biosample.tasks.submission

Complexity

Total Complexity

51

Size/Duplication

Total Lines	656
Duplicated Lines	0 %

Importance

Changes

0

24 Methods

Rating	Name	Duplication	Size	Complexity
A	SubmissionHelper.read_token()	0	31	1
A	SubmissionHelper.usi_submission_name()	0	8	1
A	SubmissionHelper.__init__()	0	20	1
A	SplitSubmissionHelper.__init__()	0	5	1
A	SubmissionHelper.mark_submission()	0	4	1
A	SubmissionHelper.recover_submission()	0	27	3
A	SubmissionHelper.mark_fail()	0	5	1
A	SubmitTask.run()	0	46	4
A	SubmissionHelper.create_submission()	0	21	1
A	SubmissionHelper.create_or_update_sample()	0	30	2
A	SubmissionHelper.team_name()	0	8	1
A	SubmissionHelper.read_samples()	0	13	2
A	SubmissionHelper.start_submission()	0	11	2
A	SubmissionHelper.mark_success()	0	5	1
A	SubmissionHelper.add_samples()	0	20	3
A	SubmissionHelper.owner()	0	11	1
A	SubmissionCompleteTask.update_message()	0	12	2
A	SplitSubmissionHelper.model_in_submission()	0	51	4
A	SplitSubmissionHelper.process_model()	0	10	2
A	SplitSubmissionHelper.create_submission()	0	17	1
B	SplitSubmissionHelper.add_to_submission_data()	0	36	5
A	SplitSubmissionTask.run()	0	41	1
B	SubmissionCompleteTask.run()	0	78	5
A	SplitSubmissionHelper.process_data()	0	27	4

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 18 14:14:06 2019

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

import redis
import traceback
import pyUSIrest.client

from celery import chord
from celery.utils.log import get_task_logger

from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.db.models import Count, F
from django.db.models.functions import Least
from django.utils import timezone

from common.constants import ERROR, READY, SUBMITTED, COMPLETED
from common.tasks import BaseTask, NotifyAdminTaskMixin
from image.celery import app as celery_app
from submissions.tasks import SubmissionTaskMixin

from ..helpers import get_auth
from ..models import (
    Submission as USISubmission, SubmissionData as USISubmissionData)

# Get an instance of a logger
logger = get_task_logger(__name__)

# how many sample for submission
MAX_SAMPLES = 100


class SubmissionError(Exception):
    """Exception call for Error with submissions"""

    pass


# HINT: move into helper module?
class SubmissionHelper():
    """
    An helper class for submission task, used to deal with pyUSIrest
    """

    # define my class attributes
    def __init__(self, submission_id):

        # ok those are my default class attributes
        self.submission_id = submission_id
        self.submission_obj = None
        self.token = None

        # here are pyUSIrest object
        self.auth = None
        self.root = None

        # here I will track a USI submission
        self.usi_submission = None

        # here I will store samples already submitted
        self.submitted_samples = {}

        # get a submission object
        self.submission_obj = USISubmission.objects.get(
            pk=self.submission_id)

        # HINT: should I check my status?

    @property
    def owner(self):
        """Recover owner from a submission object related with a UID
        Submission

        Returns:
            :py:attr:`Submission.owner`: a django
            :py:class:`django.contrib.auth.models.User` object
        """

        return self.submission_obj.uid_submission.owner

    @property
    def team_name(self):
        """Recover team_name from a submission object

        Returns:
            str: the team name"""

        return self.owner.biosample_account.team.name

    @property
    def usi_submission_name(self):
        """Get/set biosample submission id from database

        Returns:
            str: the biosample USI submission identifier"""

        return self.submission_obj.usi_submission_name

    @usi_submission_name.setter
    def usi_submission_name(self, name):

        self.submission_obj.usi_submission_name = name
        self.submission_obj.save()

    def read_token(self):
        """Read token from REDIS database and set root attribute with a
        pyUSIrest.client.Root instance

        Returns:
            str: the read token"""

        # read biosample token from redis database
        client = redis.StrictRedis(
            host=settings.REDIS_HOST,
            port=settings.REDIS_PORT,
            db=settings.REDIS_DB)

        # infere key from submission data
        key = "token:submission:{submission_id}:{user}".format(
            submission_id=self.submission_obj.uid_submission.id,
            user=self.owner)

        # create a new auth object
        logger.debug("Reading token for '%s'" % self.owner)

        # getting token from redis db and set submission data
        self.token = client.get(key).decode("utf8")

        # get a root object with auth
        self.auth = get_auth(token=self.token)

        logger.debug("getting biosample root")
        self.root = pyUSIrest.client.Root(auth=self.auth)

        return self.token

    def start_submission(self):
        """
        Get a USI submission document. Recover submission if possible,
        create a new one if not defined. If recovered submission is
        closed, raise an error
        """

        if not self.recover_submission():
            self.create_submission()

        return self.usi_submission

    def recover_submission(self):
        """Try to recover a USI submission document or raise Exception. If
        not defined, return false"""

