data.py 45.3 KB
Newer Older
Markus Scheidgen's avatar
Markus Scheidgen committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
# 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.

15
'''
Markus Scheidgen's avatar
Markus Scheidgen committed
16
17
18
19
20
21
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
Markus Scheidgen's avatar
Markus Scheidgen committed
22

Markus Scheidgen's avatar
Markus Scheidgen committed
23
.. autoclass:: Upload
Markus Scheidgen's avatar
Markus Scheidgen committed
24

25
'''
Markus Scheidgen's avatar
Markus Scheidgen committed
26

27
from typing import cast, List, Any, Tuple, Iterator, Dict, cast, Iterable
28
from mongoengine import StringField, DateTimeField, DictField, BooleanField, IntField
Markus Scheidgen's avatar
Markus Scheidgen committed
29
import logging
30
from structlog import wrap_logger
31
from contextlib import contextmanager
32
import os.path
33
34
from datetime import datetime
from pymongo import UpdateOne
35
import hashlib
36
from structlog.processors import StackInfoRenderer, format_exc_info, TimeStamper
Markus Scheidgen's avatar
Markus Scheidgen committed
37

38
from nomad import utils, config, infrastructure, search, datamodel
39
from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles, PublicUploadFiles, StagingUploadFiles
40
from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
41
from nomad.parsing import parser_dict, match_parser, Backend
Markus Scheidgen's avatar
Markus Scheidgen committed
42
43
44
from nomad.normalizing import normalizers


45
46
47
48
49
50
51
def _pack_log_event(logger, method_name, event_dict):
    try:
        log_data = dict(event_dict)
        log_data.update(**{
            key: value
            for key, value in getattr(logger, '_context', {}).items()
            if key not in ['service', 'release', 'upload_id', 'calc_id', 'mainfile', 'process_status']})
52
        log_data.update(logger=logger.name)
53
54
55
56
57
58
59
60
61
62
63

        return log_data
    except Exception:
        # raising an exception would cause an indefinite loop
        return event_dict


_log_processors = [
    StackInfoRenderer(),
    _pack_log_event,
    format_exc_info,
64
    TimeStamper(fmt="%Y-%m-%d %H:%M.%S", utc=False)]
65
66


Markus Scheidgen's avatar
Markus Scheidgen committed
67
class Calc(Proc):
68
    '''
Markus Scheidgen's avatar
Markus Scheidgen committed
69
70
71
72
73
    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.

74
75
    The attribute list, does not include the various metadata properties generated
    while parsing, including ``code_name``, ``code_version``, etc.
Markus Scheidgen's avatar
Markus Scheidgen committed
76
77

    Attributes:
78
        calc_id: the calc_id of this calc
Markus Scheidgen's avatar
Markus Scheidgen committed
79
80
81
        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
82

83
84
        metadata: the metadata record wit calc and user metadata, see :class:`datamodel.EntryMetadata`
    '''
85
    calc_id = StringField(primary_key=True)
Markus Scheidgen's avatar
Markus Scheidgen committed
86
87
88
89
    upload_id = StringField()
    mainfile = StringField()
    parser = StringField()

90
91
    metadata = DictField()

Markus Scheidgen's avatar
Markus Scheidgen committed
92
    meta: Any = {
Markus Scheidgen's avatar
Markus Scheidgen committed
93
        'indexes': [
94
95
96
97
            'upload_id',
            ('upload_id', 'mainfile'),
            ('upload_id', 'parser'),
            ('upload_id', 'tasks_status'),
98
            ('upload_id', 'process_status'),
99
100
101
            ('upload_id', 'metadata.nomad_version'),
            'metadata.published',
            'metadata.datasets'
Markus Scheidgen's avatar
Markus Scheidgen committed
102
            'metadata.pid'
Markus Scheidgen's avatar
Markus Scheidgen committed
103
104
105
106
107
        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
108
        self._parser_backend: Backend = None
109
110
        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
111
        self._calc_proc_logs: List[Any] = None
Markus Scheidgen's avatar
Markus Scheidgen committed
112

113
        self._entry_metadata = None
114

Markus Scheidgen's avatar
Markus Scheidgen committed
115
116
    @classmethod
    def get(cls, id):
117
        return cls.get_by_id(id, 'calc_id')
Markus Scheidgen's avatar
Markus Scheidgen committed
118

Markus Scheidgen's avatar
Markus Scheidgen committed
119
    @property
120
121
    def mainfile_file(self) -> PathObject:
        return self.upload_files.raw_file_object(self.mainfile)
Markus Scheidgen's avatar
Markus Scheidgen committed
122

