data.py 51.4 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.

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'''
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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
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.. autoclass:: Upload
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'''
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from typing import cast, List, Any, Tuple, Iterator, Dict, cast, Iterable
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from mongoengine import StringField, DateTimeField, DictField, BooleanField, IntField
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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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import hashlib
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from structlog.processors import StackInfoRenderer, format_exc_info, TimeStamper
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from nomad import utils, config, infrastructure, search, datamodel
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from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles, PublicUploadFiles, StagingUploadFiles
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from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
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from nomad.parsing import Backend
from nomad.parsing.parsers import parser_dict, match_parser
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from nomad.normalizing import normalizers
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from nomad.datamodel import EntryArchive
from nomad.archive import query_archive
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from nomad.datamodel.encyclopedia import (
    EncyclopediaMetadata,
)
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from nomad.metainfo import MSection
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import phonopyparser
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def _pack_log_event(logger, method_name, event_dict):
    try:
        log_data = dict(event_dict)
        log_data.update(**{
            key: value
            for key, value in getattr(logger, '_context', {}).items()
            if key not in ['service', 'release', 'upload_id', 'calc_id', 'mainfile', 'process_status']})
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        log_data.update(logger=logger.name)
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        return log_data
    except Exception:
        # raising an exception would cause an indefinite loop
        return event_dict


_log_processors = [
    StackInfoRenderer(),
    _pack_log_event,
    format_exc_info,
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    TimeStamper(fmt="%Y-%m-%d %H:%M.%S", utc=False)]
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class Calc(Proc):
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    '''
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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.

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    The attribute list, does not include the various metadata properties generated
    while parsing, including ``code_name``, ``code_version``, etc.
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    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.EntryMetadata`
    '''
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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',
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            'parser',
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            ('upload_id', 'mainfile'),
            ('upload_id', 'parser'),
            ('upload_id', 'tasks_status'),
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            ('upload_id', 'process_status'),
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            ('upload_id', 'metadata.nomad_version'),
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            'metadata.processed',
            'metadata.last_processing',
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            'metadata.published',
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            'metadata.datasets',
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            'metadata.pid'
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        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
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        self._parser_backend: Backend = None
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        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
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        self._calc_proc_logs: List[Any] = None
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        self._entry_metadata = 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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    def apply_entry_metadata(self, entry_metadata: datamodel.EntryMetadata):
        self.metadata = entry_metadata.m_to_dict(
            include_defaults=True,
            categories=[datamodel.MongoMetadata])  # TODO use embedded doc?

    def create_metadata(self) -> datamodel.EntryMetadata:
        '''
        Returns a :class:`nomad.datamodel.EntryMetadata` with values from this
        processing object, not necessarely the user metadata nor the metadata from
        the archive.
        '''
        entry_metadata = datamodel.EntryMetadata()
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        if self.parser is not None:
            entry_metadata.domain = parser_dict[self.parser].domain
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        entry_metadata.upload_id = self.upload_id
        entry_metadata.calc_id = self.calc_id
        entry_metadata.mainfile = self.mainfile
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        entry_metadata.nomad_version = config.meta.version
        entry_metadata.nomad_commit = config.meta.commit
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        entry_metadata.uploader = self.upload.user_id
        entry_metadata.upload_time = self.upload.upload_time
        entry_metadata.upload_name = self.upload.name

        return entry_metadata

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

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

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

            else:
                entry_metadata = self.create_metadata()
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        entry_metadata.m_update_from_dict(self.metadata)

        return entry_metadata

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

        return entry_metadata

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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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        '''
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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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        '''
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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_logs is None:
            self._calc_proc_logs = []
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        def save_to_calc_log(logger, method_name, event_dict):
            try:
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                # sanitize the event_dict, because all kinds of values might have been added
                dump_dict = {key: str(value) for key, value in event_dict.items()}
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                dump_dict.update(level=method_name.upper())
                self._calc_proc_logs.append(dump_dict)
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            except Exception:
                # Exceptions here will cause indefinite loop
                pass
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            return event_dict
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        return wrap_logger(logger, processors=_log_processors + [save_to_calc_log])
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    @process
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    def re_process_calc(self):
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        '''
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        Processes a calculation again. This means there is already metadata and
        instead of creating it initially, we are just updating the existing
        records.
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        '''
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        parser = match_parser(self.upload_files.raw_file_object(self.mainfile).os_path, strict=False)
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        logger = self.get_logger()
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        if parser is None and not config.reprocess_unmatched:
            self.errors = ['no parser matches during re-process, will not re-process this calc']
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            try:
                upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
                with upload_files.read_archive(self.calc_id) as archive:
                    self.upload_files.write_archive(self.calc_id, archive[self.calc_id].to_dict())

