data.py 22 KB
Newer Older
Markus Scheidgen's avatar
Markus Scheidgen committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
# 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.

"""
This module comprises a set of persistent document classes that hold all user related
data. These are information about users, their uploads and datasets, the associated
calculations, and files


.. autoclass:: Calc
    :members:
.. autoclass:: Upload
    :members:
"""

27
from typing import List, Any, ContextManager, Tuple, Generator
28
from mongoengine import StringField, DateTimeField, DictField
Markus Scheidgen's avatar
Markus Scheidgen committed
29
import logging
30
from structlog import wrap_logger
31
from contextlib import contextmanager
Markus Scheidgen's avatar
Markus Scheidgen committed
32

33
from nomad import utils, coe_repo, config, infrastructure, search
Markus Scheidgen's avatar
Markus Scheidgen committed
34
from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles
35
from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
36
from nomad.parsing import parser_dict, match_parser
Markus Scheidgen's avatar
Markus Scheidgen committed
37
from nomad.normalizing import normalizers
Markus Scheidgen's avatar
Markus Scheidgen committed
38
from nomad.datamodel import UploadWithMetadata, CalcWithMetadata
Markus Scheidgen's avatar
Markus Scheidgen committed
39
40


Markus Scheidgen's avatar
Markus Scheidgen committed
41
class Calc(Proc):
Markus Scheidgen's avatar
Markus Scheidgen committed
42
43
44
45
46
47
48
49
50
51
    """
    Instances of this class represent calculations. This class manages the elastic
    search index entry, files, and archive for the respective calculation.

    It also contains the calculations processing and its state.

    The attribute list, does not include the various repository properties generated
    while parsing, including ``program_name``, ``program_version``, etc.

    Attributes:
52
        calc_id: the calc_id of this calc
Markus Scheidgen's avatar
Markus Scheidgen committed
53
54
55
56
        parser: the name of the parser used to process this calc
        upload_id: the id of the upload used to create this calculation
        mainfile: the mainfile (including path in upload) that was used to create this calc
    """
57
    calc_id = StringField(primary_key=True)
Markus Scheidgen's avatar
Markus Scheidgen committed
58
59
60
61
62
63
    upload_id = StringField()
    mainfile = StringField()
    parser = StringField()

    meta: Any = {
        'indices': [
64
            'upload_id', 'mainfile', 'code', 'parser', 'tasks_status'
Markus Scheidgen's avatar
Markus Scheidgen committed
65
66
67
68
69
70
        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self._parser_backend = None
71
72
        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
73
        self._calc_proc_logwriter = None
74
        self._calc_proc_logwriter_ctx: ContextManager = None
Markus Scheidgen's avatar
Markus Scheidgen committed
75
76
77

    @classmethod
    def get(cls, id):
78
        return cls.get_by_id(id, 'calc_id')
Markus Scheidgen's avatar
Markus Scheidgen committed
79

Markus Scheidgen's avatar
Markus Scheidgen committed
80
    @property
81
82
    def mainfile_file(self) -> PathObject:
        return self.upload_files.raw_file_object(self.mainfile)
Markus Scheidgen's avatar
Markus Scheidgen committed
83

84
85
86
87
88
89
    @property
    def upload(self) -> 'Upload':
        if not self._upload:
            self._upload = Upload.get(self.upload_id)
        return self._upload

90
91
92
    @property
    def upload_files(self) -> ArchiveBasedStagingUploadFiles:
        if not self._upload_files:
93
            self._upload_files = ArchiveBasedStagingUploadFiles(self.upload_id, is_authorized=lambda: True, local_path=self.upload.local_path)
94
95
        return self._upload_files

Markus Scheidgen's avatar
Markus Scheidgen committed
96
    def get_logger(self, **kwargs):
97
98
99
100
        """
        Returns a wrapped logger that additionally saves all entries to the calculation
        processing log in the archive.
        """
101
102
103
        logger = super().get_logger()
        logger = logger.bind(
            upload_id=self.upload_id, mainfile=self.mainfile, calc_id=self.calc_id, **kwargs)
104