123
124
125
126
    @property
    def upload(self) -> 'Upload':
        if not self._upload:
            self._upload = Upload.get(self.upload_id)
127
            self._upload.worker_hostname = self.worker_hostname
128
129
        return self._upload

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
    def apply_entry_metadata(self, entry_metadata: datamodel.EntryMetadata):
        self.metadata = entry_metadata.m_to_dict(
            include_defaults=True,
            categories=[datamodel.MongoMetadata])  # TODO use embedded doc?

    def create_metadata(self) -> datamodel.EntryMetadata:
        '''
        Returns a :class:`nomad.datamodel.EntryMetadata` with values from this
        processing object, not necessarely the user metadata nor the metadata from
        the archive.
        '''
        entry_metadata = datamodel.EntryMetadata()
        entry_metadata.domain = parser_dict[self.parser].domain
        entry_metadata.upload_id = self.upload_id
        entry_metadata.calc_id = self.calc_id
        entry_metadata.mainfile = self.mainfile
        entry_metadata.nomad_version = config.version
        entry_metadata.nomad_commit = config.commit
        entry_metadata.uploader = self.upload.user_id
        entry_metadata.upload_time = self.upload.upload_time
        entry_metadata.upload_name = self.upload.name

        return entry_metadata

    def entry_metadata(self, upload_files: UploadFiles) -> datamodel.EntryMetadata:
        '''
        Returns a complete set of :class:`nomad.datamodel.EntryMetadata` including
        the user metadata and metadata from the archive.

        Arguments:
            upload_files:
                The :class:`nomad.files.UploadFiles` instance to read the archive from.
            cache:
                A boolean that indicates if the archive file should be left unclosed,
                e.g. if this method is called for many entries of the same upload.
        '''
        archive = upload_files.read_archive(self.calc_id)
167
168
169
170
171
172
173
174
175
176
177
178
        try:
            entry_metadata = datamodel.EntryMetadata.m_from_dict(
                archive[self.calc_id][datamodel.EntryArchive.section_metadata.name].to_dict())

        except KeyError:
            # Due hard processing failures, it might be possible that an entry might not
            # have an archive
            if self._entry_metadata is not None:
                entry_metadata = self._entry_metadata

            else:
                entry_metadata = self.create_metadata()
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194

        entry_metadata.m_update_from_dict(self.metadata)

        return entry_metadata

    def user_metadata(self) -> datamodel.EntryMetadata:
        '''
        Returns a :class:`nomad.datamodel.EntryMetadata` with values from this
        processing object and the user metadata, not necessarely the metadata from
        the archive.
        '''
        entry_metadata = self.create_metadata()
        entry_metadata.m_update_from_dict(self.metadata)

        return entry_metadata

195
196
197
    @property
    def upload_files(self) -> ArchiveBasedStagingUploadFiles:
        if not self._upload_files:
198
199
            self._upload_files = ArchiveBasedStagingUploadFiles(
                self.upload_id, is_authorized=lambda: True, upload_path=self.upload.upload_path)
200
201
        return self._upload_files

Markus Scheidgen's avatar
Markus Scheidgen committed
202
    def get_logger(self, **kwargs):
203
        '''
204
205
        Returns a wrapped logger that additionally saves all entries to the calculation
        processing log in the archive.
206
        '''
207
208
209
        logger = super().get_logger()
        logger = logger.bind(
            upload_id=self.upload_id, mainfile=self.mainfile, calc_id=self.calc_id, **kwargs)
210

211
212
        if self._calc_proc_logs is None:
            self._calc_proc_logs = []
213

214
215
        def save_to_calc_log(logger, method_name, event_dict):
            try:
216
217
                # sanitize the event_dict, because all kinds of values might have been added
                dump_dict = {key: str(value) for key, value in event_dict.items()}
218
219
                dump_dict.update(level=method_name.upper())
                self._calc_proc_logs.append(dump_dict)
220

221
222
223
            except Exception:
                # Exceptions here will cause indefinite loop
                pass
224

225
            return event_dict
226

227
        return wrap_logger(logger, processors=_log_processors + [save_to_calc_log])
228

229
230
    @process
    def re_process_calc(self):
231
        '''
232
233
234
        Processes a calculation again. This means there is already metadata and
        instead of creating it initially, we are just updating the existing
        records.
235
        '''
236
        parser = match_parser(self.upload_files.raw_file_object(self.mainfile).os_path, strict=False)
237
        logger = self.get_logger()
238
239
240

        if parser is None and not config.reprocess_unmatched:
            self.errors = ['no parser matches during re-process, will not re-process this calc']
241

