data.py 34.4 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:
"""

Markus Scheidgen's avatar
Markus Scheidgen committed
27
from typing import cast, List, Any, ContextManager, Tuple, Generator, Dict, cast
28
from mongoengine import StringField, DateTimeField, DictField, BooleanField
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
Markus Scheidgen's avatar
Markus Scheidgen committed
36

37
from nomad import utils, coe_repo, config, infrastructure, search, datamodel
38
from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles, PublicUploadFiles, StagingUploadFiles
39
from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
40
from nomad.parsing import parser_dict, match_parser, LocalBackend
Markus Scheidgen's avatar
Markus Scheidgen committed
41
from nomad.normalizing import normalizers
42
from nomad.datamodel import UploadWithMetadata, Domain
Markus Scheidgen's avatar
Markus Scheidgen committed
43
44


Markus Scheidgen's avatar
Markus Scheidgen committed
45
class Calc(Proc):
Markus Scheidgen's avatar
Markus Scheidgen committed
46
47
48
49
50
51
52
53
54
55
    """
    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:
56
        calc_id: the calc_id of this calc
Markus Scheidgen's avatar
Markus Scheidgen committed
57
58
59
        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
60

61
        metadata: the metadata record wit calc and user metadata, see :class:`datamodel.CalcWithMetadata`
Markus Scheidgen's avatar
Markus Scheidgen committed
62
    """
63
    calc_id = StringField(primary_key=True)
Markus Scheidgen's avatar
Markus Scheidgen committed
64
65
66
67
    upload_id = StringField()
    mainfile = StringField()
    parser = StringField()

68
69
    metadata = DictField()

Markus Scheidgen's avatar
Markus Scheidgen committed
70
    meta: Any = {
Markus Scheidgen's avatar
Markus Scheidgen committed
71
        'indexes': [
72
73
74
75
76
            'upload_id',
            ('upload_id', 'mainfile'),
            ('upload_id', 'parser'),
            ('upload_id', 'tasks_status'),
            ('upload_id', 'process_status')
Markus Scheidgen's avatar
Markus Scheidgen committed
77
78
79
80
81
        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
82
        self._parser_backend: LocalBackend = None
83
84
        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
85
        self._calc_proc_logwriter = None
86
        self._calc_proc_logwriter_ctx: ContextManager = None
Markus Scheidgen's avatar
Markus Scheidgen committed
87
88
89

    @classmethod
    def get(cls, id):
90
        return cls.get_by_id(id, 'calc_id')
Markus Scheidgen's avatar
Markus Scheidgen committed
91

Markus Scheidgen's avatar
Markus Scheidgen committed
92
    @property
93
94
    def mainfile_file(self) -> PathObject:
        return self.upload_files.raw_file_object(self.mainfile)
Markus Scheidgen's avatar
Markus Scheidgen committed
95

96
97
98
99
    @property
    def upload(self) -> 'Upload':
        if not self._upload:
            self._upload = Upload.get(self.upload_id)
100
            self._upload.worker_hostname = self.worker_hostname
101
102
        return self._upload

103
104
105
    @property
    def upload_files(self) -> ArchiveBasedStagingUploadFiles:
        if not self._upload_files:
106
107
            self._upload_files = ArchiveBasedStagingUploadFiles(
                self.upload_id, is_authorized=lambda: True, upload_path=self.upload.upload_path)
108
109
        return self._upload_files

Markus Scheidgen's avatar
Markus Scheidgen committed
110
    def get_logger(self, **kwargs):
111
112
113
114
        """
        Returns a wrapped logger that additionally saves all entries to the calculation
        processing log in the archive.
        """
115
116
117
        logger = super().get_logger()
        logger = logger.bind(
            upload_id=self.upload_id, mainfile=self.mainfile, calc_id=self.calc_id, **kwargs)
118

