metainfo.py 70 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
from typing import Type, TypeVar, Union, Tuple, Iterable, List, Any, Dict, Set, \
    Callable as TypingCallable, cast
17
from collections.abc import Iterable as IterableABC
18
import sys
19
import inspect
20
import re
21
import json
22
import itertools
23
import numpy as np
24
25
26
import pint
import pint.unit
import pint.quantity
27
28
29
import aniso8601
from datetime import datetime
import pytz
30
import docstring_parser
31

32
33
34

m_package: 'Package' = None

Markus Scheidgen's avatar
Markus Scheidgen committed
35
36
is_bootstrapping = True
MSectionBound = TypeVar('MSectionBound', bound='MSection')
37
T = TypeVar('T')
38

39

Markus Scheidgen's avatar
Markus Scheidgen committed
40
41
# Metainfo errors

42
class MetainfoError(Exception):
43
    """ Metainfo related errors. """
44
45
46
    pass


47
48
49
50
51
class DeriveError(MetainfoError):
    """ An error occurred while computing a derived value. """
    pass


52
53
class MetainfoReferenceError(MetainfoError):
    """ An error indicating that a reference could not be resolved. """
54
    pass
55
56


Markus Scheidgen's avatar
Markus Scheidgen committed
57
# Metainfo quantity data types
58

59
class Enum(list):
60
    """ Allows to define str types with values limited to a pre-set list of possible values. """
61
62
63
64
65
66
    def __init__(self, *args):
        if len(args) == 1 and isinstance(args[0], list):
            super().__init__(args[0])

        else:
            super().__init__(args)
67
68


69
class MProxy():
70
71
72
73
74
    """ A placeholder object that acts as reference to a value that is not yet resolved.

    Attributes:
        url: The reference represented as an URL string.
    """
75
76
77
78
79

    def __init__(self, url: str):
        self.url = url


80
81
82
83
class DataType:
    """
    Allows to define custom data types that can be used in the meta-info.

84
    The metainfo supports the most types out of the box. These includes the python build-in
85
86
    primitive types (int, bool, str, float, ...), references to sections, and enums.
    However, in some occasions you need to add custom data types.
87
88
89
90
91

    This base class lets you customize various aspects of value treatment. This includes
    type checks and various value transformations. This allows to store values in the
    section differently from how the usermight set/get them, and it allows to have non
    serializeable values that are transformed on de-/serialization.
92
    """
93
94
95
96
97
98
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        """ Transforms the given value before it is set and checks its type. """
        return value

    def get_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        """ Transforms the given value when it is get. """
99
100
        return value

101
102
    def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        """ Transforms the given value when making the section serializeable. """
103
104
        return value

105
106
    def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        """ Transforms the given value from its serializeable form. """
107
108
109
        return value


110
111
112
113
114
range_re = re.compile(r'(\d)\.\.(\d|\*)')


class _Dimension(DataType):

115
    def set_normalize(self, section, quantity_def: 'Quantity', value):
116
        if isinstance(value, int):
Markus Scheidgen's avatar
Markus Scheidgen committed
117
            return value
118
119
120

        if isinstance(value, str):
            if value.isidentifier():
Markus Scheidgen's avatar
Markus Scheidgen committed
121
                return value
122
            if re.match(range_re, value):
Markus Scheidgen's avatar
Markus Scheidgen committed
123
                return value
124
125

        if isinstance(value, Section):
Markus Scheidgen's avatar
Markus Scheidgen committed
126
            return value
127

128
        if isinstance(value, type) and hasattr(value, 'm_def'):
Markus Scheidgen's avatar
Markus Scheidgen committed
129
            return value
130
131
132

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

133
134
135
136
137
138
139
    @staticmethod
    def check_dimension(section, dimension, length):
        if isinstance(dimension, int):
            return dimension == length
        if isinstance(dimension, str):
            if dimension.isidentifier():
                return dimension == getattr(section, dimension)
140