            except Exception as e:
                logger.error('could not copy archive for non matching, non reprocessed entry', exc_info=e)
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                raise e
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            # mock the steps of actual processing
            self._continue_with('parsing')
            self._continue_with('normalizing')
            self._continue_with('archiving')
            self._complete()
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            return

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        if parser is None:
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            self.get_logger().warn('no parser matches during re-process, use the old parser')
            self.warnings = ['no matching parser found during re-processing']

        elif self.parser != parser.name:
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            if parser_dict[self.parser].name == parser.name:
                # parser was just renamed
                self.parser = parser.name

            else:
                self.parser = parser.name
                logger.info(
                    'different parser matches during re-process, use new parser',
                    parser=parser.name)
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        try:
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            self._entry_metadata = self.user_metadata()
            self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
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            self._entry_metadata.nomad_version = config.meta.version
            self._entry_metadata.nomad_commit = config.meta.commit
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            self._entry_metadata.last_processing = datetime.utcnow()
            self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)
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            self.parsing()
            self.normalizing()
            self.archiving()
        finally:
            # close loghandler that was not closed due to failures
            try:
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                if self._parser_backend and self._parser_backend.resource:
                    self._parser_backend.resource.unload()
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            except Exception as e:
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                logger.error('could unload processing results', exc_info=e)
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    def _setup_fallback_metadata(self):
        self._entry_metadata = self.create_metadata()
        self._entry_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
        self._entry_metadata.last_processing = datetime.utcnow()
        self._entry_metadata.files = self.upload_files.calc_files(self.mainfile)

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    @process
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    def process_calc(self):
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        '''
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        Processes a new calculation that has no prior records in the mongo, elastic,
        or filesystem storage. It will create an initial set of (user) metadata.
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        '''
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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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            self._setup_fallback_metadata()
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            if len(self._entry_metadata.files) >= config.auxfile_cutoff:
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                self.warning(
                    'This calc has many aux files in its directory. '
                    'Have you placed many calculations in the same directory?')

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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._parser_backend and self._parser_backend.resource:
                    self._parser_backend.resource.unload()
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            except Exception as e:
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                logger.error('could unload processing results', exc_info=e)
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    def on_fail(self):
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        # in case of failure, index a minimum set of metadata and mark
        # processing failure
        try:
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            if self._entry_metadata is None:
                self._setup_fallback_metadata()

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            self._entry_metadata.processed = False
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            self.apply_entry_metadata(self._entry_metadata)
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            if self._parser_backend and self._parser_backend.resource:
                backend = self._parser_backend
            else:
                backend = None
            self._entry_metadata.apply_domain_metadata(backend)
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            self._entry_metadata.a_elastic.index()
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        except Exception as e:
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            self.get_logger().error(
                'could not index after processing failure', exc_info=e)
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        try:
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            self.write_archive(None)
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        except Exception as e:
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            self.get_logger().error(
                'could not write archive after processing failure', exc_info=e)
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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 == 're_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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        ''' The *task* that encapsulates all parsing related actions. '''
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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._entry_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)
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                if isinstance(self._parser_backend, MSection):
                    backend = Backend(parser._metainfo_env, parser.domain)
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                    root_section = datamodel.domains[parser.domain]['root_section']
                    setattr(backend.entry_archive, root_section, self._parser_backend)
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                    backend.resource.add(self._parser_backend)
                    self._parser_backend = backend

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            except Exception as e:
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                self.fail('parser failed with exception', exc_info=e, error=str(e), **context)
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                return
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            except SystemExit:
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                self.fail('parser raised system exit', error='system exit', **context)
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                return
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        if self._parser_backend.status[0] != 'ParseSuccess':
            error = self._parser_backend.status[1]
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            self.fail('parser failed', error=error, **context)
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    def process_phonon(self):
        """Function that is run for phonon calculation before cleanup.
        This task is run by the celery process that is calling the join for the
        upload.

