metainfo.py 94.7 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

24
import numpy as np
25
26
27
import pint
import pint.unit
import pint.quantity
28
29
30
import aniso8601
from datetime import datetime
import pytz
31
import docstring_parser
32
import flask_restplus.inputs
33

34
35
36

m_package: 'Package' = None

Markus Scheidgen's avatar
Markus Scheidgen committed
37
38
is_bootstrapping = True
MSectionBound = TypeVar('MSectionBound', bound='MSection')
39
T = TypeVar('T')
40

41
42
43
44
45
46
47
48
# Make pylint believe all bootstrap quantities are actual properties even though
# we have to initialize them to None due to bootstrapping
_placeholder_quantity: 'Quantity' = property()  # type: ignore
if True:
    _placeholder_quantity: 'Quantity' = None  # type: ignore

_primitive_types = {str: str, int: int, float: float, bool: bool}

49

Markus Scheidgen's avatar
Markus Scheidgen committed
50
51
# Metainfo errors

52
class MetainfoError(Exception):
53
    ''' Metainfo related errors. '''
54
55
56
    pass


57
class DeriveError(MetainfoError):
58
    ''' An error occurred while computing a derived value. '''
59
60
61
    pass


62
class MetainfoReferenceError(MetainfoError):
63
    ''' An error indicating that a reference could not be resolved. '''
64
    pass
65
66


Markus Scheidgen's avatar
Markus Scheidgen committed
67
# Metainfo quantity data types
68

69
class MEnum():
70
    '''Allows to define str types with values limited to a pre-set list of possible values.'''
71
72
    def __init__(self, *args, **kwargs):
        # Supports one big list in place of args
73
        if len(args) == 1 and isinstance(args[0], list):
74
            args = args[0]
75

76
77
78
79
80
81
82
83
84
85
86
87
88
        # If non-named arguments are given, the default is to have them placed
        # into a dictionary with their string value as both the enum name and
        # the value.
        for arg in args:
            if arg in kwargs:
                raise ValueError("Duplicate value '{}' provided for enum".format(arg))
            kwargs[arg] = arg

        self._values = set(kwargs.values())  # For allowing constant time member check
        self._map = kwargs

    def __getattr__(self, attr):
        return self._map[attr]
89
90


91
class MProxy():
92
    ''' A placeholder object that acts as reference to a value that is not yet resolved.
93
94
95

    Attributes:
        url: The reference represented as an URL string.
96
    '''
97

98
99
100
    def __init__(
            self, m_proxy_url: str, m_proxy_section: 'MSection' = None,
            m_proxy_quantity: 'Quantity' = None):
101
102
103
        self.m_proxy_url = m_proxy_url
        self.m_proxy_section = m_proxy_section
        self.m_proxy_resolved = None
104
        self.m_proxy_quantity = m_proxy_quantity
105
106

    def m_proxy_resolve(self):
107
108
        if self.m_proxy_section and self.m_proxy_quantity and not self.m_proxy_resolved:
            self.m_proxy_resolved = self.m_proxy_quantity.type.resolve(self)
109
110
111
112
113
114
115
116

        if self.m_proxy_resolved is not None and isinstance(self, MProxy):
            setattr(self, '__class__', self.m_proxy_resolved.__class__)
            self.__dict__.update(**self.m_proxy_resolved.__dict__)

        return self.m_proxy_resolved

    def __getattr__(self, key):
117
        if self.m_proxy_resolve() is not None:
118
119
120
            return getattr(self.m_proxy_resolved, key)

        raise ReferenceError('could not resolve %s' % self.m_proxy_url)
121
122


123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
class SectionProxy(MProxy):
    def m_proxy_resolve(self):
        if self.m_proxy_section and not self.m_proxy_resolved:
            root = self.m_proxy_section
            while root is not None and not isinstance(root, Package):
                root = root.m_parent

            if isinstance(root, Package):
                self.m_proxy_resolved = root.all_definitions.get(self.m_proxy_url)

            if self.m_proxy_resolved is None:
                raise ReferenceError('could not resolve %s' % self.m_proxy_url)

        return self.m_proxy_resolved


139
class DataType:
140
    '''
141
142
    Allows to define custom data types that can be used in the meta-info.

