biosample.tasks.retrieval.RetrievalCompleteTask.update_validationsummary() - Code Metrics - Inspection of ":bookmark: Bump version: 0.9.4.dev0 → 0.9.4" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

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Push — master ( bd2622...f167a9 )

by Paolo

created 2020-03-03 14:46 UTC

RetrievalCompleteTask.update_validationsummary() A

↳ Parent: biosample.tasks.retrieval

Complexity

Conditions

Size

Total Lines	6
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	3
dl	0
loc	6
rs	10
c	0
b	0
f	0
cc	1
nop	2

#!/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 collections import Counter, defaultdict

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

import pyUSIrest.usi
import pyUSIrest.exceptions

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

from image.celery import app as celery_app
from uid.helpers import parse_image_alias, get_model_object
from uid.models import Submission
from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task
from common.constants import ERROR, NEED_REVISION, SUBMITTED, COMPLETED
from submissions.tasks import SubmissionTaskMixin
from validation.models import ValidationResult, ValidationSummary

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.usi.Root(self.auth)

        # here I will track the biosample submission
        self.submission_name = self.usi_submission.usi_submission_name

        logger.info(
            "Getting info for usi submission '%s'" % (self.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.info("Submission '%s' is currently '%s'" % (
            self.submission_name, self.submission.status))

        # 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()

            # write status into database
            self.usi_submission.samples_status = dict(status)
            self.usi_submission.save()

            # 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))

        elif self.submission.status == 'Processing':
            # 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.debug(
                "Submission '%s' is '%s'. Still waiting from BioSamples" % (
                    self.submission_name,
                    self.submission.status))

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

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

        # track errors  in validation tables
        errorMessages = validation_result.errorMessages

        # since I validated this object, I have already a ValidationResult
        # object associated to my model
        sample_obj.validationresult.status = 'Error'
        sample_obj.validationresult.messages = [
            "%s: %s" % (k, v) for k, v in errorMessages.items()]
        sample_obj.validationresult.save()

        # need to update ValidationSummary table, since here I know if this
        # is a sample or an animal
        summary = self.uid_submission.validationsummary_set.filter(
            type=table.lower()).first()

        # now update query using django F function. Decrease pass count
        # an increase error count for this object
        # HINT: should I define message here?
        summary.pass_count = F('pass_count') - 1
        summary.error_count = F('error_count') + 1
        summary.issues_count = F('issues_count') + 1
        summary.save()

        # 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.info("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 biosample names"""

        logger.info("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.status = COMPLETED
            sample_obj.biosample_id = sample.accession
            sample_obj.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, BaseTask):
    name = "Fetch USI status"
    description = """Fetch biosample using USI API"""

    @exclusive_task(task_name="Fetch USI status", 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 <uid.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 pyUSIrest.exceptions.USIConnectionError 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 <uid.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:
            logger.info("getting USI submission for UID '%s'" % (
                uid_submission))
            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"""

        logger.info("RetrievalCompleteTask started")

        # 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)

            # update validationsummary
            self.update_validationsummary(uid_submission)

            self.update_message(uid_submission, submission_qs, ERROR)

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

            self.mail_to_owner(uid_submission, subject, body)

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

            # update validationsummary
            self.update_validationsummary(uid_submission)

            self.update_message(uid_submission, submission_qs, NEED_REVISION)

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

            self.mail_to_owner(uid_submission, subject, body)

        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)

        logger.info("RetrievalCompleteTask completed")

        return "success"

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

        # 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)),
            construct_message=True)

    def update_validationsummary(self, uid_submission):
        """Update validationsummary message after our USI submission is
        completed (with errors or not)"""

        self.__generic_validationsummary(uid_submission, "animal")
        self.__generic_validationsummary(uid_submission, "sample")

    def __generic_validationsummary(self, uid_submission, model):
        # when arriving here, I have processed the USI results and maybe
        # i have update validationresult accordingly
        logger.debug("Update validationsummary(%s) for %s" % (
            model, uid_submission))

        model_type = ContentType.objects.get(app_label='uid', model=model)

        # get validation results querysets
        model_qs = ValidationResult.objects.filter(
            submission=uid_submission,
            content_type=model_type,
            status="Error")

        # ok now prepare messages
        messages_counter = Counter()
        messages_ids = defaultdict(list)

        for item in model_qs:
            for message in item.messages:
                messages_counter.update([message])
                messages_ids[message].append(item.content_object.id)

        # ok preparing to update summary object
        model_summary = ValidationSummary.objects.get(
            submission=uid_submission, type=model)
        messages = []