119
        if self._calc_proc_logwriter_ctx is None:
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
            try:
                self._calc_proc_logwriter_ctx = self.upload_files.archive_log_file(self.calc_id, 'wt')
                self._calc_proc_logwriter = self._calc_proc_logwriter_ctx.__enter__()  # pylint: disable=E1101
            except KeyError:
                # cannot open log file
                pass

        if self._calc_proc_logwriter_ctx is None:
            return logger
        else:
            def save_to_calc_log(logger, method_name, event_dict):
                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')

                return event_dict

            return wrap_logger(logger, processors=[save_to_calc_log])
145

Markus Scheidgen's avatar
Markus Scheidgen committed
146
    @process
147
    def process_calc(self):
148
        logger = self.get_logger()
149
        if self.upload is None:
150
            logger.error('calculation upload does not exist')
Markus Scheidgen's avatar
Markus Scheidgen committed
151
152

        try:
153
154
            # save preliminary minimum calc metadata in case processing fails
            # successful processing will replace it with the actual metadata
155
            calc_with_metadata = datamodel.CalcWithMetadata(
156
157
158
159
160
161
                upload_id=self.upload_id,
                calc_id=self.calc_id,
                calc_hash=self.upload_files.calc_hash(self.mainfile),
                mainfile=self.mainfile)
            calc_with_metadata.published = False
            calc_with_metadata.uploader = self.upload.uploader.to_popo()
162
            calc_with_metadata.upload_time = self.upload.upload_time
163
            calc_with_metadata.nomad_version = config.version
164
            calc_with_metadata.nomad_commit = config.commit
165
166
            calc_with_metadata.last_processing = datetime.now()
            calc_with_metadata.files = self.upload_files.calc_files(self.mainfile)
167
            self.preprocess_files(calc_with_metadata.files)
168
169
            self.metadata = calc_with_metadata.to_dict()

Markus Scheidgen's avatar
Markus Scheidgen committed
170
171
172
173
            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
Markus Scheidgen's avatar
Markus Scheidgen committed
174
            # close loghandler that was not closed due to failures
175
            try:
176
177
178
                if self._calc_proc_logwriter is not None:
                    self._calc_proc_logwriter.close()
                    self._calc_proc_logwriter = None
179
180
181
            except Exception as e:
                logger.error('could not close calculation proc log', exc_info=e)

182
183
184
185
    def fail(self, *errors, log_level=logging.ERROR, **kwargs):
        # in case of failure, index a minimum set of metadata and mark
        # processing failure
        try:
186
            calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
187
188
189
190
191
192
193
194
            calc_with_metadata.formula = config.services.not_processed_value
            calc_with_metadata.basis_set = config.services.not_processed_value
            calc_with_metadata.xc_functional = config.services.not_processed_value
            calc_with_metadata.system = config.services.not_processed_value
            calc_with_metadata.crystal_system = config.services.not_processed_value
            calc_with_metadata.spacegroup = config.services.not_processed_value
            calc_with_metadata.spacegroup_symbol = config.services.not_processed_value
            calc_with_metadata.code_version = config.services.not_processed_value
195
196
197
198
199
200
201

            calc_with_metadata.code_name = config.services.not_processed_value
            if self.parser is not None:
                parser = parser_dict[self.parser]
                if hasattr(parser, 'code_name'):
                    calc_with_metadata.code_name = parser.code_name

202
203
204
205
206
207
208
209
            calc_with_metadata.processed = False
            self.metadata = calc_with_metadata.to_dict()
            search.Entry.from_calc_with_metadata(calc_with_metadata).save()
        except Exception as e:
            self.get_logger().error('could not index after processing failure', exc_info=e)

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

210
211
212
213
214
215
216
    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
217

218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
    def preprocess_files(self, filepaths):
        for path in filepaths:
            if os.path.basename(path) == 'POTCAR':
                # create checksum
                hash = hashlib.sha224()
                with open(self.upload_files.raw_file_object(path).os_path, 'rb') as f:
                    for line in f.readlines():
                        hash.update(line)

                checksum = hash.hexdigest()

                # created stripped POTCAR
                stripped_path = path + '.stripped'
                with open(self.upload_files.raw_file_object(stripped_path).os_path, 'wt') as f:
                    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 }'
                    ''' % (
241
242
                        self.upload_files.raw_file_object(path).os_path,
                        self.upload_files.raw_file_object(stripped_path).os_path))
243
244
245
246
247

                filepaths.append(stripped_path)

        return filepaths

Markus Scheidgen's avatar
Markus Scheidgen committed
248
249
    @task
    def parsing(self):
250
        context = dict(parser=self.parser, step=self.parser)
251
        logger = self.get_logger(**context)
252
        parser = parser_dict[self.parser]
253
        self.metadata['parser_name'] = self.parser
Markus Scheidgen's avatar
Markus Scheidgen committed
254

