biosample.tasks.retrieval.RetrievalCompleteTask.update_message() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #60..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 2c16e2...2c16e2 )

by Paolo

created 2019-10-08 15:14 UTC

RetrievalCompleteTask.update_message() A

↳ Parent: biosample.tasks.retrieval

Complexity

Conditions

Size

Total Lines	12
Code Lines	6

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	6
dl	0
loc	12
rs	10
c	0
b	0
f	0
cc	2
nop	4

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 16 11:25:03 2019

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

import os
import json

from decouple import AutoConfig
from celery.utils.log import get_task_logger

import pyUSIrest.client

from django.conf import settings
from django.db.models import Count
from django.utils import timezone

from image.celery import app as celery_app
from image_app.helpers import parse_image_alias, get_model_object
from image_app.models import Submission
from common.tasks import BaseTask, ExclusiveTask, NotifyAdminTaskMixin
from common.constants import (
    ERROR, NEED_REVISION, SUBMITTED, COMPLETED)
from submissions.tasks import SubmissionTaskMixin

from ..helpers import get_manager_auth
from ..models import Submission as USISubmission

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

# define a decouple config object
settings_dir = os.path.join(settings.BASE_DIR, 'image')
config = AutoConfig(search_path=settings_dir)

# a threshold of days to determine a very long task
MAX_DAYS = 5


# HINT: how this class could be similar to SubmissionHelper?
class FetchStatusHelper():
    """Helper class to deal with submission data"""

    # define my class attributes
    def __init__(self, usi_submission):
        """
        Helper function to have info for a biosample.models.Submission

        Args:
            usi_submission (biosample.models.Submission): a biosample
                model Submission instance
        """

        # ok those are my default class attributes
        self.usi_submission = usi_submission
        self.uid_submission = usi_submission.uid_submission

        # here are pyUSIrest object
        self.auth = get_manager_auth()
        self.root = pyUSIrest.client.Root(self.auth)

        # here I will track the biosample submission
        self.submission_name = self.usi_submission.usi_submission_name
        self.submission = self.root.get_submission_by_name(
            submission_name=self.submission_name)

    def check_submission_status(self):
        """Check submission status, finalize submission, check errors etc"""

        # reload submission status
        self.usi_submission.refresh_from_db()

        if self.usi_submission.status != SUBMITTED:
            # someone else has taken this task and done something. Ignore!
            logger.warning("Ignoring submission %s current status is %s" % (
                self.usi_submission, self.usi_submission.get_status_display()))
            return

        logger.debug("Checking status for '%s'" % (
            self.submission_name))

        # Update submission status if completed
        if self.submission.status == 'Completed':
            # fetch biosample ids with a proper function
            self.complete()

        elif self.submission.status == 'Draft':
            # check for a long task
            if self.submission_has_issues():
                # return to the caller. I've just marked the submission with
                # errors and sent a mail to the user
                return

            # check validation. If it is ok, finalize submission
            status = self.submission.get_status()

            # this mean validation statuses, I want to see completed in all
            # samples
            if len(status) == 1 and 'Complete' in status:
                # check for errors and eventually finalize
                self.finalize()

            else:
                logger.warning(
                    "Biosample validation is not completed yet (%s)" %
                    (status))

        elif self.submission.status == 'Submitted':
            # check for a long task
            if self.submission_has_issues():
                # return to the caller. I've just marked the submission with
                # errors and sent a mail to the user
                return

            logger.info(
                "Submission '%s' is '%s'. Waiting for biosample ids" % (
                    self.submission_name,
                    self.submission.status))

            # debug submission status
            document = self.submission.follow_url(
                "processingStatusSummary", self.auth)

            logger.debug(
                "Current status for submission '%s' is '%s'" % (
                    self.submission_name, document.data))

        else:
            # HINT: thrown an exception?
            logger.warning("Unknown status '%s' for submission '%s'" % (
                self.submission.status,
                self.submission_name))

        logger.debug("Checking status for '%s' completed" % (
            self.submission_name))

    def submission_has_issues(self):
        """
        Check that biosample submission has not issues. For example, that
        it will remain in the same status for a long time