        # If no usi_submission_name, return False
        if not self.usi_submission_name:
            return False

        logger.info("Recovering submission %s for team %s" % (
            self.usi_submission_name,
            self.team_name))

        # get the same submission object
        self.usi_submission = self.root.get_submission_by_name(
            submission_name=self.usi_submission_name)

        # check that a submission is still editable
        if self.usi_submission.status != "Draft":
            raise SubmissionError(
                "Cannot recover submission '%s': current status is '%s'" % (
                   self.usi_submission_name,
                   self.usi_submission.status))

        # read already submitted samples
        self.read_samples()

        return True

    def create_submission(self):
        """Create a new USI submission object

        Returns:
            :py:class:`pyUSIrest.client.Submission` a pyUSIrest submission
            object
        """

        # getting team
        logger.debug("getting team '%s'" % (self.team_name))
        team = self.root.get_team_by_name(self.team_name)

        # create a new submission
        logger.info("Creating a new submission for '%s'" % (team.name))
        self.usi_submission = team.create_submission()

        # track submission_id in table
        self.usi_submission_name = self.usi_submission.name

        # return USI submission document
        return self.usi_submission

    def read_samples(self):
        """Read sample in a USI submission document and set submitted_samples
        attribute"""

        # read already submitted samples
        logger.debug("Getting info on samples...")
        samples = self.usi_submission.get_samples()
        logger.debug("Got %s samples" % (len(samples)))

        for sample in samples:
            self.submitted_samples[sample.alias] = sample

        return self.submitted_samples

    def create_or_update_sample(self, model):
        """Add or patch a sample into USI submission document. Can be
        animal or sample

        Args:
            model (:py:class:`uid.mixins.BioSampleMixin`): An animal or
                sample object"""

        # alias is used to reference the same objects
        alias = model.biosample_alias

        # check in my submitted samples
        if alias in self.submitted_samples:
            # patch sample
            logger.info("Patching %s" % (alias))

            # get usi sample
            sample = self.submitted_samples[alias]
            sample.patch(model.to_biosample())

        else:
            sample = self.usi_submission.create_sample(
                model.to_biosample())

            self.submitted_samples[alias] = sample

        # update sample status
        model.status = SUBMITTED
        model.last_submitted = timezone.now()
        model.save()

    def add_samples(self):
        """Iterate over sample data (animal/sample) and call
        create_or_update_sample (if model is in READY state)"""

        # iterate over sample data
        for submission_data in self.submission_obj.submission_data\
                .order_by('id'):
            # get model for simplicity
            model = submission_data.content_object

            if model.status == READY:
                logger.debug("Adding %s %s to submission %s" % (
                    model._meta.verbose_name,
                    model,
                    self.usi_submission_name))
                self.create_or_update_sample(model)

            else:
                logger.debug("Ignoring %s %s" % (
                    model._meta.verbose_name, model))

    def mark_submission(self, status, message):
        self.submission_obj.status = status
        self.submission_obj.message = message
        self.submission_obj.save()

    def mark_fail(self, message):
        """Set a :py:const:`ERROR <common.constants.ERROR>` status for
        :py:class:`biosample.models.Submission` and a message"""

        self.mark_submission(ERROR, message)

    def mark_success(self, message="Waiting for biosample validation"):
        """Set a :py:const:`SUBMITTED <common.constants.SUBMITTED>`
        :py:class:`biosample.models.Submission` and a message"""

        self.mark_submission(SUBMITTED, message)


class SubmitTask(NotifyAdminTaskMixin, BaseTask):
    name = "Submit to Biosample"
    description = """Submit to Biosample using USI"""

    def run(self, usi_submission_id):
        """Run task. Instantiate a SubmissionHelper with the provided
        :py:class:`biosample.models.Submission` id. Read token from database,
        start or recover a submission, add samples to it and then mark a
        status for it
        """

        # get a submission helper object
        submission_helper = SubmissionHelper(submission_id=usi_submission_id)

        # No retries, we expect always success
        try:
            submission_helper.read_token()
            submission_helper.start_submission()
            submission_helper.add_samples()
            submission_helper.mark_success()

        except ConnectionError as exc:
            logger.error("Error in biosample submission: %s" % exc)
            message = "Errors in EBI API endpoints. Please try again later"
            logger.error(message)

            # track message in submission object
            submission_helper.mark_submission(READY, message)

        # TODO: should I rename this exception with a more informative name
        # when token expires during a submission?
        except RuntimeError as exc:
            logger.error("Error in biosample submission: %s" % exc)
            message = (
                "Your token is expired: please submit again to resume "
                "submission")
            logger.error(message)

