))

        return sub_section
465

Markus Scheidgen's avatar
Markus Scheidgen committed
466
    def m_sub_sections(self, definition: SectionDef) -> List[MSectionBound]:
467
468
469
470
471
472
473
474
        """Returns all sub sections for the given section definition

        Args:
            definition: The definition of the section.

        Raises:
            KeyError: If the definition is not for a sub section
        """
475
476
        sub_section = self._resolve_sub_section(definition)
        return getattr(self, sub_section.name)
477

Markus Scheidgen's avatar
Markus Scheidgen committed
478
    def m_sub_section(self, definition: SectionDef, parent_index: int = -1) -> MSectionBound:
479
480
481
482
483
484
485
486
487
488
489
490
491
492
        """Returns the sub section for the given section definition and possible
           parent_index (for repeatable sections).

        Args:
            definition: The definition of the section.
            parent_index: The index of the desired section. This can be omitted for non
                repeatable sections. If omitted for repeatable sections a exception
                will be raised, if more then one sub-section exists. Likewise, if the given
                index is out of range.
        Raises:
            KeyError: If the definition is not for a sub section
            IndexError: If the given index is wrong, or if an index is given for a non
                repeatable section
        """
493
        sub_section = self._resolve_sub_section(definition)
494

495
        m_data_value = getattr(self, sub_section.name)
496
497

        if m_data_value is None:
498
            if sub_section.repeats:
499
500
501
                m_data_value = []
            else:
                m_data_value = None
502
503
504
505
506
507
508
509
510
511
512
513
514

        if isinstance(m_data_value, list):
            m_data_values = m_data_value
            if parent_index == -1:
                if len(m_data_values) == 1:
                    return m_data_values[0]
                else:
                    raise IndexError()
            else:
                return m_data_values[parent_index]
        else:
            if parent_index != -1:
                raise IndexError('Not a repeatable sub section.')
515
516

            return m_data_value
517

Markus Scheidgen's avatar
Markus Scheidgen committed
518
    def m_add_sub_section(self, sub_section: MSectionBound) -> MSectionBound:
519
520
        """Adds the given section instance as a sub section to this section."""

521
522
523
524
525
526
        sub_section_def = self._resolve_sub_section(sub_section.m_def.section_cls)
        sub_section.m_parent = self
        if sub_section_def.repeats:
            values = getattr(self, sub_section_def.name)
            sub_section.m_parent_index = len(values)
            values.append(sub_section)
527
528

        else:
529
530
            self.m_data[sub_section_def.name] = sub_section
            sub_section.m_parent_index = -1
531
532
533

        return sub_section

534
    def m_create(self, definition: Type[MSectionBound], **kwargs) -> MSectionBound:
535
        """Creates a subsection and adds it this this section
536

537
538
539
540
        Args:
            section: The section definition of the subsection. It is either the
                definition itself, or the python class representing the section definition.
            **kwargs: Are used to initialize the subsection.
541

542
543
        Returns:
            The created subsection
544

545
        Raises:
546
            KeyError: If the given section is not a subsection of this section.
547
        """
548
        sub_section: 'SubSection' = self._resolve_sub_section(definition)
549

550
551
        section_cls = sub_section.sub_section.section_cls
        section_instance = section_cls(m_def=section_cls.m_def, m_parent=self, **kwargs)
552

553
        return cast(MSectionBound, self.m_add_sub_section(section_instance))
554

555
556
557
    def __resolve_quantity(self, definition: Union[str, 'Quantity']) -> 'Quantity':
        """Resolves and checks the given quantity definition. """
        if isinstance(definition, str):
558
            quantity = self.m_def.all_quantities[definition]
559

560
        else:
561
            if definition.m_parent != self.m_def:
562
563
564
565
566
567
568
                raise KeyError('Quantity is not a quantity of this section.')
            quantity = definition

        return quantity

    def m_add(self, definition: Union[str, 'Quantity'], value: Any):
        """Adds the given value to the given quantity."""
569