255
        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
256
257
258
259
260
261
262
            try:
                self._parser_backend = parser.run(
                    self.upload_files.raw_file_object(self.mainfile).os_path, logger=logger)
            except Exception as e:
                self.fail(
                    'parser failed with exception', level=logging.ERROR,
                    exc_info=e, error=str(e), **context)
263
                return
Markus Scheidgen's avatar
Markus Scheidgen committed
264

265
266
        # add the non code specific calc metadata to the backend
        # all other quantities have been determined by parsers/normalizers
267
        self._parser_backend.openNonOverlappingSection('section_entry_info')
268
        self._parser_backend.addValue('upload_id', self.upload_id)
269
        self._parser_backend.addValue('calc_id', self.calc_id)
270
        self._parser_backend.addValue('calc_hash', self.metadata['calc_hash'])
271
        self._parser_backend.addValue('mainfile', self.mainfile)
272
        self._parser_backend.addValue('parser_name', self.parser)
273
274
275
276
277
278
279
280
281
282
283
284
        filepaths = self.metadata['files']
        self._parser_backend.addValue('number_of_files', len(filepaths))
        self._parser_backend.addValue('filepaths', filepaths)
        uploader = self.upload.uploader
        self._parser_backend.addValue(
            'entry_uploader_name', '%s, %s' % (uploader.first_name, uploader.last_name))
        self._parser_backend.addValue(
            'entry_uploader_id', str(uploader.user_id))
        self._parser_backend.addValue('entry_upload_time', int(self.upload.upload_time.timestamp()))
        self._parser_backend.closeNonOverlappingSection('section_entry_info')

        self.add_processor_info(self.parser)
285

Markus Scheidgen's avatar
Markus Scheidgen committed
286
        if self._parser_backend.status[0] != 'ParseSuccess':
287
            logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
288
            error = self._parser_backend.status[1]
289
            self.fail(error, level=logging.INFO, **context)
290
291
292
293
294
295
296
297

    @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:
298
        self._parser_backend.openContext('/section_entry_info/0')
299
300
301
302
303
304
305
        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')
306
                self._parser_backend.addValue('number_of_archive_processor_warnings', len(warnings))
307
308
309
310
                self._parser_backend.addArrayValues('archive_processor_warnings', [str(warning) for warning in warnings])
            else:
                self._parser_backend.addValue('archive_processor_status', 'Success')
        else:
311
            errors = self._parser_backend.status[1]
312
313
314
            self._parser_backend.addValue('archive_processor_error', str(errors))

        self._parser_backend.closeNonOverlappingSection('section_archive_processing_info')
315
        self._parser_backend.closeContext('/section_entry_info/0')
Markus Scheidgen's avatar
Markus Scheidgen committed
316
317
318
319

    @task
    def normalizing(self):
        for normalizer in normalizers:
320
321
322
            if normalizer.domain != config.domain:
                continue

Markus Scheidgen's avatar
Markus Scheidgen committed
323
            normalizer_name = normalizer.__name__
324
            context = dict(normalizer=normalizer_name, step=normalizer_name)
325
            logger = self.get_logger(**context)
Markus Scheidgen's avatar
Markus Scheidgen committed
326
327

            with utils.timer(
328
                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
329
                with self.use_parser_backend(normalizer_name) as backend:
330
331
332
333
334
335
336
                    try:
                        normalizer(backend).normalize(logger=logger)
                    except Exception as e:
                        self.fail(
                            'normalizer failed with exception', level=logging.ERROR,
                            exc_info=e, error=str(e), **context)
                        self._parser_backend.status = ['ParseFailure', str(e)]
Markus Scheidgen's avatar
Markus Scheidgen committed
337

338
339
            failed = self._parser_backend.status[0] != 'ParseSuccess'
            if failed:
340
                logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
341
                error = self._parser_backend.status[1]
342
                self.fail(error, level=logging.WARNING, error=error, **context)
343
344
345
346
                break
            else:
                logger.debug(
                    'completed normalizer successfully', normalizer=normalizer_name)
Markus Scheidgen's avatar
Markus Scheidgen committed
347
348
349

    @task
    def archiving(self):
350
351
        logger = self.get_logger()

352
        calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
353
        calc_with_metadata.apply_domain_metadata(self._parser_backend)
354
        calc_with_metadata.processed = True
355

356
357
        # persist the calc metadata
        with utils.timer(logger, 'saved calc metadata', step='metadata'):
358
            self.metadata = calc_with_metadata.to_dict()
359
360

