elasticsearch.py 8.43 KB
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import os

from typing import Tuple, List, Union, Dict, Any, Set
import mongomock
import pymongo.collection
from fastapi import HTTPException

from elasticsearch_dsl import Search, Q
from urllib.parse import urlparse

from optimade.filterparser import LarkParser
from optimade.filtertransformers.elasticsearch import ElasticTransformer
from optimade.models import EntryResource
from optimade.server.config import CONFIG
from optimade.server.entry_collections import EntryCollection
from optimade.server.logger import LOGGER
from optimade.server.mappers import BaseResourceMapper
from optimade.server.query_params import EntryListingQueryParams, SingleEntryQueryParams
from optimade.server.exceptions import BadRequest
from optimade.server.mappers import StructureMapper
from optimade.models import StructureResource


from nomad import config, datamodel, files, search, utils
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from nomad.normalizing.optimade import (
    optimade_chemical_formula_reduced, optimade_chemical_formula_anonymous,
    optimade_chemical_formula_hill)
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from .filterparser import _get_transformer as get_transformer


logger = utils.get_logger(__name__)


class ElasticsearchStructureCollection(EntryCollection):

    def __init__(self):
        super().__init__(
            collection=config.elastic.index_name,
            resource_cls=StructureResource,
            resource_mapper=StructureMapper,
            transformer=get_transformer(nomad_properties='dft', without_prefix=False))

        self.parser = LarkParser(version=(1, 0, 0), variant="default")

        # check aliases do not clash with mongo operators
        self._check_aliases(self.resource_mapper.all_aliases())
        self._check_aliases(self.resource_mapper.all_length_aliases())

        self.client = Search

    def _base_search_request(self):
        request = search.SearchRequest().owner('public', None)
        request.search_parameter('processed', True)
        # TODO use the elastic annotations when done
        request.query(Q('exists', field='dft.optimade.elements'))
        return request

    def __len__(self) -> int:
        # TODO cache
        return self._base_search_request().execute()['total']

    def count(self, **kwargs) -> int:
        # This seams solely mongodb specific
        raise NotImplementedError()

    def find(
            self,
            params: Union[EntryListingQueryParams, SingleEntryQueryParams]) \
            -> Tuple[List[StructureResource], int, bool, set]:

        criteria = self.handle_query_params(params)

        all_fields = criteria.pop("fields")
        if getattr(params, "response_fields", False):
            fields = set(params.response_fields.split(","))
            fields |= self.resource_mapper.get_required_fields()
        else:
            fields = all_fields.copy()

        sort, order = criteria.get('sort', (('chemical_formula_reduced', 1),))[0]
        sort_quantity = datamodel.OptimadeEntry.m_def.all_quantities.get(sort, None)
        if sort_quantity is None:
            raise BadRequest(detail='Unable to sort on field %s' % sort)
        sort_quantity_a_optimade = sort_quantity.m_get_annotations('optimade')
        if not sort_quantity_a_optimade.sortable:
            raise BadRequest(detail='Unable to sort on field %s' % sort)

        search_request = self._base_search_request().include('calc_id', 'upload_id')

        filter = criteria['filter']
        if filter is None:
            filter_param = getattr(params, 'filter')
            logger.error('could not parse optimade filter', filter=filter_param)
            raise NotImplementedError(
                'some features used in filter query %s are not implemented' % filter_param)
        elif filter != {}:
            search_request.query(filter)

        es_response = search_request.execute_paginated(
            page_offset=criteria.get('skip', 0),
            per_page=criteria['limit'],
            order=order,
            order_by='dft.optimade.%s' % sort)
        results = self._es_to_optimade_results(es_response['results'], response_fields=fields)

        nresults_now = len(results)
        if isinstance(params, EntryListingQueryParams):
            data_returned = es_response['pagination']['total']
            more_data_available = data_returned >= criteria.get('skip', 0) + criteria['limit']
        else:
            # SingleEntryQueryParams, e.g., /structures/{entry_id}
            data_returned = nresults_now
            more_data_available = False
            if nresults_now > 1:
                raise HTTPException(
                    status_code=404,
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                    detail=f'Instead of a single entry, {nresults_now} entries were found')
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            results = results[0] if results else None

        return results, data_returned, more_data_available, all_fields - fields

    def _check_aliases(self, aliases):
        pass

    def _es_to_optimade_result(
            self, es_result: dict,
            response_fields: Set[str],
            upload_files_cache: Dict[str, files.UploadFiles]) -> StructureResource:

        calc_id, upload_id = es_result['calc_id'], es_result['upload_id']
        upload_files = upload_files_cache.get(upload_id)

        if upload_files is None:
            upload_files = files.UploadFiles.get(upload_id, is_authorized=lambda: True)
            if upload_files is None:
                logger.error('missing upload', upload_id=upload_id)
                return None

            upload_files_cache[upload_id] = upload_files

        try:
            archive = upload_files.read_archive(calc_id)
        except KeyError:
            logger.error('missing archive entry', upload_id=upload_id, calc_id=calc_id)
            return None

        metadata = archive[calc_id]['section_metadata'].to_dict()
        entry = datamodel.EntryMetadata.m_from_dict(metadata)

        def include(key):
            return response_fields is None or (key in response_fields) or not key.startswith('_')

        attrs = {
            key: value
            for key, value in entry.dft.optimade.m_to_dict().items()
            if include(key)}

        if include('immutable_id'):
            attrs['immutable_id'] = calc_id
        if include('last_modified'):
            attrs['last_modified'] = entry.last_processing if entry.last_processing is not None else entry.upload_time

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        # TODO this should be removed, once all data is reprocessed with the right normalization
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        attrs['chemical_formula_reduced'] = optimade_chemical_formula_reduced(
            attrs['chemical_formula_reduced'])
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        attrs['chemical_formula_anonymous'] = optimade_chemical_formula_anonymous(
            attrs['chemical_formula_reduced'])
        attrs['chemical_formula_hill'] = optimade_chemical_formula_hill(
            attrs['chemical_formula_hill'])
        attrs['chemical_formula_descriptive'] = attrs['chemical_formula_hill']
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        dimension_types = attrs['dimension_types']
        if isinstance(dimension_types, int):
            attrs['dimension_types'] = [1] * dimension_types + [0] * (3 - dimension_types)
            attrs['nperiodic_dimensions'] = dimension_types
        elif isinstance(dimension_types, list):
            attrs['nperiodic_dimensions'] = sum(dimension_types)

        if response_fields is not None:
            for request_field in response_fields:
                if not request_field.startswith('_nmd_'):
                    continue

                try:
                    if request_field.startswith('_nmd_dft_'):
                        attrs[request_field] = getattr(entry.dft, request_field[9:])
                    else:
                        attrs[request_field] = getattr(entry, request_field[5:])
                except AttributeError:
                    # if unknown properties where provided, we will ignore them
                    pass

        return self.resource_cls(
            type='structures',
            id=entry.calc_id,
            attributes=attrs,
            relationships=None)

    def _es_to_optimade_results(self, es_results: List[dict], response_fields: Set[str]):
        upload_files_cache: Dict[str, files.UploadFiles] = {}
        optimade_results = []
        try:
            for es_result in es_results:
                optimade_result = self._es_to_optimade_result(
                    es_result, response_fields, upload_files_cache)
                if optimade_result is not None:
                    optimade_results.append(optimade_result)
        finally:
            for upload_files in upload_files_cache.values():
                upload_files.close()

        return optimade_results