105
        if self._calc_proc_logwriter_ctx is None:
106
            self._calc_proc_logwriter_ctx = self.upload_files.archive_log_file(self.calc_id, 'wt')
107
            self._calc_proc_logwriter = self._calc_proc_logwriter_ctx.__enter__()  # pylint: disable=E1101
108

109
        def save_to_calc_log(logger, method_name, event_dict):
110
111
112
113
114
115
116
117
118
119
120
            if self._calc_proc_logwriter is not None:
                program = event_dict.get('normalizer', 'parser')
                event = event_dict.get('event', '')
                entry = '[%s] %s: %s' % (method_name, program, event)
                if len(entry) > 120:
                    self._calc_proc_logwriter.write(entry[:120])
                    self._calc_proc_logwriter.write('...')
                else:
                    self._calc_proc_logwriter.write(entry)
                self._calc_proc_logwriter.write('\n')

121
122
            return event_dict

123
        return wrap_logger(logger, processors=[save_to_calc_log])
124

Markus Scheidgen's avatar
Markus Scheidgen committed
125
    @process
126
    def process_calc(self):
127
        logger = self.get_logger()
128
        if self.upload is None:
129
            logger.error('calculation upload does not exist')
Markus Scheidgen's avatar
Markus Scheidgen committed
130
131
132
133
134
135

        try:
            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
Markus Scheidgen's avatar
Markus Scheidgen committed
136
            # close loghandler that was not closed due to failures
137
            try:
138
139
140
                if self._calc_proc_logwriter is not None:
                    self._calc_proc_logwriter.close()
                    self._calc_proc_logwriter = None
141
142
143
            except Exception as e:
                logger.error('could not close calculation proc log', exc_info=e)

144
145
146
147
148
149
150
    def on_process_complete(self, process_name):
        # the save might be necessary to correctly read the join condition from the db
        self.save()
        # in case of error, the process_name might be unknown
        if process_name == 'process_calc' or process_name is None:
            self.upload.reload()
            self.upload.check_join()
Markus Scheidgen's avatar
Markus Scheidgen committed
151
152
153

    @task
    def parsing(self):
154
        context = dict(parser=self.parser, step=self.parser)
155
        logger = self.get_logger(**context)
156
        parser = parser_dict[self.parser]
Markus Scheidgen's avatar
Markus Scheidgen committed
157

158
        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
159
160
            self._parser_backend = parser.run(
                self.upload_files.raw_file_object(self.mainfile).os_path, logger=logger)
Markus Scheidgen's avatar
Markus Scheidgen committed
161

162
163
        self._parser_backend.openNonOverlappingSection('section_calculation_info')
        self._parser_backend.addValue('upload_id', self.upload_id)
164
165
        self._parser_backend.addValue('calc_id', self.calc_id)
        self._parser_backend.addValue('calc_hash', self.upload_files.calc_hash(self.mainfile))
166
167
168
        self._parser_backend.addValue('main_file', self.mainfile)
        self._parser_backend.addValue('parser_name', self.parser)

Markus Scheidgen's avatar
Markus Scheidgen committed
169
        if self._parser_backend.status[0] != 'ParseSuccess':
170
            logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
171
            error = self._parser_backend.status[1]
172
            self._parser_backend.addValue('parse_status', 'ParseFailure')
173
            self.fail(error, level=logging.DEBUG, **context)
174
175
176
177
178
        else:
            self._parser_backend.addValue('parse_status', 'ParseSuccess')

        self._parser_backend.closeNonOverlappingSection('section_calculation_info')

179
180
181
182
183
184
        self._parser_backend.openNonOverlappingSection('section_repository_info')
        self._parser_backend.addValue('repository_archive_gid', '%s/%s' % (self.upload_id, self.calc_id))
        self._parser_backend.addValue(
            'repository_filepaths', self.upload_files.calc_files(self.mainfile))
        self._parser_backend.closeNonOverlappingSection('section_repository_info')

185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
        self.add_processor_info(self.parser)

