legacy.py 17.5 KB
Newer Older
1
2

from typing import cast, Dict, List, Union, Any, Set, Iterable
3
import numpy as np
4
5
from pint.errors import UndefinedUnitError
import os.path
6
from jinja2 import Environment as JinjaEnvironment, PackageLoader, select_autoescape
7
import textwrap
8

9
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl, InfoKindEnv
10
11
12
import nomad_meta_info

from nomad import utils
13
14
15
from nomad.metainfo import (
    Definition, SubSection, Package, Quantity, Category, Section, Reference, units,
    Environment, MEnum)
16
17


18
logger = utils.get_logger(__name__)
19
20


21
22
23
_ignored_packages = [
    'meta_types.nomadmetainfo.json',
    'repository.nomadmetainfo.json']
24
25


26
class LegacyMetainfoEnvironment(Environment):
27
    '''
28
29
    A metainfo environment with functions to create a legacy metainfo version of
    the environment.
30
    '''
31
    def legacy_info(self, definition: Definition, *args, **kwargs) -> InfoKindEl:
32
        ''' Creates a legacy metainfo objects for the given definition. '''
33
34
35
36
37
38
39
40
41
42
43
44
45
        super_names: List[str] = list()
        result: Dict[str, Any] = dict(
            name=definition.name,
            description=definition.description,
            superNames=super_names)

        for category in definition.categories:
            super_names.append(category.name)

        if isinstance(definition, Section):
            result['kindStr'] = 'type_section'
            result['repeats'] = any(
                sub_section.repeats
46
                for sub_section in self.resolve_definitions(definition.name, SubSection))
47

48
            for sub_section in self.resolve_definitions(definition.name, SubSection):
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
                super_names.append(sub_section.m_parent_as(Definition).name)

        elif isinstance(definition, Quantity):
            result['kindStr'] = 'document_content'
            result['shape'] = definition.shape
            dtype_str = None
            if definition.type == int:
                dtype_str = 'i'
            elif definition.type == float:
                dtype_str = 'f'
            elif definition.type == bool:
                dtype_str = 'b'
            elif definition.type == str:
                dtype_str = 'C'
            elif isinstance(definition.type, Reference):
                dtype_str = 'r'
                result['referencedSections'] = [definition.type.target_section_def.name]
66
            elif isinstance(definition.type, MEnum):
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
                dtype_str = 'C'
            elif type(definition.type) == np.dtype:
                dtype_str = definition.type.name[0]
            elif definition.type == Any:
                dtype_str = 'D'
            else:
                raise TypeError(
                    'Unsupported quantity type %s in %s.' % (definition.type, definition))
            result['dtypeStr'] = dtype_str
            if definition.unit is not None:
                result['units'] = str(definition.unit)
            super_names.append(definition.m_parent_as(Definition).name)

        elif isinstance(definition, Category):
            result['kindStr'] = 'abstract_document_content'

        return InfoKindEl(*args, **result, **kwargs)

    def legacy_info_env(self, packages: List[Package] = None, *args, **kwargs) -> InfoKindEnv:
86
        ''' Creates a legacy metainfo environment with all definitions from the given packages. '''
87
        if packages is None:
88
            packages = self.packages
89
90
91
92

        env = InfoKindEnv(*args, **kwargs)
        for package in packages:
            for definition in package.all_definitions.values():
93
94
95
                if not (isinstance(definition, Section) and definition.extends_base_section):
                    env.addInfoKindEl(self.legacy_info(definition))

96
97
98
99
100
101
                if isinstance(definition, Section):
                    for quantity in definition.quantities:
                        env.addInfoKindEl(self.legacy_info(quantity))

        return env

102

103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
class EnvironmentConversion:
    def __init__(self, legacy_env_or_path: Union[InfoKindEnv, str]):
        if isinstance(legacy_env_or_path, str):
            legacy_env_or_path = os.path.normpath(os.path.join(
                os.path.dirname(nomad_meta_info.__file__), legacy_env_or_path))
            self.legacy_env, _ = loadJsonFile(filePath=legacy_env_or_path)

        else:
            self.legacy_env = cast(InfoKindEnv, legacy_env_or_path)

        self.__fix_legacy_super_names()

        self.package_conversions: Dict[str, PackageConversion] = {}

        for legacy_def in self.legacy_env.infoKindEls():
            if legacy_def.package in _ignored_packages:
                continue
            legacy_def.package = legacy_def.package.replace('.nomadmetainfo.json', '').replace('.', '_')
            package_conversion = self.package_conversions.get(legacy_def.package)
            if package_conversion is None:
                package_conversion = PackageConversion(self, legacy_def.package)
                self.package_conversions[legacy_def.package] = package_conversion

            package_conversion.legacy_defs.append(legacy_def)

        for package_conversion in self.package_conversions.values():
            package_conversion.create_definitions()

        for package_conversion in self.package_conversions.values():
            package_conversion.set_super_names()

        for package_conversion in self.package_conversions.values():
            package_conversion.init_definitions()

