data.py 34.6 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
167
168
            calc_with_metadata.last_processing = datetime.now()
            calc_with_metadata.files = self.upload_files.calc_files(self.mainfile)
            self.metadata = calc_with_metadata.to_dict()

169
170
171
172
173
            if len(calc_with_metadata.files) >= config.auxfile_cutoff:
                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
174
175
176
177
            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
Markus Scheidgen's avatar
Markus Scheidgen committed
178
            # close loghandler that was not closed due to failures
179
            try:
180
181
182
                if self._calc_proc_logwriter is not None:
                    self._calc_proc_logwriter.close()
                    self._calc_proc_logwriter = None
183
184
185
            except Exception as e:
                logger.error('could not close calculation proc log', exc_info=e)

186
187
188
189
    def fail(self, *errors, log_level=logging.ERROR, **kwargs):
        # in case of failure, index a minimum set of metadata and mark
        # processing failure
        try:
190
            calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
191
192
193
194
195
196
197
198
            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
199
200
201
202
203
204
205

            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

206
207
208
209
210
211
212
213
            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)

214
215
216
217
218
219
220
    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
221
222
223

    @task
    def parsing(self):
224
        context = dict(parser=self.parser, step=self.parser)
225
        logger = self.get_logger(**context)
226
        parser = parser_dict[self.parser]
227
        self.metadata['parser_name'] = self.parser
Markus Scheidgen's avatar
Markus Scheidgen committed
228

229
        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
230
231
232
233
234
235
236
            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)
237
                return
Markus Scheidgen's avatar
Markus Scheidgen committed
238

239
240
        # add the non code specific calc metadata to the backend
        # all other quantities have been determined by parsers/normalizers
241
        self._parser_backend.openNonOverlappingSection('section_entry_info')
242
        self._parser_backend.addValue('upload_id', self.upload_id)
243
        self._parser_backend.addValue('calc_id', self.calc_id)
244
        self._parser_backend.addValue('calc_hash', self.metadata['calc_hash'])
245
        self._parser_backend.addValue('mainfile', self.mainfile)
246
        self._parser_backend.addValue('parser_name', self.parser)
247
248
249
250
251
252
253
254
255
256
257
258
        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)
259

Markus Scheidgen's avatar
Markus Scheidgen committed
260
        if self._parser_backend.status[0] != 'ParseSuccess':
261
            logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
262
            error = self._parser_backend.status[1]
263
            self.fail(error, level=logging.INFO, **context)
264
265
266
267
268
269
270
271

    @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:
272
        self._parser_backend.openContext('/section_entry_info/0')
273
274
275
276
277
278
279
        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')
280
                self._parser_backend.addValue('number_of_archive_processor_warnings', len(warnings))
281
282
283
284
                self._parser_backend.addArrayValues('archive_processor_warnings', [str(warning) for warning in warnings])
            else:
                self._parser_backend.addValue('archive_processor_status', 'Success')
        else:
285
            errors = self._parser_backend.status[1]
286
287
288
            self._parser_backend.addValue('archive_processor_error', str(errors))

        self._parser_backend.closeNonOverlappingSection('section_archive_processing_info')
289
        self._parser_backend.closeContext('/section_entry_info/0')
Markus Scheidgen's avatar
Markus Scheidgen committed
290
291
292
293

    @task
    def normalizing(self):
        for normalizer in normalizers:
294
295
296
            if normalizer.domain != config.domain:
                continue

Markus Scheidgen's avatar
Markus Scheidgen committed
297
            normalizer_name = normalizer.__name__
298
            context = dict(normalizer=normalizer_name, step=normalizer_name)
299
            logger = self.get_logger(**context)
Markus Scheidgen's avatar
Markus Scheidgen committed
300
301

            with utils.timer(
302
                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
303
                with self.use_parser_backend(normalizer_name) as backend:
304
305
306
307
308
309
310
                    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
311

312
313
            failed = self._parser_backend.status[0] != 'ParseSuccess'
            if failed:
314
                logger.error(self._parser_backend.status[1])
Markus Scheidgen's avatar
Markus Scheidgen committed
315
                error = self._parser_backend.status[1]
316
                self.fail(error, level=logging.WARNING, error=error, **context)
317
318
319
320
                break
            else:
                logger.debug(
                    'completed normalizer successfully', normalizer=normalizer_name)
Markus Scheidgen's avatar
Markus Scheidgen committed
321
322
323

    @task
    def archiving(self):
324
325
        logger = self.get_logger()

326
        calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
327
        calc_with_metadata.apply_domain_metadata(self._parser_backend)
328
        calc_with_metadata.processed = True
329