    @contextmanager
    def use_parser_backend(self, processor_name):
        self._parser_backend.reset_status()
        yield self._parser_backend
        self.add_processor_info(processor_name)

    def add_processor_info(self, processor_name: str) -> None:
        self._parser_backend.openContext('/section_calculation_info/0')
        self._parser_backend.openNonOverlappingSection('section_archive_processing_info')
        self._parser_backend.addValue('archive_processor_name', processor_name)

        if self._parser_backend.status[0] == 'ParseSuccess':
            warnings = getattr(self._parser_backend, '_warnings', [])
            if len(warnings) > 0:
                self._parser_backend.addValue('archive_processor_status', 'WithWarnings')
                self._parser_backend.addValue('archive_processor_warning_number', len(warnings))
                self._parser_backend.addArrayValues('archive_processor_warnings', [str(warning) for warning in warnings])
            else:
                self._parser_backend.addValue('archive_processor_status', 'Success')
        else:
207
            errors = self._parser_backend.tasks_status[1]
208
209
210
211
            self._parser_backend.addValue('archive_processor_error', str(errors))

        self._parser_backend.closeNonOverlappingSection('section_archive_processing_info')
        self._parser_backend.closeContext('/section_calculation_info/0')
Markus Scheidgen's avatar
Markus Scheidgen committed
212
213
214
215
216

    @task
    def normalizing(self):
        for normalizer in normalizers:
            normalizer_name = normalizer.__name__
217
            context = dict(normalizer=normalizer_name, step=normalizer_name)
218
            logger = self.get_logger(**context)
Markus Scheidgen's avatar
Markus Scheidgen committed
219
220

            with utils.timer(
221
                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
222
223
                with self.use_parser_backend(normalizer_name) as backend:
                    normalizer(backend).normalize(logger=logger)
Markus Scheidgen's avatar
Markus Scheidgen committed
224

225
226
            failed = self._parser_backend.status[0] != 'ParseSuccess'
            if failed:
227
                logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
228
                error = self._parser_backend.status[1]
229
                self.fail(error, level=logging.WARNING, **context)
230
231
232
233
                break
            else:
                logger.debug(
                    'completed normalizer successfully', normalizer=normalizer_name)
Markus Scheidgen's avatar
Markus Scheidgen committed
234
235
236

    @task
    def archiving(self):
237
238
        logger = self.get_logger()

239
240
        calc_with_metadata = self._parser_backend.to_calc_with_metadata()

241
        # persist the repository metadata
242
243
244
245
246
        with utils.timer(logger, 'saved repo metadata', step='persist'):
            self.upload_files.metadata.insert(calc_with_metadata.to_dict())

        # index in search
        with utils.timer(logger, 'indexed', step='persist'):
247
248
            calc_with_metadata.update(published=False, uploader=self.upload.uploader.to_popo())
            search.Entry.from_calc_with_metadata(calc_with_metadata).save()
249

250
        # persist the archive
Markus Scheidgen's avatar
Markus Scheidgen committed
251
        with utils.timer(
252
                logger, 'archived', step='persist',
Markus Scheidgen's avatar
Markus Scheidgen committed
253
                input_size=self.mainfile_file.size) as log_data:
254
            with self.upload_files.archive_file(self.calc_id, 'wt') as out:
255
256
                self._parser_backend.write_json(out, pretty=True)

257
            log_data.update(archive_size=self.upload_files.archive_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
258
259
260
261

        # close loghandler
        if self._calc_proc_logwriter is not None:
            with utils.timer(
262
                    logger, 'archived log', step='persist',
Markus Scheidgen's avatar
Markus Scheidgen committed
263
                    input_size=self.mainfile_file.size) as log_data:
264
                self._calc_proc_logwriter_ctx.__exit__(None, None, None)  # pylint: disable=E1101
265
                self._calc_proc_logwriter = None
Markus Scheidgen's avatar
Markus Scheidgen committed
266

267
                log_data.update(log_size=self.upload_files.archive_log_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
268