143
    The metainfo supports the most types out of the box. These includes the python build-in
144
145
    primitive types (int, bool, str, float, ...), references to sections, and enums.
    However, in some occasions you need to add custom data types.
146
147
148
149
150

    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.
151
    '''
152
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
153
        ''' Transforms the given value before it is set and checks its type. '''
154
155
156
        return value

    def get_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
157
        ''' Transforms the given value when it is get. '''
158
159
        return value

160
    def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
161
        ''' Transforms the given value when making the section serializeable. '''
162
163
        return value

164
    def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
165
        ''' Transforms the given value from its serializeable form. '''
166
167
168
        return value


169
170
171
172
173
range_re = re.compile(r'(\d)\.\.(\d|\*)')


class _Dimension(DataType):

174
    def set_normalize(self, section, quantity_def: 'Quantity', value):
175
        if isinstance(value, int):
Markus Scheidgen's avatar
Markus Scheidgen committed
176
            return value
177
178
179

        if isinstance(value, str):
            if value.isidentifier():
Markus Scheidgen's avatar
Markus Scheidgen committed
180
                return value
181
            if re.match(range_re, value):
Markus Scheidgen's avatar
Markus Scheidgen committed
182
                return value
183
184

        if isinstance(value, Section):
Markus Scheidgen's avatar
Markus Scheidgen committed
185
            return value
186

187
        if isinstance(value, type) and hasattr(value, 'm_def'):
Markus Scheidgen's avatar
Markus Scheidgen committed
188
            return value
189

190
191
192
193
        if isinstance(value, str):
            # TODO error/warning?
            return '0..*'

194
195
        raise TypeError('%s is not a valid dimension' % str(value))

196
197
198
199
200
201
202
    @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)
203

204
205
206
207
208
209
210
            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):
211
    def set_normalize(self, section, quantity_def: 'Quantity', value):
212
213
214
        if isinstance(value, str):
            value = units.parse_units(value)

215
        elif not isinstance(value, pint.unit._Unit):
216
217
218
219
            raise TypeError('Units must be given as str or pint Unit instances.')

        return value

220
    def serialize(self, section, quantity_def: 'Quantity', value):
221
222
        return value.__str__()

223
    def deserialize(self, section, quantity_def: 'Quantity', value):
224
225
        return units.parse_units(value)

226

227
units = pint.UnitRegistry()
228
''' The default pint unit registry that should be used to give units to quantity definitions. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
229
230


231
class _Callable(DataType):
232
233
234
235
236
237
238
    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')


239
class _QuantityType(DataType):
240
    ''' Data type for defining the type of a metainfo quantity.
241
242
243
244
245
246

    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
247
    - an MEnum instance to use it's values as possible str values
248
249
    - a custom datatype, i.e. instance of :class:`DataType`
    - Any
250
    '''
251
252
253
254
255

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

256
257
        if isinstance(value, MEnum):
            for enum_value in value._values:
258
                if not isinstance(enum_value, str):
259
                    raise TypeError('MEnum value %s is not a string.' % enum_value)
260
261
262
263
264
265
266
267
            return value

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

        if isinstance(value, Section):
            return value

268
269
270
271
272
273
        if isinstance(value, Reference) and isinstance(value.target_section_def, MProxy):
            proxy = value.target_section_def
            proxy.m_proxy_section = section
            proxy.m_proxy_quantity = quantity_def
            return value

274
275
276
277
278
279
280
281
282
283
284
        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)

285
        if isinstance(value, MProxy):
286
287
            value.m_proxy_section = section
            value.m_proxy_quantity = quantity_def
288
289
            return value

290
291
292
293
294
        raise MetainfoError(
            'Type %s of %s is not a valid metainfo quantity type' %
            (value, quantity_def))

    def serialize(self, section, quantity_def, value):
295
        if value is str or value is int or value is float or value is bool:
296
297
            return dict(type_kind='python', type_data=value.__name__)

298
        if isinstance(value, MEnum):
299
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
            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):
325
    ''' Datatype used for reference quantities. '''
326