141
142
143
144
145
146
147
            m = re.match(range_re, dimension)
            start = int(m.group(1))
            end = -1 if m.group(2) == '*' else int(m.group(2))
            return start <= length and (end == -1 or length <= end)


class _Unit(DataType):
148
    def set_normalize(self, section, quantity_def: 'Quantity', value):
149
150
151
        if isinstance(value, str):
            value = units.parse_units(value)

152
        elif not isinstance(value, pint.unit._Unit):
153
154
155
156
            raise TypeError('Units must be given as str or pint Unit instances.')

        return value

157
    def serialize(self, section, quantity_def: 'Quantity', value):
158
159
        return value.__str__()

160
    def deserialize(self, section, quantity_def: 'Quantity', value):
161
162
        return units.parse_units(value)

163

164
units = pint.UnitRegistry()
Markus Scheidgen's avatar
Markus Scheidgen committed
165
166
167
""" The default pint unit registry that should be used to give units to quantity definitions. """


168
class _Callable(DataType):
169
170
171
172
173
174
175
    def serialize(self, section, quantity_def: 'Quantity', value):
        raise MetainfoError('Callables cannot be serialized')

    def deserialize(self, section, quantity_def: 'Quantity', value):
        raise MetainfoError('Callables cannot be serialized')


176
class _QuantityType(DataType):
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
    """ Data type for defining the type of a metainfo quantity.

    A metainfo quantity type can be one of

    - python build-in primitives: int, float, bool, str
    - numpy dtypes, e.g. f, int32
    - a section definition to define references
    - an Enum instance to use it's values as possible str values
    - a custom datatype, i.e. instance of :class:`DataType`
    - Any
    """

    def set_normalize(self, section, quantity_def, value):
        if value in [str, int, float, bool]:
            return value

        if isinstance(value, Enum):
            for enum_value in value:
                if not isinstance(enum_value, str):
                    raise TypeError('Enum value %s is not a string.' % enum_value)
            return value

        if type(value) == np.dtype:
            return value

        if isinstance(value, Section):
            return value

        if isinstance(value, DataType):
            return value

        if value == Any:
            return value

        if isinstance(value, type):
            section = getattr(value, 'm_def', None)
            if section is not None:
                return Reference(section)

        raise MetainfoError(
            'Type %s of %s is not a valid metainfo quantity type' %
            (value, quantity_def))

    def serialize(self, section, quantity_def, value):
        if value in [str, int, float, bool]:
            return dict(type_kind='python', type_data=value.__name__)

        if isinstance(value, Enum):
            return dict(type_kind='Enum', type_data=list(value))

        if type(value) == np.dtype:
            return dict(type_kind='numpy', type_data=str(value))

        if isinstance(value, Reference):
            return dict(type_kind='reference', type_data=value.target_section_def.m_path())

        if isinstance(value, DataType):
            module = value.__class__.__module__
            if module is None or module == str.__class__.__module__:
                type_data = value.__class__.__name__
            else:
                type_data = '%s.%s' % (module, value.__class__.__name__)

            return dict(type_kind='custom', type_data=type_data)

        if value == Any:
            return dict(type_kind='Any')

        raise MetainfoError(
            'Type %s of %s is not a valid metainfo quantity type' %
            (value, quantity_def))


class Reference(DataType):
    """ Datatype used for reference quantities. """

    def __init__(self, section_def: 'Section'):
        if not isinstance(section_def, Section):
            raise MetainfoError('%s is not a section definition.' % section_def)
        self.target_section_def = section_def

    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        if self.target_section_def.m_follows(Definition.m_def):
            # special case used in metainfo definitions, where we reference metainfo definitions
            # using their Python class. E.g. referencing a section definition using its
            # class instead of the object: Run vs. Run.m_def
            if isinstance(value, type):
                definition = getattr(value, 'm_def', None)
                if definition is not None and definition.m_follows(self.target_section_def):
                    return definition

        if isinstance(value, MProxy):
            return value

        if not isinstance(value, MSection):
            raise TypeError(
                'The value %s is not a section and can not be used as a reference.' % value)

        if not value.m_follows(self.target_section_def):
            raise TypeError(
                '%s is not a %s and therefore an invalid value of %s.' %
                (value, self.target_section_def, quantity_def))

        return value

    def get_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        if isinstance(value, MProxy):
            resolved: 'MSection' = section.m_resolve(value.url)
            if resolved is None:
                raise ReferenceError('Could not resolve %s from %s.' % (value, section))
            section.m_set(quantity_def, value)
            return resolved

        return value

    def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        return value.m_path()

    def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        return MProxy(value)


