data.py

# 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:
"""

from typing import cast, List, Any, ContextManager, Tuple, Generator, Dict, cast
from mongoengine import StringField, DateTimeField, DictField, BooleanField
import logging
from structlog import wrap_logger
from contextlib import contextmanager
import os.path
from datetime import datetime
from pymongo import UpdateOne
import hashlib

from nomad import utils, coe_repo, config, infrastructure, search, datamodel
from nomad.files import PathObject, UploadFiles, ExtractError, ArchiveBasedStagingUploadFiles, PublicUploadFiles, StagingUploadFiles
from nomad.processing.base import Proc, process, task, PENDING, SUCCESS, FAILURE
from nomad.parsing import parser_dict, match_parser, LocalBackend
from nomad.normalizing import normalizers
from nomad.datamodel import UploadWithMetadata, Domain


class Calc(Proc):
    """
    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:
        calc_id: the calc_id of this calc
        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

        metadata: the metadata record wit calc and user metadata, see :class:`datamodel.CalcWithMetadata`
    """
    calc_id = StringField(primary_key=True)
    upload_id = StringField()
    mainfile = StringField()
    parser = StringField()

    metadata = DictField()

    meta: Any = {
        'indexes': [
            'upload_id',
            ('upload_id', 'mainfile'),
            ('upload_id', 'parser'),
            ('upload_id', 'tasks_status'),
            ('upload_id', 'process_status'),
            ('upload_id', 'metadata.nomad_version')
        ]
    }

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self._parser_backend: LocalBackend = None
        self._upload: Upload = None
        self._upload_files: ArchiveBasedStagingUploadFiles = None
        self._calc_proc_logwriter = None
        self._calc_proc_logwriter_ctx: ContextManager = None

    @classmethod
    def get(cls, id):
        return cls.get_by_id(id, 'calc_id')

    @property
    def mainfile_file(self) -> PathObject:
        return self.upload_files.raw_file_object(self.mainfile)

    @property
    def upload(self) -> 'Upload':
        if not self._upload:
            self._upload = Upload.get(self.upload_id)
            self._upload.worker_hostname = self.worker_hostname
        return self._upload

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

    def get_logger(self, **kwargs):
        """
        Returns a wrapped logger that additionally saves all entries to the calculation
        processing log in the archive.
        """
        logger = super().get_logger()
        logger = logger.bind(
            upload_id=self.upload_id, mainfile=self.mainfile, calc_id=self.calc_id, **kwargs)

        if self._calc_proc_logwriter_ctx is None:
            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: %s' % (method_name, datetime.utcnow().isoformat(), program, event)
                    if len(entry) > 140:
                        self._calc_proc_logwriter.write(entry[:140])
                        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])

    @process
    def re_process_calc(self):
        """
        Processes a calculation again. This means there is already metadata and
        instead of creating it initially, we are just updating the existing
        records.
        """
        logger = self.get_logger()

        try:
            calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
            calc_with_metadata.upload_id = self.upload_id
            calc_with_metadata.calc_id = self.calc_id
            calc_with_metadata.calc_hash = self.upload_files.calc_hash(self.mainfile)
            calc_with_metadata.mainfile = self.mainfile
            calc_with_metadata.nomad_version = config.version
            calc_with_metadata.nomad_commit = config.commit
            calc_with_metadata.last_processing = datetime.utcnow()
            calc_with_metadata.files = self.upload_files.calc_files(self.mainfile)
            self.metadata = calc_with_metadata.to_dict()

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

    @process
    def process_calc(self):
        """
        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.
        """
        logger = self.get_logger()
        if self.upload is None:
            logger.error('calculation upload does not exist')

        try:
            # save preliminary minimum calc metadata in case processing fails
            # successful processing will replace it with the actual metadata
            calc_with_metadata = datamodel.CalcWithMetadata(
                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()
            calc_with_metadata.upload_time = self.upload.upload_time
            calc_with_metadata.nomad_version = config.version
            calc_with_metadata.nomad_commit = config.commit
            calc_with_metadata.last_processing = datetime.utcnow()
            calc_with_metadata.files = self.upload_files.calc_files(self.mainfile)
            self.metadata = calc_with_metadata.to_dict()