327
    def __init__(self, section_def: Union['Section', 'SectionProxy']):
328
329
        self.target_section_def = section_def

330
331
332
333
334
335
336
    def resolve(self, proxy) -> 'MSection':
        '''
        Resolve the given proxy. The proxy is gurantied to have a context and
        will to be not yet resolved.
        '''
        return proxy.m_proxy_section.m_resolve(proxy.m_proxy_url)

337
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
338
339
340
341
342
343
        if isinstance(self.target_section_def, MProxy):
            proxy = self.target_section_def
            proxy.m_proxy_section = section
            proxy.m_proxy_quantity = quantity_def
            self.target_section_def = proxy.m_proxy_resolve()

344
345
346
347
348
349
350
351
352
        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

353
354
355
        if isinstance(value, str):
            return MProxy(value, m_proxy_section=section, m_proxy_quantity=quantity_def)

356
        if isinstance(value, MProxy):
357
            value.m_proxy_section = section
358
            value.m_proxy_quantity = quantity_def
359
360
361
362
363
364
            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)

365
        if not value.m_follows(self.target_section_def):  # type: ignore
366
367
368
369
370
371
372
373
374
375
            raise TypeError(
                '%s is not a %s and therefore an invalid value of %s.' %
                (value, self.target_section_def, quantity_def))

        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:
376
        return MProxy(value, m_proxy_section=section, m_proxy_quantity=quantity_def)
377
378


379
class _Datetime(DataType):
380

381
    def _parse(self, datetime_str: str) -> datetime:
382
        try:
383
384
385
            return aniso8601.parse_datetime(datetime_str)
        except ValueError:
            pass
386

387
388
389
390
391
392
393
394
395
396
397
398
399
400
        try:
            return aniso8601.parse_date(datetime_str)
        except ValueError:
            pass

        try:
            # TODO necessary?
            return flask_restplus.inputs.datetime_from_rfc822(datetime_str)
        except ValueError:
            pass

        raise TypeError('Invalid date literal "{0}"'.format(datetime_str))

    def _convert(self, value):
401
402
403
        if value is None:
            return None

404
        if isinstance(value, str):
405
406
407
408
            value = self._parse(value)

        elif isinstance(value, (int, float)):
            value = datetime.fromtimestamp(value)
409

410
411
412
        elif isinstance(value, pint.Quantity):
            value = datetime.fromtimestamp(value.magnitude)

413
414
415
416
417
        if not isinstance(value, datetime):
            raise TypeError('%s is not a datetime.' % value)

        return value

418
419
420
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        return self._convert(value)

421
    def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
422
423
424
        if value is None:
            return None

425
426
427
428
        value.replace(tzinfo=pytz.utc)
        return value.isoformat()

    def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
429
        return self._convert(value)
430
431


432
433
434
435
436
Dimension = _Dimension()
Unit = _Unit()
QuantityType = _QuantityType()
Callable = _Callable()
Datetime = _Datetime()
437
438


Markus Scheidgen's avatar
Markus Scheidgen committed
439
440
# Metainfo data storage and reflection interface

441
class MObjectMeta(type):
442

443
    def __new__(self, cls_name, bases, dct):
444
445
446
447
448
449
        do_init = dct.get('do_init', None)
        if do_init is not None:
            del(dct['do_init'])
        else:
            do_init = True

450
        cls = super().__new__(self, cls_name, bases, dct)
Markus Scheidgen's avatar
Markus Scheidgen committed
451

Markus Scheidgen's avatar
Markus Scheidgen committed
452
        init = getattr(cls, '__init_cls__')
453
        if init is not None and do_init and not is_bootstrapping:
454
455
            init()
        return cls
456
457


458
SectionDef = Union[str, 'Section', 'SubSection', Type[MSectionBound]]
459
''' Type for section definition references.
460
461
462
463
464
465
466

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
467
'''
468
469


470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
def constraint(warning):
    ''' A decorator for methods implementing constraints. '''
    f = None
    if not isinstance(warning, bool):
        f = warning
        warning = False

    def decorator(f):
        setattr(f, 'm_constraint', True)
        setattr(f, 'm_warning', warning)
        return f

    if f is None:
        return decorator
    else:
        return decorator(f)