    def create_env(self) -> LegacyMetainfoEnvironment:
        env = LegacyMetainfoEnvironment()
        for package_conv in self.package_conversions.values():
            package = package_conv.package
            errors, warnings = package.m_all_validate()
            if len(errors) > 0:
                logger.error(
                    '%s. There are %d more errors in converted legacy package %s' %
                    (errors[0], len(errors) - 1, package))
            if len(warnings) > 0:
                logger.warn(
                    '%s. There are %d more warnings in converted legacy package %s' %
                    (warnings[0], len(warnings) - 1, package))
            env.m_add_sub_section(Environment.packages, package)
            package.init_metainfo()

        return env

    def __fix_legacy_super_names(self):

        def get_super_names(legacy_def: InfoKindEl, super_categories: Set[str] = None):
            super_section: str = None
            if super_categories is None:
                super_categories = set()

            for super_name in legacy_def.superNames:
                super_def = self.legacy_env.infoKindEl(super_name)

                if super_def.kindStr == 'type_section':
                    super_section = super_def.name

                elif super_def.kindStr == 'type_abstract_document_content':
                    super_categories.add(super_def.name)
                    super_super_section, _ = get_super_names(super_def, super_categories=super_categories)
171

172
173
                    if super_super_section is None:
                        pass
174

175
176
                    elif super_section is None:
                        super_section = super_super_section
177

178
179
                    elif super_section == super_super_section:
                        pass
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
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
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
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
                    else:
                        logger.error('conflicting parent sections %s, %s for %s' % (
                            super_section, super_def.name, legacy_def.name))

            return super_section, super_categories

        for legacy_def in self.legacy_env.infoKindEls():
            super_section, super_categories = get_super_names(legacy_def)

            if super_section is None:
                legacy_def.superNames = list(super_categories)

            else:
                legacy_def.superNames = [super_section] + list(super_categories)

    def resolve(self, name: str) -> Iterable[Definition]:
        for package_conversion in self.package_conversions.values():
            definition = package_conversion.package.all_definitions.get(name)
            if definition is not None:
                yield definition


class PackageConversion:

    def __init__(self, env_conversion: EnvironmentConversion, name: str):
        self.env_conversion = env_conversion
        self.legacy_defs: List[InfoKindEl] = []

        self.package = Package(name=name)
        self.quantities: Dict[str, Quantity] = {}

        self.logger = logger.bind(package=name)

    def create_definitions(self):
        for legacy_def in self.legacy_defs:
            name = legacy_def.name

            if legacy_def.kindStr == 'type_abstract_document_content':
                self.package.m_create(Category, name=name)

            elif legacy_def.kindStr == 'type_section':
                self.package.m_create(Section, name=name)

            elif legacy_def.kindStr in ['type_dimension', 'type_document_content']:
                definition = Quantity(name=name)
                self.quantities[name] = (definition)

            else:
                logger.error('unknown kindStr %s for %s' % (legacy_def.kindStr, name))

    def __resolve(self, name: str, create_extends: bool = False):
        definition: Definition = self.package.all_definitions.get(name)
        if definition is None:
            definition = self.quantities.get(name)

        if definition is not None:
            if not (isinstance(definition, Section) and definition.extends_base_section) or create_extends:
                return definition

        for definition in self.env_conversion.resolve(name):
            if isinstance(definition, Section) and definition.extends_base_section:
                continue

            if create_extends and isinstance(definition, Section):
                extending_def = self.package.m_create(Section, name=definition.name)
                extending_def.base_sections = [definition]
                extending_def.extends_base_section = True
                return extending_def

            return definition

        assert False, 'definition %s must be created now' % name

    def set_super_names(self):
        for legacy_def in self.legacy_defs:
            definition = self.__resolve(legacy_def.name)
            assert definition is not None, 'definition %s must exist' % legacy_def.name

            if isinstance(definition, Section):
                parent_section: Section = None
                for super_name in legacy_def.superNames:
                    super_def = self.__resolve(super_name, create_extends=True)
                    if isinstance(super_def, Section):
                        parent_section = cast(Section, super_def)

                if parent_section is not None:
                    sub_section = parent_section.m_create(SubSection, name=definition.name)
                    sub_section.sub_section = definition
                    sub_section.repeats = legacy_def.repeats is None or legacy_def.repeats

            if isinstance(definition, Quantity):
                parent_section: Section = None
                for super_name in legacy_def.superNames:
                    super_def = self.__resolve(super_name, create_extends=True)
                    if isinstance(super_def, Section):
                        parent_section = cast(Section, super_def)

                parent_section.m_add_sub_section(Section.quantities, definition)

    def init_definitions(self):
        for legacy_def in self.legacy_defs:
            definition = self.__resolve(legacy_def.name)
            assert definition is not None, 'definition %s must exist' % legacy_def.name
            logger = self.logger.bind(definition=definition.name)