242
243
244
245
246
247
248
            try:
                upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
                with upload_files.read_archive(self.calc_id) as archive:
                    self.upload_files.write_archive(self.calc_id, archive[self.calc_id].to_dict())

            except Exception as e:
                logger.error('could not copy archive for non matching, non reprocessed entry', exc_info=e)
249
                raise e
250

251
252
253
254
255
            # mock the steps of actual processing
            self._continue_with('parsing')
            self._continue_with('normalizing')
            self._continue_with('archiving')
            self._complete()
256
257
            return

258
        if parser is None:
259
260
            self.get_logger().error('no parser matches during re-process, use the old parser')
            self.errors = ['no matching parser found during re-processing']
261
        if self.parser != parser.name:
262
263
264
            self.parser = parser.name
            logger.info(
                'different parser matches during re-process, use new parser',
265
                parser=parser.name)
266

267
        try:
268
269
270
271
272
273
            self._entry_metadata = self.user_metadata()
            self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
            self._entry_metadata.nomad_version = config.version
            self._entry_metadata.nomad_commit = config.commit
            self._entry_metadata.last_processing = datetime.utcnow()
            self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)
274
275
276
277
278
279

            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
            # close loghandler that was not closed due to failures
280
281
282
283
284
285
            try:
                if self._parser_backend and self._parser_backend.resource:
                    self._parser_backend.resource.unload()
            except Exception as e:
                logger.error('could unload processing results', exc_info=e)

Markus Scheidgen's avatar
Markus Scheidgen committed
286
    @process
287
    def process_calc(self):
288
        '''
289
290
        Processes a new calculation that has no prior records in the mongo, elastic,
        or filesystem storage. It will create an initial set of (user) metadata.
291
        '''
292
        logger = self.get_logger()
293
        if self.upload is None:
294
            logger.error('calculation upload does not exist')
Markus Scheidgen's avatar
Markus Scheidgen committed
295
296

        try:
297
298
            # save preliminary minimum calc metadata in case processing fails
            # successful processing will replace it with the actual metadata
299
300
301
302
303
304
            self._entry_metadata = self.create_metadata()
            self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
            self._entry_metadata.last_processing = datetime.utcnow()
            self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)

            if len(self._entry_metadata.files) >= config.auxfile_cutoff:
305
306
307
308
                self.warning(
                    'This calc has many aux files in its directory. '
                    'Have you placed many calculations in the same directory?')

Markus Scheidgen's avatar
Markus Scheidgen committed
309
310
311
312
            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
Markus Scheidgen's avatar
Markus Scheidgen committed
313
            # close loghandler that was not closed due to failures
314
315
316
317
318
319
            try:
                if self._parser_backend and self._parser_backend.resource:
                    self._parser_backend.resource.unload()
            except Exception as e:
                logger.error('could unload processing results', exc_info=e)

320
321
322
323
    def fail(self, *errors, log_level=logging.ERROR, **kwargs):
        # in case of failure, index a minimum set of metadata and mark
        # processing failure
        try:
324
325
326
            if self.parser is not None:
                parser = parser_dict[self.parser]
                if hasattr(parser, 'code_name'):
327
                    self._entry_metadata.code_name = parser.code_name
328

329
330
331
            self._entry_metadata.processed = False
            self.apply_entry_metadata(self._entry_metadata)
            self._entry_metadata.a_elastic.index()
332
        except Exception as e:
333
334
            self.get_logger().error(
                'could not index after processing failure', exc_info=e)
335

336
        try:
337
            self.write_archive(None)
338
        except Exception as e:
339
340
            self.get_logger().error(
                'could not write archive after processing failure', exc_info=e)
341

342
343
        super().fail(*errors, log_level=log_level, **kwargs)

344
345
346
347
    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
348
        if process_name == 'process_calc' or process_name == 're_process_calc' or process_name is None:
349
350
            self.upload.reload()
            self.upload.check_join()
Markus Scheidgen's avatar
Markus Scheidgen committed
351
352
353

    @task
    def parsing(self):
354
        ''' The *task* that encapsulates all parsing related actions. '''
355
        context = dict(parser=self.parser, step=self.parser)
356
        logger = self.get_logger(**context)
357
        parser = parser_dict[self.parser]
358
        self._entry_metadata.parser_name = self.parser
Markus Scheidgen's avatar
Markus Scheidgen committed
359

360
        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
361
362
363
364
            try:
                self._parser_backend = parser.run(
                    self.upload_files.raw_file_object(self.mainfile).os_path, logger=logger)
            except Exception as e:
365
                self.fail('parser failed with exception', exc_info=e, error=str(e), **context)
366
                return
367
            except SystemExit:
368
                self.fail('parser raised system exit', error='system exit', **context)
369
                return
Markus Scheidgen's avatar
Markus Scheidgen committed
370

