biosample.tasks.submission.SubmissionHelper.create_or_update_sample() - Code Metrics - Inspection of ":zap: Batch submission to Biosamples" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#44)

by Paolo

created 2019-09-07 12:57 UTC

SubmissionHelper.create_or_update_sample() A

↳ Parent: biosample.tasks.submission

Complexity

Conditions

Size

Total Lines	28
Code Lines	11

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	11
dl	0
loc	28
rs	9.85
c	0
b	0
f	0
cc	2
nop	2

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

@author: Paolo Cozzi <[email protected]>
"""

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
from django.utils import timezone

from common.constants import ERROR, READY, SUBMITTED, COMPLETED
from image.celery import app as celery_app, MyTask
from image_app.models import Submission, Animal
from submissions.helpers import send_message

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


# TODO: promote this to become a common mixin for tasks
class TaskFailureMixin():
    """Mixin candidate to become the common behaviour of task failure which
    mark submission with ERROR status and send message to owner"""

    # Ovverride default on failure method
    def on_failure(self, exc, task_id, args, kwargs, einfo):
        """Mark submission with error status, send async message and a
        mail to the owner or such submission"""

        logger.error('{0!r} failed: {1!r}'.format(task_id, exc))

        # get submission object
        submission_obj = Submission.objects.get(pk=args[0])

        submission_obj.status = ERROR
        submission_obj.message = (
            "Error in biosample submission: %s" % str(exc))
        submission_obj.save()

        # send async message
        send_message(submission_obj)

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

        # TODO: submit mail to admin


# 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:`image_app.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:
            self.usi_submission.create_sample(
                model.to_biosample())

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

    def add_samples(self):
        """Iterate over sample data (animal/sample) and call
        create_or_update_sample"""

        # 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.name.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(MyTask):
    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`image_app.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"""

        for animal in Animal.objects.filter(
                name__submission=self.uid_submission):

            # add animal if not yet submitted, or patch it
            if animal.name.status == READY:
                self.add_to_submission_data(animal)

            else:
                # already submitted, so could be ignored
                logger.debug("Ignoring animal %s" % (animal))

            # Add their specimen
            for sample in animal.sample_set.all():
                # add sample if not yet submitted
                if sample.name.status == READY:
                    self.add_to_submission_data(sample)

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

            # end of cicle for animal.

    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:`image_app.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:`image_app.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.info("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(TaskFailureMixin, MyTask):
    """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"""

    def run(self, submission_id):
        """Call :py:class:`SplitSubmissionHelper` to split
        :py:class:`image_app.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 = Submission.objects.get(
            pk=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(TaskFailureMixin, MyTask):
    """Update submission status after batch submission"""

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

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

        submission_statuses = args[0]

        # 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)

        # get UID submission
        uid_submission = Submission.objects.get(
            pk=kwargs['uid_submission_id'])

        # 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)

        # send async message
        send_message(uid_submission)

        return "success"

    def __update_message(self, uid_submission, submission_qs, status):
        """Read biosample.models.Submission message and set
        image_app.models.Submission message"""

        # get error messages for submission
        message = []

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

        uid_submission.status = status
        uid_submission.message = "\n".join(set(message))
        uid_submission.save()


