excel.helpers.fill_uid

Complexity

Total Complexity

34

Size/Duplication

Total Lines	458
Duplicated Lines	0 %

Importance

Changes

0

5 Functions

Rating	Name	Duplication	Size	Complexity
B	fill_uid_breeds()	0	50	5
B	fill_uid_names()	0	36	5
C	fill_uid_animals()	0	112	7
D	fill_uid_samples()	0	137	11
B	upload_template()	0	87	6

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jul  5 16:37:48 2019

@author: Paolo Cozzi <cozzi@ibba.cnr.it>
"""

import logging

from common.constants import (
    ERROR, LOADED, ACCURACIES, SAMPLE_STORAGE, SAMPLE_STORAGE_PROCESSING)
from common.helpers import image_timedelta, parse_image_timedelta
from image_app.models import (
    DictBreed, DictCountry, DictSpecie, DictSex, DictUberon, Name, Animal,
    Sample, DictDevelStage, DictPhysioStage)
from submissions.helpers import send_message
from validation.helpers import construct_validation_message
from validation.models import ValidationSummary

from .exceptions import ExcelImportError
from .exceltemplate import ExcelTemplateReader

# Get an instance of a logger
logger = logging.getLogger(__name__)


def fill_uid_breeds(submission_obj, template):
    """Fill DictBreed from a excel record"""

    logger.info("fill_uid_breeds() started")

    # ok get languages from submission (useful for translation)
    language = submission_obj.gene_bank_country.label

    # iterate among excel template
    for record in template.get_breed_records():
        # TODO: move this in a helper module (image_app.helpers?)
        # get a DictSpecie object. Species are in latin names, but I can
        # find also a common name in translation tables
        try:
            specie = DictSpecie.objects.get(label=record.species)

        except DictSpecie.DoesNotExist:
            logger.info("Search %s in synonyms" % (record.species))
            # search for language synonym (if I arrived here a synonym should
            # exists)
            specie = DictSpecie.get_by_synonym(
                synonym=record.species,
                language=language)

        # get country for breeds. Ideally will be the same of submission,
        # however, it could be possible to store data from other contries
        country, created = DictCountry.objects.get_or_create(
            label=record.efabis_breed_country)

        # I could create a country from a v_breed_specie instance. That's
        # ok, maybe I could have a lot of breed from different countries and
        # a few organizations submitting them
        if created:
            logger.info("Created %s" % country)

        else:
            logger.debug("Found %s" % country)

        breed, created = DictBreed.objects.get_or_create(
            supplied_breed=record.supplied_breed,
            specie=specie,
            country=country)

        if created:
            logger.info("Created %s" % breed)

        else:
            logger.debug("Found %s" % breed)

    logger.info("fill_uid_breeds() completed")


def fill_uid_names(submission_obj, template):
    """fill Names table from crbanim record"""

    # debug
    logger.info("called fill_uid_names()")

    # iterate among excel template
    for record in template.get_animal_records():
        # in the same record I have the sample identifier and animal identifier
        # a name record for animal
        animal_name, created = Name.objects.get_or_create(
            name=record.animal_id_in_data_source,
            submission=submission_obj,
            owner=submission_obj.owner)

        if created:
            logger.debug("Created animal name %s" % animal_name)

        else:
            logger.debug("Found animal name %s" % animal_name)

    # iterate among excel template
    for record in template.get_sample_records():
        # name record for sample
        sample_name, created = Name.objects.get_or_create(
            name=record.sample_id_in_data_source,
            submission=submission_obj,
            owner=submission_obj.owner)

        if created:
            logger.debug("Created sample name %s" % sample_name)

        else:
            logger.debug("Found sample name %s" % sample_name)

    logger.info("fill_uid_names() completed")


def fill_uid_animals(submission_obj, template):
    # debug
    logger.info("called fill_uid_animals()")

    # get submission language
    language = submission_obj.gene_bank_country.label

    # iterate among excel template
    for record in template.get_animal_records():
        # determine sex. Check for values
        sex = DictSex.objects.get(label__iexact=record.sex)

        # get specie
        specie = DictSpecie.objects.get(label=record.species)

        # how I can get breed from my data?
        breeds = [breed for breed in template.get_breed_records()
                  if breed.supplied_breed == record.breed and
                  breed.species == record.species]