299
class _Datetime(DataType):
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327

    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)


328
329
330
331
332
Dimension = _Dimension()
Unit = _Unit()
QuantityType = _QuantityType()
Callable = _Callable()
Datetime = _Datetime()
333
334


Markus Scheidgen's avatar
Markus Scheidgen committed
335
336
# Metainfo data storage and reflection interface

337
class MObjectMeta(type):
338

339
340
    def __new__(self, cls_name, bases, dct):
        cls = super().__new__(self, cls_name, bases, dct)
Markus Scheidgen's avatar
Markus Scheidgen committed
341

Markus Scheidgen's avatar
Markus Scheidgen committed
342
343
        init = getattr(cls, '__init_cls__')
        if init is not None and not is_bootstrapping:
344
345
            init()
        return cls
346
347


348
Content = Tuple['MSection', int, 'SubSection', 'MSection']
349
350
351
352
353
354
355
356
357
358
359

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
"""
360
361


362
363
364
365
366
class MData:
    """ An interface for low-level metainfo data objects.

    Metainfo data objects store the data of a single section instance. This interface
    constitutes the minimal functionality for accessing and modifying section data.
367
    Different implementations of this interface, can realize different storage backends.
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420

    All section instances will implement this interface, usually be delegating calls to
    a standalone implementation of this interface. This allows to configure various
    data backends on section instance creation.
    """

    def __getitem__(self, key):
        raise NotImplementedError()

    def __setitem__(self, key, value):
        raise NotImplementedError()

    def m_set(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> None:
        """ Set the given value for the given quantity. """
        raise NotImplementedError()

    def m_get(self, section: 'MSection', quantity_def: 'Quantity') -> Any:
        """ Retrieve the given value for the given quantity. """
        raise NotImplementedError()

    def m_is_set(self, section: 'MSection', quantity_def: 'Quantity') -> bool:
        """ True iff this quantity was explicitely set. """
        raise NotImplementedError()

    def m_add_values(
            self, section: 'MSection', quantity_def: 'Quantity', values: Any,
            offset: int) -> None:
        """ Add (partial) values for the given quantity of higher dimensionality. """
        raise NotImplementedError()

    def m_add_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            sub_section: 'MSection') -> None:
        """ Adds the given section instance as a sub section of the given sub section definition. """
        raise NotImplementedError()

    def m_get_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            index: int) -> 'MSection':
        """ Retrieves a single sub section of the given sub section definition. """
        raise NotImplementedError()

    def m_get_sub_sections(
            self, section: 'MSection', sub_section_def: 'SubSection') -> Iterable['MSection']:
        """ Retrieves  all sub sections of the given sub section definition. """
        raise NotImplementedError()

    def m_sub_section_count(self, section: 'MSection', sub_section_def: 'SubSection') -> int:
        """ Returns the number of sub sections for the given sub section definition. """
        raise NotImplementedError()


class MDataDict(MData):
421
    """ A simple dict backed implementaton of :class:`MData`. It is used by default. """
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494

    def __init__(self, dct: Dict[str, Any] = None):
        if dct is None:
            dct = {}

        self.dct = dct

    def __getitem__(self, key):
        return self.dct[key]

    def __setitem__(self, key, value):
        self.dct[key] = value

    def m_set(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> None:
        self.dct[quantity_def.name] = value

    def m_get(self, section: 'MSection', quantity_def: 'Quantity') -> Any:
        quantity_name = quantity_def.name
        if quantity_name not in self.dct:
            return quantity_def.default
        else:
            return self.dct[quantity_name]

    def m_is_set(self, section: 'MSection', quantity_def: 'Quantity') -> bool:
        return quantity_def.name in self.dct

    def m_add_values(
            self, section: 'MSection', quantity_def: 'Quantity', values: Any,
            offset: int) -> None:

        # TODO
        raise NotImplementedError()

    def m_add_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            sub_section: 'MSection') -> None:

        sub_section_name = sub_section_def.name
        if sub_section_def.repeats:
            sub_section_lst = self.dct.get(sub_section_name, None)
            if sub_section_lst is None:
                sub_section_lst = self.dct.setdefault(sub_section_name, [])

            sub_section_lst.append(sub_section)

        else:
            self.dct[sub_section_name] = sub_section

    def m_get_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            index: int) -> 'MSection':

        if sub_section_def.repeats:
            return self.dct[sub_section_def.name][index]

        else:
            return self.dct.get(sub_section_def.name, None)

    def m_get_sub_sections(
            self, section: 'MSection', sub_section_def: 'SubSection') -> Iterable['MSection']:
        return self.dct.get(sub_section_def.name, [])

    def m_sub_section_count(self, section: 'MSection', sub_section_def: 'SubSection') -> int:
        sub_section_name = sub_section_def.name
        if sub_section_name not in self.dct:
            return 0

        if not sub_section_def.repeats:
            return 1

        return len(self.dct[sub_section_name])


Markus Scheidgen's avatar
Markus Scheidgen committed
495
496
class MSection(metaclass=MObjectMeta):
    """Base class for all section instances on all meta-info levels.
497

498
499
500
501
502
    All `section instances` indirectly instantiate the :class:`MSection` and therefore all
    members of :class:`MSection` are available on all `section instances`. :class:`MSection`
    provides many special attributes and functions (they all start with ``m_``) that allow
    to reflect on a `section's definition` and allow to manipulate the `section instance`
    without a priori knowledge of the `section defintion`.
503
504
505
506

    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.

507
508
509
    Attributes:
        m_def: The `section definition` that this `section instance` follows as a
            :class:`Section` object.
510

511
512
        m_parent:
            If this section is a sub-section, this references the parent section instance.
513

514
515
516
        m_parent_sub_section:
            If this section is a sub-section, this is the :class:`SubSection` that defines
            this relationship.
517

518
519
520
521
522
523
524
        m_parent_index:
            For repeatable sections, parent keep a list of sub-sections. This is the index
            of this section in the respective parent sub-section list.

        m_data: The :class:`MData` implementations that stores the section data. It keeps
            the quantity values and sub-section. It should only be read directly
            (and never manipulated).
525
526
527

    """

528
    m_def: 'Section' = None
529

530
531
    def __init__(self, m_def: 'Section' = None, m_data: MData = None, **kwargs):

532
        self.m_def: 'Section' = m_def
533
534
        self.m_parent: 'MSection' = None
        self.m_parent_sub_section: 'SubSection' = None
535
        self.m_parent_index = -1
536

537
        # get missing m_def from class
538
        cls = self.__class__
539
540
        if self.m_def is None:
            self.m_def = cls.m_def
541

542
        # check m_def
543
        if cls.m_def is not None:
544
545
546
547
548
549
550
551
552
            if self.m_def != cls.m_def:
                MetainfoError('Section class and section definition must match.')

            if self.m_def.extends_base_section:
                MetainfoError('Section extends another section and cannot be instantiated.')

        else:
            if not is_bootstrapping:
                MetainfoError('Section has not m_def.')
553

554
        # get annotations from kwargs
555
        self.m_annotations: Dict[str, Any] = {}
Markus Scheidgen's avatar
Markus Scheidgen committed
556
        rest = {}
557
558
559
560
        for key, value in kwargs.items():
            if key.startswith('a_'):
                self.m_annotations[key[2:]] = value
            else:
Markus Scheidgen's avatar
Markus Scheidgen committed
561
562
                rest[key] = value

563
564
565
        # initialize data
        self.m_data = m_data
        if self.m_data is None:
566
            self.m_data = MDataDict()
567

568
569
        # set remaining kwargs
        if is_bootstrapping:
570
            self.m_data.dct.update(**rest)  # type: ignore
Markus Scheidgen's avatar
Markus Scheidgen committed
571
        else:
572
            self.m_update(**rest)
573