# 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)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Thu Jul 18 14:14:06 2019
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import redis
10			import traceback
11			import pyUSIrest.client
12
13			from celery import chord
14			from celery.utils.log import get_task_logger
15
16			from django.conf import settings
17			from django.contrib.contenttypes.models import ContentType
18			from django.db.models import Count
19			from django.utils import timezone
20
21			from common.constants import ERROR, READY, SUBMITTED, COMPLETED
22			from image.celery import app as celery_app, MyTask
23			from image_app.models import Submission, Animal
24			from submissions.helpers import send_message
25
26			from ..helpers import get_auth
27			from ..models import (
28			Submission as USISubmission, SubmissionData as USISubmissionData)
29
30			# Get an instance of a logger
31			logger = get_task_logger(__name__)
32
33			# how many sample for submission
34			MAX_SAMPLES = 100
35
36
37			class SubmissionError(Exception):
38			"""Exception call for Error with submissions"""
39
40			pass
41
42
43			# TODO: promote this to become a common mixin for tasks
44			class TaskFailureMixin():
45			"""Mixin candidate to become the common behaviour of task failure which
46			mark submission with ERROR status and send message to owner"""
47
48			# Ovverride default on failure method
49			def on_failure(self, exc, task_id, args, kwargs, einfo):
50			"""Mark submission with error status, send async message and a
51			mail to the owner or such submission"""
52
53			logger.error('{0!r} failed: {1!r}'.format(task_id, exc))
54
55			# get submission object
56			submission_obj = Submission.objects.get(pk=args[0])
57
58			submission_obj.status = ERROR
59			submission_obj.message = (
60			"Error in biosample submission: %s" % str(exc))
61			submission_obj.save()
62
63			# send async message
64			send_message(submission_obj)
65
66			# send a mail to the user with the stacktrace (einfo)
67			submission_obj.owner.email_user(
68			"Error in biosample submission %s" % (
69			submission_obj.id),
70			("Something goes wrong with biosample submission. Please report "
71			"this to InjectTool team\n\n %s" % str(einfo)),
72			)
73
74			# TODO: submit mail to admin
75
76
77			# HINT: move into helper module?
78			class SubmissionHelper():
79			"""
80			An helper class for submission task, used to deal with pyUSIrest
81			"""
82
83			# define my class attributes
84			def __init__(self, submission_id):
85
86			# ok those are my default class attributes
87			self.submission_id = submission_id
88			self.submission_obj = None
89			self.token = None
90
91			# here are pyUSIrest object
92			self.auth = None
93			self.root = None
94
95			# here I will track a USI submission
96			self.usi_submission = None
97
98			# here I will store samples already submitted
99			self.submitted_samples = {}
100
101			# get a submission object
102			self.submission_obj = USISubmission.objects.get(
103			pk=self.submission_id)
104
105			# HINT: should I check my status?
106
107			@property
108			def owner(self):
109			"""Recover owner from a submission object related with a UID
110			Submission
111
112			Returns:
113			:py:attr:`Submission.owner`: a django
114			:py:class:`django.contrib.auth.models.User` object
115			"""
116
117			return self.submission_obj.uid_submission.owner
118
119			@property
120			def team_name(self):
121			"""Recover team_name from a submission object
122
123			Returns:
124			str: the team name"""
125
126			return self.owner.biosample_account.team.name
127
128			@property
129			def usi_submission_name(self):
130			"""Get/set biosample submission id from database
131
132			Returns:
133			str: the biosample USI submission identifier"""
134
135			return self.submission_obj.usi_submission_name
136
137			@usi_submission_name.setter
138			def usi_submission_name(self, name):
139
140			self.submission_obj.usi_submission_name = name
141			self.submission_obj.save()
142
143			def read_token(self):
144			"""Read token from REDIS database and set root attribute with a
145			pyUSIrest.client.Root instance
146
147			Returns:
148			str: the read token"""
149
150			# read biosample token from redis database
151			client = redis.StrictRedis(
152			host=settings.REDIS_HOST,
153			port=settings.REDIS_PORT,
154			db=settings.REDIS_DB)
155
156			# infere key from submission data
157			key = "token:submission:{submission_id}:{user}".format(
158			submission_id=self.submission_obj.uid_submission.id,
159			user=self.owner)
160
161			# create a new auth object
162			logger.debug("Reading token for '%s'" % self.owner)
163
164			# getting token from redis db and set submission data
165			self.token = client.get(key).decode("utf8")
166
167			# get a root object with auth
168			self.auth = get_auth(token=self.token)
169
170			logger.debug("getting biosample root")
171			self.root = pyUSIrest.client.Root(auth=self.auth)
172
173			return self.token
174
175			def start_submission(self):
176			"""
177			Get a USI submission document. Recover submission if possible,
178			create a new one if not defined. If recovered submission is