        Returns:
            bool: True if an issue is detected
        """

        logger.debug(
            "Check if submission '%s' remained in the same status "
            "for a long time" % (
                self.submission_name))

        if (timezone.now() - self.usi_submission.updated_at).days > MAX_DAYS:
            message = (
                "Biosample submission '%s' remained with the same status "
                "for more than %s days. Please report it to InjectTool "
                "team" % (self.submission_name, MAX_DAYS))

            self.usi_submission.status = ERROR
            self.usi_submission.message = message
            self.usi_submission.save()

            logger.error(
                "Errors for submission: %s" % (
                    self.submission_name))
            logger.error(message)

            return True

        else:
            return False

    def __sample_has_errors(self, sample, table, pk):
        """
        Helper metod to mark a (animal/sample) with its own errors. Table
        sould be Animal or Sample to update the approriate object. Sample
        is a USI sample object

        Args:
            sample (pyUSIrest.client.sample): a USI sample object
            table (str): ``Animal`` or ``Sample``, mean the table where this
                object should be searched
            pk (int): table primary key
        """

        # get sample/animal object relying on table name and pk
        sample_obj = get_model_object(table, pk)

        sample_obj.name.status = NEED_REVISION
        sample_obj.name.save()

        # get a USI validation result
        validation_result = sample.get_validation_result()

        # TODO: should I store validation_result error in validation tables?
        errorMessages = validation_result.errorMessages

        # return an error for each object
        return {str(sample_obj): errorMessages}

    def finalize(self):
        """Finalize a submission by closing document and send it to
        biosample"""

        logger.debug("Finalizing submission '%s'" % (
            self.submission_name))

        # get errors for a submission
        errors = self.submission.has_errors()

        # collect all error messages in a list
        messages = []

        if True in errors:
            # get sample with errors then update database
            samples = self.submission.get_samples(has_errors=True)

            for sample in samples:
                # derive pk and table from alias
                table, pk = parse_image_alias(sample.alias)

                # need to check if this sample/animals has errors or not
                if sample.has_errors():
                    logger.warning(
                        "%s in table %s has errors!!!" % (sample, table))

                    # mark this sample since has problems
                    errorMessages = self.__sample_has_errors(
                        sample, table, pk)

                    # append this into error messages list
                    messages.append(errorMessages)

                # if a sample has no errors, status will be the same

            logger.error(
                "Errors for submission: '%s'" % (self.submission_name))
            logger.error("Fix them, then finalize")

            # report error
            message = json.dumps(messages, indent=2)

            # Update status for biosample.models.Submission
            self.usi_submission.status = NEED_REVISION
            self.usi_submission.message = message
            self.usi_submission.save()

        else:
            # raising an exception while finalizing will result
            # in a failed task.
            # TODO: model and test exception in finalization
            self.submission.finalize()

    def complete(self):
        """Complete a submission and fetch name objects"""

        logger.debug("Completing submission '%s'" % (
            self.submission_name))

        for sample in self.submission.get_samples():
            # derive pk and table from alias
            table, pk = parse_image_alias(sample.alias)

            # if no accession, return without doing anything
            if sample.accession is None:
                logger.error("No accession found for sample '%s'" % (sample))
                logger.error("Ignoring submission '%s'" % (self.submission))
                return

            # get sample/animal object relying on table name and pk
            sample_obj = get_model_object(table, pk)

            # update statuses
            sample_obj.name.status = COMPLETED
            sample_obj.name.biosample_id = sample.accession
            sample_obj.name.save()

        # update submission
        self.usi_submission.status = COMPLETED
        self.usi_submission.message = "Successful submission into biosample"
        self.usi_submission.save()

        logger.info(
            "Submission %s is now completed and recorded into UID" % (
                self.submission))


class FetchStatusTask(NotifyAdminTaskMixin, ExclusiveTask):
    name = "Fetch USI status"
    description = """Fetch biosample using USI API"""
    lock_id = "FetchStatusTask"

    def run(self):
        """
        This function is called when delay is called. It will acquire a lock
        in redis, so those tasks are mutually exclusive

        Returns:
            str: success if everything is ok. Different messages if task is
            already running or exception is caught"""

        # debugging instance
        self.debug_task()

        # do stuff and return something
        return self.fetch_status()

    def fetch_status(self):
        """
        Fetch status from pending submissions. Called from
        :py:meth:`run`, handles exceptions from USI, select
        all :py:class:`Submission <image_app.models.Submission>` objects
        with :py:const:`SUBMITTED <common.constants.SUBMITTED>` status
        from :ref:`UID <The Unified Internal Database>` and call
        :py:meth:`fetch_queryset` with this data
        """

        logger.info("fetch_status started")