Markus Scheidgen's avatar
Markus Scheidgen committed
269
270
271
272
    def to_calc_with_metadata(self) -> CalcWithMetadata:
        upload_files = UploadFiles.get(self.upload_id, is_authorized=lambda: True)
        if self.upload_files is None:
            raise KeyError
273

Markus Scheidgen's avatar
Markus Scheidgen committed
274
275
        _data = upload_files.metadata.get(self.calc_id)
        return CalcWithMetadata(**_data)
276
277


278
class Upload(Proc):
Markus Scheidgen's avatar
Markus Scheidgen committed
279
280
281
282
283
284
    """
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

    Attributes:
        name: optional user provided upload name
285
        local_path: optional local path, e.g. for files that are already somewhere on the server
286
        metadata: optional user provided additional meta data
Markus Scheidgen's avatar
Markus Scheidgen committed
287
288
        upload_id: the upload id generated by the database
        upload_time: the timestamp when the system realised the upload
289
        user_id: the id of the user that created this upload
Markus Scheidgen's avatar
Markus Scheidgen committed
290
291
292
293
294
295
    """
    id_field = 'upload_id'

    upload_id = StringField(primary_key=True)

    name = StringField(default=None)
296
    local_path = StringField(default=None)
297
    metadata = DictField(default=None)
Markus Scheidgen's avatar
Markus Scheidgen committed
298
    upload_time = DateTimeField()
299
    user_id = StringField(required=True)
Markus Scheidgen's avatar
Markus Scheidgen committed
300
301
302

    meta: Any = {
        'indexes': [
303
            'user_id', 'tasks_status'
Markus Scheidgen's avatar
Markus Scheidgen committed
304
305
306
307
308
        ]
    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
309
        self._upload_files: ArchiveBasedStagingUploadFiles = None
Markus Scheidgen's avatar
Markus Scheidgen committed
310
311
312
313
314
315

    @classmethod
    def get(cls, id):
        return cls.get_by_id(id, 'upload_id')

    @classmethod
316
    def user_uploads(cls, user: coe_repo.User) -> List['Upload']:
Markus Scheidgen's avatar
Markus Scheidgen committed
317
        """ Returns all uploads for the given user. Currently returns all uploads. """
318
        return cls.objects(user_id=str(user.user_id))
Markus Scheidgen's avatar
Markus Scheidgen committed
319

320
321
322
323
    @property
    def uploader(self):
        return coe_repo.User.from_user_id(self.user_id)

Markus Scheidgen's avatar
Markus Scheidgen committed
324
325
326
327
328
329
330
331
332
333
334
    def get_logger(self, **kwargs):
        logger = super().get_logger()
        logger = logger.bind(upload_id=self.upload_id, **kwargs)
        return logger

    @classmethod
    def create(cls, **kwargs) -> 'Upload':
        """
        Creates a new upload for the given user, a user given name is optional.
        It will populate the record with a signed url and pending :class:`UploadProc`.
        The upload will be already saved to the database.
335
336

        Arguments:
337
            user (coe_repo.User): The user that created the upload.
Markus Scheidgen's avatar
Markus Scheidgen committed
338
        """
339
        user: coe_repo.User = kwargs['user']
340
341
342
        del(kwargs['user'])
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
343
        kwargs.update(user_id=str(user.user_id))
Markus Scheidgen's avatar
Markus Scheidgen committed
344
        self = super().create(**kwargs)
345

Markus Scheidgen's avatar
Markus Scheidgen committed
346
        self._continue_with('uploading')
347

Markus Scheidgen's avatar
Markus Scheidgen committed
348
349
        return self

350
351
352
353
354
355
356
357
358
359
360
361
362
363
    def delete(self):
        """ Deletes this upload process state entry and its calcs. """
        Calc.objects(upload_id=self.upload_id).delete()
        super().delete()

    @process
    def delete_upload(self):
        """
        Deletes of the upload, including its processing state and
        staging files.
        """
        logger = self.get_logger()

        with utils.lnr(logger, 'staged upload delete failed'):
364
365
366
367
368
            with utils.timer(
                    logger, 'upload deleted from index', step='delete',
                    upload_size=self.upload_files.size):
                search.Entry.delete_upload(self.upload_id)