        # index in search
361
        with utils.timer(logger, 'indexed', step='index'):
362
            search.Entry.from_calc_with_metadata(calc_with_metadata).save()
363

364
        # persist the archive
Markus Scheidgen's avatar
Markus Scheidgen committed
365
        with utils.timer(
366
                logger, 'archived', step='archive',
Markus Scheidgen's avatar
Markus Scheidgen committed
367
                input_size=self.mainfile_file.size) as log_data:
368
            with self.upload_files.archive_file(self.calc_id, 'wt') as out:
369
                self._parser_backend.write_json(out, pretty=True, root_sections=Domain.instance.root_sections)
370

371
            log_data.update(archive_size=self.upload_files.archive_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
372
373
374
375

        # close loghandler
        if self._calc_proc_logwriter is not None:
            with utils.timer(
376
                    logger, 'archived log', step='logs',
Markus Scheidgen's avatar
Markus Scheidgen committed
377
                    input_size=self.mainfile_file.size) as log_data:
378
                self._calc_proc_logwriter_ctx.__exit__(None, None, None)  # pylint: disable=E1101
379
                self._calc_proc_logwriter = None
Markus Scheidgen's avatar
Markus Scheidgen committed
380

381
                log_data.update(log_size=self.upload_files.archive_log_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
382

383
    def __str__(self):
384
        return 'calc %s calc_id=%s upload_id%s' % (super().__str__(), self.calc_id, self.upload_id)
385

386

387
class Upload(Proc):
Markus Scheidgen's avatar
Markus Scheidgen committed
388
389
390
391
392
393
    """
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

    Attributes:
        name: optional user provided upload name
394
395
        upload_path: the path were the uploaded files was stored
        temporary: True if the uploaded file should be removed after extraction
396
        metadata: optional user provided additional meta data
Markus Scheidgen's avatar
Markus Scheidgen committed
397
398
        upload_id: the upload id generated by the database
        upload_time: the timestamp when the system realised the upload
399
        user_id: the id of the user that created this upload
Markus Scheidgen's avatar
Markus Scheidgen committed
400
401
402
403
    """
    id_field = 'upload_id'

    upload_id = StringField(primary_key=True)
404
405
    upload_path = StringField(default=None)
    temporary = BooleanField(default=False)
Markus Scheidgen's avatar
Markus Scheidgen committed
406
407
408

    name = StringField(default=None)
    upload_time = DateTimeField()
409
    user_id = StringField(required=True)
410
411
    published = BooleanField(default=False)
    publish_time = DateTimeField()
412
    last_update = DateTimeField()
Markus Scheidgen's avatar
Markus Scheidgen committed
413
414
415

    meta: Any = {
        'indexes': [
416
            'user_id', 'tasks_status', 'process_status', 'published', 'upload_time'
Markus Scheidgen's avatar
Markus Scheidgen committed
417
418
419
420
421
        ]
    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
422
        self._upload_files: ArchiveBasedStagingUploadFiles = None
Markus Scheidgen's avatar
Markus Scheidgen committed
423

424
425
    @property
    def metadata(self) -> dict:
426
427
428
429
430
431
        # TODO user_metadata needs to be stored in the public bucket, since staging data might not be shared
        try:
            upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
        except KeyError:
            return None
        return upload_files.user_metadata
432
433
434

    @metadata.setter
    def metadata(self, data: dict) -> None:
435
436
437
        # TODO user_metadata needs to be stored in the public bucket, since staging data might not be shared
        upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True, create=True)
        upload_files.user_metadata = data
438

Markus Scheidgen's avatar
Markus Scheidgen committed
439
    @classmethod
440
    def get(cls, id: str, include_published: bool = True) -> 'Upload':
441
        upload = cls.get_by_id(id, 'upload_id')
442
        if upload is not None:
443
444
445
            return upload

        raise KeyError()
Markus Scheidgen's avatar
Markus Scheidgen committed
446
447

    @classmethod
448
449
450
    def user_uploads(cls, user: coe_repo.User, **kwargs) -> List['Upload']:
        """ Returns all uploads for the given user. Kwargs are passed to mongo query. """
        return cls.objects(user_id=str(user.user_id), **kwargs)
Markus Scheidgen's avatar
Markus Scheidgen committed
451

452
453
454
455
    @property
    def uploader(self):
        return coe_repo.User.from_user_id(self.user_id)