488
class MResource():
489
    '''
490
491
492
    Represents a collection of related metainfo data, i.e. a set of :class:`MSection` instances.
    '''

493
494
495
496
497
    def __init__(self):
        self.__data: Dict['Section', List['MSection']] = dict()
        self.contents: List['MSection'] = []

    def create(self, section_cls: Type[MSectionBound], *args, **kwargs) -> MSectionBound:
498
499
500
501
502
503
504
505
506
507
        '''
        Create an instance of the given section class and adds it to this resource as
        a root section. The m_parent_index will be set sequentially among root sections of
        the same section definition starting with 0.
        '''
        index = 0
        for content in self.contents:
            if content.m_follows(section_cls.m_def):
                index = max(index, content.m_parent_index + 1)

508
        result = section_cls(*args, **kwargs)
509
510
        result.m_parent_index = index

511
512
513
514
515
516
517
518
519
520
        self.add(result)
        return cast(MSectionBound, result)

    def add(self, section):
        section.m_resource = self
        self.__data.setdefault(section.m_def, []).append(section)
        if section.m_parent is None:
            self.contents.append(section)

    def remove(self, section):
521
522
        import traceback
        traceback.print_stack()
523
524
525
526
527
528
529
        assert section.m_resource == self, 'Can only remove section from the resource that contains it.'
        section.m_resource = None
        self.__data.get(section.m_def).remove(section)
        if section.m_parent is not None:
            self.contents.remove(section)

    def all(self, section_cls: Type[MSectionBound]) -> List[MSectionBound]:
530
        ''' Returns all instances of the given section class in this resource. '''
531
532
533
        return cast(List[MSectionBound], self.__data.get(section_cls.m_def, []))

    def unload(self):
534
        ''' Breaks all references among the contain metainfo sections to allow GC. '''
535
536
537
538
539
540
541
        for collections in self.__data.values():
            for section in collections:
                section.m_parent = None
            collections.clear()

        # TODO break actual references via quantities

542
543
544
545
546
547
548
549
550
551
    def m_to_dict(self, filter: TypingCallable[['MSection'], bool] = None):
        if filter is None:
            def filter(_):  # pylint: disable=function-redefined
                return True

        return {
            section.m_def.name: section.m_to_dict()
            for section in self.contents
            if filter(section)}

552

553
554
class MSection(metaclass=MObjectMeta):  # TODO find a way to make this a subclass of collections.abs.Mapping
    '''Base class for all section instances on all meta-info levels.
555

556
557
558
559
560
    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`.
561
562
563
564

    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.

565
566
567
    Attributes:
        m_def: The `section definition` that this `section instance` follows as a
            :class:`Section` object.
568

569
570
        m_parent:
            If this section is a sub-section, this references the parent section instance.
571

572
573
574
        m_parent_sub_section:
            If this section is a sub-section, this is the :class:`SubSection` that defines
            this relationship.
575

576
577
578
579
        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.

580
581
        m_resource: The :class:`MResource` that contains and manages this section.

582
    '''
583

584
    m_def: 'Section' = None
585

586
    def __init__(
587
            self, m_def: 'Section' = None, m_resource: MResource = None, **kwargs):
588

589
        self.m_def: 'Section' = m_def
590
591
        self.m_parent: 'MSection' = None
        self.m_parent_sub_section: 'SubSection' = None
592
        self.m_parent_index = -1
593
        self.m_resource = m_resource
594
        self.m_mod_count = 0
595

596
        # get missing m_def from class
597
        cls = self.__class__
598
599
        if self.m_def is None:
            self.m_def = cls.m_def
600

601
        # check m_def
602
        if cls.m_def is not None:
603
604
605
606
607
608
609
610
611
            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.')
612

613
        # get annotations from kwargs
614
615
        self.m_annotations: Dict[str, Any] = {}
        other_kwargs = {}
616
617
618
619
        for key, value in kwargs.items():
            if key.startswith('a_'):
                self.m_annotations[key[2:]] = value
            else:
620
621
622
623
                other_kwargs[key] = value

