metainfo.py 81.4 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

Markus Scheidgen's avatar
Markus Scheidgen committed
42
43
# Metainfo errors

44
class MetainfoError(Exception):
45
    ''' Metainfo related errors. '''
46
47
48
    pass


49
class DeriveError(MetainfoError):
50
    ''' An error occurred while computing a derived value. '''
51
52
53
    pass


54
class MetainfoReferenceError(MetainfoError):
55
    ''' An error indicating that a reference could not be resolved. '''
56
    pass
57
58


Markus Scheidgen's avatar
Markus Scheidgen committed
59
# Metainfo quantity data types
60

61
class MEnum():
62
    '''Allows to define str types with values limited to a pre-set list of possible values.'''
63
64
    def __init__(self, *args, **kwargs):
        # Supports one big list in place of args
65
        if len(args) == 1 and isinstance(args[0], list):
66
            args = args[0]
67

68
69
70
71
72
73
74
75
76
77
78
79
80
        # 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]
81
82


83
class MProxy():
84
    ''' A placeholder object that acts as reference to a value that is not yet resolved.
85
86
87

    Attributes:
        url: The reference represented as an URL string.
88
    '''
89
90
91
92
93

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


94
class DataType:
95
    '''
96
97
    Allows to define custom data types that can be used in the meta-info.

98
    The metainfo supports the most types out of the box. These includes the python build-in
99
100
    primitive types (int, bool, str, float, ...), references to sections, and enums.
    However, in some occasions you need to add custom data types.
101
102
103
104
105

    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.
106
    '''
107
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
108
        ''' Transforms the given value before it is set and checks its type. '''
109
110
111
        return value

    def get_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
112
        ''' Transforms the given value when it is get. '''
113
114
        return value

115
    def serialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
116
        ''' Transforms the given value when making the section serializeable. '''
117
118
        return value

119
    def deserialize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
120
        ''' Transforms the given value from its serializeable form. '''
121
122
123
        return value


124
125
126
127
128
range_re = re.compile(r'(\d)\.\.(\d|\*)')


class _Dimension(DataType):

129
    def set_normalize(self, section, quantity_def: 'Quantity', value):
130
        if isinstance(value, int):
Markus Scheidgen's avatar
Markus Scheidgen committed
131
            return value
132
133
134

        if isinstance(value, str):
            if value.isidentifier():
Markus Scheidgen's avatar
Markus Scheidgen committed
135
                return value
136
            if re.match(range_re, value):
Markus Scheidgen's avatar
Markus Scheidgen committed
137
                return value
138
139

        if isinstance(value, Section):
Markus Scheidgen's avatar
Markus Scheidgen committed
140
            return value
141

142
        if isinstance(value, type) and hasattr(value, 'm_def'):
Markus Scheidgen's avatar
Markus Scheidgen committed
143
            return value
144
145
146

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

147
148
149
150
151
152
153
    @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)
154

155
156
157
158
159
160
161
            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):
162
    def set_normalize(self, section, quantity_def: 'Quantity', value):
163
164
165
        if isinstance(value, str):
            value = units.parse_units(value)

166
        elif not isinstance(value, pint.unit._Unit):
167
168
169
170
            raise TypeError('Units must be given as str or pint Unit instances.')

        return value

171
    def serialize(self, section, quantity_def: 'Quantity', value):
172
173
        return value.__str__()

174
    def deserialize(self, section, quantity_def: 'Quantity', value):
175
176
        return units.parse_units(value)

177

178
units = pint.UnitRegistry()
179
''' The default pint unit registry that should be used to give units to quantity definitions. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
180
181


182
class _Callable(DataType):
183
184
185
186
187
188
189
    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')


190
class _QuantityType(DataType):
191
    ''' Data type for defining the type of a metainfo quantity.
192
193
194
195
196
197

    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
198
    - an MEnum instance to use it's values as possible str values
199
200
    - a custom datatype, i.e. instance of :class:`DataType`
    - Any
201
    '''
202
203
204
205
206

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

207
208
        if isinstance(value, MEnum):
            for enum_value in value._values:
209
                if not isinstance(enum_value, str):
210
                    raise TypeError('MEnum value %s is not a string.' % enum_value)
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
            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):
235
        if value is str or value is int or value is float or value is bool:
236
237
            return dict(type_kind='python', type_data=value.__name__)