570
571
        quantity = self.__resolve_quantity(definition)

Markus Scheidgen's avatar
Markus Scheidgen committed
572
        value = self.m_type_check(quantity, value, check_item=True)
573
574
575
576
577
578
579
580
581

        m_data_values = self.m_data.setdefault(quantity.name, [])
        m_data_values.append(value)

    def m_add_values(self, definition: Union[str, 'Quantity'], values: Iterable[Any]):
        """Adds the given values to the given quantity."""

        quantity = self.__resolve_quantity(definition)

Markus Scheidgen's avatar
Markus Scheidgen committed
582
        values = [self.m_type_check(quantity, value, check_item=True) for value in values]
583
584
585
586
587

        m_data_values = self.m_data.setdefault(quantity.name, [])
        for value in values:
            m_data_values.append(value)

588
589
590
    def m_update(self, **kwargs):
        """ Updates all quantities and sub-sections with the given arguments. """
        for name, value in kwargs.items():
591
592
            prop = self.m_def.all_properties.get(name, None)
            if prop is None:
593
                raise KeyError('%s is not an attribute of this section %s' % (name, self))
594

595
596
            if isinstance(prop, SubSection):
                if prop.repeats:
597
598
599
600
                    if isinstance(value, List):
                        for item in value:
                            self.m_add_sub_section(item)
                    else:
601
                        raise TypeError('Sub section %s repeats, but no list was given' % prop.name)
602
603
604
605
606
607
                else:
                    self.m_add_sub_section(item)

            else:
                setattr(self, name, value)

608
609
610
    def m_follows(self, definition: 'Section') -> bool:
        return self.m_def == definition or self.m_def in definition.all_base_sections

611
612
    def m_to_dict(self) -> Dict[str, Any]:
        """Returns the data of this section as a json serializeable dictionary. """
613
614

        def items() -> Iterable[Tuple[str, Any]]:
615
            yield 'm_def', self.m_def.name
616
            if self.m_parent_index != -1:
617
                yield 'm_parent_index', self.m_parent_index
618

619
            for name, sub_section in self.m_def.all_sub_sections.items():
620
621
622
623
624
625
626
627
                if name not in self.m_data:
                    continue

                if sub_section.repeats:
                    yield name, [item.m_to_dict() for item in self.m_data[name]]
                else:
                    yield name, self.m_data[name].m_to_dict()

628
            for name, quantity in self.m_def.all_quantities.items():
629
630
631
632
                if name in self.m_data:
                    value = getattr(self, name)
                    if hasattr(value, 'tolist'):
                        value = value.tolist()
633
634
635
636
637
638
639
640
641
642
643
644
645
646

                    # TODO
                    if isinstance(quantity.type, Section):
                        value = str(value)
                    # TODO
                    if isinstance(value, type):
                        value = str(value)
                    # TODO
                    if isinstance(value, np.dtype):
                        value = str(value)
                    # TODO
                    if isinstance(value, _Unit):
                        value = str(value)

647
648
649
                    yield name, value

        return {key: value for key, value in items()}
650

651
    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
652
    def m_from_dict(cls: Type[MSectionBound], dct: Dict[str, Any]) -> MSectionBound:
653
        section_def = cls.m_def
654

655
656
        # remove m_def and m_parent_index, they set themselves automatically
        assert section_def.name == dct.pop('m_def', None)
657
658
659
        dct.pop('m_parent_index', -1)

        def items():
660
            for name, sub_section_def in section_def.all_sub_sections.items():
661
662
663
664
                if name in dct:
                    sub_section_value = dct.pop(name)
                    if sub_section_def.repeats:
                        yield name, [
665
                            sub_section_def.sub_section.section_cls.m_from_dict(sub_section_dct)
666
667
                            for sub_section_dct in sub_section_value]
                    else:
668
                        yield name, sub_section_def.sub_section.section_cls.m_from_dict(sub_section_value)
669
670
671
672
673

            for key, value in dct.items():
                yield key, value

        dct = {key: value for key, value in items()}
Markus Scheidgen's avatar
Markus Scheidgen committed
674
        section_instance = cast(MSectionBound, section_def.section_cls())
675
676
677
        section_instance.m_update(**dct)
        return section_instance