Markus Scheidgen's avatar
Markus Scheidgen committed
456
457
    def get_logger(self, **kwargs):
        logger = super().get_logger()
458
        logger = logger.bind(upload_id=self.upload_id, upload_name=self.name, **kwargs)
Markus Scheidgen's avatar
Markus Scheidgen committed
459
460
461
462
463
464
465
466
        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.
467
468

        Arguments:
469
            user (coe_repo.User): The user that created the upload.
Markus Scheidgen's avatar
Markus Scheidgen committed
470
        """
471
        user: coe_repo.User = kwargs['user']
472
473
474
        del(kwargs['user'])
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
475
        kwargs.update(user_id=str(user.user_id))
Markus Scheidgen's avatar
Markus Scheidgen committed
476
        self = super().create(**kwargs)
477

Markus Scheidgen's avatar
Markus Scheidgen committed
478
        self._continue_with('uploading')
479

Markus Scheidgen's avatar
Markus Scheidgen committed
480
481
        return self

482
483
484
485
486
    def delete(self):
        """ Deletes this upload process state entry and its calcs. """
        Calc.objects(upload_id=self.upload_id).delete()
        super().delete()

487
    def delete_upload_local(self, with_coe_repo: bool = False):
488
489
        """
        Deletes of the upload, including its processing state and
490
        staging files. Local version without celery processing.
491
492
493
494
        """
        logger = self.get_logger()

        with utils.lnr(logger, 'staged upload delete failed'):
495

496
497
498
499
500
            if with_coe_repo and self.published:
                with utils.timer(
                        logger, 'upload deleted from repo db', step='repo',
                        upload_size=self.upload_files.size):
                    coe_repo.Upload.delete(self.upload_id)
501

502
            with utils.timer(
503
                    logger, 'upload deleted from index', step='index',
504
                    upload_size=self.upload_files.size):
505
                search.delete_upload(self.upload_id)
506

507
            with utils.timer(
508
                    logger, 'staged upload deleted', step='files',
509
510
511
512
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
                self.delete()

513
514
515
516
517
518
519
520
    @process
    def delete_upload(self, with_coe_repo: bool = False):
        """
        Deletes of the upload, including its processing state and
        staging files. This starts the celery process of deleting the upload.
        """
        self.delete_upload_local(with_coe_repo=with_coe_repo)

521
        return True  # do not save the process status on the delete upload
522

523
    @process
524
    def publish_upload(self):
525
526
527
528
529
        """
        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.
530
531
532

        If the upload is already published (i.e. re-publish), it will update user metadata from
        repository db, publish to repository db if not exists, update the search index.
533
        """
534
535
        assert self.processed_calcs > 0

536
        logger = self.get_logger()
537
        logger.info('started to publish')
538

539
540
        with utils.lnr(logger, '(re-)publish failed'):
            upload_with_metadata = self.to_upload_with_metadata(self.metadata)
541
            calcs = upload_with_metadata.calcs
542

543
            if config.repository_db.publish_enabled:
544
545
546
547
548
549
550
                if config.repository_db.mode == 'coe' and isinstance(self.upload_files, StagingUploadFiles):
                    with utils.timer(
                            logger, 'coe extracted raw-file copy created', step='repo',
                            upload_size=self.upload_files.size):

                        self.upload_files.create_extracted_copy()

551
552
553
554
555
556
557
                coe_upload = coe_repo.Upload.from_upload_id(upload_with_metadata.upload_id)
                if coe_upload is None:
                    with utils.timer(
                            logger, 'upload added to repository', step='repo',
                            upload_size=self.upload_files.size):
                        coe_upload = coe_repo.Upload.publish(upload_with_metadata)

558
                with utils.timer(
559
                        logger, 'upload PIDs read from repository', step='repo',
560
                        upload_size=self.upload_files.size):
561
562
                    for calc, coe_calc in zip(calcs, coe_upload.calcs):
                        calc.pid = coe_calc.coe_calc_id
563

564
            with utils.timer(
565
                    logger, 'upload metadata updated', step='metadata',
566
                    upload_size=self.upload_files.size):
567
568

                def create_update(calc):
569
                    calc.published = True
570
571
572
573
574
                    return UpdateOne(
                        {'_id': calc.calc_id},
                        {'$set': {'metadata': calc.to_dict()}})

                Calc._get_collection().bulk_write([create_update(calc) for calc in calcs])
575

576
577
578
579
580
            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(upload_with_metadata)
581
582
583
584

            with utils.timer(
                    logger, 'index updated', step='index',
                    upload_size=self.upload_files.size):
585
                search.publish(calcs)
586