238
        if isinstance(value, MEnum):
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
            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):
265
    ''' Datatype used for reference quantities. '''
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

    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

296
297
298
    def resolve(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> 'MSection':
        return section.m_resolve(value.url)

299
300
    def get_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        if isinstance(value, MProxy):
301
            resolved: 'MSection' = self.resolve(section, quantity_def, value)
302
303
            if resolved is None:
                raise ReferenceError('Could not resolve %s from %s.' % (value, section))
304

305
306
307
308
309
310
311
312
313
314
315
            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)


316
class _Datetime(DataType):
317

318
    def _parse(self, datetime_str: str) -> datetime:
319
        try:
320
321
322
            return aniso8601.parse_datetime(datetime_str)
        except ValueError:
            pass
323

324
325
326
327
328
329
330
331
332
333
334
335
336
337
        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):
338
        if isinstance(value, str):
339
340
341
342
            value = self._parse(value)

        elif isinstance(value, (int, float)):
            value = datetime.fromtimestamp(value)
343
344
345
346
347
348

        if not isinstance(value, datetime):
            raise TypeError('%s is not a datetime.' % value)

        return value

349
350
351
    def set_normalize(self, section: 'MSection', quantity_def: 'Quantity', value: Any) -> Any:
        return self._convert(value)

352
353
354
355
356
    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:
357
        return self._convert(value)
358
359


360
361
362
363
364
Dimension = _Dimension()
Unit = _Unit()
QuantityType = _QuantityType()
Callable = _Callable()
Datetime = _Datetime()
365
366


Markus Scheidgen's avatar
Markus Scheidgen committed
367
368
# Metainfo data storage and reflection interface

369
class MObjectMeta(type):
370

371
    def __new__(self, cls_name, bases, dct):
372
373
374
375
376
377
        do_init = dct.get('do_init', None)
        if do_init is not None:
            del(dct['do_init'])
        else:
            do_init = True

378
        cls = super().__new__(self, cls_name, bases, dct)
Markus Scheidgen's avatar
Markus Scheidgen committed
379

Markus Scheidgen's avatar
Markus Scheidgen committed
380
        init = getattr(cls, '__init_cls__')
381
        if init is not None and do_init and not is_bootstrapping:
382
383
            init()
        return cls
384
385


386
SectionDef = Union[str, 'Section', 'SubSection', Type[MSectionBound]]
387
''' Type for section definition references.
388
389
390
391
392
393
394

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
395
'''
396
397


398
class MData:
399
    ''' An interface for low-level metainfo data objects.
400
401
402

    Metainfo data objects store the data of a single section instance. This interface
    constitutes the minimal functionality for accessing and modifying section data.
403
    Different implementations of this interface, can realize different storage backends.
404
405
406
407

    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.
408
    '''
409
410
411
412
413
414
415
416

    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:
417
        ''' Set the given value for the given quantity. '''
418
419
420
        raise NotImplementedError()

    def m_get(self, section: 'MSection', quantity_def: 'Quantity') -> Any:
421
        ''' Retrieve the given value for the given quantity. '''
422
423
424
        raise NotImplementedError()

    def m_is_set(self, section: 'MSection', quantity_def: 'Quantity') -> bool:
425
        ''' True iff this quantity was explicitely set. '''
426
427
428
429
430
        raise NotImplementedError()

    def m_add_values(
            self, section: 'MSection', quantity_def: 'Quantity', values: Any,
            offset: int) -> None:
431
        ''' Add (partial) values for the given quantity of higher dimensionality. '''
432
433
434
435
436
        raise NotImplementedError()

    def m_add_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            sub_section: 'MSection') -> None:
437
438
439
440
441
442
        ''' Adds the given section instance as a sub section of the given sub section definition. '''
        raise NotImplementedError()

    def m_remove_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection', index: int) -> None:
        ''' Removes the given section instance as a sub section of the given sub section definition. '''
443
444
445
446
447
        raise NotImplementedError()

    def m_get_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection',
            index: int) -> 'MSection':
448
        ''' Retrieves a single sub section of the given sub section definition. '''
449
450
451
452
        raise NotImplementedError()

    def m_get_sub_sections(
            self, section: 'MSection', sub_section_def: 'SubSection') -> Iterable['MSection']:
453
        ''' Retrieves  all sub sections of the given sub section definition. '''
454
455
456
        raise NotImplementedError()

    def m_sub_section_count(self, section: 'MSection', sub_section_def: 'SubSection') -> int:
457
        ''' Returns the number of sub sections for the given sub section definition. '''
458
459
460
461
        raise NotImplementedError()


class MDataDict(MData):
462
    ''' A simple dict backed implementaton of :class:`MData`. It is used by default. '''
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
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510