            # track message in submission object
            submission_helper.mark_submission(READY, message)

        except Exception as exc:
            logger.error("Unmanaged error: %s" % exc)
            # get exception info
            einfo = traceback.format_exc()

            # track traceback in message
            submission_helper.mark_fail(einfo)

        return "success", usi_submission_id


# HINT: move into helper module?
class SplitSubmissionHelper():
    """
    helper class to split py:class`uid.models.Submission` data in
    bacthes limited in sizes"""

    def __init__(self, uid_submission):
        self.counter = 0
        self.uid_submission = uid_submission
        self.usi_submission = None
        self.submission_ids = []

    def process_data(self):
        """Add animal and its samples to a submission"""

        # here we try to submit first animal without parents, then animal
        # with parent with lowest foreign keys, supposing that when uploadimg
        # a chiuld, his parents need to be defined and so they have a lower id
        # the postgres LEAST is a function that will return the column with
        # the lowest value, then we have to order explicitely with F in
        # order to apply the NULLS FIRST condition (animal without parents)
        for animal in self.uid_submission.animal_set.annotate(
                least=Least('father_id', 'mother_id')).order_by(
                    F('least').asc(nulls_first=True), F('id')):

            # ignore not READY models
            self.process_model(animal)

            # Add their specimen
            for sample in animal.sample_set.all():
                # ignore not READY models
                self.process_model(sample)

            # end of cicle for animal

        # are there orphaned samples (a submission with only samples)?
        for sample in self.uid_submission.sample_set.all():
            # ignore not READY models
            self.process_model(sample)

    def process_model(self, model):
        """Test for a model in a biosample submission. Ignore a model if
        status is not READY"""

        if model.status == READY:
            self.add_to_submission_data(model)

        else:
            # already submittes, so could be ignored
            logger.debug("Ignoring %s %s" % (model._meta.verbose_name, model))

    def create_submission(self):
        """
        Create a new :py:class:`biosample.models.Submission` object and
        set sample counter to 0"""

        self.usi_submission = USISubmission.objects.create(
            uid_submission=self.uid_submission,
            status=READY)

        # track object pks
        self.usi_submission.refresh_from_db()
        self.submission_ids.append(self.usi_submission.id)

        logger.debug("Created submission %s" % (self.usi_submission))

        # reset couter object
        self.counter = 0

    def model_in_submission(self, model):
        """
        Check if :py:class:`uid.mixins.BioSampleMixin` is already in an
        opened submission"""

        logger.debug("Searching %s %s in submissions" % (
            model._meta.verbose_name,
            model))

        # get content type
        ct = ContentType.objects.get_for_model(model)

        # define a queryset
        data_qs = USISubmissionData.objects.filter(
            content_type=ct,
            object_id=model.id)

        # exclude opened submission
        data_qs = data_qs.exclude(submission__status__in=[COMPLETED])

        if data_qs.count() == 1:
            usi_submission = data_qs.first().submission

            logger.debug("Found %s %s in %s" % (
                model._meta.verbose_name,
                model,
                usi_submission))

            # mark this batch to be called like it was created
            if usi_submission.id not in self.submission_ids:
                self.submission_ids.append(usi_submission.id)

                logger.debug(
                    "Reset status for submission %s" % (usi_submission))
                usi_submission.status = READY
                usi_submission.save()

            return True

        elif data_qs.count() >= 1:
            raise SubmissionError(
                "More than one submission opened for %s %s" % (
                    model._meta.verbose_name,
                    model))

        else:
            # no sample in data. I could append model into submission
            logger.debug("No %s %s in submission data" % (
                model._meta.verbose_name,
                model))
            return False

    def add_to_submission_data(self, model):
        """Add a :py:class:`uid.mixins.BioSampleMixin` to a
        :py:class:`biosample.models.Submission` object, or create a new
        one if there are more samples than required"""

        # get model type (animal or sample)
        model_type = model._meta.verbose_name

        # check if model is already in an opened submission
        if self.model_in_submission(model):
            logger.debug("Ignoring %s %s: already in a submission" % (
                model_type,
                model))
            return

        # Create a new submission if necessary
        if self.usi_submission is None:
            self.create_submission()

        # every time I split data in chunks I need to call the
        # submission task. Do it only on animals, to prevent
        # to put samples in a different submission
        if model_type == 'animal' and self.counter >= MAX_SAMPLES:
            self.create_submission()

        logger.info("Appending %s %s to %s" % (
            model._meta.verbose_name,
            model,
            self.usi_submission))