369
370
371
372
373
374
375
            with utils.timer(
                    logger, 'staged upload deleted', step='delete',
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
                self.delete()

        return True  # do not save the process status on the delete upload
376

377
    @process
378
    def publish_upload(self):
379
380
381
382
383
384
385
        """
        Moves the upload out of staging to add it to the coe repository. It will
        pack the staging upload files in to public upload files, add entries to the
        coe repository db and remove this instance and its calculation from the
        processing state db.
        """
        logger = self.get_logger()
386

387
        with utils.lnr(logger, 'publish failed'):
388
389
            upload_with_metadata = self.to_upload_with_metadata()

390
            with utils.timer(
391
                    logger, 'upload added to repository', step='publish',
392
                    upload_size=self.upload_files.size):
393
                coe_repo.Upload.add(upload_with_metadata)
394
395

            with utils.timer(
396
                    logger, 'staged upload files packed', step='publish',
397
398
399
                    upload_size=self.upload_files.size):
                self.upload_files.pack()

400
401
402
            with utils.timer(
                    logger, 'index updated', step='publish',
                    upload_size=self.upload_files.size):
403
404
405
406
407
408
409
                coe_upload = coe_repo.Upload.from_upload_id(upload_with_metadata.upload_id)
                if coe_upload is not None:
                    for coe_calc in coe_upload.calcs:
                        entry = search.Entry.from_calc_with_metadata(
                            coe_calc.to_calc_with_metadata())
                        entry.published = True
                        entry.save(refresh=True)
410

411
            with utils.timer(
412
                    logger, 'staged upload deleted', step='publish',
413
414
415
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
                self.delete()
Markus Scheidgen's avatar
Markus Scheidgen committed
416

417
        return True  # do not save the process status on the delete upload
418

Markus Scheidgen's avatar
Markus Scheidgen committed
419
    @process
420
    def process_upload(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
421
422
423
424
425
426
427
        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
        pass

428
    @property
429
430
    def upload_files(self) -> ArchiveBasedStagingUploadFiles:
        if not self._upload_files:
431
            self._upload_files = ArchiveBasedStagingUploadFiles(self.upload_id, is_authorized=lambda: True, local_path=self.local_path)
432
        return self._upload_files
433

Markus Scheidgen's avatar
Markus Scheidgen committed
434
435
    @task
    def extracting(self):
436
437
438
439
440
441
        """
        Task performed before the actual parsing/normalizing. Extracting and bagging
        the uploaded files, computing all keys, create an *upload* entry in the NOMAD-coe
        repository db, etc.
        """
        # extract the uploaded file, this will also create a bagit bag.
Markus Scheidgen's avatar
Markus Scheidgen committed
442
443
        logger = self.get_logger()
        try:
Markus Scheidgen's avatar
Markus Scheidgen committed
444
445
            with utils.timer(
                    logger, 'upload extracted', step='extracting',
446
447
                    upload_size=self.upload_files.size):
                self.upload_files.extract()
448
        except KeyError:
449
            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
450
451
452
            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
Markus Scheidgen's avatar
Markus Scheidgen committed
453
454
            return

455
    def match_mainfiles(self) -> Generator[Tuple[str, object], None, None]:
456
457
458
459
460
461
462
        """
        Generator function that matches all files in the upload to all parsers to
        determine the upload's mainfiles.

        Returns:
            Tuples of mainfile, filename, and parsers
        """
463
        for filename in self.upload_files.raw_file_manifest():
464
            try:
465
                parser = match_parser(filename, self.upload_files)
466
467
468
469
470
471
                if parser is not None:
                    yield filename, parser
            except Exception as e:
                self.get_logger().error(
                    'exception while matching pot. mainfile',
                    mainfile=filename, exc_info=e)
472

Markus Scheidgen's avatar
Markus Scheidgen committed
473
474
    @task
    def parse_all(self):
475
        """
476
        Identified mainfile/parser combinations among the upload's files, creates
477
478
        respective :class:`Calc` instances, and triggers their processing.
        """
479
480
        logger = self.get_logger()