    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

511
512
513
514
515
516
517
518
519
    def m_remove_sub_section(
            self, section: 'MSection', sub_section_def: 'SubSection', index: int) -> None:

        if sub_section_def.repeats:
            del(self.dct[sub_section_def.name][index])

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

520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
    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])


545
class MResource():
546
    '''Represents a collection of related metainfo data, i.e. a set of :class:`MSection` instances.
547
548
549

    MResource allows to keep related objects together and resolve sections of certain
    section definitions.
550
    '''
551
552
553
554
555
    def __init__(self):
        self.__data: Dict['Section', List['MSection']] = dict()
        self.contents: List['MSection'] = []

    def create(self, section_cls: Type[MSectionBound], *args, **kwargs) -> MSectionBound:
556
        ''' Create an instance of the given section class and adds it to this resource. '''
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
        result = section_cls(*args, **kwargs)
        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):
        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]:
575
        ''' Returns all instances of the given section class in this resource. '''
576
577
578
        return cast(List[MSectionBound], self.__data.get(section_cls.m_def, []))

    def unload(self):
579
        ''' Breaks all references among the contain metainfo sections to allow GC. '''
580
581
582
583
584
585
586
587
        for collections in self.__data.values():
            for section in collections:
                section.m_parent = None
            collections.clear()

        # TODO break actual references via quantities


588
589
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.
590

591
592
593
594
595
    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`.
596
597
598
599

    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.

600
601
602
    Attributes:
        m_def: The `section definition` that this `section instance` follows as a
            :class:`Section` object.
603

604
605
        m_parent:
            If this section is a sub-section, this references the parent section instance.
606

607
608
609
        m_parent_sub_section:
            If this section is a sub-section, this is the :class:`SubSection` that defines
            this relationship.
610

611
612
613
614
615
616
617
        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).
618

619
620
        m_resource: The :class:`MResource` that contains and manages this section.

621
    '''
622

623
    m_def: 'Section' = None
624

625
626
627
    def __init__(
            self, m_def: 'Section' = None, m_data: MData = None,
            m_resource: MResource = None, **kwargs):
628

629
        self.m_def: 'Section' = m_def
630
631
        self.m_parent: 'MSection' = None
        self.m_parent_sub_section: 'SubSection' = None
632
        self.m_parent_index = -1
633
        self.m_resource = m_resource
634

635
        # get missing m_def from class
636
        cls = self.__class__
637
638
        if self.m_def is None:
            self.m_def = cls.m_def
639

640
        # check m_def
641
        if cls.m_def is not None:
642
643
644
645
646
647
648
649
650
            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.')
651

652
        # get annotations from kwargs
653
        self.m_annotations: Dict[str, Any] = {}
Markus Scheidgen's avatar
Markus Scheidgen committed
654
        rest = {}
655
656
657
658
        for key, value in kwargs.items():
            if key.startswith('a_'):
                self.m_annotations[key[2:]] = value
            else:
Markus Scheidgen's avatar
Markus Scheidgen committed
659
660
                rest[key] = value

661
662
663
        # initialize data
        self.m_data = m_data
        if self.m_data is None:
664
            self.m_data = MDataDict()
665

666
667
        # set remaining kwargs
        if is_bootstrapping:
668
            self.m_data.dct.update(**rest)  # type: ignore
Markus Scheidgen's avatar
Markus Scheidgen committed
669
        else:
670
            self.m_update(**rest)
671

672
    @classmethod
Markus Scheidgen's avatar
Markus Scheidgen committed
673
    def __init_cls__(cls):
674
675
        # ensure that the m_def is defined
        m_def = cls.m_def
Markus Scheidgen's avatar
Markus Scheidgen committed
676
        if m_def is None:
677
678
            m_def = Section()
            setattr(cls, 'm_def', m_def)
679

680
        # transfer name m_def
681
682
        m_def.name = cls.__name__
        m_def.section_cls = cls
683