574
    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
575
    def __init_cls__(cls):
576
577
        # ensure that the m_def is defined
        m_def = cls.m_def
Markus Scheidgen's avatar
Markus Scheidgen committed
578
        if m_def is None:
579
580
            m_def = Section()
            setattr(cls, 'm_def', m_def)
581

582
        # transfer name m_def
583
584
        m_def.name = cls.__name__
        m_def.section_cls = cls
585

586
        # add base sections
587
        extended_base_section = None
588
589
590
591
592
593
        if m_def.extends_base_section:
            base_sections_count = len(cls.__bases__)
            if base_sections_count == 0:
                raise MetainfoError(
                    'Section %s extend the base section, but has no base section.' % m_def)

Markus Scheidgen's avatar
Markus Scheidgen committed
594
            if base_sections_count > 1:
595
596
597
598
                raise MetainfoError(
                    'Section %s extend the base section, but has more than one base section' % m_def)

            base_section_cls = cls.__bases__[0]
599
            extended_base_section = base_section = getattr(base_section_cls, 'm_def', None)
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
            if base_section is None:
                raise MetainfoError(
                    'The base section of %s is not a section class.' % m_def)

            for name, attr in cls.__dict__.items():
                if isinstance(attr, Property):
                    setattr(base_section_cls, name, attr)

            section_to_add_properties_to = base_section
        else:
            for base_cls in cls.__bases__:
                if base_cls != MSection:
                    base_section = getattr(base_cls, 'm_def')
                    if base_section is None:
                        raise TypeError(
                            'Section defining classes must have MSection or a decendant as '
                            'base classes.')

                    base_sections = list(m_def.m_get(Section.base_sections))
                    base_sections.append(base_section)
                    m_def.m_set(Section.base_sections, base_sections)

            section_to_add_properties_to = m_def

624
625
        constraints: Set[str] = set()
        event_handlers: Set[Callable] = set(m_def.event_handlers)
626
        for name, attr in cls.__dict__.items():
627
628
            # transfer names and descriptions for properties
            if isinstance(attr, Property):
629
                attr.name = name
630
                if attr.description is not None:
631
                    attr.description = inspect.cleandoc(attr.description).strip()
632
                    attr.__doc__ = attr.description
633

634
                if isinstance(attr, Quantity):
635
                    section_to_add_properties_to.m_add_sub_section(Section.quantities, attr)
636
                elif isinstance(attr, SubSection):
637
                    section_to_add_properties_to.m_add_sub_section(Section.sub_sections, attr)
638
639
                else:
                    raise NotImplementedError('Unknown property kind.')
640

641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
            if inspect.isfunction(attr):
                method_name = attr.__name__

                # transfer constraints
                if method_name.startswith('c_'):
                    constraint = method_name[2:]
                    constraints.add(constraint)

                # register event_handlers from event_handler methods
                if method_name.startswith('on_set') or method_name.startswith('on_add_sub_section'):
                    if attr not in event_handlers:
                        event_handlers.add(attr)

        # add handler and constraints from base sections
        for base_section in m_def.all_base_sections:
            for constraint in base_section.constraints:
                constraints.add(constraint)
            for event_handler in base_section.event_handlers:
                event_handlers.add(event_handler)
Markus Scheidgen's avatar
Markus Scheidgen committed
660

661
662
        m_def.constraints = list(constraints)
        m_def.event_handlers = list(event_handlers)
Markus Scheidgen's avatar
Markus Scheidgen committed
663

664
665
666
        # add section cls' section to the module's package
        module_name = cls.__module__
        pkg = Package.from_module(module_name)
667
        pkg.m_add_sub_section(Package.section_definitions, cls.m_def)
668

669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
        # apply_google_docstrings
        # Parses the google doc string of the given class and properly updates the
        # definition descriptions.