678
    def m_to_json(self, **kwargs):
679
        """Returns the data of this section as a json string. """
680
        return json.dumps(self.m_to_dict(), **kwargs)
681

682
    def m_all_contents(self) -> Iterable[Content]:
683
        """Returns an iterable over all sub and sub subs sections. """
684
685
686
        for content in self.m_contents():
            for sub_content in content[0].m_all_contents():
                yield sub_content
687

688
            yield content
689

690
    def m_contents(self) -> Iterable[Content]:
691
        """Returns an iterable over all direct subs sections. """
692
693
694
        for name, attr in self.m_data.items():
            if isinstance(attr, list):
                for value in attr:
Markus Scheidgen's avatar
Markus Scheidgen committed
695
                    if isinstance(value, MSection):
696
                        yield value, attr, name, self
697

Markus Scheidgen's avatar
Markus Scheidgen committed
698
            elif isinstance(attr, MSection):
699
                yield value, value, name, self
700

701
    def __repr__(self):
702
        m_section_name = self.m_def.name
703
704
705
706
707
        name = ''
        if 'name' in self.m_data:
            name = self.m_data['name']

        return '%s:%s' % (name, m_section_name)
708
709


Markus Scheidgen's avatar
Markus Scheidgen committed
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
class MCategory(metaclass=MObjectMeta):

    m_def: 'Category' = None

    @classmethod
    def __init_cls__(cls):
        # ensure that the m_def is defined
        m_def = cls.m_def
        if m_def is None:
            m_def = Category()
            setattr(cls, 'm_def', m_def)

        # transfer name and description to m_def
        m_def.name = cls.__name__
        if cls.__doc__ is not None:
725
            m_def.description = inspect.cleandoc(cls.__doc__).strip()
Markus Scheidgen's avatar
Markus Scheidgen committed
726
727
728
729
730
731
732

        # add section cls' section to the module's package
        module_name = cls.__module__
        pkg = Package.from_module(module_name)
        pkg.m_add_sub_section(cls.m_def)


733
734
735
736
737
738
739
# M3, the definitions that are used to write definitions. These are the section definitions
# for sections Section and Quantity.They define themselves; i.e. the section definition
# for Section is the same section definition.
# Due to this circular nature (hen-egg-problem), the classes for sections Section and
# Quantity do only contain placeholder for their own section and quantity definitions.
# These placeholder are replaced, once the necessary classes are defined. This process
# is referred to as 'bootstrapping'.
740

741
742
743
_definition_change_counter = 0


744
745
class cached_property:
    """ A property that allows to cache the property value.
746
747
748
749
750

    The cache will be invalidated whenever a new definition is added. Once all definitions
    are loaded, the cache becomes stable and complex derived results become available
    instantaneous.
    """
751
752
753
754
755
    def __init__(self, f):
        self.__doc__ = getattr(f, "__doc__")
        self.f = f
        self.change = -1
        self.values: Dict[type(self), Any] = {}
756

757
758
759
760
761
762
763
    def __get__(self, obj, cls):
        if obj is None:
            return self

        global _definition_change_counter
        if self.change != _definition_change_counter:
            self.values = {}
764

765
766
767
768
        value = self.values.get(obj, None)
        if value is None:
            value = self.f(obj)
            self.values[obj] = value
769
770
771
772

        return value


Markus Scheidgen's avatar
Markus Scheidgen committed
773
class Definition(MSection):
774

Markus Scheidgen's avatar
Markus Scheidgen committed
775
    __all_definitions: Dict[Type[MSection], List[MSection]] = {}
776