        # search for submission with SUBMITTED status. Other submission are
        # not yet finalized. This function need to be called by exclusives
        # tasks
        qs = Submission.objects.filter(status=SUBMITTED)

        # check for queryset length
        if qs.count() != 0:
            try:
                # fetch biosample status
                self.fetch_queryset(qs)

            # retry a task under errors
            # http://docs.celeryproject.org/en/latest/userguide/tasks.html#retrying
            except ConnectionError as exc:
                raise self.retry(exc=exc)

        else:
            logger.debug("No pending submission in UID database")

        # debug
        logger.info("fetch_status completed")

        return "success"

    # a function to retrieve biosample submission
    def fetch_queryset(self, queryset):
        """Fetch biosample against a queryset (a list of
        :py:const:`SUBMITTED <common.constants.SUBMITTED>`
        :py:class:`Submission <image_app.models.Submission>` objects). Iterate
        through submission to get USI info. Calls
        :py:class:`FetchStatusHelper`
        """

        logger.info("Searching for submissions into biosample")

        for uid_submission in queryset:
            usi_submissions = USISubmission.objects.filter(
                uid_submission=uid_submission,
                status=SUBMITTED)

            # HINT: fetch statuses using tasks?
            for usi_submission in usi_submissions:
                status_helper = FetchStatusHelper(usi_submission)
                status_helper.check_submission_status()

            # set the final status for a submission like SubmissionCompleteTask
            retrievalcomplete = RetrievalCompleteTask()

            # assign kwargs to chord
            res = retrievalcomplete.delay(uid_submission_id=uid_submission.id)

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

        logger.info("fetch_queryset completed")


class RetrievalCompleteTask(SubmissionTaskMixin, BaseTask):
    """Update submission status after fetching status"""

    name = "Complete Retrieval Process"
    description = """Check submission status after retrieval nd update stuff"""
    action = "biosample retrieval"

    def run(self, *args, **kwargs):
        """Fetch submission data and then update UID submission status"""

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

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

        # annotate biosample submission by statuses
        statuses = {}

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

        if SUBMITTED in statuses:
            # ignoring the other models. No errors thrown until there is
            # as SUBMITTED USISubmission
            logger.info("Submission %s not yet finished" % uid_submission)

            return "success"

        # if there is ANY errors in biosample.models.Submission for a
        # particoular submission, I will mark it as ERROR
        elif 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),
            )

        # check if submission need revision
        elif NEED_REVISION in statuses:
            # submission failed
            logger.info("Submission %s failed" % uid_submission)

            self.update_message(uid_submission, submission_qs, NEED_REVISION)

            # send a mail to the user
            uid_submission.owner.email_user(
                "Error in biosample submission %s" % (
                    uid_submission.id),
                "Some items needs revision:\n\n" + uid_submission.message,
            )

        elif COMPLETED in statuses and len(statuses) == 1:
            # if all status are complete, the submission is completed
            logger.info(
                "Submission %s completed with success" % uid_submission)

            self.update_message(uid_submission, submission_qs, COMPLETED)

        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)