        # get additional annotations from the section definition
        if not is_bootstrapping:
624
            for section_annotation in self.m_def.m_get_annotations(SectionAnnotation, as_list=True):
625
626
627
628
629
630
                for name, annotation in section_annotation.new(self).items():
                    self.m_annotations[name] = annotation

        # add annotation attributes for names annotations
        for annotation_name, annotation in self.m_annotations.items():
            setattr(self, 'a_%s' % annotation_name, annotation)
Markus Scheidgen's avatar
Markus Scheidgen committed
631

632
633
        # set remaining kwargs
        if is_bootstrapping:
634
            self.__dict__.update(**other_kwargs)  # type: ignore
Markus Scheidgen's avatar
Markus Scheidgen committed
635
        else:
636
            self.m_update(**other_kwargs)
637

638
    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
639
    def __init_cls__(cls):
640
        # ensure that the m_def is defined
641
        m_def = cls.__dict__.get('m_def')  # do not accedentally get the m_def from a potential base section
Markus Scheidgen's avatar
Markus Scheidgen committed
642
        if m_def is None:
643
644
            m_def = Section()
            setattr(cls, 'm_def', m_def)
645

646
        # transfer name m_def
647
        m_def.name = cls.__name__
648
        m_def._section_cls = cls
649

650
        # add base sections
651
652
653
654
655
656
657
658
659
        base_sections: List[Section] = []
        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.append(base_section)
660

661
662
663
        m_def.m_set(Section.base_sections, base_sections)

        # transfer names, descriptions, constraints, event_handlers
664
665
        constraints: Set[str] = set()
        event_handlers: Set[Callable] = set(m_def.event_handlers)
666
        for name, attr in cls.__dict__.items():
667
            # transfer names and descriptions for properties, init properties
668
            if isinstance(attr, Property):
669
                attr.name = name
670
                if attr.description is not None:
671
                    attr.description = inspect.cleandoc(attr.description).strip()
672
                    attr.__doc__ = attr.description
673

674
                if isinstance(attr, Quantity):
675
                    m_def.m_add_sub_section(Section.quantities, attr)
676
                elif isinstance(attr, SubSection):
677
                    m_def.m_add_sub_section(Section.sub_sections, attr)
678
679
                else:
                    raise NotImplementedError('Unknown property kind.')
680

681
682
683
684
            if inspect.isfunction(attr):
                method_name = attr.__name__

                # transfer constraints
685
686
                if getattr(attr, 'm_constraint', False):
                    constraint = method_name
687
688
689
690
691
692
693
694
695
696
697
698
699
                    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
700

701
702
        m_def.constraints = list(constraints)
        m_def.event_handlers = list(event_handlers)
Markus Scheidgen's avatar
Markus Scheidgen committed
703

704
705
706
        # add section cls' section to the module's package
        module_name = cls.__module__
        pkg = Package.from_module(module_name)
707
        pkg.m_add_sub_section(Package.section_definitions, cls.m_def)
708

709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
        # 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

740
741
        for content in m_def.m_all_contents(depth_first=True, include_self=True):
            cast(Definition, content).__init_metainfo__()
742

743
744
745
746
    def __getattr__(self, name):
        # This will make mypy and pylint ignore 'missing' dynamic attributes and functions
        # and wrong types of those.
        # Ideally we have a plugin for both that add the corrent type info
747
        raise AttributeError(name)
748

749
750
751
752
753
754
755
    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))

756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
        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))

777
778
        elif isinstance(quantity_def.type, MEnum):
            if value not in quantity_def.type._values:
779
780
781
782
783
784
785
                raise TypeError(
                    'The value %s is not an enum value for quantity %s.' %
                    (value, quantity_def))

        elif quantity_def.type == Any:
            pass

786
787
788
789
790
791
        elif quantity_def.type == str and type(value) == np.str_:
            return str(value)

        elif quantity_def.type == bool and type(value) == np.bool_:
            return bool(value)

792
        else:
793
            if value is not None and type(value) != quantity_def.type:
794
795
796
797
798
799
                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

800
801
802
803
    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
804

805
806
807
808
809
810
811
812
    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

