data.py 29 KB
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# 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:
"""

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from typing import List, Any, ContextManager, Tuple, Generator, Dict, cast
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from mongoengine import StringField, DateTimeField, DictField, BooleanField
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import logging
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from structlog import wrap_logger
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from contextlib import contextmanager
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import os.path
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from datetime import datetime
from pymongo import UpdateOne
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from nomad import utils, coe_repo, config, infrastructure, search, datamodel
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from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles, PublicUploadFiles
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from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
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from nomad.parsing import parser_dict, match_parser, LocalBackend
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from nomad.normalizing import normalizers
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from nomad.datamodel import UploadWithMetadata, Domain
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class Calc(Proc):
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    """
    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:
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        calc_id: the calc_id of this calc
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        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
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        metadata: the metadata record wit calc and user metadata, see :class:`datamodel.CalcWithMetadata`
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    """
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    calc_id = StringField(primary_key=True)
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    upload_id = StringField()
    mainfile = StringField()
    parser = StringField()

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    metadata = DictField()

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    meta: Any = {
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        'indexes': [
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            'upload_id', 'mainfile', 'parser', 'tasks_status', 'process_status'
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        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
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        self._parser_backend: LocalBackend = None
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        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
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        self._calc_proc_logwriter = None
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        self._calc_proc_logwriter_ctx: ContextManager = None
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    @classmethod
    def get(cls, id):
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        return cls.get_by_id(id, 'calc_id')
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    @property
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    def mainfile_file(self) -> PathObject:
        return self.upload_files.raw_file_object(self.mainfile)
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    @property
    def upload(self) -> 'Upload':
        if not self._upload:
            self._upload = Upload.get(self.upload_id)
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            self._upload.worker_hostname = self.worker_hostname
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        return self._upload

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    @property
    def upload_files(self) -> ArchiveBasedStagingUploadFiles:
        if not self._upload_files:
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            self._upload_files = ArchiveBasedStagingUploadFiles(
                self.upload_id, is_authorized=lambda: True, upload_path=self.upload.upload_path)
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        return self._upload_files

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    def get_logger(self, **kwargs):
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        """
        Returns a wrapped logger that additionally saves all entries to the calculation
        processing log in the archive.
        """
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        logger = super().get_logger()
        logger = logger.bind(
            upload_id=self.upload_id, mainfile=self.mainfile, calc_id=self.calc_id, **kwargs)
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        if self._calc_proc_logwriter_ctx is None:
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            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])
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    @process
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    def process_calc(self):
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        logger = self.get_logger()
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        if self.upload is None:
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            logger.error('calculation upload does not exist')
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        try:
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            # save preliminary minimum calc metadata in case processing fails
            # successful processing will replace it with the actual metadata
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            calc_with_metadata = datamodel.CalcWithMetadata(
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                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()
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            calc_with_metadata.upload_time = self.upload.upload_time
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            calc_with_metadata.nomad_version = config.version
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            calc_with_metadata.nomad_commit = config.commit
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            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()

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            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
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            # close loghandler that was not closed due to failures
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            try:
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                if self._calc_proc_logwriter is not None:
                    self._calc_proc_logwriter.close()
                    self._calc_proc_logwriter = None
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            except Exception as e:
                logger.error('could not close calculation proc log', exc_info=e)

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    def fail(self, *errors, log_level=logging.ERROR, **kwargs):
        # in case of failure, index a minimum set of metadata and mark
        # processing failure
        try:
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            calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
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            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
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            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

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            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)