777
778
779
    name: 'Quantity' = None
    description: 'Quantity' = None
    links: 'Quantity' = None
780
    categories: 'Quantity' = None
781

782
783
784
785
786
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        global _definition_change_counter
        _definition_change_counter += 1

787
788
789
790
791
        for cls in self.__class__.mro() + [self.__class__]:
            definitions = Definition.__all_definitions.setdefault(cls, [])
            definitions.append(self)

    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
792
    def all_definitions(cls: Type[MSectionBound]) -> Iterable[MSectionBound]:
793
        """ Returns all definitions of this definition class. """
Markus Scheidgen's avatar
Markus Scheidgen committed
794
        return cast(Iterable[MSectionBound], Definition.__all_definitions.get(cls, []))
795

796
797
798
799
    @cached_property
    def all_categories(self):
        """ All categories of this definition and its categories. """
        all_categories = list(self.categories)
Markus Scheidgen's avatar
Markus Scheidgen committed
800
        for category in self.categories:  # pylint: disable=not-an-iterable
801
802
803
804
805
            for super_category in category.all_categories:
                all_categories.append(super_category)

        return all_categories

806

807
808
809
810
811
class Property(Definition):
    pass


class Quantity(Property):
812
813
814
815
816
817
818
819
820
821
822
    """Used to define quantities that store a certain piece of (meta-)data.

    Quantities are the basic building block with meta-info data. The Quantity class is
    used to define quantities within sections. A quantity definition
    is a (physics) quantity with name, type, shape, and potentially a unit.

    In Python terms, quantities are descriptors. Descriptors define how to get, set, and
    delete values for a object attribute. Meta-info descriptors ensure that
    type and shape fit the set values.
    """

823
824
    type: 'Quantity' = None
    shape: 'Quantity' = None
825
826
    unit: 'Quantity' = None
    default: 'Quantity' = None
Markus Scheidgen's avatar
Markus Scheidgen committed
827
    synonym_for: 'Quantity' = None
828
829
830
831
832

    # 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.
833
834
835
836
837

    # Some quantities of Quantity cannot be read as normal quantities due to bootstraping.
    # Those can be accessed internally through the following replacement properties that
    # read directly from m_data.
    __name = property(lambda self: self.m_data['name'])
Markus Scheidgen's avatar
Markus Scheidgen committed
838
    __synonym_for = property(lambda self: self.m_data.get('synonym_for', None))
839
    __default = property(lambda self: self.m_data.get('default', None))
840

841
    def __get__(self, obj, cls):
842
843
844
845
846
        if obj is None:
            # class (def) attribute case
            return self

        # object (instance) attribute case
Markus Scheidgen's avatar
Markus Scheidgen committed
847
        if self.__synonym_for is not None:
848
            return getattr(obj, self.__synonym_for)
Markus Scheidgen's avatar
Markus Scheidgen committed
849

850
851
852
853
        try:
            return obj.m_data[self.__name]
        except KeyError:
            return self.__default
854

855
    def __set__(self, obj, value):
856
857
858
859
860
        if obj is None:
            # class (def) case
            raise KeyError('Cannot overwrite quantity definition. Only values can be set.')

        # object (instance) case
Markus Scheidgen's avatar
Markus Scheidgen committed
861
        if self.__synonym_for is not None:
862
            return setattr(obj, self.__synonym_for, value)
Markus Scheidgen's avatar
Markus Scheidgen committed
863

864
865
866
867
868
869
870
871
872
        if type(self.type) == np.dtype:
            if type(value) != np.ndarray:
                value = np.array(value, dtype=self.type)
            elif self.type != value.dtype:
                value = np.array(value, dtype=self.type)

        elif type(value) == np.ndarray:
            value = value.tolist()

Markus Scheidgen's avatar
Markus Scheidgen committed
873
        value = obj.m_type_check(self, value)
874

875
        obj.m_data[self.__name] = value
876

877
    def __delete__(self, obj):
878
879
880
881
882
        if obj is None:
            # class (def) case
            raise KeyError('Cannot delete quantity definition. Only values can be deleted.')