Markus Scheidgen's avatar
Markus Scheidgen committed
371
372
        if self._parser_backend.status[0] != 'ParseSuccess':
            error = self._parser_backend.status[1]
373
            self.fail('parser failed', error=error, **context)
374
375
376
377
378
379
380
381

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

        if self._parser_backend.status[0] == 'ParseSuccess':
            warnings = getattr(self._parser_backend, '_warnings', [])
382

383
            if len(warnings) > 0:
384
385
386
387
                self.get_logger().warn(
                    'processor completed successful with warnings',
                    processor=processor_name, warnings=[str(warning) for warning in warnings])

388
            else:
389
390
391
392
                self.get_logger().info(
                    'processor completed successful',
                    processor=processor_name)

393
        else:
394
            errors = self._parser_backend.status[1]
395
396
397
            self.get_logger().error(
                'processor completed with failure',
                processor=processor_name, errors=str(errors))
Markus Scheidgen's avatar
Markus Scheidgen committed
398
399
400

    @task
    def normalizing(self):
401
        ''' The *task* that encapsulates all normalizing related actions. '''
402
403
404
405
406

        # allow normalizer to access and add data to the entry metadata
        self._parser_backend.entry_archive.m_add_sub_section(
            datamodel.EntryArchive.section_metadata, self._entry_metadata)

Markus Scheidgen's avatar
Markus Scheidgen committed
407
        for normalizer in normalizers:
408
            if normalizer.domain != parser_dict[self.parser].domain:
409
410
                continue

Markus Scheidgen's avatar
Markus Scheidgen committed
411
            normalizer_name = normalizer.__name__
412
            context = dict(normalizer=normalizer_name, step=normalizer_name)
413
            logger = self.get_logger(**context)
Markus Scheidgen's avatar
Markus Scheidgen committed
414
415

            with utils.timer(
416
                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
417
                with self.use_parser_backend(normalizer_name) as backend:
418
419
420
                    try:
                        normalizer(backend).normalize(logger=logger)
                    except Exception as e:
421
                        self._parser_backend.finishedParsingSession('ParseFailure', [str(e)])
422
423
424
                        logger.error(
                            'normalizer failed with exception', exc_info=e,
                            error=str(e), **context)
425
426
427
428
429
430
431
432
433
                        break
                    else:
                        if self._parser_backend.status[0] != 'ParseSuccess':
                            error = self._parser_backend.status[1]
                            self.fail('normalizer failed', error=error, **context)
                            break
                        else:
                            logger.debug(
                                'completed normalizer successfully', normalizer=normalizer_name)
Markus Scheidgen's avatar
Markus Scheidgen committed
434
435
436

    @task
    def archiving(self):
437
        ''' The *task* that encapsulates all archival related actions. '''
438
439
        logger = self.get_logger()

440
441
        self._entry_metadata.apply_domain_metadata(self._parser_backend)
        self._entry_metadata.processed = True
442

443
444
        # persist the calc metadata
        with utils.timer(logger, 'saved calc metadata', step='metadata'):
445
            self.apply_entry_metadata(self._entry_metadata)
446
447

        # index in search
448
        with utils.timer(logger, 'indexed', step='index'):
449
            self._entry_metadata.a_elastic.index()
450

451
        # persist the archive
Markus Scheidgen's avatar
Markus Scheidgen committed
452
        with utils.timer(
453
                logger, 'archived', step='archive',
Markus Scheidgen's avatar
Markus Scheidgen committed
454
                input_size=self.mainfile_file.size) as log_data:
455

456
            archive_size = self.write_archive(self._parser_backend)
457
            log_data.update(archive_size=archive_size)
Markus Scheidgen's avatar
Markus Scheidgen committed
458

459
460
461
462
463
464
465
466
467
    def write_archive(self, backend: Backend):
        if self._calc_proc_logs is None:
            self._calc_proc_logs = []

        if backend is not None:
            entry_archive = backend.entry_archive.m_copy()
        else:
            entry_archive = datamodel.EntryArchive()

468
469
470
        if entry_archive.section_metadata is None:
            entry_archive.m_add_sub_section(datamodel.EntryArchive.section_metadata, self._entry_metadata)

471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
        entry_archive.processing_logs = self._calc_proc_logs

        try:
            return self.upload_files.write_archive(self.calc_id, entry_archive.m_to_dict())
        except Exception as e:
            if backend is None:
                raise e