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    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()
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    @task
    def parsing(self):
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        context = dict(parser=self.parser, step=self.parser)
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        logger = self.get_logger(**context)
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        parser = parser_dict[self.parser]
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        self.metadata['parser_name'] = self.parser
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        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
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            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)
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                return
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        # add the non code specific calc metadata to the backend
        # all other quantities have been determined by parsers/normalizers
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        self._parser_backend.openNonOverlappingSection('section_entry_info')
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        self._parser_backend.addValue('upload_id', self.upload_id)
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        self._parser_backend.addValue('calc_id', self.calc_id)
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        self._parser_backend.addValue('calc_hash', self.metadata['calc_hash'])
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        self._parser_backend.addValue('mainfile', self.mainfile)
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        self._parser_backend.addValue('parser_name', self.parser)
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        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)
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        if self._parser_backend.status[0] != 'ParseSuccess':
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            logger.error(self._parser_backend.status[1])
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            error = self._parser_backend.status[1]
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            self.fail(error, level=logging.INFO, **context)
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    @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:
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        self._parser_backend.openContext('/section_entry_info/0')
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        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')
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                self._parser_backend.addValue('number_of_archive_processor_warnings', len(warnings))
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                self._parser_backend.addArrayValues('archive_processor_warnings', [str(warning) for warning in warnings])
            else:
                self._parser_backend.addValue('archive_processor_status', 'Success')
        else:
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            errors = self._parser_backend.status[1]
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            self._parser_backend.addValue('archive_processor_error', str(errors))

        self._parser_backend.closeNonOverlappingSection('section_archive_processing_info')
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        self._parser_backend.closeContext('/section_entry_info/0')
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    @task
    def normalizing(self):
        for normalizer in normalizers:
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            if normalizer.domain != config.domain:
                continue

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            normalizer_name = normalizer.__name__
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            context = dict(normalizer=normalizer_name, step=normalizer_name)
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            logger = self.get_logger(**context)
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            with utils.timer(
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                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
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                with self.use_parser_backend(normalizer_name) as backend:
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                    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)]
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            failed = self._parser_backend.status[0] != 'ParseSuccess'
            if failed:
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                logger.error(self._parser_backend.status[1])
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                error = self._parser_backend.status[1]
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                self.fail(error, level=logging.WARNING, error=error, **context)
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                break
            else:
                logger.debug(
                    'completed normalizer successfully', normalizer=normalizer_name)
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    @task
    def archiving(self):
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        logger = self.get_logger()

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        calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
        print(calc_with_metadata.__class__.__name__)
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        calc_with_metadata.apply_domain_metadata(self._parser_backend)
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        calc_with_metadata.processed = True
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        # persist the calc metadata
        with utils.timer(logger, 'saved calc metadata', step='metadata'):
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            self.metadata = calc_with_metadata.to_dict()
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        # index in search
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        with utils.timer(logger, 'indexed', step='index'):
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            search.Entry.from_calc_with_metadata(calc_with_metadata).save()
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        # persist the archive
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        with utils.timer(
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                logger, 'archived', step='archive',
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                input_size=self.mainfile_file.size) as log_data:
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            with self.upload_files.archive_file(self.calc_id, 'wt') as out:
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                self._parser_backend.write_json(out, pretty=True, root_sections=Domain.instance.root_sections)
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            log_data.update(archive_size=self.upload_files.archive_file_object(self.calc_id).size)
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        # close loghandler
        if self._calc_proc_logwriter is not None:
            with utils.timer(
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                    logger, 'archived log', step='logs',
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                    input_size=self.mainfile_file.size) as log_data:
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                self._calc_proc_logwriter_ctx.__exit__(None, None, None)  # pylint: disable=E1101
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                self._calc_proc_logwriter = None
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                log_data.update(log_size=self.upload_files.archive_log_file_object(self.calc_id).size)
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    def __str__(self):
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        return 'calc %s calc_id=%s upload_id%s' % (super().__str__(), self.calc_id, self.upload_id)
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class Upload(Proc):
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    """
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

    Attributes:
        name: optional user provided upload name
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        upload_path: the path were the uploaded files was stored
        temporary: True if the uploaded file should be removed after extraction
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        metadata: optional user provided additional meta data
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        upload_id: the upload id generated by the database
        upload_time: the timestamp when the system realised the upload
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        user_id: the id of the user that created this upload
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    """
    id_field = 'upload_id'

    upload_id = StringField(primary_key=True)
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    upload_path = StringField(default=None)
    temporary = BooleanField(default=False)
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    name = StringField(default=None)
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    metadata = DictField(default=None)
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    upload_time = DateTimeField()
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    user_id = StringField(required=True)
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    published = BooleanField(default=False)
    publish_time = DateTimeField()
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    meta: Any = {
        'indexes': [
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            'user_id', 'tasks_status', 'process_status', 'published'
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        ]
    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
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        self._upload_files: ArchiveBasedStagingUploadFiles = None
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    @classmethod
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    def get(cls, id: str, include_published: bool = False) -> 'Upload':
        upload = cls.get_by_id(id, 'upload_id')
        # TODO published uploads should not be hidden by this and API
        if upload is not None and (not upload.published or include_published):
            return upload

        raise KeyError()
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    @classmethod
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    def user_uploads(cls, user: coe_repo.User) -> List['Upload']:
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        """ Returns all uploads for the given user. Currently returns all uploads. """
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        return cls.objects(user_id=str(user.user_id), published=False)
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    @property
    def uploader(self):
        return coe_repo.User.from_user_id(self.user_id)