813
        if len(quantity_def.shape) > 0 and type(value) != np.ndarray:
814
815
816
817
818
819
            try:
                value = np.asarray(value)
            except TypeError:
                raise TypeError(
                    'Could not convert value %s of %s to a numpy array' %
                    (value, quantity_def))
820
821
822
823
824
825
826
        elif type(value) != quantity_def.type.type:
            try:
                value = quantity_def.type.type(value)
            except TypeError:
                raise TypeError(
                    'Could not convert value %s of %s to a numpy scalar' %
                    (value, quantity_def))
827
828
829

        return self.__check_np(quantity_def, value)

830
    def m_set(self, quantity_def: 'Quantity', value: Any) -> None:
831
        ''' Set the given value for the given quantity. '''
832
        self.m_mod_count += 1
833
        quantity_def = self.__resolve_synonym(quantity_def)
834

835
836
        if quantity_def.derived is not None:
            raise MetainfoError('The quantity %s is derived and cannot be set.' % quantity_def)
837
838

        if type(quantity_def.type) == np.dtype:
839
            value = self.__to_np(quantity_def, value)
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856

        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 '
857
                    'quantities: %s' % quantity_def)
858

859
        self.__dict__[quantity_def.name] = value
860

861
862
863
864
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_set'):
                handler(self, quantity_def, value)

865
    def m_get(self, quantity_def: 'Quantity') -> Any:
866
        ''' Retrieve the given value for the given quantity. '''
867
        return quantity_def.__get__(self, Quantity)
868

869
    def m_is_set(self, quantity_def: 'Quantity') -> bool:
870
        ''' True if the given quantity is set. '''
871
        quantity_def = self.__resolve_synonym(quantity_def)
872
873
874
        if quantity_def.derived is not None:
            return True

875
        return quantity_def.name in self.__dict__
Markus Scheidgen's avatar
Markus Scheidgen committed
876

877
    def m_add_values(self, quantity_def: 'Quantity', values: Any, offset: int) -> None:
878
        ''' Add (partial) values for the given quantity of higher dimensionality. '''
879
880
        # TODO
        raise NotImplementedError()
881

882
    def m_add_sub_section(self, sub_section_def: 'SubSection', sub_section: 'MSection') -> None:
883
        ''' Adds the given section instance as a sub section of the given sub section definition. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
884

885
        self.m_mod_count += 1
886
        parent_index = -1
887
        if sub_section_def.repeats:
888
            parent_index = self.m_sub_section_count(sub_section_def)
889
890

        else:
891
            old_sub_section = self.__dict__.get(sub_section_def.name)
892
893
894
895
896
897
898
            if old_sub_section is not None:
                old_sub_section.m_parent = None
                old_sub_section.m_parent_sub_section = None
                old_sub_section.m_parent_index = -1
                if self.m_resource is not None:
                    self.m_resource.remove(sub_section)

899
900
901
        sub_section.m_parent = self
        sub_section.m_parent_sub_section = sub_section_def
        sub_section.m_parent_index = parent_index
902
903
904
905
        if sub_section.m_resource is not None:
            sub_section.m_resource.remove(sub_section)
        if self.m_resource is not None:
            self.m_resource.add(sub_section)
906

907
908
909
910
911
912
913
914
915
916
        sub_section_name = sub_section_def.name
        if sub_section_def.repeats:
            sub_section_lst = self.__dict__.get(sub_section_name)
            if sub_section_lst is None:
                sub_section_lst = self.__dict__.setdefault(sub_section_name, [])

            sub_section_lst.append(sub_section)

        else:
            self.__dict__[sub_section_name] = sub_section
917

918
919
920
921
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_add_sub_section'):
                handler(self, sub_section_def, sub_section)

922
923
    def m_remove_sub_section(self, sub_section_def: 'SubSection', index: int) -> None:
        ''' Removes the exiting section for a non repeatable sub section '''
924
        self.m_mod_count += 1
925
926
927
928
929
        if sub_section_def.repeats:
            del(self.__dict__[sub_section_def.name][index])

        elif sub_section_def.name in self.__dict__:
            del(self.__dict__[sub_section_def.name])
930