            # most likely failed due to domain data, try to write metadata and processing logs
            entry_archive = datamodel.EntryArchive()
            entry_archive.m_add_sub_section(datamodel.EntryArchive.section_metadata, self._entry_metadata)
            entry_archive.processing_logs = self._calc_proc_logs
            self.upload_files.write_archive(self.calc_id, entry_archive.m_to_dict())
            raise e

486
    def __str__(self):
487
        return 'calc %s calc_id=%s upload_id%s' % (super().__str__(), self.calc_id, self.upload_id)
488

489

490
class Upload(Proc):
491
    '''
Markus Scheidgen's avatar
Markus Scheidgen committed
492
493
494
495
496
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

    Attributes:
        name: optional user provided upload name
497
498
        upload_path: the path were the uploaded files was stored
        temporary: True if the uploaded file should be removed after extraction
Markus Scheidgen's avatar
Markus Scheidgen committed
499
500
        upload_id: the upload id generated by the database
        upload_time: the timestamp when the system realised the upload
501
        user_id: the id of the user that created this upload
Markus Scheidgen's avatar
Markus Scheidgen committed
502
503
        published: Boolean that indicates the publish status
        publish_time: Date when the upload was initially published
504
        last_update: Date of the last publishing/re-processing
Markus Scheidgen's avatar
Markus Scheidgen committed
505
        joined: Boolean indicates if the running processing has joined (:func:`check_join`)
506
    '''
Markus Scheidgen's avatar
Markus Scheidgen committed
507
508
509
    id_field = 'upload_id'

    upload_id = StringField(primary_key=True)
510
511
    upload_path = StringField(default=None)
    temporary = BooleanField(default=False)
512
    embargo_length = IntField(default=36)
Markus Scheidgen's avatar
Markus Scheidgen committed
513
514
515

    name = StringField(default=None)
    upload_time = DateTimeField()
516
    user_id = StringField(required=True)
517
518
    published = BooleanField(default=False)
    publish_time = DateTimeField()
519
    last_update = DateTimeField()
Markus Scheidgen's avatar
Markus Scheidgen committed
520

521
522
    joined = BooleanField(default=False)

Markus Scheidgen's avatar
Markus Scheidgen committed
523
524
    meta: Any = {
        'indexes': [
525
            'user_id', 'tasks_status', 'process_status', 'published', 'upload_time'
Markus Scheidgen's avatar
Markus Scheidgen committed
526
527
528
529
530
        ]
    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
531
        self._upload_files: ArchiveBasedStagingUploadFiles = None
Markus Scheidgen's avatar
Markus Scheidgen committed
532

533
534
    @property
    def metadata(self) -> dict:
535
        '''
Markus Scheidgen's avatar
Markus Scheidgen committed
536
537
538
539
540
        Getter, setter for user metadata. Metadata is pickled to and from the public
        bucket to allow sharing among all processes. Usually uploads do not have (much)
        user defined metadata, but users provide all metadata per upload as part of
        the publish process. This will change, when we introduce editing functionality
        and metadata will be provided through different means.
541
        '''
542
543
544
545
546
        try:
            upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
        except KeyError:
            return None
        return upload_files.user_metadata
547
548
549

    @metadata.setter
    def metadata(self, data: dict) -> None:
550
551
        upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True, create=True)
        upload_files.user_metadata = data
552

Markus Scheidgen's avatar
Markus Scheidgen committed
553
    @classmethod
554
    def get(cls, id: str, include_published: bool = True) -> 'Upload':
555
        return cls.get_by_id(id, 'upload_id')
Markus Scheidgen's avatar
Markus Scheidgen committed
556
557

    @classmethod
558
    def user_uploads(cls, user: datamodel.User, **kwargs) -> List['Upload']:
559
        ''' Returns all uploads for the given user. Kwargs are passed to mongo query. '''
560
        return cls.objects(user_id=str(user.user_id), **kwargs)
Markus Scheidgen's avatar
Markus Scheidgen committed
561

562
563
    @property
    def uploader(self):
564
        return datamodel.User.get(self.user_id)
565

Markus Scheidgen's avatar
Markus Scheidgen committed
566
567
    def get_logger(self, **kwargs):
        logger = super().get_logger()
568
569
        user = self.uploader
        user_name = '%s %s' % (user.first_name, user.last_name)
570
        # We are not using 'user_id' because logstash (?) will filter these entries ?!
571
572
        logger = logger.bind(
            upload_id=self.upload_id, upload_name=self.name, user_name=user_name,
573
            user=user.user_id, **kwargs)
Markus Scheidgen's avatar
Markus Scheidgen committed
574
575
576
577
        return logger

    @classmethod
    def create(cls, **kwargs) -> 'Upload':
578
        '''
Markus Scheidgen's avatar
Markus Scheidgen committed
579
580
581
        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.
582
583