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

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

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

            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

            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)

    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()

    @task
    def parsing(self):
        context = dict(parser=self.parser, step=self.parser)
        logger = self.get_logger(**context)
        parser = parser_dict[self.parser]
        self.metadata['parser_name'] = self.parser

        with utils.timer(logger, 'parser executed', input_size=self.mainfile_file.size):
            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)
                return

        # add the non code specific calc metadata to the backend
        # all other quantities have been determined by parsers/normalizers
        self._parser_backend.openNonOverlappingSection('section_entry_info')
        self._parser_backend.addValue('upload_id', self.upload_id)
        self._parser_backend.addValue('calc_id', self.calc_id)
        self._parser_backend.addValue('calc_hash', self.metadata['calc_hash'])
        self._parser_backend.addValue('mainfile', self.mainfile)
        self._parser_backend.addValue('parser_name', self.parser)
        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)

        if self._parser_backend.status[0] != 'ParseSuccess':
            logger.error(self._parser_backend.status[1])
            error = self._parser_backend.status[1]
            self.fail(error, level=logging.INFO, **context)

    @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:
        self._parser_backend.openContext('/section_entry_info/0')
        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')
                self._parser_backend.addValue('number_of_archive_processor_warnings', len(warnings))
                self._parser_backend.addArrayValues('archive_processor_warnings', [str(warning) for warning in warnings])
            else:
                self._parser_backend.addValue('archive_processor_status', 'Success')
        else:
            errors = self._parser_backend.status[1]
            self._parser_backend.addValue('archive_processor_error', str(errors))

        self._parser_backend.closeNonOverlappingSection('section_archive_processing_info')
        self._parser_backend.closeContext('/section_entry_info/0')

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

            normalizer_name = normalizer.__name__
            context = dict(normalizer=normalizer_name, step=normalizer_name)
            logger = self.get_logger(**context)

            with utils.timer(
                    logger, 'normalizer executed', input_size=self.mainfile_file.size):
                with self.use_parser_backend(normalizer_name) as backend:
                    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)]

            failed = self._parser_backend.status[0] != 'ParseSuccess'
            if failed:
                logger.error(self._parser_backend.status[1])
                error = self._parser_backend.status[1]
                self.fail(error, level=logging.WARNING, error=error, **context)
                break
            else:
                logger.debug(
                    'completed normalizer successfully', normalizer=normalizer_name)

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

        calc_with_metadata = datamodel.CalcWithMetadata(**self.metadata)
        calc_with_metadata.apply_domain_metadata(self._parser_backend)
        calc_with_metadata.processed = True

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

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

        # persist the archive
        with utils.timer(
                logger, 'archived', step='archive',
                input_size=self.mainfile_file.size) as log_data:
            with self.upload_files.archive_file(self.calc_id, 'wt') as out:
                self._parser_backend.write_json(out, pretty=True, root_sections=Domain.instance.root_sections)

            log_data.update(archive_size=self.upload_files.archive_file_object(self.calc_id).size)

        # close loghandler
        if self._calc_proc_logwriter is not None:
            with utils.timer(
                    logger, 'archived log', step='logs',
                    input_size=self.mainfile_file.size) as log_data:
                self._calc_proc_logwriter_ctx.__exit__(None, None, None)  # pylint: disable=E1101
                self._calc_proc_logwriter = None

                log_data.update(log_size=self.upload_files.archive_log_file_object(self.calc_id).size)

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


class Upload(Proc):
    """
    Represents uploads in the databases. Provides persistence access to the files storage,
    and processing state.