        # create messages. No offending column since is not always possible
        # to determine a column from USI error. With this, I have a record
        # in ValidationSummary page, but I don't have a link to batch update
        # since is not possible to determine and change a column in my
        # data
        for message, count in messages_counter.items():
            messages.append({
                'message': message,
                'count': count,
                'ids': messages_ids[message],
                'offending_column': ''})

        model_summary.messages = messages
        model_summary.save()


# 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			from collections import Counter, defaultdict
12
13			from decouple import AutoConfig
14			from celery.utils.log import get_task_logger
15
16			import pyUSIrest.usi
17			import pyUSIrest.exceptions
18
19			from django.conf import settings
20			from django.contrib.contenttypes.models import ContentType
21			from django.db.models import Count, F
22			from django.utils import timezone
23
24			from image.celery import app as celery_app
25			from uid.helpers import parse_image_alias, get_model_object
26			from uid.models import Submission
27			from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task
28			from common.constants import ERROR, NEED_REVISION, SUBMITTED, COMPLETED
29			from submissions.tasks import SubmissionTaskMixin
30			from validation.models import ValidationResult, ValidationSummary
31
32			from ..helpers import get_manager_auth
33			from ..models import Submission as USISubmission
34
35			# Get an instance of a logger
36			logger = get_task_logger(__name__)
37
38			# define a decouple config object
39			settings_dir = os.path.join(settings.BASE_DIR, 'image')
40			config = AutoConfig(search_path=settings_dir)
41
42			# a threshold of days to determine a very long task
43			MAX_DAYS = 5
44
45
46			# HINT: how this class could be similar to SubmissionHelper?
47			class FetchStatusHelper():
48			"""Helper class to deal with submission data"""
49
50			# define my class attributes
51			def __init__(self, usi_submission):
52			"""
53			Helper function to have info for a biosample.models.Submission
54
55			Args:
56			usi_submission (biosample.models.Submission): a biosample
57			model Submission instance
58			"""
59
60			# ok those are my default class attributes
61			self.usi_submission = usi_submission
62			self.uid_submission = usi_submission.uid_submission
63
64			# here are pyUSIrest object
65			self.auth = get_manager_auth()
66			self.root = pyUSIrest.usi.Root(self.auth)
67
68			# here I will track the biosample submission
69			self.submission_name = self.usi_submission.usi_submission_name
70
71			logger.info(
72			"Getting info for usi submission '%s'" % (self.submission_name))
73			self.submission = self.root.get_submission_by_name(
74			submission_name=self.submission_name)
75
76			def check_submission_status(self):
77			"""Check submission status, finalize submission, check errors etc"""
78
79			# reload submission status
80			self.usi_submission.refresh_from_db()
81
82			if self.usi_submission.status != SUBMITTED:
83			# someone else has taken this task and done something. Ignore!
84			logger.warning("Ignoring submission %s current status is %s" % (
85			self.usi_submission, self.usi_submission.get_status_display()))
86			return
87
88			logger.info("Submission '%s' is currently '%s'" % (
89			self.submission_name, self.submission.status))
90
91			# Update submission status if completed
92			if self.submission.status == 'Completed':
93			# fetch biosample ids with a proper function
94			self.complete()
95
96			elif self.submission.status == 'Draft':
97			# check for a long task
98			if self.submission_has_issues():
99			# return to the caller. I've just marked the submission with
100			# errors and sent a mail to the user
101			return
102
103			# check validation. If it is ok, finalize submission
104			status = self.submission.get_status()
105
106			# write status into database
107			self.usi_submission.samples_status = dict(status)
108			self.usi_submission.save()
109
110			# this mean validation statuses, I want to see completed in all
111			# samples
112			if len(status) == 1 and 'Complete' in status:
113			# check for errors and eventually finalize
114			self.finalize()
115
116			else:
117			logger.warning(
118			"Biosample validation is not completed yet (%s)" %
119			(status))
120
121			elif self.submission.status == 'Submitted':
122			# check for a long task
123			if self.submission_has_issues():
124			# return to the caller. I've just marked the submission with
125			# errors and sent a mail to the user
126			return
127
128			logger.info(
129			"Submission '%s' is '%s'. Waiting for biosample ids" % (
130			self.submission_name,
131			self.submission.status))
132
133			# debug submission status
134			document = self.submission.follow_url(
135			"processingStatusSummary", self.auth)
136
137			logger.debug(