        # This allows to document quantities and sub-sections with 'Args:' in the section
        # class. It will remove the 'Args' section from the section definition and will
        # set the respective pieces to the quantity and sub-section descriptions.
        docstring = cls.__doc__
        if docstring is not None:
            parsed_docstring = docstring_parser.parse(docstring)
            short = parsed_docstring.short_description
            dsc = parsed_docstring.long_description

            if short and dsc:
                description = '%s %s' % (short.strip(), dsc.strip())
            elif short:
                description = short.strip()
            elif dsc:
                description = dsc.strip()
            else:
                description = None

            if m_def.description is None:
                m_def.description = description

            for param in parsed_docstring.params:
                prop = m_def.all_properties.get(param.arg_name)
                if prop is not None:
                    if prop.description is None:
                        prop.description = param.description

700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
        # validate
        def validate(definition):
            errors = definition.m_all_validate()
            if len(errors) > 0:
                raise MetainfoError(
                    '%s. The section definition %s violates %d more constraints' %
                    (str(errors[0]).strip('.'), definition, len(errors) - 1))

        if extended_base_section is not None:
            validate(extended_base_section)
        validate(m_def)

    def __check_np(self, quantity_def: 'Quantity', value: np.ndarray) -> np.ndarray:
        # TODO this feels expensive, first check, then possible convert very often?
        # if quantity_ref.type != value.dtype:
        #     raise MetainfoError(
        #         'Quantity dtype %s and value dtype %s do not match.' %
        #         (quantity_ref.type, value.dtype))

719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
        return value

    def __set_normalize(self, quantity_def: 'Quantity', value: Any) -> Any:

        if isinstance(quantity_def.type, DataType):
            return quantity_def.type.set_normalize(self, quantity_def, value)

        elif isinstance(quantity_def.type, Section):
            if isinstance(value, MProxy):
                return value

            if not isinstance(value, MSection):
                raise TypeError(
                    'The value %s for reference quantity %s is not a section instance.' %
                    (value, quantity_def))

            if not value.m_follows(quantity_def.type):
                raise TypeError(
                    'The value %s for quantity %s does not follow %s' %
                    (value, quantity_def, quantity_def.type))

        elif isinstance(quantity_def.type, Enum):
            if value not in quantity_def.type:
                raise TypeError(
                    'The value %s is not an enum value for quantity %s.' %
                    (value, quantity_def))

        elif quantity_def.type == Any:
            pass

        else:
            if type(value) != quantity_def.type:
                raise TypeError(
                    'The value %s with type %s for quantity %s is not of type %s' %
                    (value, type(value), quantity_def, quantity_def.type))

        return value

757
758
759
760
    def __resolve_synonym(self, quantity_def: 'Quantity') -> 'Quantity':
        if quantity_def.synonym_for is not None:
            return self.m_def.all_quantities[quantity_def.synonym_for]
        return quantity_def
761

762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
    def __to_np(self, quantity_def: 'Quantity', value):
        if isinstance(value, pint.quantity._Quantity):
            if quantity_def.unit is None:
                raise MetainfoError(
                    'The quantity %s has not a unit, but value %s has.' %
                    (quantity_def, value))
            value = value.to(quantity_def.unit).magnitude

        if type(value) != np.ndarray:
            try:
                value = np.asarray(value)
            except TypeError:
                raise TypeError(
                    'Could not convert value %s of %s to a numpy array' %
                    (value, quantity_def))

        return self.__check_np(quantity_def, value)

780
781
782
    def m_set(self, quantity_def: 'Quantity', value: Any) -> None:
        """ Set the given value for the given quantity. """
        quantity_def = self.__resolve_synonym(quantity_def)
783

784
785
        if quantity_def.derived is not None:
            raise MetainfoError('The quantity %s is derived and cannot be set.' % quantity_def)
786
787
788

        if type(quantity_def.type) == np.dtype:
            if type(value) != np.ndarray:
789
                value = self.__to_np(quantity_def, value)
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810

            value = self.__check_np(quantity_def, value)

        else:
            dimensions = len(quantity_def.shape)
            if dimensions == 0:
                value = self.__set_normalize(quantity_def, value)

            elif dimensions == 1:
                if type(value) == str or not isinstance(value, IterableABC):
                    raise TypeError(
                        'The shape of %s requires an iterable value, but %s is not iterable.' %
                        (quantity_def, value))

                value = list(self.__set_normalize(quantity_def, item) for item in value)

            else:
                raise MetainfoError(
                    'Only numpy arrays and dtypes can be used for higher dimensional '
                    'quantities.')