        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(FetchStatusTask)
celery_app.tasks.register(RetrievalCompleteTask)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Tue Jul 16 11:25:03 2019
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import os
10			import json
11
12			from decouple import AutoConfig
13			from celery.utils.log import get_task_logger
14
15			import pyUSIrest.client
16
17			from django.conf import settings
18			from django.db.models import Count
19			from django.utils import timezone
20
21			from image.celery import app as celery_app
22			from image_app.helpers import parse_image_alias, get_model_object
23			from image_app.models import Submission
24			from common.tasks import BaseTask, ExclusiveTask, NotifyAdminTaskMixin
25			from common.constants import (
26			ERROR, NEED_REVISION, SUBMITTED, COMPLETED)
27			from submissions.tasks import SubmissionTaskMixin
28
29			from ..helpers import get_manager_auth
30			from ..models import Submission as USISubmission
31
32			# Get an instance of a logger
33			logger = get_task_logger(__name__)
34
35			# define a decouple config object
36			settings_dir = os.path.join(settings.BASE_DIR, 'image')
37			config = AutoConfig(search_path=settings_dir)
38
39			# a threshold of days to determine a very long task
40			MAX_DAYS = 5
41
42
43			# HINT: how this class could be similar to SubmissionHelper?
44			class FetchStatusHelper():
45			"""Helper class to deal with submission data"""
46
47			# define my class attributes
48			def __init__(self, usi_submission):
49			"""
50			Helper function to have info for a biosample.models.Submission
51
52			Args:
53			usi_submission (biosample.models.Submission): a biosample
54			model Submission instance
55			"""
56
57			# ok those are my default class attributes
58			self.usi_submission = usi_submission
59			self.uid_submission = usi_submission.uid_submission
60
61			# here are pyUSIrest object
62			self.auth = get_manager_auth()
63			self.root = pyUSIrest.client.Root(self.auth)
64
65			# here I will track the biosample submission
66			self.submission_name = self.usi_submission.usi_submission_name
67			self.submission = self.root.get_submission_by_name(
68			submission_name=self.submission_name)
69
70			def check_submission_status(self):
71			"""Check submission status, finalize submission, check errors etc"""
72
73			# reload submission status
74			self.usi_submission.refresh_from_db()
75
76			if self.usi_submission.status != SUBMITTED:
77			# someone else has taken this task and done something. Ignore!
78			logger.warning("Ignoring submission %s current status is %s" % (
79			self.usi_submission, self.usi_submission.get_status_display()))
80			return
81
82			logger.debug("Checking status for '%s'" % (
83			self.submission_name))
84
85			# Update submission status if completed
86			if self.submission.status == 'Completed':
87			# fetch biosample ids with a proper function
88			self.complete()
89
90			elif self.submission.status == 'Draft':
91			# check for a long task
92			if self.submission_has_issues():
93			# return to the caller. I've just marked the submission with
94			# errors and sent a mail to the user
95			return
96
97			# check validation. If it is ok, finalize submission
98			status = self.submission.get_status()
99
100			# this mean validation statuses, I want to see completed in all
101			# samples
102			if len(status) == 1 and 'Complete' in status:
103			# check for errors and eventually finalize
104			self.finalize()
105
106			else:
107			logger.warning(
108			"Biosample validation is not completed yet (%s)" %
109			(status))
110
111			elif self.submission.status == 'Submitted':
112			# check for a long task
113			if self.submission_has_issues():
114			# return to the caller. I've just marked the submission with
115			# errors and sent a mail to the user
116			return
117
118			logger.info(
119			"Submission '%s' is '%s'. Waiting for biosample ids" % (
120			self.submission_name,
121			self.submission.status))
122
123			# debug submission status
124			document = self.submission.follow_url(
125			"processingStatusSummary", self.auth)
126
127			logger.debug(
128			"Current status for submission '%s' is '%s'" % (
129			self.submission_name, document.data))
130
131			else:
132			# HINT: thrown an exception?
133			logger.warning("Unknown status '%s' for submission '%s'" % (
134			self.submission.status,
135			self.submission_name))
136
137			logger.debug("Checking status for '%s' completed" % (
138			self.submission_name))
139
140			def submission_has_issues(self):
141			"""
142			Check that biosample submission has not issues. For example, that
143			it will remain in the same status for a long time
144
145			Returns:
146			bool: True if an issue is detected
147			"""
148
149			logger.debug(
150			"Check if submission '%s' remained in the same status "
151			"for a long time" % (
152			self.submission_name))
153
154			if (timezone.now() - self.usi_submission.updated_at).days > MAX_DAYS:
155			message = (
156			"Biosample submission '%s' remained with the same status "
157			"for more than %s days. Please report it to InjectTool "
158			"team" % (self.submission_name, MAX_DAYS))