330
331
        # persist the calc metadata
        with utils.timer(logger, 'saved calc metadata', step='metadata'):
332
            self.metadata = calc_with_metadata.to_dict()
333
334

        # index in search
335
        with utils.timer(logger, 'indexed', step='index'):
336
            search.Entry.from_calc_with_metadata(calc_with_metadata).save()
337

338
        # persist the archive
Markus Scheidgen's avatar
Markus Scheidgen committed
339
        with utils.timer(
340
                logger, 'archived', step='archive',
Markus Scheidgen's avatar
Markus Scheidgen committed
341
                input_size=self.mainfile_file.size) as log_data:
342
            with self.upload_files.archive_file(self.calc_id, 'wt') as out:
343
                self._parser_backend.write_json(out, pretty=True, root_sections=Domain.instance.root_sections)
344

345
            log_data.update(archive_size=self.upload_files.archive_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
346
347
348
349

        # close loghandler
        if self._calc_proc_logwriter is not None:
            with utils.timer(
350
                    logger, 'archived log', step='logs',
Markus Scheidgen's avatar
Markus Scheidgen committed
351
                    input_size=self.mainfile_file.size) as log_data:
352
                self._calc_proc_logwriter_ctx.__exit__(None, None, None)  # pylint: disable=E1101
353
                self._calc_proc_logwriter = None
Markus Scheidgen's avatar
Markus Scheidgen committed
354

355
                log_data.update(log_size=self.upload_files.archive_log_file_object(self.calc_id).size)
Markus Scheidgen's avatar
Markus Scheidgen committed
356

357
    def __str__(self):
358
        return 'calc %s calc_id=%s upload_id%s' % (super().__str__(), self.calc_id, self.upload_id)
359

360

361
class Upload(Proc):
Markus Scheidgen's avatar
Markus Scheidgen committed
362
363
364
365
366
367
    """
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

    Attributes:
        name: optional user provided upload name
368
369
        upload_path: the path were the uploaded files was stored
        temporary: True if the uploaded file should be removed after extraction
370
        metadata: optional user provided additional meta data
Markus Scheidgen's avatar
Markus Scheidgen committed
371
372
        upload_id: the upload id generated by the database
        upload_time: the timestamp when the system realised the upload
373
        user_id: the id of the user that created this upload
Markus Scheidgen's avatar
Markus Scheidgen committed
374
375
376
377
    """
    id_field = 'upload_id'

    upload_id = StringField(primary_key=True)
378
379
    upload_path = StringField(default=None)
    temporary = BooleanField(default=False)
Markus Scheidgen's avatar
Markus Scheidgen committed
380
381
382

    name = StringField(default=None)
    upload_time = DateTimeField()
383
    user_id = StringField(required=True)
384
385
    published = BooleanField(default=False)
    publish_time = DateTimeField()
386
    last_update = DateTimeField()
Markus Scheidgen's avatar
Markus Scheidgen committed
387
388
389

    meta: Any = {
        'indexes': [
390
            'user_id', 'tasks_status', 'process_status', 'published', 'upload_time'
Markus Scheidgen's avatar
Markus Scheidgen committed
391
392
393
394
395
        ]
    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
396
        self._upload_files: ArchiveBasedStagingUploadFiles = None
Markus Scheidgen's avatar
Markus Scheidgen committed
397

398
399
    @property
    def metadata(self) -> dict:
400
401
402
403
404
405
        # 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
406
407
408

    @metadata.setter
    def metadata(self, data: dict) -> None:
409
410
411
        # 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
412

Markus Scheidgen's avatar
Markus Scheidgen committed
413
    @classmethod
414
    def get(cls, id: str, include_published: bool = True) -> 'Upload':
415
        upload = cls.get_by_id(id, 'upload_id')
416
        if upload is not None:
417
418
419
            return upload

        raise KeyError()
Markus Scheidgen's avatar
Markus Scheidgen committed
420
421

    @classmethod
422
423
424
    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
425

426
427
428
429
    @property
    def uploader(self):
        return coe_repo.User.from_user_id(self.user_id)

Markus Scheidgen's avatar
Markus Scheidgen committed
430
431
    def get_logger(self, **kwargs):
        logger = super().get_logger()
432
        logger = logger.bind(upload_id=self.upload_id, upload_name=self.name, **kwargs)
Markus Scheidgen's avatar
Markus Scheidgen committed
433
434
435
436
437
438
439
440
        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.
441
442

        Arguments:
443
            user (coe_repo.User): The user that created the upload.
Markus Scheidgen's avatar
Markus Scheidgen committed
444
        """
445
        user: coe_repo.User = kwargs['user']
446
447
448
        del(kwargs['user'])
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
449
        kwargs.update(user_id=str(user.user_id))
Markus Scheidgen's avatar
Markus Scheidgen committed
450
        self = super().create(**kwargs)
451