811
        self.m_data.m_set(self, quantity_def, value)
812

813
814
815
816
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_set'):
                handler(self, quantity_def, value)

817
818
819
    def m_get(self, quantity_def: 'Quantity') -> Any:
        """ Retrieve the given value for the given quantity. """
        quantity_def = self.__resolve_synonym(quantity_def)
820
821
822
823
824
825
        if quantity_def.derived is not None:
            try:
                return quantity_def.derived(self)
            except Exception as e:
                raise DeriveError('Could not derive value for %s: %s' % (quantity_def, str(e)))

826
827
        value = self.m_data.m_get(self, quantity_def)

828
829
830
831
832
833
834
835
836
837
838
839
840
841
        if isinstance(quantity_def.type, DataType) and quantity_def.type.get_normalize != DataType.get_normalize:
            dimensions = len(quantity_def.shape)
            if dimensions == 0:
                value = quantity_def.type.get_normalize(self, quantity_def, value)

            elif dimensions == 1:
                value = list(
                    quantity_def.type.get_normalize(self, quantity_def, item)
                    for item in value)

            else:
                raise MetainfoError(
                    'Only numpy arrays and dtypes can be used for higher dimensional '
                    'quantities.')
842

843
844
845
846
        elif type(quantity_def.type) == np.dtype:
            if quantity_def.unit is not None:
                value = value * quantity_def.unit

847
        return value
848

849
    def m_is_set(self, quantity_def: 'Quantity') -> bool:
850
        """ True if the given quantity is set. """
851
        quantity_def = self.__resolve_synonym(quantity_def)
852
853
854
        if quantity_def.derived is not None:
            return True

855
        return self.m_data.m_is_set(self, quantity_def)
Markus Scheidgen's avatar
Markus Scheidgen committed
856

857
858
859
    def m_add_values(self, quantity_def: 'Quantity', values: Any, offset: int) -> None:
        """ Add (partial) values for the given quantity of higher dimensionality. """
        self.m_data.m_add_values(self, quantity_def, values, offset)
860

861
862
    def m_add_sub_section(self, sub_section_def: 'SubSection', sub_section: 'MSection') -> None:
        """ Adds the given section instance as a sub section of the given sub section definition. """
Markus Scheidgen's avatar
Markus Scheidgen committed
863

864
        parent_index = -1
865
        if sub_section_def.repeats:
866
867
868
869
            parent_index = self.m_sub_section_count(sub_section_def)
        sub_section.m_parent = self
        sub_section.m_parent_sub_section = sub_section_def
        sub_section.m_parent_index = parent_index
870

871
        self.m_data.m_add_sub_section(self, sub_section_def, sub_section)
872

873
874
875
876
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_add_sub_section'):
                handler(self, sub_section_def, sub_section)

877
878
879
    def m_get_sub_section(self, sub_section_def: 'SubSection', index: int) -> 'MSection':
        """ Retrieves a single sub section of the given sub section definition. """
        return self.m_data.m_get_sub_section(self, sub_section_def, index)
880

881
882
883
    def m_get_sub_sections(self, sub_section_def: 'SubSection') -> Iterable['MSection']:
        """ Retrieves  all sub sections of the given sub section definition. """
        return self.m_data.m_get_sub_sections(self, sub_section_def)
884

885
886
887
    def m_sub_section_count(self, sub_section_def: 'SubSection') -> int:
        """ Returns the number of sub sections for the given sub section definition. """
        return self.m_data.m_sub_section_count(self, sub_section_def)
888

889
890
891
    def m_create(self, section_cls: Type[MSectionBound], **kwargs) -> MSectionBound:
        """ Creates a section instance and adds it to this section provided there is a
        corresponding sub section.
892
        """
893