        This function re-opens the Archive for this calculation to add method
        information from another referenced archive. Updates the method
        information in section_encyclopedia as well as the DFT domain metadata.
        """
        try:
            # Re-create a backend
            context = dict(parser=self.parser, step=self.parser)
            logger = self.get_logger(**context)
            metainfo = phonopyparser.metainfo.m_env
            backend = Backend(metainfo, logger=logger, domain="dft")

            # Open the archive of the phonon calculation.
            upload_files = StagingUploadFiles(self.upload_id, is_authorized=lambda: True)
            with upload_files.read_archive(self.calc_id) as archive:
                arch = query_archive(archive, {self.calc_id: self.calc_id})[self.calc_id]
                phonon_archive = EntryArchive.m_from_dict(arch)
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            # Save Archive contents, metadata and logs from the old entry
            backend.entry_archive = phonon_archive
            self._parser_backend = backend
            self._entry_metadata = backend.entry_archive.section_metadata
            self._calc_proc_logs = phonon_archive.processing_logs
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            # Read in the first referenced calculation. The reference is given as
            # an absolute path which needs to be converted into a path that is
            # relative to upload root.
            scc = backend.entry_archive.section_run[0].section_single_configuration_calculation[0]
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            relative_ref = scc.section_calculation_to_calculation_refs[0].calculation_to_calculation_external_url
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            ref_id = upload_files.calc_id(relative_ref)
            with upload_files.read_archive(ref_id) as archive:
                arch = query_archive(archive, {ref_id: ref_id})[ref_id]
                ref_archive = EntryArchive.m_from_dict(arch)

            # Get encyclopedia method information directly from the referenced calculation.
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            ref_enc_method = ref_archive.section_metadata.encyclopedia.method
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            if ref_enc_method is None or len(ref_enc_method) == 0 or ref_enc_method.functional_type is None:
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                raise ValueError("No method information available in referenced calculation.")
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            backend.entry_archive.section_metadata.encyclopedia.method = ref_enc_method
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            # Overwrite old entry with new data. The metadata is updated with
            # new timestamp and method details taken from the referenced
            # archive.
            self._entry_metadata.last_processing = datetime.utcnow()
            self._entry_metadata.dft.xc_functional = ref_archive.section_metadata.dft.xc_functional
            self._entry_metadata.dft.basis_set = ref_archive.section_metadata.dft.basis_set
            self._entry_metadata.dft.update_group_hash()
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            self._entry_metadata.encyclopedia.status = EncyclopediaMetadata.status.type.success
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        except Exception as e:
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            logger.error("Could not retrieve method information for phonon calculation.", exc_info=e)
            try:
                if self._entry_metadata.encyclopedia is None:
                    self._entry_metadata.encyclopedia = EncyclopediaMetadata()
                self._entry_metadata.encyclopedia.status = EncyclopediaMetadata.status.type.failure
            except Exception as e:
                logger.error("Could set encyclopedia status.", exc_info=e)
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        finally:
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            # persist the calc metadata
            with utils.timer(logger, 'saved calc metadata', step='metadata'):
                self.apply_entry_metadata(self._entry_metadata)

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

            # persist the archive
            with utils.timer(
                    logger, 'archived', step='archive',
                    input_size=self.mainfile_file.size) as log_data:

                archive_size = self.write_archive(self._parser_backend)
                log_data.update(archive_size=archive_size)

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

        if self._parser_backend.status[0] == 'ParseSuccess':
            warnings = getattr(self._parser_backend, '_warnings', [])
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            if len(warnings) > 0:
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                self.get_logger().warn(
                    'processor completed successful with warnings',
                    processor=processor_name, warnings=[str(warning) for warning in warnings])

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            else:
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                self.get_logger().info(
                    'processor completed successful',
                    processor=processor_name)