Markus Scheidgen's avatar
Markus Scheidgen committed
481
482
        with utils.timer(
                logger, 'upload extracted', step='matching',
483
484
                upload_size=self.upload_files.size):
            for filename, parser in self.match_mainfiles():
485
                calc = Calc.create(
486
                    calc_id=self.upload_files.calc_id(filename),
487
488
489
                    mainfile=filename, parser=parser.name,
                    upload_id=self.upload_id)

490
                calc.process_calc()
Markus Scheidgen's avatar
Markus Scheidgen committed
491

492
493
494
495
496
497
498
499
500
501
502
503
    def on_process_complete(self, process_name):
        if process_name == 'process_upload':
            self.check_join()

    def check_join(self):
        total_calcs = self.total_calcs
        processed_calcs = self.processed_calcs

        self.get_logger().debug('check join', processed_calcs=processed_calcs, total_calcs=total_calcs)
        if not self.process_running and processed_calcs >= total_calcs:
            self.get_logger().debug('join')
            self.join()
504
505
506

    def join(self):
        self.cleanup()
Markus Scheidgen's avatar
Markus Scheidgen committed
507
508
509

    @task
    def cleanup(self):
510
511
512
513
514
515
516
517
518
519
        # send email about process finish
        user = self.uploader
        name = '%s %s' % (user.first_name, user.last_name)
        message = '\n'.join([
            'Dear %s,' % name,
            '',
            'your data %suploaded %s has completed processing.' % (
                self.name if self.name else '', self.upload_time.isoformat()),
            'You can review your data on your upload page: %s' % config.services.upload_url
        ])
520
521
522
523
524
525
526
        try:
            infrastructure.send_mail(
                name=name, email=user.email, message=message, subject='Processing completed')
        except Exception as e:
            # probably due to email configuration problems
            # don't fail or present this error to clients
            self.logger.error('could not send after processing email', exc_info=e)
Markus Scheidgen's avatar
Markus Scheidgen committed
527
528

    @property
529
    def processed_calcs(self):
530
        return Calc.objects(upload_id=self.upload_id, tasks_status__in=[SUCCESS, FAILURE]).count()
531
532
533
534
535
536
537

    @property
    def total_calcs(self):
        return Calc.objects(upload_id=self.upload_id).count()

    @property
    def failed_calcs(self):
538
        return Calc.objects(upload_id=self.upload_id, tasks_status=FAILURE).count()
539

540
541
    @property
    def pending_calcs(self):
542
        return Calc.objects(upload_id=self.upload_id, tasks_status=PENDING).count()
543

544
545
    def all_calcs(self, start, end, order_by='mainfile'):
        return Calc.objects(upload_id=self.upload_id)[start:end].order_by(order_by)
546
547
548

    @property
    def calcs(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
549
        return Calc.objects(upload_id=self.upload_id, tasks_status=SUCCESS)
Markus Scheidgen's avatar
Markus Scheidgen committed
550
551
552
553
554
555
556
557
558
559
560

    def to_upload_with_metadata(self) -> UploadWithMetadata:
        calc_metadata = dict()
        user_upload_time = None
        if self.metadata is not None:
            user_upload_time = self.metadata.get('_upload_time')
            for calc in self.metadata.get('calculations', []):
                calc_metadata[calc['mainfile']] = calc

        def apply_metadata(calc):
            metadata = calc_metadata.get(calc.mainfile, self.metadata)
561
562
            if metadata is not None:
                calc.apply_user_metadata(metadata)
Markus Scheidgen's avatar
Markus Scheidgen committed
563
564
565
566
567
568
569
570
571
572
573
            return calc

        result = UploadWithMetadata(
            upload_id=self.upload_id,
            uploader=utils.POPO(id=int(self.user_id)),
            upload_time=self.upload_time if user_upload_time is None else user_upload_time)

        result.calcs = [
            apply_metadata(calc.to_calc_with_metadata()) for calc in self.calcs]

        return result