138			"Current status for submission '%s' is '%s'" % (
139			self.submission_name, document.data))
140
141			elif self.submission.status == 'Processing':
142			# check for a long task
143			if self.submission_has_issues():
144			# return to the caller. I've just marked the submission with
145			# errors and sent a mail to the user
146			return
147
148			logger.debug(
149			"Submission '%s' is '%s'. Still waiting from BioSamples" % (
150			self.submission_name,
151			self.submission.status))
152
153			else:
154			# HINT: thrown an exception?
155			logger.warning("Unknown status '%s' for submission '%s'" % (
156			self.submission.status,
157			self.submission_name))
158
159			logger.debug("Checking status for '%s' completed" % (
160			self.submission_name))
161
162			def submission_has_issues(self):
163			"""
164			Check that biosample submission has not issues. For example, that
165			it will remain in the same status for a long time
166
167			Returns:
168			bool: True if an issue is detected
169			"""
170
171			logger.debug(
172			"Check if submission '%s' remained in the same status "
173			"for a long time" % (
174			self.submission_name))
175
176			if (timezone.now() - self.usi_submission.updated_at).days > MAX_DAYS:
177			message = (
178			"Biosample submission '%s' remained with the same status "
179			"for more than %s days. Please report it to InjectTool "
180			"team" % (self.submission_name, MAX_DAYS))
181
182			self.usi_submission.status = ERROR
183			self.usi_submission.message = message
184			self.usi_submission.save()
185
186			logger.error(
187			"Errors for submission: %s" % (
188			self.submission_name))
189			logger.error(message)
190
191			return True
192
193			else:
194			return False
195
196			def sample_has_errors(self, sample, table, pk):
197			"""
198			Helper metod to mark a (animal/sample) with its own errors. Table
199			sould be Animal or Sample to update the approriate object. Sample
200			is a USI sample object
201
202			Args:
203			sample (pyUSIrest.usi.sample): a USI sample object
204			table (str): ``Animal`` or ``Sample``, mean the table where this
205			object should be searched
206			pk (int): table primary key
207			"""
208
209			# get sample/animal object relying on table name and pk
210			sample_obj = get_model_object(table, pk)
211
212			sample_obj.status = NEED_REVISION
213			sample_obj.save()
214
215			# get a USI validation result
216			validation_result = sample.get_validation_result()
217
218			# track errors in validation tables
219			errorMessages = validation_result.errorMessages
220
221			# since I validated this object, I have already a ValidationResult
222			# object associated to my model
223			sample_obj.validationresult.status = 'Error'
224			sample_obj.validationresult.messages = [
225			"%s: %s" % (k, v) for k, v in errorMessages.items()]
226			sample_obj.validationresult.save()
227
228			# need to update ValidationSummary table, since here I know if this
229			# is a sample or an animal
230			summary = self.uid_submission.validationsummary_set.filter(
231			type=table.lower()).first()
232
233			# now update query using django F function. Decrease pass count
234			# an increase error count for this object
235			# HINT: should I define message here?
236			summary.pass_count = F('pass_count') - 1
237			summary.error_count = F('error_count') + 1
238			summary.issues_count = F('issues_count') + 1
239			summary.save()
240
241			# return an error for each object
242			return {str(sample_obj): errorMessages}
243
244			def finalize(self):
245			"""Finalize a submission by closing document and send it to
246			biosample"""
247
248			logger.info("Finalizing submission '%s'" % (
249			self.submission_name))
250
251			# get errors for a submission
252			errors = self.submission.has_errors()
253
254			# collect all error messages in a list
255			messages = []
256
257			if True in errors:
258			# get sample with errors then update database
259			samples = self.submission.get_samples(has_errors=True)
260
261			for sample in samples:
262			# derive pk and table from alias
263			table, pk = parse_image_alias(sample.alias)
264
265			# need to check if this sample/animals has errors or not
266			if sample.has_errors():
267			logger.warning(
268			"%s in table %s has errors!!!" % (sample, table))
269
270			# mark this sample since has problems
271			errorMessages = self.sample_has_errors(
272			sample, table, pk)
273
274			# append this into error messages list
275			messages.append(errorMessages)
276
277			# if a sample has no errors, status will be the same
278
279			logger.error(
280			"Errors for submission: '%s'" % (self.submission_name))
281			logger.error("Fix them, then finalize")
282
283			# report error
284			message = json.dumps(messages, indent=2)
285
286			# Update status for biosample.models.Submission
287			self.usi_submission.status = NEED_REVISION
288			self.usi_submission.message = message
289			self.usi_submission.save()
290
291			else:
292			# raising an exception while finalizing will result
293			# in a failed task.
294			# TODO: model and test exception in finalization
295			self.submission.finalize()
296
297			def complete(self):
298			"""Complete a submission and fetch biosample names"""
299
300			logger.info("Completing submission '%s'" % (
301			self.submission_name))
302
303			for sample in self.submission.get_samples():
304			# derive pk and table from alias
305			table, pk = parse_image_alias(sample.alias)
306
307			# if no accession, return without doing anything
308			if sample.accession is None:
309			logger.error("No accession found for sample '%s'" % (sample))
310			logger.error("Ignoring submission '%s'" % (self.submission))
311			return
312
313			# get sample/animal object relying on table name and pk
314			sample_obj = get_model_object(table, pk)
315
316			# update statuses
317			sample_obj.status = COMPLETED
318			sample_obj.biosample_id = sample.accession
319			sample_obj.save()
320
321			# update submission
322			self.usi_submission.status = COMPLETED
323			self.usi_submission.message = "Successful submission into biosample"
324			self.usi_submission.save()
325
326			logger.info(
327			"Submission %s is now completed and recorded into UID" % (
328			self.submission))
329
330
331			class FetchStatusTask(NotifyAdminTaskMixin, BaseTask):
332			name = "Fetch USI status"
333			description = """Fetch biosample using USI API"""
334
335			@exclusive_task(task_name="Fetch USI status", lock_id="FetchStatusTask")
336			def run(self):
337			"""
338			This function is called when delay is called. It will acquire a lock
339			in redis, so those tasks are mutually exclusive
340
341			Returns:
342			str: success if everything is ok. Different messages if task is
343			already running or exception is caught"""
344
345			# debugging instance
346			self.debug_task()
347
348			# do stuff and return something
349			return self.fetch_status()
350
351			def fetch_status(self):
352			"""
353			Fetch status from pending submissions. Called from
354			:py:meth:`run`, handles exceptions from USI, select
355			all :py:class:`Submission <uid.models.Submission>` objects
356			with :py:const:`SUBMITTED <common.constants.SUBMITTED>` status
357			from :ref:`UID <The Unified Internal Database>` and call
358			:py:meth:`fetch_queryset` with this data
359			"""
360
361			logger.info("fetch_status started")
362
363			# search for submission with SUBMITTED status. Other submission are
364			# not yet finalized. This function need to be called by exclusives
365			# tasks
366			qs = Submission.objects.filter(status=SUBMITTED)
367
368			# check for queryset length
369			if qs.count() != 0:
370			try:
371			# fetch biosample status
372			self.fetch_queryset(qs)
373
374			# retry a task under errors
375			# http://docs.celeryproject.org/en/latest/userguide/tasks.html#retrying
376			except pyUSIrest.exceptions.USIConnectionError as exc:
377			raise self.retry(exc=exc)
378
379			else:
380			logger.debug("No pending submission in UID database")
381
382			# debug
383			logger.info("fetch_status completed")
384
385			return "success"
386
387			# a function to retrieve biosample submission
388			def fetch_queryset(self, queryset):
389			"""Fetch biosample against a queryset (a list of
390			:py:const:`SUBMITTED <common.constants.SUBMITTED>`
391			:py:class:`Submission <uid.models.Submission>` objects). Iterate
392			through submission to get USI info. Calls
393			:py:class:`FetchStatusHelper`
394			"""
395
396			logger.info("Searching for submissions into biosample")
397
398			for uid_submission in queryset:
399			logger.info("getting USI submission for UID '%s'" % (
400			uid_submission))
401			usi_submissions = USISubmission.objects.filter(
402			uid_submission=uid_submission,
403			status=SUBMITTED)
404
405			# HINT: fetch statuses using tasks?
406			for usi_submission in usi_submissions:
407			status_helper = FetchStatusHelper(usi_submission)
408			status_helper.check_submission_status()
409
410			# set the final status for a submission like SubmissionCompleteTask
411			retrievalcomplete = RetrievalCompleteTask()
412
413			# assign kwargs to chord
414			res = retrievalcomplete.delay(uid_submission_id=uid_submission.id)
415
416			logger.info(
417			"Start RetrievalCompleteTask process for '%s' "
418			"with task '%s'" % (uid_submission, res.task_id))
419
420			logger.info("fetch_queryset completed")
421
422
423			class RetrievalCompleteTask(SubmissionTaskMixin, BaseTask):
424			"""Update submission status after fetching status"""
425
426			name = "Complete Retrieval Process"
427			description = """Check submission status after retrieval nd update stuff"""
428			action = "biosample retrieval"
429
430			def run(self, args, *kwargs):
431			"""Fetch submission data and then update UID submission status"""
432
433			logger.info("RetrievalCompleteTask started")
434
435			# get UID submission
436			uid_submission = self.get_uid_submission(kwargs['uid_submission_id'])
437