        Arguments:
584
            user: The user that created the upload.
585
        '''
586
587
        # use kwargs to keep compatibility with super method
        user: datamodel.User = kwargs['user']
588
        del(kwargs['user'])
589

590
591
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
592
        kwargs.update(user_id=user.user_id)
Markus Scheidgen's avatar
Markus Scheidgen committed
593
        self = super().create(**kwargs)
594

Markus Scheidgen's avatar
Markus Scheidgen committed
595
        self._continue_with('uploading')
596

Markus Scheidgen's avatar
Markus Scheidgen committed
597
598
        return self

599
    def delete(self):
600
        ''' Deletes this upload process state entry and its calcs. '''
601
602
603
        Calc.objects(upload_id=self.upload_id).delete()
        super().delete()

604
    def delete_upload_local(self):
605
        '''
606
        Deletes the upload, including its processing state and
607
        staging files. Local version without celery processing.
608
        '''
609
610
611
        logger = self.get_logger()

        with utils.lnr(logger, 'staged upload delete failed'):
612
            with utils.timer(
613
                    logger, 'upload deleted from index', step='index',
614
                    upload_size=self.upload_files.size):
615
                search.delete_upload(self.upload_id)
616

617
            with utils.timer(
618
                    logger, 'staged upload deleted', step='files',
619
620
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
621
622

            self.delete()
623

624
    @process
625
    def delete_upload(self):
626
        '''
627
628
        Deletes of the upload, including its processing state and
        staging files. This starts the celery process of deleting the upload.
629
        '''
630
        self.delete_upload_local()
631

632
        return True  # do not save the process status on the delete upload
633

634
    @process
635
    def publish_upload(self):
636
        '''
637
638
        Moves the upload out of staging to the public area. It will
        pack the staging upload files in to public upload files.
639
        '''
640
641
        assert self.processed_calcs > 0

642
        logger = self.get_logger()
643
        logger.info('started to publish')
644

645
        with utils.lnr(logger, 'publish failed'):
646
            with self.entries_metadata(self.metadata) as calcs:
647

648
                with utils.timer(
649
                        logger, 'upload metadata updated', step='metadata',
650
                        upload_size=self.upload_files.size):
651

652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
                    def create_update(calc):
                        calc.published = True
                        calc.with_embargo = calc.with_embargo if calc.with_embargo is not None else False
                        return UpdateOne(
                            {'_id': calc.calc_id},
                            {'$set': {'metadata': calc.m_to_dict(
                                include_defaults=True, categories=[datamodel.MongoMetadata])}})

                    Calc._get_collection().bulk_write([create_update(calc) for calc in calcs])

                if isinstance(self.upload_files, StagingUploadFiles):
                    with utils.timer(
                            logger, 'staged upload files packed', step='pack',
                            upload_size=self.upload_files.size):
                        self.upload_files.pack(calcs)
667

668
                with utils.timer(
669
                        logger, 'index updated', step='index',
670
                        upload_size=self.upload_files.size):
671
672
673
674
675
676
677
678
679
680
681
682
                    search.publish(calcs)

                if isinstance(self.upload_files, StagingUploadFiles):
                    with utils.timer(
                            logger, 'staged upload deleted', step='delete staged',
                            upload_size=self.upload_files.size):
                        self.upload_files.delete()
                        self.published = True
                        self.publish_time = datetime.utcnow()
                        self.last_update = datetime.utcnow()
                        self.save()
                else:
683
                    self.last_update = datetime.utcnow()
684
                    self.save()
685

686
687
    @process
    def re_process_upload(self):
688
        '''
Markus Scheidgen's avatar
Markus Scheidgen committed
689
690
691
        A *process* that performs the re-processing of a earlier processed
        upload.

692
693
694
695
696
697
        Runs the distributed process of fully reparsing/renormalizing an existing and
        already published upload. Will renew the archive part of the upload and update
        mongo and elastic search entries.