587
588
589
590
591
592
593
594
595
596
597
            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.now()
                    self.last_update = datetime.now()
                    self.save()
            else:
                self.last_update = datetime.now()
598
                self.save()
599

Markus Scheidgen's avatar
Markus Scheidgen committed
600
    @process
601
    def process_upload(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
602
603
604
605
606
607
608
        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
        pass

609
    @property
610
611
    def upload_files(self) -> UploadFiles:
        upload_files_class = ArchiveBasedStagingUploadFiles if not self.published else PublicUploadFiles
612
        kwargs = dict(upload_path=self.upload_path) if not self.published else {}
613
614
615

        if not self._upload_files or not isinstance(self._upload_files, upload_files_class):
            self._upload_files = upload_files_class(
616
                self.upload_id, is_authorized=lambda: True, **kwargs)
617

618
        return self._upload_files
619

620
621
622
623
624
    @property
    def staging_upload_files(self) -> ArchiveBasedStagingUploadFiles:
        assert not self.published
        return cast(ArchiveBasedStagingUploadFiles, self.upload_files)

Markus Scheidgen's avatar
Markus Scheidgen committed
625
626
    @task
    def extracting(self):
627
628
629
630
631
        """
        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.
        """
632
633
634
635
636
        # 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
637
638
        logger = self.get_logger()
        try:
Markus Scheidgen's avatar
Markus Scheidgen committed
639
640
            with utils.timer(
                    logger, 'upload extracted', step='extracting',
641
642
                    upload_size=self.upload_files.size):
                self.upload_files.extract()
643
644
645
646

            if self.temporary:
                os.remove(self.upload_path)
                self.upload_path = None
647

648
        except KeyError:
649
            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
650
651
652
            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
Markus Scheidgen's avatar
Markus Scheidgen committed
653
654
            return

655
    def match_mainfiles(self) -> Generator[Tuple[str, object], None, None]:
656
657
658
659
660
661
662
        """
        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
        """
663
        directories_with_match: Dict[str, str] = dict()
664
665
        upload_files = self.staging_upload_files
        for filename in upload_files.raw_file_manifest():
666
            try:
667
                parser = match_parser(filename, upload_files)
668
                if parser is not None:
669
670
                    directory = os.path.dirname(filename)
                    if directory in directories_with_match:
671
672
673
                        # TODO this might give us the chance to store directory based relationship
                        # between calcs for the future?
                        pass
674
675
                    else:
                        directories_with_match[directory] = filename
676
677

                    yield filename, parser
678
679
680
681
            except Exception as e:
                self.get_logger().error(
                    'exception while matching pot. mainfile',
                    mainfile=filename, exc_info=e)
682

Markus Scheidgen's avatar
Markus Scheidgen committed
683
684
    @task
    def parse_all(self):
685
        """
686
        Identified mainfile/parser combinations among the upload's files, creates
687
688
        respective :class:`Calc` instances, and triggers their processing.
        """
689
690
        logger = self.get_logger()

Markus Scheidgen's avatar
Markus Scheidgen committed
691
692
        with utils.timer(
                logger, 'upload extracted', step='matching',
693
694
                upload_size=self.upload_files.size):
            for filename, parser in self.match_mainfiles():
695
                calc = Calc.create(
696
                    calc_id=self.upload_files.calc_id(filename),
697
                    mainfile=filename, parser=parser.name,
698
                    worker_hostname=self.worker_hostname,
699
700
                    upload_id=self.upload_id)

701
                calc.process_calc()
Markus Scheidgen's avatar
Markus Scheidgen committed
702

703
704
705
706
707
708
709
710
711
712
713
714
    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()
715
716
717

    def join(self):
        self.cleanup()
Markus Scheidgen's avatar
Markus Scheidgen committed
718

719
720
721
722
723
724
725
    @property
    def gui_url(self):
        base = config.api_url()[:-3]
        if base.endswith('/'):
            base = base[:-1]
        return '%s/uploads/' % base

Markus Scheidgen's avatar
Markus Scheidgen committed
726
727
    @task
    def cleanup(self):
728
729
        search.refresh()