894
895
896
        section_def = section_cls.m_def
        sub_section_def = self.m_def.all_sub_sections_by_section.get(section_def, None)
        if sub_section_def is None:
897
            raise TypeError('There is no sub section to hold a %s in %s.' % (section_def, self.m_def))
898

899
900
        sub_section = section_cls(**kwargs)
        self.m_add_sub_section(sub_section_def, sub_section)
901

902
        return cast(MSectionBound, sub_section)
903

904
    def m_update(self, safe: bool = True, **kwargs):
905
        """ Updates all quantities and sub-sections with the given arguments. """
906
907
908
909
910
911
912
913
914
915
916
917
918
        if safe:
            for name, value in kwargs.items():
                prop = self.m_def.all_properties.get(name, None)
                if prop is None:
                    raise KeyError('%s is not an attribute of this section %s' % (name, self))

                if isinstance(prop, SubSection):
                    if prop.repeats:
                        if isinstance(value, List):
                            for item in value:
                                self.m_add_sub_section(prop, item)
                        else:
                            raise TypeError('Sub section %s repeats, but no list was given' % prop.name)
919
                    else:
920
921
                        self.m_add_sub_section(prop, item)

922
                else:
923
                    self.m_set(prop, value)
924

925
926
        else:
            self.m_data.m_data.dct.update(**kwargs)  # type: ignore
927

928
929
930
931
    def m_as(self, section_cls: Type[MSectionBound]) -> MSectionBound:
        """ 'Casts' this section to the given extending sections. """
        return cast(MSectionBound, self)

932
    def m_follows(self, definition: 'Section') -> bool:
933
        """ Determines if this section's definition is or is derived from the given definition. """
934
        return self.m_def == definition or definition in self.m_def.all_base_sections
935

936
    def m_to_dict(self, with_meta: bool = False) -> Dict[str, Any]:
937
        """Returns the data of this section as a json serializeable dictionary. """
938
939

        def items() -> Iterable[Tuple[str, Any]]:
940
941
942
943
944
945
946
947
948
            # metadata
            if with_meta:
                yield 'm_def', self.m_def.name
                if self.m_parent_index != -1:
                    yield 'm_parent_index', self.m_parent_index
                if self.m_parent_sub_section is not None:
                    yield 'm_parent_sub_section', self.m_parent_sub_section.name

            # quantities
949
            for name, quantity in self.m_def.all_quantities.items():
950
                if quantity.virtual or not self.m_is_set(quantity):
951
952
                    continue

953
                if self.m_is_set(quantity) and quantity.derived is None:
954
                    serialize: TypingCallable[[Any], Any] = str
955
                    if isinstance(quantity.type, DataType):
956
957

                        def data_type_serialize(value):
Markus Scheidgen's avatar
Markus Scheidgen committed
958
                            return quantity.type.serialize(self, quantity, value)
959
960

                        serialize = data_type_serialize
961

962
                    elif quantity.type in [str, int, float, bool]:
963
                        serialize = quantity.type
964

965
                    elif type(quantity.type) == np.dtype:
966
967
                        pass

968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
                    elif isinstance(quantity.type, Enum):
                        pass

                    elif quantity.type == Any:
                        def _serialize(value: Any):
                            if type(value) not in [str, int, float, bool, list, type(None)]:
                                raise MetainfoError(
                                    'Only python primitives are allowed for Any typed non '
                                    'virtual quantities: %s of quantity %s in section %s' %
                                    (value, quantity, self))

                            return value

                        serialize = _serialize

                    else:
                        raise MetainfoError(
                            'Do not know how to serialize data with type %s for quantity %s' %
                            (quantity.type, quantity))

988
                    value = cast(MDataDict, self.m_data).dct[name]
989

990
                    if type(quantity.type) == np.dtype:
991
992
993
994
                        serializable_value = value.tolist()

                    else:
                        if len(quantity.shape) == 0:
995
                            serializable_value = serialize(value)
996
                        elif len(quantity.shape) == 1:
997
                            serializable_value = [serialize(i) for i in value]
998
999
1000
                        else:
                            raise NotImplementedError('Higher shapes (%s) not supported: %s' % (quantity.shape, quantity))