        TODO this implementation does not do any re-matching. This will be more complex
        due to handling of new or missing matches.
698
        '''
699
700
701
        logger = self.get_logger()
        logger.info('started to re-process')

702
703
704
705
706
        # mock the steps of actual processing
        self._continue_with('uploading')

        # extract the published raw files into a staging upload files instance
        self._continue_with('extracting')
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721

        if self.published:
            try:
                staging_upload_files = StagingUploadFiles(self.upload_id)
                # public files exist and there is a staging directory, it is probably old
                # and we delete it first
                staging_upload_files.delete()
                logger.warn('deleted old staging files')

            except KeyError as e:
                logger.info('reprocessing published files')
        else:
            logger.info('reprocessing staging files')

        staging_upload_files = self.upload_files.to_staging_upload_files(create=True)
722
723

        self._continue_with('parse_all')
724
        try:
725
            # check if a calc is already/still processing
726
727
728
729
730
731
732
733
            processing = Calc.objects(
                upload_id=self.upload_id,
                **Calc.process_running_mongoengine_query()).count()

            if processing > 0:
                logger.warn(
                    'processes are still/already running on calc, they will be resetted',
                    count=processing)
734
735

            # reset all calcs
736
            Calc._get_collection().update_many(
737
738
739
                dict(upload_id=self.upload_id),
                {'$set': Calc.reset_pymongo_update(worker_hostname=self.worker_hostname)})

740
            # process call calcs
741
742
743
            Calc.process_all(Calc.re_process_calc, dict(upload_id=self.upload_id), exclude=['metadata'])

            logger.info('completed to trigger re-process of all calcs')
744
745
        except Exception as e:
            # try to remove the staging copy in failure case
746
747
            logger.error('failed to trigger re-process of all calcs', exc_info=e)

748
749
750
            if self.published:
                if staging_upload_files is not None and staging_upload_files.exists():
                    staging_upload_files.delete()
751
752

            raise e
753
754
755
756

        # the packing and removing of the staging upload files, will be trigged by
        # the 'cleanup' task after processing all calcs

757
758
    @process
    def re_pack(self):
759
        ''' A *process* that repacks the raw and archive data based on the current embargo data. '''
760
761
762
763
764
765
766
767
        assert self.published

        # mock the steps of actual processing
        self._continue_with('uploading')
        self._continue_with('extracting')
        self._continue_with('parse_all')
        self._continue_with('cleanup')

768
        self.upload_files.re_pack(self.user_metadata())
769
770
771
        self.joined = True
        self._complete()

Markus Scheidgen's avatar
Markus Scheidgen committed
772
    @process
773
    def process_upload(self):
774
        ''' A *process* that performs the initial upload processing. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
775
776
777
778
779
        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
780
        ''' A no-op *task* as a stand-in for receiving upload data. '''
Markus Scheidgen's avatar
Markus Scheidgen committed
781
782
        pass

783
    @property
784
785
    def upload_files(self) -> UploadFiles:
        upload_files_class = ArchiveBasedStagingUploadFiles if not self.published else PublicUploadFiles
786
        kwargs = dict(upload_path=self.upload_path) if not self.published else {}
787
788
789

        if not self._upload_files or not isinstance(self._upload_files, upload_files_class):
            self._upload_files = upload_files_class(
790
                self.upload_id, is_authorized=lambda: True, **kwargs)
791

792
        return self._upload_files
793

794
795
796
797
798
    @property
    def staging_upload_files(self) -> ArchiveBasedStagingUploadFiles:
        assert not self.published
        return cast(ArchiveBasedStagingUploadFiles, self.upload_files)

Markus Scheidgen's avatar
Markus Scheidgen committed
799
800
    @task
    def extracting(self):
801
        '''
802
803
        The *task* performed before the actual parsing/normalizing: extracting
        the uploaded files.
804
        '''
805
806
807
808
809
        # extract the uploaded file
        self._upload_files = ArchiveBasedStagingUploadFiles(
            upload_id=self.upload_id, is_authorized=lambda: True, create=True,
            upload_path=self.upload_path)

Markus Scheidgen's avatar
Markus Scheidgen committed
810
811
        logger = self.get_logger()
        try:
Markus Scheidgen's avatar
Markus Scheidgen committed
812
813
            with utils.timer(
                    logger, 'upload extracted', step='extracting',
814
815
                    upload_size=self.upload_files.size):
                self.upload_files.extract()
816
817
818
819

            if self.temporary:
                os.remove(self.upload_path)
                self.upload_path = None
820

821
        except KeyError:
822
            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
823
824
825
            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
Markus Scheidgen's avatar
Markus Scheidgen committed
826
827
            return

828
    def _preprocess_files(self, path):
829
        '''
830
831
        Some files need preprocessing. Currently we need to add a stripped POTCAR version
        and always restrict/embargo the original.
832
        '''
833
        if os.path.basename(path).startswith('POTCAR'):
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
            # create checksum
            hash = hashlib.sha224()
            with open(self.staging_upload_files.raw_file_object(path).os_path, 'rb') as orig_f:
                for line in orig_f.readlines():
                    hash.update(line)

            checksum = hash.hexdigest()