        # object (instance) case
Markus Scheidgen's avatar
Markus Scheidgen committed
883
884
885
        if self.__synonym_for is not None:
            return self.__synonym_for.__delete__(obj)

886
        del obj.m_data[self.__name]
887
888


889
890
891
892
893
894
class SubSection(Property):
    """ Allows to assign a section class as a sub-section to another section class. """

    sub_section: 'Quantity' = None
    repeats: 'Quantity' = None

895
    def __get__(self, obj, type=None):
896
897
898
899
900
901
902
903
904
905
906
907
908
909
        if obj is None:
            # the class attribute case
            return self

        else:
            # the object attribute case
            m_data_value = obj.m_data.get(self.name, None)
            if m_data_value is None:
                if self.repeats:
                    m_data_value = []
                    obj.m_data[self.name] = m_data_value

            return m_data_value

910
    def __set__(self, obj, value):
911
912
913
914
915
916
        raise NotImplementedError('Sub sections cannot be set directly. Use m_create.')

    def __delete__(self, obj):
        raise NotImplementedError('Sub sections cannot be deleted directly.')


917
class Section(Definition):
918
919
920
    """Used to define section that organize meta-info data into containment hierarchies.

    Section definitions determine what quantities and sub-sections can appear in a section
921
    instance.
922

923
    In Python terms, sections are classes. Sub-sections and quantities are attributes of
924
925
926
927
928
929
    respective instantiating objects. For each section class there is a corresponding
    :class:`Section` instance that describes this class as a section. This instance
    is referred to as 'section definition' in contrast to the Python class that we call
    'section class'.
    """

Markus Scheidgen's avatar
Markus Scheidgen committed
930
    section_cls: Type[MSection] = None
931
932
    """ The section class that corresponse to this section definition. """

933
934
    quantities: 'SubSection' = None
    sub_sections: 'SubSection' = None
935

Markus Scheidgen's avatar
Markus Scheidgen committed
936
    base_sections: 'Quantity' = None
937
938
    # TODO extends = Quantity(type=bool), denotes this section as a container for
    #      new quantities that belong to the base-class section definitions
939
940
941
942
943
944
945
946
947
    @cached_property
    def all_base_sections(self) -> Set['Section']:
        all_base_sections: Set['Section'] = set()
        for base_section in self.base_sections:  # pylint: disable=not-an-iterable
            for base_base_section in base_section.all_base_sections:
                all_base_sections.add(base_base_section)

            all_base_sections.add(base_section)
        return all_base_sections
948

949
    @cached_property
950
    def all_properties(self) -> Dict[str, Union['SubSection', Quantity]]:
951
        """ All attribute (sub section and quantity) definitions. """
952

953
954
955
        properties: Dict[str, Union[SubSection, Quantity]] = dict(**self.all_quantities)
        properties.update(**self.all_sub_sections)
        return properties
956

957
    @cached_property
958
    def all_quantities(self) -> Dict[str, Quantity]:
959
        """ All quantity definition in the given section definition. """
960

Markus Scheidgen's avatar
Markus Scheidgen committed
961
        all_quantities: Dict[str, Quantity] = {}
962
        for section in itertools.chain(self.all_base_sections, [self]):
Markus Scheidgen's avatar
Markus Scheidgen committed
963
964
965
966
            for quantity in section.m_data.get('quantities', []):
                all_quantities[quantity.name] = quantity

        return all_quantities
967

968
    @cached_property
969
970
    def all_sub_sections(self) -> Dict[str, 'SubSection']:
        """ All sub section definitions for this section definition by name. """
971

972
973
        return {
            sub_section.name: sub_section
974
            for sub_section in self.m_data.get('sub_sections', [])}
975