931
    def m_get_sub_section(self, sub_section_def: 'SubSection', index: int) -> 'MSection':
932
        ''' Retrieves a single sub section of the given sub section definition. '''
933
934
935
936
937
        if sub_section_def.repeats:
            return self.__dict__[sub_section_def.name][index]

        else:
            return self.__dict__.get(sub_section_def.name, None)
938

939
    def m_get_sub_sections(self, sub_section_def: 'SubSection') -> Iterable['MSection']:
940
        ''' Retrieves  all sub sections of the given sub section definition. '''
941
        try:
942
943
944
945
            if sub_section_def.repeats:
                return self.__dict__[sub_section_def.name]
            else:
                return [self.__dict__[sub_section_def.name]]
946
947
        except KeyError:
            return []
948

949
    def m_sub_section_count(self, sub_section_def: 'SubSection') -> int:
950
        ''' Returns the number of sub sections for the given sub section definition. '''
951
952
953
954
955
956
957
958
        try:
            value = self.__dict__[sub_section_def.name]
            if sub_section_def.repeats:
                return len(value)
            else:
                return 1
        except KeyError:
            return 0
959

960
961
962
    def m_create(
            self, section_cls: Type[MSectionBound], sub_section_def: 'SubSection' = None,
            **kwargs) -> MSectionBound:
963
        ''' Creates a section instance and adds it to this section provided there is a
964
        corresponding sub section.
965
966
967
968
969

        Args:
            section_cls: The section class for the sub-secton to create
            sub_section_def: If there are multiple sub-sections for the given class,
                this must be used to explicitely state the sub-section definition.
970
        '''
971

972
        section_def = section_cls.m_def
973
974
975
        sub_section_defs = self.m_def.all_sub_sections_by_section.get(section_def, [])
        n_sub_section_defs = len(sub_section_defs)
        if n_sub_section_defs == 0:
976
            raise TypeError('There is no sub section to hold a %s in %s.' % (section_def, self.m_def))
977

978
979
980
981
982
983
984
985
986
987
988
989
990
        if n_sub_section_defs > 1 and sub_section_def is None:
            raise MetainfoError(
                'There are multiple sub section to hold a %s in %s, '
                'but no sub-section was explicitely given.' % (section_def, self.m_def))

        if sub_section_def is not None and sub_section_def not in sub_section_defs:
            raise MetainfoError(
                'The given sub-section class %s does not match the given sub-section '
                'definition %s.' % (section_cls, sub_section_def))

        if sub_section_def is None:
            sub_section_def = sub_section_defs[0]

991
992
        sub_section = section_cls(**kwargs)
        self.m_add_sub_section(sub_section_def, sub_section)
993

994
        return cast(MSectionBound, sub_section)
995

996
    def m_update(self, safe: bool = True, **kwargs):
997
        ''' Updates all quantities and sub-sections with the given arguments. '''
998
        self.m_mod_count += 1
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
        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)
1012
                    else:
1013
1014
                        self.m_add_sub_section(prop, item)

1015
                else:
1016
                    self.m_set(prop, value)
1017

1018
        else:
1019
            self.__dict__.update(**kwargs)
1020

1021
    def m_as(self, section_cls: Type[MSectionBound]) -> MSectionBound:
1022
        ''' 'Casts' this section to the given extending sections. '''
1023
1024
        return cast(MSectionBound, self)

1025
    def m_follows(self, definition: 'Section') -> bool:
1026
        ''' Determines if this section's definition is or is derived from the given definition. '''
1027
1028
        if not isinstance(definition, Section):
            raise TypeError('%s is of class Section' % definition)
1029
        return self.m_def == definition or definition in self.m_def.all_base_sections
1030

1031
1032
1033
1034
1035
1036
1037
1038
1039
    def m_to_dict(self, with_meta: bool = False, include_defaults: bool = False) -> Dict[str, Any]:
        '''
        Returns the data of this section as a json serializeable dictionary.

        Arguments:
            with_meta: Include information about the section definition and the sections
                position in its parent.
            include_defaults: Include default values of unset quantities.
        '''
1040
1041

        def items() -> Iterable[Tuple[str, Any]]:
1042
1043
1044
1045
1046