684
        # add base sections
685
        extended_base_section = None
686
687
688
689
690
691
        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
692
            if base_sections_count > 1:
693
694
695
696
                raise MetainfoError(
                    'Section %s extend the base section, but has more than one base section' % m_def)

            base_section_cls = cls.__bases__[0]
697
            extended_base_section = base_section = getattr(base_section_cls, 'm_def', None)
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
            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

722
723
        constraints: Set[str] = set()
        event_handlers: Set[Callable] = set(m_def.event_handlers)
724
        for name, attr in cls.__dict__.items():
725
            # transfer names and descriptions for properties, init properties
726
            if isinstance(attr, Property):
727
                attr.name = name
728
                if attr.description is not None:
729
                    attr.description = inspect.cleandoc(attr.description).strip()
730
                    attr.__doc__ = attr.description
731

732
                if isinstance(attr, Quantity):
733
                    section_to_add_properties_to.m_add_sub_section(Section.quantities, attr)
734
                elif isinstance(attr, SubSection):
735
                    section_to_add_properties_to.m_add_sub_section(Section.sub_sections, attr)
736
737
                else:
                    raise NotImplementedError('Unknown property kind.')
738

739
740
                attr.__init_property__()

741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
            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
760

761
762
        m_def.constraints = list(constraints)
        m_def.event_handlers = list(event_handlers)
Markus Scheidgen's avatar
Markus Scheidgen committed
763

764
765
766
        # add section cls' section to the module's package
        module_name = cls.__module__
        pkg = Package.from_module(module_name)
767
        pkg.m_add_sub_section(Package.section_definitions, cls.m_def)
768

769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
        # 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

800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
        # 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))

819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
        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))

840
841
        elif isinstance(quantity_def.type, MEnum):
            if value not in quantity_def.type._values:
842
843
844
845
846
847
848
                raise TypeError(
                    'The value %s is not an enum value for quantity %s.' %
                    (value, quantity_def))

        elif quantity_def.type == Any:
            pass

849
850
851
852
853
854
        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)

855
        else:
856
            if value is not None and type(value) != quantity_def.type:
857
858
859
860
861
862
                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

863
864
865
866
    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
867

868
869
870
871
872
873
874
875
    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

876
        if len(quantity_def.shape) > 0 and type(value) != np.ndarray:
877
878
879
880
881
882
            try:
                value = np.asarray(value)
            except TypeError:
                raise TypeError(
                    'Could not convert value %s of %s to a numpy array' %
                    (value, quantity_def))
883
884
885
886
887
888
889
        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))
890
891
892

        return self.__check_np(quantity_def, value)

893
    def m_set(self, quantity_def: 'Quantity', value: Any) -> None:
894
        ''' Set the given value for the given quantity. '''
895
        quantity_def = self.__resolve_synonym(quantity_def)
896

897
898
        if quantity_def.derived is not None:
            raise MetainfoError('The quantity %s is derived and cannot be set.' % quantity_def)
899
900

        if type(quantity_def.type) == np.dtype:
901
            value = self.__to_np(quantity_def, value)
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920

        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.')

921
        self.m_data.m_set(self, quantity_def, value)
922

923
924
925
926
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_set'):
                handler(self, quantity_def, value)

927
    def m_get(self, quantity_def: 'Quantity') -> Any:
928
        ''' Retrieve the given value for the given quantity. '''
929
        quantity_def = self.__resolve_synonym(quantity_def)
930
931
932
933
934
935
        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)))

936
937
        value = self.m_data.m_get(self, quantity_def)

938
939
940
        if value is None:
            return value

941
942
943
944
945
946
947
948
949
950
951
952
953
954
        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.')
955

956
957
958
959
            if isinstance(quantity_def.type, Reference):
                # save the resolved values for the next access to avoid re-resolve
                self.m_data.m_set(self, quantity_def, value)

960
961
962
963
        elif type(quantity_def.type) == np.dtype:
            if quantity_def.unit is not None:
                value = value * quantity_def.unit

964
        return value
965

966
    def m_is_set(self, quantity_def: 'Quantity') -> bool:
967
        ''' True if the given quantity is set. '''
968
        quantity_def = self.__resolve_synonym(quantity_def)
969
970
971
        if quantity_def.derived is not None:
            return True

972
        return self.m_data.m_is_set(self, quantity_def)
Markus Scheidgen's avatar
Markus Scheidgen committed
973