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    def get_logger(self, **kwargs):
        logger = super().get_logger()
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        logger = logger.bind(upload_id=self.upload_id, upload_name=self.name, **kwargs)
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        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.
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        Arguments:
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            user (coe_repo.User): The user that created the upload.
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        """
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        user: coe_repo.User = kwargs['user']
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        del(kwargs['user'])
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
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        kwargs.update(user_id=str(user.user_id))
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        self = super().create(**kwargs)
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        self._continue_with('uploading')
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        return self

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

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

        with utils.lnr(logger, 'staged upload delete failed'):
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            with utils.timer(
                    logger, 'upload deleted from repo db', step='repo',
                    upload_size=self.upload_files.size):
                coe_repo.Upload.delete(self.upload_id)

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            with utils.timer(
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                    logger, 'upload deleted from index', step='index',
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                    upload_size=self.upload_files.size):
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                search.delete_upload(self.upload_id)
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            with utils.timer(
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                    logger, 'staged upload deleted', step='files',
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                    upload_size=self.upload_files.size):
                self.upload_files.delete()
                self.delete()

        return True  # do not save the process status on the delete upload
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    @process
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    def publish_upload(self):
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        """
        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.
        """
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        assert self.processed_calcs > 0

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        logger = self.get_logger()
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        logger.info('started to publish')
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        with utils.lnr(logger, 'publish failed'):
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            upload_with_metadata = self.to_upload_with_metadata()

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            if config.repository_db.publish_enabled:
                with utils.timer(
                        logger, 'upload added to repository', step='repo',
                        upload_size=self.upload_files.size):
                    coe_repo.Upload.publish(upload_with_metadata)

            if config.repository_db.publish_enabled:
                coe_upload = coe_repo.Upload.from_upload_id(upload_with_metadata.upload_id)
                if coe_upload is not None:
                    calcs = [coe_calc.to_calc_with_metadata() for coe_calc in coe_upload.calcs]
                else:
                    calcs = []
            else:
                calcs = upload_with_metadata.calcs

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            with utils.timer(
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                    logger, 'upload metadata updated', step='metadata',
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                    upload_size=self.upload_files.size):
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                def create_update(calc):
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                    calc.published = True
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                    return UpdateOne(
                        {'_id': calc.calc_id},
                        {'$set': {'metadata': calc.to_dict()}})

                Calc._get_collection().bulk_write([create_update(calc) for calc in calcs])
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            with utils.timer(
                    logger, 'staged upload files packed', step='pack',
                    upload_size=self.upload_files.size):
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                self.upload_files.pack(upload_with_metadata)
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            with utils.timer(
                    logger, 'index updated', step='index',
                    upload_size=self.upload_files.size):
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                search.publish(calcs)
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            with utils.timer(
                    logger, 'staged upload deleted', step='delete staged',
                    upload_size=self.upload_files.size):
                self.upload_files.delete()
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                self.published = True
                self.publish_time = datetime.now()
                self.save()
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    @process
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    def process_upload(self):
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        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
        pass

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    @property
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    def upload_files(self) -> UploadFiles:
        upload_files_class = ArchiveBasedStagingUploadFiles if not self.published else PublicUploadFiles

        if not self._upload_files or not isinstance(self._upload_files, upload_files_class):
            self._upload_files = upload_files_class(
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                self.upload_id, is_authorized=lambda: True, upload_path=self.upload_path)
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        return self._upload_files
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    @property
    def staging_upload_files(self) -> ArchiveBasedStagingUploadFiles:
        assert not self.published
        return cast(ArchiveBasedStagingUploadFiles, self.upload_files)