            # created stripped POTCAR
            stripped_path = path + '.stripped'
            with open(self.staging_upload_files.raw_file_object(stripped_path).os_path, 'wt') as stripped_f:
                stripped_f.write('Stripped POTCAR file. Checksum of original file (sha224): %s\n' % checksum)
            os.system(
                '''
                    awk < %s >> %s '
                    BEGIN { dump=1 }
                    /End of Dataset/ { dump=1 }
                    dump==1 { print }
                    /END of PSCTR/ { dump=0 }'
                ''' % (
                    self.staging_upload_files.raw_file_object(path).os_path,
                    self.staging_upload_files.raw_file_object(stripped_path).os_path))

857
    def match_mainfiles(self) -> Iterator[Tuple[str, object]]:
858
        '''
859
860
861
862
863
        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
864
        '''
865
        directories_with_match: Dict[str, str] = dict()
866
867
        upload_files = self.staging_upload_files
        for filename in upload_files.raw_file_manifest():
868
            self._preprocess_files(filename)
869
            try:
870
                parser = match_parser(upload_files.raw_file_object(filename).os_path)
871
                if parser is not None:
872
873
                    directory = os.path.dirname(filename)
                    if directory in directories_with_match:
874
875
876
                        # TODO this might give us the chance to store directory based relationship
                        # between calcs for the future?
                        pass
877
878
                    else:
                        directories_with_match[directory] = filename
879
880

                    yield filename, parser
881
882
883
884
            except Exception as e:
                self.get_logger().error(
                    'exception while matching pot. mainfile',
                    mainfile=filename, exc_info=e)
885

Markus Scheidgen's avatar
Markus Scheidgen committed
886
887
    @task
    def parse_all(self):
888
        '''
Markus Scheidgen's avatar
Markus Scheidgen committed
889
        The *task* used to identify mainfile/parser combinations among the upload's files, creates
890
        respective :class:`Calc` instances, and triggers their processing.
891
        '''
892
893
        logger = self.get_logger()

Markus Scheidgen's avatar
Markus Scheidgen committed
894
895
        with utils.timer(
                logger, 'upload extracted', step='matching',
896
897
                upload_size=self.upload_files.size):
            for filename, parser in self.match_mainfiles():
898
                calc = Calc.create(
899
                    calc_id=self.upload_files.calc_id(filename),
900
                    mainfile=filename, parser=parser.name,
901
                    worker_hostname=self.worker_hostname,
902
903
                    upload_id=self.upload_id)

904
                calc.process_calc()
Markus Scheidgen's avatar
Markus Scheidgen committed
905

906
    def on_process_complete(self, process_name):
907
        if process_name == 'process_upload' or process_name == 're_process_upload':
908
909
910
            self.check_join()

    def check_join(self):
911
        '''
Markus Scheidgen's avatar
Markus Scheidgen committed
912
913
914
915
916
917
        Performs an evaluation of the join condition and triggers the :func:`cleanup`
        task if necessary. The join condition allows to run the ``cleanup`` after
        all calculations have been processed. The upload processing stops after all
        calculation processings have been triggered (:func:`parse_all` or
        :func:`re_process_upload`). The cleanup task is then run within the last
        calculation process (the one that triggered the join by calling this method).
918
        '''
919
920
921
922
        total_calcs = self.total_calcs
        processed_calcs = self.processed_calcs

        self.get_logger().debug('check join', processed_calcs=processed_calcs, total_calcs=total_calcs)
923
924
        # check if process is not running anymore, i.e. not still spawining new processes to join
        # check the join condition, i.e. all calcs have been processed
925
        if not self.process_running and processed_calcs >= total_calcs:
926
            # this can easily be called multiple times, e.g. upload finished after all calcs finished
927
928
929
            modified_upload = self._get_collection().find_one_and_update(
                {'_id': self.upload_id, 'joined': {'$ne': True}},
                {'$set': {'joined': True}})
930
931
932
933
934
935
            if modified_upload is not None:
                self.get_logger().debug('join')
                self.cleanup()
            else:
                # the join was already done due to a prior call
                pass
936

937
938
939
    def reset(self):
        self.joined = False
        super().reset()
Markus Scheidgen's avatar
Markus Scheidgen committed
940

941
942
943
944
945
946
    @classmethod
    def reset_pymongo_update(cls, worker_hostname: str = None):
        update = super().reset_pymongo_update()
        update.update(joined=False)
        return update

947
    def _cleanup_after_processing(self):
948
949
950
951
952
953
        # send email about process finish
        user = self.uploader
        name = '%s %s' % (user.first_name, user.last_name)
        message = '\n'.join([
            'Dear %s,' % name,
            '',
954
            'your data %suploaded at %s has completed processing.' % (
955
                '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()),  # pylint: disable=no-member
956