976
977
978
979
980
981
    @cached_property
    def all_sub_sections_by_section(self) -> Dict['Section', 'SubSection']:
        """ All sub section definitions for this section definition by their section definition. """
        return {
            sub_section.sub_section: sub_section
            for sub_section in self.m_data.get('sub_sections', [])}
982

983

984
class Package(Definition):
985

986
987
988
    section_definitions: 'SubSection'
    category_definitions: 'SubSection'

989
990
991
992
993
994
995
996
997
998
999
    @staticmethod
    def from_module(module_name: str):
        module = sys.modules[module_name]

        pkg: 'Package' = getattr(module, 'm_package', None)
        if pkg is None:
            pkg = Package()
            setattr(module, 'm_package', pkg)

        pkg.name = module_name
        if pkg.description is None and module.__doc__ is not None:
1000
            pkg.description = inspect.cleandoc(module.__doc__).strip()
1001
1002

        return pkg
1003
1004


1005
1006
1007
1008
1009
class Category(Definition):
    """Can be used to define categories for definitions.

    Each definition, including categories themselves, can belong to a set of categories.
    Categories therefore form a hierarchy of concepts that definitions can belong to, i.e.
1010
    they form a `is a` relationship.
1011

1012
1013
    In the old meta-info this was known as `abstract types`.
    """
1014
1015
1016
1017
1018
1019

    @cached_property
    def definitions(self) -> Iterable[Definition]:
        """ All definitions that are directly or indirectly in this category. """
        return list([
            definition for definition in Definition.all_definitions()
1020
            if self in definition.all_categories])
1021
1022


Markus Scheidgen's avatar
Markus Scheidgen committed
1023
Section.m_def = Section(name='Section')
1024
1025
Section.m_def.m_def = Section.m_def
Section.m_def.section_cls = Section
1026

Markus Scheidgen's avatar
Markus Scheidgen committed
1027
1028
1029
1030
Definition.m_def = Section(name='Definition')
Property.m_def = Section(name='Property')
Quantity.m_def = Section(name='Quantity')
SubSection.m_def = Section(name='SubSection')
1031
1032
Category.m_def = Section(name='Category')
Package.m_def = Section(name='Package')
1033
1034

Definition.name = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1035
    type=str, name='name', description='''
1036
1037
1038
    The name of the quantity. Must be unique within a section.
    ''')
Definition.description = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1039
    type=str, name='description', description='''
1040
1041
1042
    An optional human readable description.
    ''')
Definition.links = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1043
    type=str, shape=['0..*'], name='links', description='''
1044
1045
    A list of URLs to external resource that describe this definition.
    ''')
1046
Definition.categories = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1047
    type=Category.m_def, shape=['0..*'], default=[], name='categories',
1048
1049
1050
    description='''
    The categories that this definition belongs to. See :class:`Category`.
    ''')
1051

1052
1053
1054
1055
1056
1057
1058
Section.quantities = SubSection(
    sub_section=Quantity.m_def, repeats=True,
    description='''The quantities of this section.''')

Section.sub_sections = SubSection(
    sub_section=SubSection.m_def, repeats=True,
    description='''The sub sections of this section.''')
Markus Scheidgen's avatar
Markus Scheidgen committed
1059
1060
1061
1062
1063
1064
1065
Section.base_sections = Quantity(
    type=Section, shape=['0..*'], default=[], name='base_sections',
    description='''
    Inherit all quantity and sub section definitions from the given sections.
    Will be derived from Python base classes.
    ''')

1066
1067

SubSection.repeats = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1068
    type=bool, name='repeats', default=False,
1069
1070
1071
    description='''Wether this sub section can appear only once or multiple times. ''')

SubSection.sub_section = Quantity(
Markus Scheidgen's avatar
Markus Scheidgen committed
1072
    type=Section.m_def, name='sub_section', description='''