179			closed, raise an error
180			"""
181
182			if not self.recover_submission():
183			self.create_submission()
184
185			return self.usi_submission
186
187			def recover_submission(self):
188			"""Try to recover a USI submission document or raise Exception. If
189			not defined, return false"""
190
191			# If no usi_submission_name, return False
192			if not self.usi_submission_name:
193			return False
194
195			logger.info("Recovering submission %s for team %s" % (
196			self.usi_submission_name,
197			self.team_name))
198
199			# get the same submission object
200			self.usi_submission = self.root.get_submission_by_name(
201			submission_name=self.usi_submission_name)
202
203			# check that a submission is still editable
204			if self.usi_submission.status != "Draft":
205			raise SubmissionError(
206			"Cannot recover submission '%s': current status is '%s'" % (
207			self.usi_submission_name,
208			self.usi_submission.status))
209
210			# read already submitted samples
211			self.read_samples()
212
213			return True
214
215			def create_submission(self):
216			"""Create a new USI submission object
217
218			Returns:
219			:py:class:`pyUSIrest.client.Submission` a pyUSIrest submission
220			object
221			"""
222
223			# getting team
224			logger.debug("getting team '%s'" % (self.team_name))
225			team = self.root.get_team_by_name(self.team_name)
226
227			# create a new submission
228			logger.info("Creating a new submission for '%s'" % (team.name))
229			self.usi_submission = team.create_submission()
230
231			# track submission_id in table
232			self.usi_submission_name = self.usi_submission.name
233
234			# return USI submission document
235			return self.usi_submission
236
237			def read_samples(self):
238			"""Read sample in a USI submission document and set submitted_samples
239			attribute"""
240
241			# read already submitted samples
242			logger.debug("Getting info on samples...")
243			samples = self.usi_submission.get_samples()
244			logger.debug("Got %s samples" % (len(samples)))
245
246			for sample in samples:
247			self.submitted_samples[sample.alias] = sample
248
249			return self.submitted_samples
250
251			def create_or_update_sample(self, model):
252			"""Add or patch a sample into USI submission document. Can be
253			animal or sample
254
255			Args:
256			model (:py:class:`image_app.mixins.BioSampleMixin`): An animal or
257			sample object"""
258
259			# alias is used to reference the same objects
260			alias = model.biosample_alias
261
262			# check in my submitted samples
263			if alias in self.submitted_samples:
264			# patch sample
265			logger.info("Patching %s" % (alias))
266
267			# get usi sample
268			sample = self.submitted_samples[alias]
269			sample.patch(model.to_biosample())
270
271			else:
272			self.usi_submission.create_sample(
273			model.to_biosample())
274
275			# update sample status
276			model.name.status = SUBMITTED
277			model.name.last_submitted = timezone.now()
278			model.name.save()
279
280			def add_samples(self):
281			"""Iterate over sample data (animal/sample) and call
282			create_or_update_sample"""
283
284			# iterate over sample data
285			for submission_data in self.submission_obj.submission_data\
286			.order_by('id'):
287			# get model for simplicity
288			model = submission_data.content_object
289
290			if model.name.status == READY:
291			logger.debug("Adding %s %s to submission %s" % (
292			model._meta.verbose_name,
293			model,
294			self.usi_submission_name))
295			self.create_or_update_sample(model)
296
297			else:
298			logger.debug("Ignoring %s %s" % (
299			model._meta.verbose_name, model))
300
301			def mark_submission(self, status, message):
302			self.submission_obj.status = status
303			self.submission_obj.message = message
304			self.submission_obj.save()
305
306			def mark_fail(self, message):
307			"""Set a :py:const:`ERROR <common.constants.ERROR>` status for
308			:py:class:`biosample.models.Submission` and a message"""
309
310			self.mark_submission(ERROR, message)
311
312			def mark_success(self, message="Waiting for biosample validation"):
313			"""Set a :py:const:`SUBMITTED <common.constants.SUBMITTED>`
314			:py:class:`biosample.models.Submission` and a message"""
315
316			self.mark_submission(SUBMITTED, message)
317
318
319			class SubmitTask(MyTask):
320			name = "Submit to Biosample"
321			description = """Submit to Biosample using USI"""
322
323			def run(self, usi_submission_id):
324			"""Run task. Instantiate a SubmissionHelper with the provided
325			:py:class:`biosample.models.Submission` id. Read token from database,
326			start or recover a submission, add samples to it and then mark a
327			status for it
328			"""
329
330			# get a submission helper object
331			submission_helper = SubmissionHelper(submission_id=usi_submission_id)
332
333			# No retries, we expect always success
334			try:
335			submission_helper.read_token()
336			submission_helper.start_submission()
337			submission_helper.add_samples()
338			submission_helper.mark_success()
339
340			except ConnectionError as exc:
341			logger.error("Error in biosample submission: %s" % exc)