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    @task
    def extracting(self):
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        """
        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.
        """
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        # extract the uploaded file
        self._upload_files = ArchiveBasedStagingUploadFiles(
            upload_id=self.upload_id, is_authorized=lambda: True, create=True,
            upload_path=self.upload_path)

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        logger = self.get_logger()
        try:
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            with utils.timer(
                    logger, 'upload extracted', step='extracting',
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                    upload_size=self.upload_files.size):
                self.upload_files.extract()
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            if self.temporary:
                os.remove(self.upload_path)
                self.upload_path = None
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        except KeyError:
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            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
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            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
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            return

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    def match_mainfiles(self) -> Generator[Tuple[str, object], None, None]:
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        """
        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
        """
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        directories_with_match: Dict[str, str] = dict()
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        upload_files = self.staging_upload_files
        for filename in upload_files.raw_file_manifest():
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            try:
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                parser = match_parser(filename, upload_files)
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                if parser is not None:
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                    directory = os.path.dirname(filename)
                    if directory in directories_with_match:
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                        # TODO this might give us the chance to store directory based relationship
                        # between calcs for the future?
                        pass
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                    else:
                        directories_with_match[directory] = filename
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                    yield filename, parser
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            except Exception as e:
                self.get_logger().error(
                    'exception while matching pot. mainfile',
                    mainfile=filename, exc_info=e)
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    @task
    def parse_all(self):
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        """
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        Identified mainfile/parser combinations among the upload's files, creates
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        respective :class:`Calc` instances, and triggers their processing.
        """
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        logger = self.get_logger()

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        with utils.timer(
                logger, 'upload extracted', step='matching',
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                upload_size=self.upload_files.size):
            for filename, parser in self.match_mainfiles():
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                calc = Calc.create(
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                    calc_id=self.upload_files.calc_id(filename),
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                    mainfile=filename, parser=parser.name,
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                    worker_hostname=self.worker_hostname,
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                    upload_id=self.upload_id)

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                calc.process_calc()
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    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()
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    def join(self):
        self.cleanup()
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    @task
    def cleanup(self):
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        search.refresh()

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        # send email about process finish
        user = self.uploader
        name = '%s %s' % (user.first_name, user.last_name)
        message = '\n'.join([
            'Dear %s,' % name,
            '',
            'your data %suploaded %s has completed processing.' % (
                self.name if self.name else '', self.upload_time.isoformat()),
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            'You can review your data on your upload page: %s/uploads' % config.api_url()[:-3]
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        ])
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        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)
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    def get_calc(self, calc_id) -> Calc:
        return Calc.objects(upload_id=self.upload_id, calc_id=calc_id).first()

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    @property
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    def processed_calcs(self):
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        return Calc.objects(upload_id=self.upload_id, tasks_status__in=[SUCCESS, FAILURE]).count()
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    @property
    def total_calcs(self):
        return Calc.objects(upload_id=self.upload_id).count()

    @property
    def failed_calcs(self):
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        return Calc.objects(upload_id=self.upload_id, tasks_status=FAILURE).count()
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    @property
    def pending_calcs(self):
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        return Calc.objects(upload_id=self.upload_id, tasks_status=PENDING).count()
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    def all_calcs(self, start, end, order_by='mainfile'):
        return Calc.objects(upload_id=self.upload_id)[start:end].order_by(order_by)
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    @property
    def calcs(self):
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        return Calc.objects(upload_id=self.upload_id, tasks_status=SUCCESS)
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    def to_upload_with_metadata(self) -> UploadWithMetadata:
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        # prepare user metadata per upload and per calc
        calc_metadatas: Dict[str, Any] = dict()
        upload_metadata: Dict[str, Any] = dict()

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        if self.metadata is not None:
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            upload_metadata.update(self.metadata)
            if 'calculations' in upload_metadata:
                del(upload_metadata['calculations'])
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            for calc in self.metadata.get('calculations', []):
                calc_metadatas[calc['mainfile']] = calc
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        user_upload_time = upload_metadata.get('_upload_time', None)
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        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)

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

            return calc_with_metadata

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        result.calcs = [get_metadata(calc) for calc in Calc.objects(upload_id=self.upload_id)]
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        return result
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    def __str__(self):
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        return 'upload %s upload_id%s' % (super().__str__(), self.upload_id)