159
160			self.usi_submission.status = ERROR
161			self.usi_submission.message = message
162			self.usi_submission.save()
163
164			logger.error(
165			"Errors for submission: %s" % (
166			self.submission_name))
167			logger.error(message)
168
169			return True
170
171			else:
172			return False
173
174			def __sample_has_errors(self, sample, table, pk):
175			"""
176			Helper metod to mark a (animal/sample) with its own errors. Table
177			sould be Animal or Sample to update the approriate object. Sample
178			is a USI sample object
179
180			Args:
181			sample (pyUSIrest.client.sample): a USI sample object
182			table (str): ``Animal`` or ``Sample``, mean the table where this
183			object should be searched
184			pk (int): table primary key
185			"""
186
187			# get sample/animal object relying on table name and pk
188			sample_obj = get_model_object(table, pk)
189
190			sample_obj.name.status = NEED_REVISION
191			sample_obj.name.save()
192
193			# get a USI validation result
194			validation_result = sample.get_validation_result()
195
196			# TODO: should I store validation_result error in validation tables?
197			errorMessages = validation_result.errorMessages
198
199			# return an error for each object
200			return {str(sample_obj): errorMessages}
201
202			def finalize(self):
203			"""Finalize a submission by closing document and send it to
204			biosample"""
205
206			logger.debug("Finalizing submission '%s'" % (
207			self.submission_name))
208
209			# get errors for a submission
210			errors = self.submission.has_errors()
211
212			# collect all error messages in a list
213			messages = []
214
215			if True in errors:
216			# get sample with errors then update database
217			samples = self.submission.get_samples(has_errors=True)
218
219			for sample in samples:
220			# derive pk and table from alias
221			table, pk = parse_image_alias(sample.alias)
222
223			# need to check if this sample/animals has errors or not
224			if sample.has_errors():
225			logger.warning(
226			"%s in table %s has errors!!!" % (sample, table))
227
228			# mark this sample since has problems
229			errorMessages = self.__sample_has_errors(
230			sample, table, pk)
231
232			# append this into error messages list
233			messages.append(errorMessages)
234
235			# if a sample has no errors, status will be the same
236
237			logger.error(
238			"Errors for submission: '%s'" % (self.submission_name))
239			logger.error("Fix them, then finalize")
240
241			# report error
242			message = json.dumps(messages, indent=2)
243
244			# Update status for biosample.models.Submission
245			self.usi_submission.status = NEED_REVISION
246			self.usi_submission.message = message
247			self.usi_submission.save()
248
249			else:
250			# raising an exception while finalizing will result
251			# in a failed task.
252			# TODO: model and test exception in finalization
253			self.submission.finalize()
254
255			def complete(self):
256			"""Complete a submission and fetch name objects"""
257
258			logger.debug("Completing submission '%s'" % (
259			self.submission_name))
260
261			for sample in self.submission.get_samples():
262			# derive pk and table from alias
263			table, pk = parse_image_alias(sample.alias)
264
265			# if no accession, return without doing anything
266			if sample.accession is None:
267			logger.error("No accession found for sample '%s'" % (sample))
268			logger.error("Ignoring submission '%s'" % (self.submission))
269			return
270
271			# get sample/animal object relying on table name and pk
272			sample_obj = get_model_object(table, pk)
273
274			# update statuses
275			sample_obj.name.status = COMPLETED
276			sample_obj.name.biosample_id = sample.accession
277			sample_obj.name.save()
278
279			# update submission
280			self.usi_submission.status = COMPLETED
281			self.usi_submission.message = "Successful submission into biosample"
282			self.usi_submission.save()
283
284			logger.info(
285			"Submission %s is now completed and recorded into UID" % (
286			self.submission))
287
288
289			class FetchStatusTask(NotifyAdminTaskMixin, ExclusiveTask):
290			name = "Fetch USI status"
291			description = """Fetch biosample using USI API"""
292			lock_id = "FetchStatusTask"
293
294			def run(self):
295			"""
296			This function is called when delay is called. It will acquire a lock
297			in redis, so those tasks are mutually exclusive
298
299			Returns:
300			str: success if everything is ok. Different messages if task is
301			already running or exception is caught"""
302
303			# debugging instance
304			self.debug_task()
305
306			# do stuff and return something
307			return self.fetch_status()
308
309			def fetch_status(self):
310			"""
311			Fetch status from pending submissions. Called from
312			:py:meth:`run`, handles exceptions from USI, select
313			all :py:class:`Submission <image_app.models.Submission>` objects
314			with :py:const:`SUBMITTED <common.constants.SUBMITTED>` status
315			from :ref:`UID <The Unified Internal Database>` and call
316			:py:meth:`fetch_queryset` with this data
317			"""
318
319			logger.info("fetch_status started")
320
321			# search for submission with SUBMITTED status. Other submission are