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        else:
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            errors = self._parser_backend.status[1]
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            self.get_logger().error(
                'processor completed with failure',
                processor=processor_name, errors=str(errors))
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    @task
    def normalizing(self):
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        ''' The *task* that encapsulates all normalizing related actions. '''
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        # allow normalizer to access and add data to the entry metadata
        self._parser_backend.entry_archive.m_add_sub_section(
            datamodel.EntryArchive.section_metadata, self._entry_metadata)

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        for normalizer in normalizers:
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            if normalizer.domain != parser_dict[self.parser].domain:
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                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:
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                        self._parser_backend.finishedParsingSession('ParseFailure', [str(e)])
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                        logger.error(
                            'normalizer failed with exception', exc_info=e,
                            error=str(e), **context)
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                        break
                    else:
                        if self._parser_backend.status[0] != 'ParseSuccess':
                            error = self._parser_backend.status[1]
                            self.fail('normalizer failed', error=error, **context)
                            break
                        else:
                            logger.debug(
                                'completed normalizer successfully', normalizer=normalizer_name)
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    @task
    def archiving(self):
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        ''' The *task* that encapsulates all archival related actions. '''
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        logger = self.get_logger()

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        self._entry_metadata.apply_domain_metadata(self._parser_backend)
        self._entry_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.apply_entry_metadata(self._entry_metadata)
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        # index in search
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        with utils.timer(logger, 'indexed', step='index'):
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            self._entry_metadata.a_elastic.index()
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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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            archive_size = self.write_archive(self._parser_backend)
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            log_data.update(archive_size=archive_size)
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    def write_archive(self, backend: Backend):
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        def filter_processing_logs(logs):
            if len(logs) > 100:
                return [
                    log for log in logs
                    if log.get('level') != 'DEBUG']
            return logs
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        if self._calc_proc_logs is None:
            self._calc_proc_logs = []

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

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

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

            # most likely failed due to domain data, try to write metadata and processing logs
            entry_archive = datamodel.EntryArchive()
            entry_archive.m_add_sub_section(datamodel.EntryArchive.section_metadata, self._entry_metadata)
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            entry_archive.processing_logs = filter_processing_logs(self._calc_proc_logs)
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            self.upload_files.write_archive(self.calc_id, entry_archive.m_to_dict())
            raise e
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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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    '''
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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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        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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        published: Boolean that indicates the publish status
        publish_time: Date when the upload was initially published
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        last_update: Date of the last publishing/re-processing
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        joined: Boolean indicates if the running processing has joined (:func:`check_join`)
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    '''
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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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    embargo_length = IntField(default=36)
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    name = StringField(default=None)
    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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    last_update = DateTimeField()
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    joined = BooleanField(default=False)

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    meta: Any = {
        'indexes': [
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            'user_id', 'tasks_status', 'process_status', 'published', 'upload_time'
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        ]
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    }

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
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        self._upload_files: ArchiveBasedStagingUploadFiles = None
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    @property
    def metadata(self) -> dict:
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        '''
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        Getter, setter for user metadata. Metadata is pickled to and from the public
        bucket to allow sharing among all processes. Usually uploads do not have (much)
        user defined metadata, but users provide all metadata per upload as part of
        the publish process. This will change, when we introduce editing functionality
        and metadata will be provided through different means.
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        '''
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        try:
            upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
        except KeyError:
            return None
        return upload_files.user_metadata
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    @metadata.setter
    def metadata(self, data: dict) -> None:
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        upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True, create=True)
        upload_files.user_metadata = data
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    @classmethod
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    def get(cls, id: str, include_published: bool = True) -> 'Upload':
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        return cls.get_by_id(id, 'upload_id')
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    @classmethod
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    def user_uploads(cls, user: datamodel.User, **kwargs) -> List['Upload']:
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        ''' Returns all uploads for the given user. Kwargs are passed to mongo query. '''
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        return cls.objects(user_id=str(user.user_id), **kwargs)
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    @property
    def uploader(self):
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        return datamodel.User.get(self.user_id)
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    def get_logger(self, **kwargs):
        logger = super().get_logger()
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        user = self.uploader
        user_name = '%s %s' % (user.first_name, user.last_name)
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        # We are not using 'user_id' because logstash (?) will filter these entries ?!
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        logger = logger.bind(
            upload_id=self.upload_id, upload_name=self.name, user_name=user_name,
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            user=user.user_id, **kwargs)
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        return logger