Markus Scheidgen's avatar
Markus Scheidgen committed
452
        self._continue_with('uploading')
453

Markus Scheidgen's avatar
Markus Scheidgen committed
454
455
        return self

456
457
458
459
460
    def delete(self):
        """ Deletes this upload process state entry and its calcs. """
        Calc.objects(upload_id=self.upload_id).delete()
        super().delete()

461
    def delete_upload_local(self, with_coe_repo: bool = False):
462
463
        """
        Deletes of the upload, including its processing state and
464
        staging files. Local version without celery processing.
465
466
467
468
        """
        logger = self.get_logger()

        with utils.lnr(logger, 'staged upload delete failed'):
469

470
471
472
473
474
            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)
475

476
            with utils.timer(
477
                    logger, 'upload deleted from index', step='index',
478
                    upload_size=self.upload_files.size):
479
                search.delete_upload(self.upload_id)
480

481
            with utils.timer(
482
                    logger, 'staged upload deleted', step='files',
483
484
485
486
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
                self.delete()

487
488
489
490
491
492
493
494
    @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)

495
        return True  # do not save the process status on the delete upload
496

497
    @process
498
    def publish_upload(self):
499
500
501
502
503
        """
        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.
504
505
506

        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.
507
        """
508
509
        assert self.processed_calcs > 0

510
        logger = self.get_logger()
511
        logger.info('started to publish')
512

513
514
        with utils.lnr(logger, '(re-)publish failed'):
            upload_with_metadata = self.to_upload_with_metadata(self.metadata)
515
            calcs = upload_with_metadata.calcs
516

517
            if config.repository_db.publish_enabled:
518
519
520
521
522
523
524
                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()

525
526
527
528
529
530
531
                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)

532
                with utils.timer(
533
                        logger, 'upload PIDs read from repository', step='repo',
534
                        upload_size=self.upload_files.size):
535
536
                    for calc, coe_calc in zip(calcs, coe_upload.calcs):
                        calc.pid = coe_calc.coe_calc_id
537

538
            with utils.timer(
539
                    logger, 'upload metadata updated', step='metadata',
540
                    upload_size=self.upload_files.size):
541
542

                def create_update(calc):
543
                    calc.published = True
544
545
546
547
548
                    return UpdateOne(
                        {'_id': calc.calc_id},
                        {'$set': {'metadata': calc.to_dict()}})

                Calc._get_collection().bulk_write([create_update(calc) for calc in calcs])
549

550
551
552
553
554
            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)
555
556
557
558

            with utils.timer(
                    logger, 'index updated', step='index',
                    upload_size=self.upload_files.size):
559
                search.publish(calcs)
560

561
562
563
564
565
566
567
568
569
570
571
            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()
572
                self.save()
573

Markus Scheidgen's avatar
Markus Scheidgen committed
574
    @process
575
    def process_upload(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
576
577
578
579
580
581
582
        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
        pass

583
    @property
584
585
    def upload_files(self) -> UploadFiles:
        upload_files_class = ArchiveBasedStagingUploadFiles if not self.published else PublicUploadFiles
586
        kwargs = dict(upload_path=self.upload_path) if not self.published else {}
587
588
589

        if not self._upload_files or not isinstance(self._upload_files, upload_files_class):
            self._upload_files = upload_files_class(
590
                self.upload_id, is_authorized=lambda: True, **kwargs)
591

592
        return self._upload_files
593

594
595
596
597
598
    @property
    def staging_upload_files(self) -> ArchiveBasedStagingUploadFiles:
        assert not self.published
        return cast(ArchiveBasedStagingUploadFiles, self.upload_files)

Markus Scheidgen's avatar
Markus Scheidgen committed
599
600
    @task
    def extracting(self):
601
602
603
604
605
        """
        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.
        """
606
607
608
609
610
        # 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
611
612
        logger = self.get_logger()
        try:
Markus Scheidgen's avatar
Markus Scheidgen committed
613
614
            with utils.timer(
                    logger, 'upload extracted', step='extracting',
615
616
                    upload_size=self.upload_files.size):
                self.upload_files.extract()
617
618
619
620

            if self.temporary:
                os.remove(self.upload_path)
                self.upload_path = None
621

622
        except KeyError:
623
            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
624
625
626
            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
Markus Scheidgen's avatar
Markus Scheidgen committed
627
628
            return