        # breed is supposed to be unique, from UID constraints. However
        # I could place the same breed name for two countries. In that case,
        # I cant derive a unique breed from users data
        if len(breeds) != 1:
            raise ExcelImportError(
                "Can't determine a unique breed for '%s:%s' from user data" %
                (record.breed, record.species))

        # get a country for this breed
        country = DictCountry.objects.get(
            label=breeds[0].efabis_breed_country)

        # ok get a real dictbreed object
        breed = DictBreed.objects.get(
            supplied_breed=record.breed,
            specie=specie,
            country=country)

        logger.debug("Selected breed is %s" % (breed))

        # define names
        name, mother, father = None, None, None

        # get name for this animal and for mother and father
        logger.debug("Getting %s as my name" % (
            record.animal_id_in_data_source))

        name = Name.objects.get(
            name=record.animal_id_in_data_source,
            submission=submission_obj)

        if record.father_id_in_data_source:
            logger.debug("Getting %s as father" % (
                record.father_id_in_data_source))

            father = Name.objects.get(
                name=record.father_id_in_data_source,
                submission=submission_obj)

        if record.mother_id_in_data_source:
            logger.debug("Getting %s as mother" % (
                record.mother_id_in_data_source))

            mother = Name.objects.get(
                name=record.mother_id_in_data_source,
                submission=submission_obj)

        # now get accuracy
        accuracy = ACCURACIES.get_value_by_desc(
            record.birth_location_accuracy)

        # create a new object. Using defaults to avoid collisions when
        # updating data
        defaults = {
            'alternative_id': record.alternative_animal_id,
            'description': record.animal_description,
            'breed': breed,
            'sex': sex,
            'father': father,
            'mother': mother,
            'birth_date': record.birth_date,
            'birth_location': record.birth_location,
            'birth_location_latitude': record.birth_location_latitude,
            'birth_location_longitude': record.birth_location_longitude,
            'birth_location_accuracy': accuracy,
            'owner': submission_obj.owner
        }

        animal, created = Animal.objects.update_or_create(
            name=name,
            defaults=defaults)

        if created:
            logger.debug("Created %s" % animal)

        else:
            logger.debug("Updating %s" % animal)

    # create a validation summary object and set all_count
    validation_summary, created = ValidationSummary.objects.get_or_create(
        submission=submission_obj, type="animal")

    if created:
        logger.debug(
            "ValidationSummary animal created for submission %s" %
            submission_obj)

    # reset counts
    validation_summary.reset_all_count()

    # debug
    logger.info("fill_uid_animals() completed")


def fill_uid_samples(submission_obj, template):
    # debug
    logger.info("called fill_uid_samples()")

    # iterate among excel template
    for record in template.get_sample_records():
        # get name for this sample
        name = Name.objects.get(
            name=record.sample_id_in_data_source,
            submission=submission_obj,
            owner=submission_obj.owner)

        # get animal by reading record
        animal = Animal.objects.get(
            name__name=record.animal_id_in_data_source,
            name__submission=submission_obj)

        # get a organism part. Organism parts need to be in lowercases
        organism_part, created = DictUberon.objects.get_or_create(
            label=record.organism_part
        )

        if created:
            logger.info("Created %s" % organism_part)

        else:
            logger.debug("Found %s" % organism_part)

        # get developmental_stage and physiological_stage terms
        # they are not mandatory
        if record.developmental_stage:
            devel_stage, created = DictDevelStage.objects.get_or_create(
                label=record.developmental_stage
            )

            if created:
                logger.info("Created %s" % devel_stage)

            else:
                logger.debug("Found %s" % devel_stage)

        else:
            devel_stage = None

        if record.physiological_stage:
            physio_stage, created = DictPhysioStage.objects.get_or_create(
                    label=record.physiological_stage
            )

            if created:
                logger.info("Created %s" % physio_stage)

            else:
                logger.debug("Found %s" % physio_stage)

        else:
            physio_stage = None

        # animal age could be present or not
        if record.animal_age_at_collection:
            animal_age_at_collection, time_units = parse_image_timedelta(
                record.animal_age_at_collection)

        else:
            # derive animal age at collection
            animal_age_at_collection, time_units = image_timedelta(
                record.collection_date, animal.birth_date)