342			message = "Errors in EBI API endpoints. Please try again later"
343			logger.error(message)
344
345			# track message in submission object
346			submission_helper.mark_submission(READY, message)
347
348			# TODO: should I rename this exception with a more informative name
349			# when token expires during a submission?
350			except RuntimeError as exc:
351			logger.error("Error in biosample submission: %s" % exc)
352			message = (
353			"Your token is expired: please submit again to resume "
354			"submission")
355			logger.error(message)
356
357			# track message in submission object
358			submission_helper.mark_submission(READY, message)
359
360			except Exception as exc:
361			logger.error("Unmanaged error: %s" % exc)
362			# get exception info
363			einfo = traceback.format_exc()
364
365			# track traceback in message
366			submission_helper.mark_fail(einfo)
367
368			return "success", usi_submission_id
369
370
371			# HINT: move into helper module?
372			class SplitSubmissionHelper():
373			"""
374			helper class to split py:class`image_app.models.Submission` data in
375			bacthes limited in sizes"""
376
377			def __init__(self, uid_submission):
378			self.counter = 0
379			self.uid_submission = uid_submission
380			self.usi_submission = None
381			self.submission_ids = []
382
383			def process_data(self):
384			"""Add animal and its samples to a submission"""
385
386			for animal in Animal.objects.filter(
387			name__submission=self.uid_submission):
388
389			# add animal if not yet submitted, or patch it
390			if animal.name.status == READY:
391			self.add_to_submission_data(animal)
392
393			else:
394			# already submitted, so could be ignored
395			logger.debug("Ignoring animal %s" % (animal))
396
397			# Add their specimen
398			for sample in animal.sample_set.all():
399			# add sample if not yet submitted
400			if sample.name.status == READY:
401			self.add_to_submission_data(sample)
402
403			else:
404			# already submittes, so could be ignored
405			logger.debug("Ignoring sample %s" % (sample))
406
407			# end of cicle for animal.
408
409			def create_submission(self):
410			"""
411			Create a new :py:class:`biosample.models.Submission` object and
412			set sample counter to 0"""
413
414			self.usi_submission = USISubmission.objects.create(
415			uid_submission=self.uid_submission,
416			status=READY)
417
418			# track object pks
419			self.usi_submission.refresh_from_db()
420			self.submission_ids.append(self.usi_submission.id)
421
422			logger.debug("Created submission %s" % (self.usi_submission))
423
424			# reset couter object
425			self.counter = 0
426
427			def model_in_submission(self, model):
428			"""
429			Check if :py:class:`image_app.mixins.BioSampleMixin` is already in an
430			opened submission"""
431
432			logger.debug("Searching %s %s in submissions" % (
433			model._meta.verbose_name,
434			model))
435
436			# get content type
437			ct = ContentType.objects.get_for_model(model)
438
439			# define a queryset
440			data_qs = USISubmissionData.objects.filter(
441			content_type=ct,
442			object_id=model.id)
443
444			# exclude opened submission
445			data_qs = data_qs.exclude(submission__status__in=[COMPLETED])
446
447			if data_qs.count() == 1:
448			usi_submission = data_qs.first().submission
449
450			logger.debug("Found %s %s in %s" % (
451			model._meta.verbose_name,
452			model,
453			usi_submission))
454
455			# mark this batch to be called like it was created
456			if usi_submission.id not in self.submission_ids:
457			self.submission_ids.append(usi_submission.id)
458
459			logger.debug(
460			"Reset status for submission %s" % (usi_submission))
461			usi_submission.status = READY
462			usi_submission.save()
463
464			return True
465
466			elif data_qs.count() >= 1:
467			raise SubmissionError(
468			"More than one submission opened for %s %s" % (
469			model._meta.verbose_name,
470			model))
471
472			else:
473			# no sample in data. I could append model into submission
474			logger.debug("No %s %s in submission data" % (
475			model._meta.verbose_name,
476			model))
477			return False
478
479			def add_to_submission_data(self, model):
480			"""Add a :py:class:`image_app.mixins.BioSampleMixin` to a
481			:py:class:`biosample.models.Submission` object, or create a new
482			one if there are more samples than required"""
483
484			# get model type (animal or sample)
485			model_type = model._meta.verbose_name
486
487			# check if model is already in an opened submission
488			if self.model_in_submission(model):
489			logger.info("Ignoring %s %s: already in a submission" % (
490			model_type,
491			model))
492			return
493
494			# Create a new submission if necessary
495			if self.usi_submission is None:
496			self.create_submission()
497
498			# every time I split data in chunks I need to call the
499			# submission task. Do it only on animals, to prevent
500			# to put samples in a different submission
501			if model_type == 'animal' and self.counter >= MAX_SAMPLES:
502			self.create_submission()
503
504			logger.info("Appending %s %s to %s" % (
505			model._meta.verbose_name,
506			model,
507			self.usi_submission))
508
509			# add object to submission data and updating counter