    @classmethod
    def create(cls, **kwargs) -> 'Upload':
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        '''
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        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: The user that created the upload.
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        '''
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        # use kwargs to keep compatibility with super method
        user: datamodel.User = kwargs['user']
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        del(kwargs['user'])
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        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
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        kwargs.update(user_id=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):
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        ''' Deletes this upload process state entry and its calcs. '''
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        Calc.objects(upload_id=self.upload_id).delete()
        super().delete()

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    def delete_upload_local(self):
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        '''
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        Deletes the upload, including its processing state and
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        staging files. Local version without celery processing.
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        '''
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        logger = self.get_logger()

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        with utils.lnr(logger, 'upload delete failed'):
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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, 'upload deleted', step='files',
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                    upload_size=self.upload_files.size):
                self.upload_files.delete()
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            self.delete()
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    @process
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    def delete_upload(self):
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        '''
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        Deletes of the upload, including its processing state and
        staging files. This starts the celery process of deleting the upload.
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        '''
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        self.delete_upload_local()
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        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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        '''
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        Moves the upload out of staging to the public area. It will
        pack the staging upload files in to public upload files.
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        '''
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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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            with self.entries_metadata(self.metadata) as 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):
                        calc.published = True
                        calc.with_embargo = calc.with_embargo if calc.with_embargo is not None else False
                        return UpdateOne(
                            {'_id': calc.calc_id},
                            {'$set': {'metadata': calc.m_to_dict(
                                include_defaults=True, categories=[datamodel.MongoMetadata])}})

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

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

                if isinstance(self.upload_files, StagingUploadFiles):
                    with utils.timer(
                            logger, 'staged upload deleted', step='delete staged',
                            upload_size=self.upload_files.size):
                        self.upload_files.delete()
                        self.published = True
                        self.publish_time = datetime.utcnow()
                        self.last_update = datetime.utcnow()
                        self.save()
                else:
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                    self.last_update = datetime.utcnow()
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                    self.save()
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    @process
    def re_process_upload(self):
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        '''
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        A *process* that performs the re-processing of a earlier processed
        upload.

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

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

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

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

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

        staging_upload_files = self.upload_files.to_staging_upload_files(create=True)
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        self._continue_with('parse_all')
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        try:
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            # check if a calc is already/still processing
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            processing = Calc.objects(
                upload_id=self.upload_id,
                **Calc.process_running_mongoengine_query()).count()

            if processing > 0:
                logger.warn(
                    'processes are still/already running on calc, they will be resetted',
                    count=processing)
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            # reset all calcs
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            Calc._get_collection().update_many(
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                dict(upload_id=self.upload_id),
                {'$set': Calc.reset_pymongo_update(worker_hostname=self.worker_hostname)})

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            # process call calcs
            Calc.process_all(Calc.re_process_calc, dict(upload_id=self.upload_id), exclude=['metadata'])
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            logger.info('completed to trigger re-process of all calcs')
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        except Exception as e:
            # try to remove the staging copy in failure case
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            logger.error('failed to trigger re-process of all calcs', exc_info=e)

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            if self.published:
                if staging_upload_files is not None and staging_upload_files.exists():
                    staging_upload_files.delete()
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            raise e
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        # the packing and removing of the staging upload files, will be trigged by
        # the 'cleanup' task after processing all calcs

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    @process
    def re_pack(self):
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        ''' A *process* that repacks the raw and archive data based on the current embargo data. '''
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        assert self.published

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

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        self.upload_files.re_pack(self.user_metadata())
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        self.joined = True
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        self._complete()

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    @process
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    def process_upload(self):
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        ''' A *process* that performs the initial upload processing. '''
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        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
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        ''' A no-op *task* as a stand-in for receiving upload data. '''
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        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
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        kwargs = dict(upload_path=self.upload_path) if not self.published else {}
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        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, **kwargs)
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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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        '''
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        The *task* performed before the actual parsing/normalizing: extracting
        the uploaded files.
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        '''
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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 _preprocess_files(self, path):
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        '''
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