730
731
732
733
734
735
        # send email about process finish
        user = self.uploader
        name = '%s %s' % (user.first_name, user.last_name)
        message = '\n'.join([
            'Dear %s,' % name,
            '',
736
            'your data %suploaded at %s has completed processing.' % (
737
                '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()),  # pylint: disable=no-member
738
739
740
741
742
            'You can review your data on your upload page: %s' % self.gui_url,
            '',
            'If you encouter any issues with your upload, please let us know and replay to this email.',
            '',
            'The nomad team'
743
        ])
744
745
746
747
748
749
750
        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
751

752
753
754
    def get_calc(self, calc_id) -> Calc:
        return Calc.objects(upload_id=self.upload_id, calc_id=calc_id).first()

Markus Scheidgen's avatar
Markus Scheidgen committed
755
    @property
756
    def processed_calcs(self):
757
        return Calc.objects(upload_id=self.upload_id, tasks_status__in=[SUCCESS, FAILURE]).count()
758
759
760
761
762
763
764

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

    @property
    def failed_calcs(self):
765
        return Calc.objects(upload_id=self.upload_id, tasks_status=FAILURE).count()
766

767
768
    @property
    def pending_calcs(self):
769
        return Calc.objects(upload_id=self.upload_id, tasks_status=PENDING).count()
770

771
772
773
    def all_calcs(self, start, end, order_by=None):
        query = Calc.objects(upload_id=self.upload_id)[start:end]
        return query.order_by(order_by) if order_by is not None else query
774
775
776

    @property
    def calcs(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
777
        return Calc.objects(upload_id=self.upload_id, tasks_status=SUCCESS)
Markus Scheidgen's avatar
Markus Scheidgen committed
778

779
    def to_upload_with_metadata(self, user_metadata: dict = None) -> UploadWithMetadata:
780
        # prepare user metadata per upload and per calc
781
782
783
        if user_metadata is not None:
            calc_metadatas: Dict[str, Any] = dict()
            upload_metadata: Dict[str, Any] = dict()
784

785
            upload_metadata.update(user_metadata)
786
787
            if 'calculations' in upload_metadata:
                del(upload_metadata['calculations'])
Markus Scheidgen's avatar
Markus Scheidgen committed
788

789
            for calc in user_metadata.get('calculations', []):  # pylint: disable=no-member
790
                calc_metadatas[calc['mainfile']] = calc
Markus Scheidgen's avatar
Markus Scheidgen committed
791

792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
            user_upload_time = upload_metadata.get('_upload_time', None)

            def get_metadata(calc: Calc):
                """
                Assemble metadata from calc's processed calc metadata and the uploads
                user metadata.
                """
                calc_data = calc.metadata
                calc_with_metadata = datamodel.CalcWithMetadata(**calc_data)
                calc_metadata = dict(upload_metadata)
                calc_metadata.update(calc_metadatas.get(calc.mainfile, {}))
                calc_with_metadata.apply_user_metadata(calc_metadata)

                return calc_with_metadata
        else:
            user_upload_time = None

            def get_metadata(calc: Calc):
                return datamodel.CalcWithMetadata(**calc.metadata)

Markus Scheidgen's avatar
Markus Scheidgen committed
812
813
814
815
816
        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)

817
        result.calcs = [get_metadata(calc) for calc in Calc.objects(upload_id=self.upload_id)]
818

Markus Scheidgen's avatar
Markus Scheidgen committed
819
        return result
820

821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
    def compress_and_set_metadata(self, metadata: Dict[str, Any]) -> None:
        """
        Stores the given user metadata in the upload document. This is the metadata
        adhering to the API model (``UploadMetaData``). Most quantities can be stored
        for the upload and for each calculation. This method will try to move same values
        from the calculation to the upload to "compress" the data.
        """
        compressed = {
            key: value for key, value in metadata.items() if key != 'calculations'}
        calculations: List[Dict[str, Any]] = []
        compressed['calculations'] = calculations

        for calc in metadata.get('calculations', []):
            compressed_calc: Dict[str, Any] = {}
            calculations.append(compressed_calc)
            for key, value in calc.items():
                if key in ['_pid', 'mainfile']:
                    # these quantities are explicitly calc specific and have to stay with
                    # the calc
                    compressed_calc[key] = value
                else:
                    if key not in compressed:
                        compressed[key] = value
                    elif compressed[key].__repr__ != value.__repr__:
                        compressed_calc[key] = value
                    else:
                        compressed[key] = value

        self.metadata = compressed

851
    def __str__(self):
852
        return 'upload %s upload_id%s' % (super().__str__(), self.upload_id)