510			USISubmissionData.objects.create(
511			submission=self.usi_submission,
512			content_object=model)
513
514			self.counter += 1
515
516
517			class SplitSubmissionTask(TaskFailureMixin, MyTask):
518			"""Split submission data in chunks in order to submit data through
519			multiple tasks/processes and with smaller submissions"""
520
521			name = "Split submission data"
522			description = """Split submission data in chunks"""
523
524			def run(self, submission_id):
525			"""Call :py:class:`SplitSubmissionHelper` to split
526			:py:class:`image_app.models.Submission` data.
527			Call :py:class:`SubmitTask` for each
528			batch of data and then call :py:class:`SubmissionCompleteTask` after
529			all data were submitted"""
530
531			logger.info("Starting %s for submission %s" % (
532			self.name, submission_id))
533
534			uid_submission = Submission.objects.get(
535			pk=submission_id)
536
537			# call an helper class to create database objects
538			submission_data_helper = SplitSubmissionHelper(uid_submission)
539
540			# iterate over animal and samples
541			submission_data_helper.process_data()
542
543			# prepare to launch chord tasks
544			submissioncomplete = SubmissionCompleteTask()
545
546			# assign kwargs to chord
547			callback = submissioncomplete.s(uid_submission_id=submission_id)
548
549			submit = SubmitTask()
550			header = [submit.s(pk) for pk in submission_data_helper.submission_ids]
551
552			logger.debug("Preparing chord for %s tasks" % len(header))
553
554			# call chord task. Chord will be called only after all tasks
555			res = chord(header)(callback)
556
557			logger.info(
558			"Start submission chord process for %s with task %s" % (
559			uid_submission,
560			res.task_id))
561
562			logger.info("%s completed" % self.name)
563
564			# return a status
565			return "success"
566
567
568			class SubmissionCompleteTask(TaskFailureMixin, MyTask):
569			"""Update submission status after batch submission"""
570
571			name = "Complete Submission Process"
572			description = """Check submission status and update stuff"""
573
574			def run(self, args, *kwargs):
575			"""Fetch submission data and then update
576			:py:class:`image_app.models.Submission` status"""
577
578			submission_statuses = args[0]
579
580			# submission_statuses will be an array like this
581			# [("success", 1), ("success"), 2]
582			usi_submission_ids = [status[1] for status in submission_statuses]
583
584			# fetch data from database
585			submission_qs = USISubmission.objects.filter(
586			pk__in=usi_submission_ids)
587
588			# get UID submission
589			uid_submission = Submission.objects.get(
590			pk=kwargs['uid_submission_id'])
591
592			# annotate biosample submission by statuses
593			statuses = {}
594
595			for res in submission_qs.values('status').annotate(
596			count=Count('status')):
597			statuses[res['status']] = res['count']
598
599			# check for errors in submission. Those are statuses setted by
600			# SubmitTask
601			if ERROR in statuses:
602			# submission failed
603			logger.info("Submission %s failed" % uid_submission)
604
605			self.__update_message(uid_submission, submission_qs, ERROR)
606
607			# send a mail to the user
608			uid_submission.owner.email_user(
609			"Error in biosample submission %s" % (
610			uid_submission.id),
611			("Something goes wrong with biosample submission. Please "
612			"report this to InjectTool team\n\n"
613			"%s" % uid_submission.message),
614			)
615
616			elif READY in statuses:
617			# submission failed
618			logger.info("Temporary error for %s" % uid_submission)
619
620			self.__update_message(uid_submission, submission_qs, READY)
621
622			# send a mail to the user
623			uid_submission.owner.email_user(
624			"Temporary error in biosample submission %s" % (
625			uid_submission.id),
626			("Something goes wrong with biosample submission. Please "
627			"try again\n\n"
628			"%s" % uid_submission.message),
629			)
630
631			else:
632			# Update submission status: a completed but not yet finalized
633			# submission
634			logger.info("Submission %s success" % uid_submission)
635
636			self.__update_message(uid_submission, submission_qs, SUBMITTED)
637
638			# send async message
639			send_message(uid_submission)
640
641			return "success"
642
643			def __update_message(self, uid_submission, submission_qs, status):
644			"""Read biosample.models.Submission message and set
645			image_app.models.Submission message"""
646
647			# get error messages for submission
648			message = []
649
650			for submission in submission_qs.filter(status=status):
651			message.append(submission.message)
652
653			uid_submission.status = status
654			uid_submission.message = "\n".join(set(message))
655			uid_submission.save()
656
657
658			# register explicitly tasks
659			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
660			celery_app.tasks.register(SubmitTask)
661			celery_app.tasks.register(SplitSubmissionTask)
662			celery_app.tasks.register(SubmissionCompleteTask)
663

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#44)

SubmissionHelper.create_or_update_sample() A

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