            # common properties
            definition.description = legacy_def.description

            if isinstance(definition, Definition):
                # deal with categories
                categories: List[Category] = []
                for super_name in legacy_def.superNames:
                    super_def = self.__resolve(super_name)
                    if isinstance(super_def, Category):
                        categories.append(super_def)

                definition.categories = categories

            if isinstance(definition, Quantity):
                # type
                referenced_sections = legacy_def.extra_args.get('referencedSections', [])
                if len(referenced_sections) == 1:
                    referenced_section = self.__resolve(referenced_sections[0])
                    if referenced_section is None:
                        logger.error('could not find referencedSection %s of %s' % (
                            referenced_sections[0], definition.name))
                        definition.type = int
                    else:
                        definition.type = Reference(referenced_section)

                elif len(referenced_sections) > 1:
                    logger.error(
                        'higher dimensional references not yet supported: %s' % legacy_def.name)
                    definition.type = np.dtype(int)

                elif legacy_def.kindStr == 'type_dimension':
                    definition.type = int
                elif legacy_def.dtypeStr == 'D':
                    definition.type = Any
                elif legacy_def.dtypeStr == 'C':
                    definition.type = str
                elif legacy_def.dtypeStr == 'r':
                    logger.error('r typed quantity %s  doesn\'t have referencedSections' % legacy_def.name)
                    definition.type = int
                elif legacy_def.dtypeStr == 'b':
                    definition.type = bool
                elif legacy_def.dtypeStr == 'i64':
                    definition.type = np.dtype(np.int64)
                elif legacy_def.dtypeStr == 'f':
                    definition.type = np.dtype(np.float64)
                else:
                    definition.type = np.dtype(legacy_def.dtypeStr)

                # shapes
                legacy_shape = legacy_def.shape
                if legacy_shape is None:
                    legacy_shape = []

                definition.shape = legacy_shape
                if len(definition.shape) > 1 and definition.type == str:
                    # Usually only np types have higher shapes in old metainfo;
                    # str is one exception.
                    definition.type = np.dtype('U')

                # units
                if legacy_def.units is not None:
                    try:
                        definition.unit = units.parse_units(legacy_def.units)
                    except UndefinedUnitError:
                        logger.error('unknown unit %s' % legacy_def.units)
                    except ValueError as e:
                        logger.error('cannot parse unit %s' % legacy_def.units, exc_info=e)


def convert(metainfo_path: str) -> LegacyMetainfoEnvironment:
    return EnvironmentConversion(metainfo_path).create_env()


def generate_metainfo_code(metainfo_env: Environment, directory: str = None):
    '''
    Generates python code with metainfo definitions for all packages in the given
    environement

    Arguments:
        env: The metainfo environment.
        directory: An optional directory path. The directory must exist. Default
            is the working directory.
    '''

    if directory is None:
        directory = '.'

    def format_description(description, indent=0, width=90):
        paragraphs = [paragraph.strip() for paragraph in description.split('\n')]

        def format_paragraph(paragraph, first):
            lines = textwrap.wrap(text=paragraph, width=width - indent * 4)
            lines = [l.replace('\\', '\\\\') for l in lines]
            return textwrap.indent(
                '\n'.join(lines), ' ' * 4 * indent, lambda x: not (first and x.startswith(lines[0])))

        return '\n\n'.join([
            format_paragraph(p, i == 0)
            for i, p in enumerate(paragraphs) if p != ''])

    def format_type(mi_type):
        if type(mi_type) == np.dtype:
            return 'np.dtype(np.%s)' % mi_type
        if mi_type in [int, float, str, bool]:
            return mi_type.__name__
        if isinstance(mi_type, Reference):
            return "SectionProxy('%s')" % mi_type.target_section_def.name
        else:
            return str(mi_type)

    def format_unit(unit):
        return "'%s'" % unit

    def format_definition_refs(pkg, definitions):
        def format_definition_ref(definition: Definition):
            if pkg == definition.m_parent:
                return definition.name
403
            else:
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
                return definition.qualified_name()

        return ', '.join([format_definition_ref(definition) for definition in definitions])

    env = JinjaEnvironment(
        loader=PackageLoader('nomad.metainfo', 'templates'),
        autoescape=select_autoescape(['python']))
    env.globals.update(
        format_description=format_description,
        format_type=format_type,
        format_unit=format_unit,
        format_definition_refs=format_definition_refs)

    for package in metainfo_env.packages:
        file_name = package.name
        with open(os.path.join(directory, '%s.py' % file_name), 'wt') as f:
420
421
422
423
424
            code = env.get_template('package.j2').render(pkg=package)
            code = '\n'.join([
                line.rstrip() if line.strip() != '' else ''
                for line in code.split('\n')])
            f.write(code)
425
426


427
428
429
430
431
432
433
434
435
436
437
438
439
440
# if __name__ == '__main__':
#     output = 'output'

#     env = convert('vasp.nomadmetainfo.json')
#     assert env.resolve_definition('x_vasp_incar_EFIELD_PEAD', Quantity) is not None
#     assert 'x_vasp_incar_EFIELD_PEAD' in env.legacy_info_env()
#     generate_metainfo_code(env, output)

#     from output import public
#     import json

#     run = public.section_run()
#     system = run.m_create(public.section_system)
#     system.atom_labels = ['H', 'H', 'O']
441

442
#     print(json.dumps(run.m_to_dict(with_meta=True), indent=2))