974
    def m_add_values(self, quantity_def: 'Quantity', values: Any, offset: int) -> None:
975
        ''' Add (partial) values for the given quantity of higher dimensionality. '''
976
        self.m_data.m_add_values(self, quantity_def, values, offset)
977

978
    def m_add_sub_section(self, sub_section_def: 'SubSection', sub_section: 'MSection') -> None:
979
        ''' Adds the given section instance as a sub section of the given sub section definition. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
980

981
        parent_index = -1
982
        if sub_section_def.repeats:
983
            parent_index = self.m_sub_section_count(sub_section_def)
984
985
986
987
988
989
990
991
992
993

        else:
            old_sub_section = self.m_data.m_get_sub_section(self, sub_section_def, -1)
            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)

994
995
996
        sub_section.m_parent = self
        sub_section.m_parent_sub_section = sub_section_def
        sub_section.m_parent_index = parent_index
997
998
999
1000
        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)
1001

1002
        self.m_data.m_add_sub_section(self, sub_section_def, sub_section)
1003

1004
1005
1006
1007
        for handler in self.m_def.event_handlers:
            if handler.__name__.startswith('on_add_sub_section'):
                handler(self, sub_section_def, sub_section)

1008
1009
1010
1011
    def m_remove_sub_section(self, sub_section_def: 'SubSection', index: int) -> None:
        ''' Removes the exiting section for a non repeatable sub section '''
        self.m_data.m_remove_sub_section(self, sub_section_def, index)

1012
    def m_get_sub_section(self, sub_section_def: 'SubSection', index: int) -> 'MSection':
1013
        ''' Retrieves a single sub section of the given sub section definition. '''
1014
        return self.m_data.m_get_sub_section(self, sub_section_def, index)
1015

1016
    def m_get_sub_sections(self, sub_section_def: 'SubSection') -> Iterable['MSection']:
1017
        ''' Retrieves  all sub sections of the given sub section definition. '''
1018
        return self.m_data.m_get_sub_sections(self, sub_section_def)
1019

1020
    def m_sub_section_count(self, sub_section_def: 'SubSection') -> int:
1021
        ''' Returns the number of sub sections for the given sub section definition. '''
1022
        return self.m_data.m_sub_section_count(self, sub_section_def)
1023

1024
1025
1026
    def m_create(
            self, section_cls: Type[MSectionBound], sub_section_def: 'SubSection' = None,
            **kwargs) -> MSectionBound:
1027
        ''' Creates a section instance and adds it to this section provided there is a
1028
        corresponding sub section.
1029
1030
1031
1032
1033

        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.
1034
        '''
1035

1036
        section_def = section_cls.m_def
1037
1038
1039
        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:
1040
            raise TypeError('There is no sub section to hold a %s in %s.' % (section_def, self.m_def))
1041

1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
        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]

1055
1056
        sub_section = section_cls(**kwargs)
        self.m_add_sub_section(sub_section_def, sub_section)
1057

1058
        return cast(MSectionBound, sub_section)
1059

1060
    def m_update(self, safe: bool = True, **kwargs):
1061
        ''' Updates all quantities and sub-sections with the given arguments. '''
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
        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)
1075
                    else:
1076
1077
                        self.m_add_sub_section(prop, item)

1078
                else:
1079
                    self.m_set(prop, value)
1080

1081
1082
        else:
            self.m_data.m_data.dct.update(**kwargs)  # type: ignore
1083

1084
    def m_as(self, section_cls: Type[MSectionBound]) -> MSectionBound:
1085
        ''' 'Casts' this section to the given extending sections. '''
1086
1087
        return cast(MSectionBound, self)

1088
    def m_follows(self, definition: 'Section') -> bool:
1089
        ''' Determines if this section's definition is or is derived from the given definition. '''
1090
        return self.m_def == definition or definition in self.m_def.all_base_sections
1091

1092
1093
1094
1095
1096
1097
1098
1099
1100
    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.
        '''
1101
1102

        def items() -> Iterable[Tuple[str, Any]]:
1103
1104
1105
1106
1107
1108
1109
1110
1111
            # 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
1112
            for name, quantity in self.m_def.all_quantities.items():
1113
                if quantity.virtual:
1114
1115
                    continue

1116
1117
1118
1119
                is_set = self.m_is_set(quantity)
                if not is_set:
                    if not include_defaults or not quantity.m_is_set(Quantity.default):
                        continue
1120