322			# not yet finalized. This function need to be called by exclusives
323			# tasks
324			qs = Submission.objects.filter(status=SUBMITTED)
325
326			# check for queryset length
327			if qs.count() != 0:
328			try:
329			# fetch biosample status
330			self.fetch_queryset(qs)
331
332			# retry a task under errors
333			# http://docs.celeryproject.org/en/latest/userguide/tasks.html#retrying
334			except ConnectionError as exc:
335			raise self.retry(exc=exc)
336
337			else:
338			logger.debug("No pending submission in UID database")
339
340			# debug
341			logger.info("fetch_status completed")
342
343			return "success"
344
345			# a function to retrieve biosample submission
346			def fetch_queryset(self, queryset):
347			"""Fetch biosample against a queryset (a list of
348			:py:const:`SUBMITTED <common.constants.SUBMITTED>`
349			:py:class:`Submission <image_app.models.Submission>` objects). Iterate
350			through submission to get USI info. Calls
351			:py:class:`FetchStatusHelper`
352			"""
353
354			logger.info("Searching for submissions into biosample")
355
356			for uid_submission in queryset:
357			usi_submissions = USISubmission.objects.filter(
358			uid_submission=uid_submission,
359			status=SUBMITTED)
360
361			# HINT: fetch statuses using tasks?
362			for usi_submission in usi_submissions:
363			status_helper = FetchStatusHelper(usi_submission)
364			status_helper.check_submission_status()
365
366			# set the final status for a submission like SubmissionCompleteTask
367			retrievalcomplete = RetrievalCompleteTask()
368
369			# assign kwargs to chord
370			res = retrievalcomplete.delay(uid_submission_id=uid_submission.id)
371
372			logger.info(
373			"Start RetrievalCompleteTask process for %s with task %s" % (
374			uid_submission,
375			res.task_id))
376
377			logger.info("fetch_queryset completed")
378
379
380			class RetrievalCompleteTask(SubmissionTaskMixin, BaseTask):
381			"""Update submission status after fetching status"""
382
383			name = "Complete Retrieval Process"
384			description = """Check submission status after retrieval nd update stuff"""
385			action = "biosample retrieval"
386
387			def run(self, args, *kwargs):
388			"""Fetch submission data and then update UID submission status"""
389
390			# get UID submission
391			uid_submission = self.get_uid_submission(kwargs['uid_submission_id'])
392
393			# fetch data from database
394			submission_qs = USISubmission.objects.filter(
395			uid_submission=uid_submission)
396
397			# annotate biosample submission by statuses
398			statuses = {}
399
400			for res in submission_qs.values('status').annotate(
401			count=Count('status')):
402			statuses[res['status']] = res['count']
403
404			if SUBMITTED in statuses:
405			# ignoring the other models. No errors thrown until there is
406			# as SUBMITTED USISubmission
407			logger.info("Submission %s not yet finished" % uid_submission)
408
409			return "success"
410
411			# if there is ANY errors in biosample.models.Submission for a
412			# particoular submission, I will mark it as ERROR
413			elif ERROR in statuses:
414			# submission failed
415			logger.info("Submission %s failed" % uid_submission)
416
417			self.update_message(uid_submission, submission_qs, ERROR)
418
419			# send a mail to the user
420			uid_submission.owner.email_user(
421			"Error in biosample submission %s" % (
422			uid_submission.id),
423			("Something goes wrong with biosample submission. Please "
424			"report this to InjectTool team\n\n"
425			"%s" % uid_submission.message),
426			)
427
428			# check if submission need revision
429			elif NEED_REVISION in statuses:
430			# submission failed
431			logger.info("Submission %s failed" % uid_submission)
432
433			self.update_message(uid_submission, submission_qs, NEED_REVISION)
434
435			# send a mail to the user
436			uid_submission.owner.email_user(
437			"Error in biosample submission %s" % (
438			uid_submission.id),
439			"Some items needs revision:\n\n" + uid_submission.message,
440			)
441
442			elif COMPLETED in statuses and len(statuses) == 1:
443			# if all status are complete, the submission is completed
444			logger.info(
445			"Submission %s completed with success" % uid_submission)
446
447			self.update_message(uid_submission, submission_qs, COMPLETED)
448
449			return "success"
450
451			def update_message(self, uid_submission, submission_qs, status):
452			"""Read biosample.models.Submission message and set
453			image_app.models.Submission message"""
454
455			# get error messages for submission
456			message = []
457
458			for submission in submission_qs.filter(status=status):
459			message.append(submission.message)
460
461			self.update_submission_status(
462			uid_submission, status, "\n".join(set(message)))
463
464
465			# register explicitly tasks
466			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
467			celery_app.tasks.register(FetchStatusTask)
468			celery_app.tasks.register(RetrievalCompleteTask)
469

cnr-ibba / IMAGE-InjectTool

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RetrievalCompleteTask.update_message() A

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