        # add object to submission data and updating counter
        USISubmissionData.objects.create(
            submission=self.usi_submission,
            content_object=model)

        self.counter += 1


class SplitSubmissionTask(SubmissionTaskMixin, NotifyAdminTaskMixin, BaseTask):
    """Split submission data in chunks in order to submit data through
    multiple tasks/processes and with smaller submissions"""

    name = "Split submission data"
    description = """Split submission data in chunks"""
    action = "biosample submission"

    def run(self, submission_id):
        """Call :py:class:`SplitSubmissionHelper` to split
        :py:class:`uid.models.Submission` data.
        Call :py:class:`SubmitTask` for each
        batch of data and then call :py:class:`SubmissionCompleteTask` after
        all data were submitted"""

        logger.info("Starting %s for submission %s" % (
            self.name, submission_id))

        uid_submission = self.get_uid_submission(submission_id)

        # call an helper class to create database objects
        submission_data_helper = SplitSubmissionHelper(uid_submission)

        # iterate over animal and samples
        submission_data_helper.process_data()

        # prepare to launch chord tasks
        submissioncomplete = SubmissionCompleteTask()

        # assign kwargs to chord
        callback = submissioncomplete.s(uid_submission_id=submission_id)

        submit = SubmitTask()
        header = [submit.s(pk) for pk in submission_data_helper.submission_ids]

        logger.debug("Preparing chord for %s tasks" % len(header))

        # call chord task. Chord will be called only after all tasks
        res = chord(header)(callback)

        logger.info(
            "Start submission chord process for %s with task %s" % (
                uid_submission,
                res.task_id))

        logger.info("%s completed" % self.name)

        # return a status
        return "success"


class SubmissionCompleteTask(
        SubmissionTaskMixin, NotifyAdminTaskMixin, BaseTask):
    """Update submission status after batch submission"""

    name = "Complete Submission Process"
    description = """Check submission status and update stuff"""
    action = "biosample submission"

    def run(self, *args, **kwargs):
        """Fetch submission data and then update
        :py:class:`uid.models.Submission` status"""

        # those are the output of SubmitTask, as a tuple of
        # biosample.model.Submission.pk and "success"
        submission_statuses = args[0]

        # get UID submission
        uid_submission = self.get_uid_submission(kwargs['uid_submission_id'])

        # mark as completed if submission_statuses is empty, for example when
        # submitting a uid submission with no data
        if not submission_statuses:
            message = "Submission %s is empty!" % uid_submission
            logger.warning(message)

            # update submission status. No more queries on this
            self.update_submission_status(
                uid_submission, ERROR, message)

            return "success"

        # submission_statuses will be an array like this
        # [("success", 1), ("success"), 2]
        usi_submission_ids = [status[1] for status in submission_statuses]

        # fetch data from database
        submission_qs = USISubmission.objects.filter(
            pk__in=usi_submission_ids)

        # annotate biosample submission by statuses
        statuses = {}

        for res in submission_qs.values('status').annotate(
                count=Count('status')):
            statuses[res['status']] = res['count']

        # check for errors in submission. Those are statuses setted by
        # SubmitTask
        if ERROR in statuses:
            # submission failed
            logger.info("Submission %s failed" % uid_submission)

            self.update_message(uid_submission, submission_qs, ERROR)

            # send a mail to the user
            uid_submission.owner.email_user(
                "Error in biosample submission %s" % (
                    uid_submission.id),
                ("Something goes wrong with biosample submission. Please "
                 "report this to InjectTool team\n\n"
                 "%s" % uid_submission.message),
            )

        elif READY in statuses:
            # submission failed
            logger.info("Temporary error for %s" % uid_submission)

            self.update_message(uid_submission, submission_qs, READY)

            # send a mail to the user
            uid_submission.owner.email_user(
                "Temporary error in biosample submission %s" % (
                    uid_submission.id),
                ("Something goes wrong with biosample submission. Please "
                 "try again\n\n"
                 "%s" % uid_submission.message),
            )

        else:
            # Update submission status: a completed but not yet finalized
            # submission
            logger.info("Submission %s success" % uid_submission)

            self.update_message(uid_submission, submission_qs, SUBMITTED)

        return "success"

    def update_message(self, uid_submission, submission_qs, status):
        """Read :py:class:`biosample.models.Submission` message and set
        :py:class:`uid.models.Submission` message"""

        # get error messages for submission
        message = []

        for submission in submission_qs.filter(status=status):
            message.append(submission.message)

        self.update_submission_status(
            uid_submission, status, "\n".join(set(message)))


# register explicitly tasks
# https://github.com/celery/celery/issues/3744#issuecomment-271366923
celery_app.tasks.register(SubmitTask)
celery_app.tasks.register(SplitSubmissionTask)
celery_app.tasks.register(SubmissionCompleteTask)