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

    upload_id = StringField(primary_key=True)
    upload_path = StringField(default=None)
    temporary = BooleanField(default=False)

    name = StringField(default=None)
    upload_time = DateTimeField()
    user_id = StringField(required=True)
    published = BooleanField(default=False)
    publish_time = DateTimeField()
    last_update = DateTimeField()

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

    def __init__(self, **kwargs):
        super().__init__(**kwargs)
        self._upload_files: ArchiveBasedStagingUploadFiles = None

    @property
    def metadata(self) -> dict:
        # TODO user_metadata needs to be stored in the public bucket, since staging data might not be shared
        try:
            upload_files = PublicUploadFiles(self.upload_id, is_authorized=lambda: True)
        except KeyError:
            return None
        return upload_files.user_metadata

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

    @classmethod
    def get(cls, id: str, include_published: bool = True) -> 'Upload':
        upload = cls.get_by_id(id, 'upload_id')
        if upload is not None:
            return upload

        raise KeyError()

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

    @property
    def uploader(self):
        return coe_repo.User.from_user_id(self.user_id)

    def get_logger(self, **kwargs):
        logger = super().get_logger()
        logger = logger.bind(upload_id=self.upload_id, upload_name=self.name, **kwargs)
        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.

        Arguments:
            user (coe_repo.User): The user that created the upload.
        """
        user: coe_repo.User = kwargs['user']
        del(kwargs['user'])
        if 'upload_id' not in kwargs:
            kwargs.update(upload_id=utils.create_uuid())
        kwargs.update(user_id=str(user.user_id))
        self = super().create(**kwargs)

        self._continue_with('uploading')

        return self

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

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

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

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

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

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

    @process
    def delete_upload(self, with_coe_repo: bool = False):
        """
        Deletes of the upload, including its processing state and
        staging files. This starts the celery process of deleting the upload.
        """
        self.delete_upload_local(with_coe_repo=with_coe_repo)

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

    @process
    def publish_upload(self):
        """
        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.

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

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

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

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

                        self.upload_files.create_extracted_copy()

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

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

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

                def create_update(calc):
                    calc.published = True
                    return UpdateOne(
                        {'_id': calc.calc_id},
                        {'$set': {'metadata': calc.to_dict()}})

                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(upload_with_metadata)

            with utils.timer(
                    logger, 'index updated', step='index',
                    upload_size=self.upload_files.size):
                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:
                self.last_update = datetime.utcnow()
                self.save()

    @process
    def re_process_upload(self):
        """
        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.
        """
        assert self.published

        logger = self.get_logger()
        logger.info('started to re-process')

        # 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')
        public_upload_files = cast(PublicUploadFiles, self.upload_files)
        public_upload_files.to_staging_upload_files(create=True)

        self._continue_with('parse_all')
        try:
            # we use a copy of the mongo queryset; reasons are cursor timeouts and
            # changing results on modifying the calc entries
            calcs = list(Calc.objects(upload_id=self.upload_id))
            for calc in calcs:
                if calc.process_running:
                    if calc.current_process == 're_process_calc':
                        logger.warn('re_process_calc is already running', calc_id=calc.calc_id)
                    else:
                        logger.warn('a process is already running on calc', calc_id=calc.calc_id)

                    continue

                calc.reset()
                calc.re_process_calc()
        except Exception as e:
            # try to remove the staging copy in failure case
            staging_upload_files = self.upload_files.to_staging_upload_files()
            if staging_upload_files.exist():
                staging_upload_files.delete()

            raise e

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

    @process
    def process_upload(self):
        self.extracting()
        self.parse_all()

    @task
    def uploading(self):
        pass

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

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

        return self._upload_files

    @property
    def staging_upload_files(self) -> ArchiveBasedStagingUploadFiles:
        assert not self.published
        return cast(ArchiveBasedStagingUploadFiles, self.upload_files)

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

        logger = self.get_logger()
        try:
            with utils.timer(
                    logger, 'upload extracted', step='extracting',
                    upload_size=self.upload_files.size):
                self.upload_files.extract()