629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
    def _preprocess_files(self, path):
        """
        Some files need preprocessing. Currently we need to add a stripped POTCAR version
        and always restrict/embargo the original.
        """
        if os.path.basename(path) == 'POTCAR':
            # 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))

658
    def match_mainfiles(self) -> Generator[Tuple[str, object], None, None]:
659
660
661
662
663
664
665
        """
        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
        """
666
        directories_with_match: Dict[str, str] = dict()
667
668
        upload_files = self.staging_upload_files
        for filename in upload_files.raw_file_manifest():
669
            self._preprocess_files(filename)
670
            try:
671
                parser = match_parser(filename, upload_files)
672
                if parser is not None:
673
674
                    directory = os.path.dirname(filename)
                    if directory in directories_with_match:
675
676
677
                        # TODO this might give us the chance to store directory based relationship
                        # between calcs for the future?
                        pass
678
679
                    else:
                        directories_with_match[directory] = filename
680
681

                    yield filename, parser
682
683
684
685
            except Exception as e:
                self.get_logger().error(
                    'exception while matching pot. mainfile',
                    mainfile=filename, exc_info=e)
686

Markus Scheidgen's avatar
Markus Scheidgen committed
687
688
    @task
    def parse_all(self):
689
        """
690
        Identified mainfile/parser combinations among the upload's files, creates
691
692
        respective :class:`Calc` instances, and triggers their processing.
        """
693
694
        logger = self.get_logger()

Markus Scheidgen's avatar
Markus Scheidgen committed
695
696
        with utils.timer(
                logger, 'upload extracted', step='matching',
697
698
                upload_size=self.upload_files.size):
            for filename, parser in self.match_mainfiles():
699
                calc = Calc.create(
700
                    calc_id=self.upload_files.calc_id(filename),
701
                    mainfile=filename, parser=parser.name,
702
                    worker_hostname=self.worker_hostname,
703
704
                    upload_id=self.upload_id)

705
                calc.process_calc()
Markus Scheidgen's avatar
Markus Scheidgen committed
706

707
708
709
710
711
712
713
714
715
716
717
718
    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()
719
720
721

    def join(self):
        self.cleanup()
Markus Scheidgen's avatar
Markus Scheidgen committed
722

723
724
725
726
727
728
729
    @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
730
731
    @task
    def cleanup(self):
732
733
        search.refresh()

734
735
736
737
738
739
        # send email about process finish
        user = self.uploader
        name = '%s %s' % (user.first_name, user.last_name)
        message = '\n'.join([
            'Dear %s,' % name,
            '',
740
            'your data %suploaded at %s has completed processing.' % (
741
                '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()),  # pylint: disable=no-member
742
743
744
745
746
            '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'
747
        ])
748
749
750
751
752
753
754
        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
755

756
757
758
    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
759
    @property
760
    def processed_calcs(self):
761
        return Calc.objects(upload_id=self.upload_id, tasks_status__in=[SUCCESS, FAILURE]).count()
762
763
764
765
766
767
768

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

    @property
    def failed_calcs(self):
769
        return Calc.objects(upload_id=self.upload_id, tasks_status=FAILURE).count()
770

771
772
    @property
    def pending_calcs(self):
773
        return Calc.objects(upload_id=self.upload_id, tasks_status=PENDING).count()
774

775
776
777
    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
778
779
780

    @property
    def calcs(self):
Markus Scheidgen's avatar
Markus Scheidgen committed
781
        return Calc.objects(upload_id=self.upload_id, tasks_status=SUCCESS)
Markus Scheidgen's avatar
Markus Scheidgen committed
782

783
    def to_upload_with_metadata(self, user_metadata: dict = None) -> UploadWithMetadata:
784
        # prepare user metadata per upload and per calc
785
786
787
        if user_metadata is not None:
            calc_metadatas: Dict[str, Any] = dict()
            upload_metadata: Dict[str, Any] = dict()
788

789
            upload_metadata.update(user_metadata)
790
791
            if 'calculations' in upload_metadata:
                del(upload_metadata['calculations'])
Markus Scheidgen's avatar
Markus Scheidgen committed
792

793
            for calc in user_metadata.get('calculations', []):  # pylint: disable=no-member
794
                calc_metadatas[calc['mainfile']] = calc
Markus Scheidgen's avatar
Markus Scheidgen committed
795

796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
            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
816
817
818
819
820
        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)

821
        result.calcs = [get_metadata(calc) for calc in Calc.objects(upload_id=self.upload_id)]
822

Markus Scheidgen's avatar
Markus Scheidgen committed
823
        return result
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
851
852
853
854
    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

855
    def __str__(self):
856
        return 'upload %s upload_id%s' % (super().__str__(), self.upload_id)