        # another time column
        if record.sampling_to_preparation_interval:
            preparation_interval, preparation_interval_units = \
                parse_image_timedelta(record.sampling_to_preparation_interval)

        else:
            preparation_interval, preparation_interval_units = None, None

        # now get accuracy
        accuracy = ACCURACIES.get_value_by_desc(
            record.collection_place_accuracy)

        # now get storage and storage processing
        # TODO; check those values in excel columns
        storage = SAMPLE_STORAGE.get_value_by_desc(
            record.sample_storage)

        storage_processing = SAMPLE_STORAGE_PROCESSING.get_value_by_desc(
            record.sample_storage_processing)

        # create a new object. Using defaults to avoid collisions when
        # updating data
        defaults = {
            'alternative_id': record.alternative_sample_id,
            'description': record.sample_description,
            'animal': animal,
            'protocol': record.specimen_collection_protocol,
            'collection_date': record.collection_date,
            'collection_place_latitude': record.collection_place_latitude,
            'collection_place_longitude': record.collection_place_longitude,
            'collection_place': record.collection_place,
            'collection_place_accuracy': accuracy,
            'organism_part': organism_part,
            'developmental_stage': devel_stage,
            'physiological_stage': physio_stage,
            'animal_age_at_collection': animal_age_at_collection,
            'animal_age_at_collection_units': time_units,
            'availability': record.availability,
            'storage': storage,
            'storage_processing': storage_processing,
            'preparation_interval': preparation_interval,
            'preparation_interval_units': preparation_interval_units,
            'owner': submission_obj.owner,
        }

        sample, created = Sample.objects.update_or_create(
            name=name,
            defaults=defaults)

        if created:
            logger.debug("Created %s" % sample)

        else:
            logger.debug("Updating %s" % sample)

    # create a validation summary object and set all_count
    validation_summary, created = ValidationSummary.objects.get_or_create(
        submission=submission_obj, type="sample")

    if created:
        logger.debug(
            "ValidationSummary animal created for submission %s" %
            submission_obj)

    # reset counts
    validation_summary.reset_all_count()

    # debug
    logger.info("fill_uid_samples() completed")


def upload_template(submission_obj):
    # debug
    logger.info("Importing from Excel template file")

    # this is the full path in docker container
    fullpath = submission_obj.get_uploaded_file_path()

    # read submission data
    reader = ExcelTemplateReader()
    reader.read_file(fullpath)

    # start data loading
    try:
        # check for species and sex in a similar way as cryoweb does
        # TODO: identical to CRBanim. Move to a mixin
        check, not_found = reader.check_sex()

        if not check:
            message = (
                "Not all Sex terms are loaded into database: "
                "check for %s in your dataset" % (not_found))

            raise ExcelImportError(message)

        check, not_found = reader.check_species(
            submission_obj.gene_bank_country)

        if not check:
            raise ExcelImportError(
                "Some species are not loaded in UID database: "
                "%s" % (not_found))

        check, not_found = reader.check_accuracies()

        if not check:
            message = (
                "Not all accuracy levels are defined in database: "
                "check for %s in your dataset" % (not_found))

            raise ExcelImportError(message)

        # BREEDS
        fill_uid_breeds(submission_obj, reader)

        # NAME
        fill_uid_names(submission_obj, reader)

        # ANIMALS
        fill_uid_animals(submission_obj, reader)

        # SAMPLES
        fill_uid_samples(submission_obj, reader)

    except Exception as exc:
        # set message:
        message = "Error in importing data: %s" % (str(exc))

        # save a message in database
        submission_obj.status = ERROR
        submission_obj.message = message
        submission_obj.save()

        # send async message
        send_message(submission_obj)

        # debug
        logger.error("Error in importing from Template: %s" % (exc))
        logger.exception(exc)

        return False

    else:
        message = "Template import completed for submission: %s" % (
            submission_obj.id)

        submission_obj.message = message
        submission_obj.status = LOADED
        submission_obj.save()

        # send async message
        send_message(
            submission_obj,
            validation_message=construct_validation_message(submission_obj))

    logger.info("Import from Template is complete")

    return True