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

        except KeyError:
            self.fail('processing requested for non existing upload', log_level=logging.ERROR)
            return
        except ExtractError:
            self.fail('bad .zip/.tar file', log_level=logging.INFO)
            return

    def _preprocess_files(self, path):
        """
        Some files need preprocessing. Currently we need to add a stripped POTCAR version
        and always restrict/embargo the original.
        """
        if os.path.basename(path) == 'POTCAR':
            # create checksum
            hash = hashlib.sha224()
            with open(self.staging_upload_files.raw_file_object(path).os_path, 'rb') as orig_f:
                for line in orig_f.readlines():
                    hash.update(line)

            checksum = hash.hexdigest()

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

    def match_mainfiles(self) -> Generator[Tuple[str, object], None, None]:
        """
        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
        """
        directories_with_match: Dict[str, str] = dict()
        upload_files = self.staging_upload_files
        for filename in upload_files.raw_file_manifest():
            self._preprocess_files(filename)
            try:
                parser = match_parser(filename, upload_files)
                if parser is not None:
                    directory = os.path.dirname(filename)
                    if directory in directories_with_match:
                        # TODO this might give us the chance to store directory based relationship
                        # between calcs for the future?
                        pass
                    else:
                        directories_with_match[directory] = filename

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

    @task
    def parse_all(self):
        """
        Identified mainfile/parser combinations among the upload's files, creates
        respective :class:`Calc` instances, and triggers their processing.
        """
        logger = self.get_logger()

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

                calc.process_calc()

    def on_process_complete(self, process_name):
        if process_name == 'process_upload' or process_name == 're_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()

    def join(self):
        self.cleanup()

    @property
    def gui_url(self):
        base = config.api_url()[:-3]
        if base.endswith('/'):
            base = base[:-1]
        return '%s/uploads/' % base

    def _cleanup_after_processing(self):
        # 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 at %s has completed processing.' % (
                '"%s" ' % self.name if self.name else '', self.upload_time.isoformat()),  # pylint: disable=no-member
            'You can review your data on your upload page: %s' % self.gui_url,
            '',
            'If you encouter any issues with your upload, please let us know and replay to this email.',
            '',
            'The nomad team'
        ])
        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)

    def _cleanup_after_re_processing(self):
        logger = self.get_logger()
        logger.info('started to repack re-processed upload')

        staging_upload_files = self.upload_files.to_staging_upload_files()

        with utils.timer(
                logger, 'reprocessed staged upload packed', step='delete staged',
                upload_size=self.upload_files.size):

            staging_upload_files.pack(self.to_upload_with_metadata())

        with utils.timer(
                logger, 'reprocessed staged upload deleted', step='delete staged',
                upload_size=self.upload_files.size):

            staging_upload_files.delete()
            self.last_update = datetime.utcnow()
            self.save()

    @task
    def cleanup(self):
        search.refresh()

        if self.current_process == 're_process_upload':
            self._cleanup_after_re_processing()
        else:
            self._cleanup_after_processing()

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

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

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

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

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

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

    @property
    def outdated_calcs(self):
        return Calc.objects(
            upload_id=self.upload_id, tasks_status=SUCCESS,
            metadata__nomad_version__ne=config.version)

    @property
    def calcs(self):
        return Calc.objects(upload_id=self.upload_id, tasks_status=SUCCESS)

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

            upload_metadata.update(user_metadata)
            if 'calculations' in upload_metadata:
                del(upload_metadata['calculations'])

            for calc in user_metadata.get('calculations', []):  # pylint: disable=no-member
                calc_metadatas[calc['mainfile']] = calc

            user_upload_time = upload_metadata.get('_upload_time', None)

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

                return calc_with_metadata
        else:
            user_upload_time = None

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

        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)

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

        return result

    def compress_and_set_metadata(self, metadata: Dict[str, Any]) -> None:
        """
        Stores the given user metadata in the upload document. This is the metadata
        adhering to the API model (``UploadMetaData``). Most quantities can be stored
        for the upload and for each calculation. This method will try to move same values
        from the calculation to the upload to "compress" the data.
        """
        compressed = {
            key: value for key, value in metadata.items() if key != 'calculations'}
        calculations: List[Dict[str, Any]] = []
        compressed['calculations'] = calculations

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

        self.metadata = compressed

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