438			# fetch data from database
439			submission_qs = USISubmission.objects.filter(
440			uid_submission=uid_submission)
441
442			# annotate biosample submission by statuses
443			statuses = {}
444
445			for res in submission_qs.values('status').annotate(
446			count=Count('status')):
447			statuses[res['status']] = res['count']
448
449			if SUBMITTED in statuses:
450			# ignoring the other models. No errors thrown until there is
451			# as SUBMITTED USISubmission
452			logger.info("Submission %s not yet finished" % uid_submission)
453
454			return "success"
455
456			# if there is ANY errors in biosample.models.Submission for a
457			# particoular submission, I will mark it as ERROR
458			elif ERROR in statuses:
459			# submission failed
460			logger.info("Submission %s failed" % uid_submission)
461
462			# update validationsummary
463			self.update_validationsummary(uid_submission)
464
465			self.update_message(uid_submission, submission_qs, ERROR)
466
467			# send a mail to the user
468			subject = "Error in biosample submission %s" % (
469			uid_submission.id)
470			body = (
471			"Something goes wrong with biosample submission. Please "
472			"report this to InjectTool team\n\n"
473			"%s" % uid_submission.message)
474
475			self.mail_to_owner(uid_submission, subject, body)
476
477			# check if submission need revision
478			elif NEED_REVISION in statuses:
479			# submission failed
480			logger.info("Submission %s failed" % uid_submission)
481
482			# update validationsummary
483			self.update_validationsummary(uid_submission)
484
485			self.update_message(uid_submission, submission_qs, NEED_REVISION)
486
487			# send a mail to the user
488			subject = "Error in biosample submission %s" % (
489			uid_submission.id)
490			body = "Some items needs revision:\n\n" + uid_submission.message
491
492			self.mail_to_owner(uid_submission, subject, body)
493
494			elif COMPLETED in statuses and len(statuses) == 1:
495			# if all status are complete, the submission is completed
496			logger.info(
497			"Submission %s completed with success" % uid_submission)
498
499			self.update_message(uid_submission, submission_qs, COMPLETED)
500
501			logger.info("RetrievalCompleteTask completed")
502
503			return "success"
504
505			def update_message(self, uid_submission, submission_qs, status):
506			"""Read biosample.models.Submission message and set
507			uid.models.Submission message relying on status"""
508
509			# get error messages for submission
510			message = []
511
512			for submission in submission_qs.filter(status=status):
513			message.append(submission.message)
514
515			self.update_submission_status(
516			uid_submission,
517			status,
518			"\n".join(set(message)),
519			construct_message=True)
520
521			def update_validationsummary(self, uid_submission):
522			"""Update validationsummary message after our USI submission is
523			completed (with errors or not)"""
524
525			self.__generic_validationsummary(uid_submission, "animal")
526			self.__generic_validationsummary(uid_submission, "sample")
527
528			def __generic_validationsummary(self, uid_submission, model):
529			# when arriving here, I have processed the USI results and maybe
530			# i have update validationresult accordingly
531			logger.debug("Update validationsummary(%s) for %s" % (
532			model, uid_submission))
533
534			model_type = ContentType.objects.get(app_label='uid', model=model)
535
536			# get validation results querysets
537			model_qs = ValidationResult.objects.filter(
538			submission=uid_submission,
539			content_type=model_type,
540			status="Error")
541
542			# ok now prepare messages
543			messages_counter = Counter()
544			messages_ids = defaultdict(list)
545
546			for item in model_qs:
547			for message in item.messages:
548			messages_counter.update([message])
549			messages_ids[message].append(item.content_object.id)
550
551			# ok preparing to update summary object
552			model_summary = ValidationSummary.objects.get(
553			submission=uid_submission, type=model)
554			messages = []
555
556			# create messages. No offending column since is not always possible
557			# to determine a column from USI error. With this, I have a record
558			# in ValidationSummary page, but I don't have a link to batch update
559			# since is not possible to determine and change a column in my
560			# data
561			for message, count in messages_counter.items():
562			messages.append({
563			'message': message,
564			'count': count,
565			'ids': messages_ids[message],
566			'offending_column': ''})
567
568			model_summary.messages = messages
569			model_summary.save()
570
571
572			# register explicitly tasks
573			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
574			celery_app.tasks.register(FetchStatusTask)
575			celery_app.tasks.register(RetrievalCompleteTask)
576

cnr-ibba / IMAGE-InjectTool

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RetrievalCompleteTask.update_validationsummary() A

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