biosample.tasks.cleanup.check_orphan_sample() - Code Metrics - Inspection of ":sparkles: clean up orphaned BioSample IDs" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — devel (#90)

by Paolo

created 2020-01-27 16:17 UTC

biosample.tasks.cleanup.check_orphan_sample() A

↳ Parent: biosample.tasks.cleanup

Complexity

Conditions

Size

Total Lines	22
Code Lines	14

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	14
dl	0
loc	22
rs	9.7
c	0
b	0
f	0
cc	4
nop	1

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Nov 14 16:06:10 2019

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

import asyncio
import aiohttp
import requests

from yarl import URL
from multidict import MultiDict

from datetime import timedelta
from celery.utils.log import get_task_logger
from django.utils import timezone
from django.utils.dateparse import parse_date

from common.constants import COMPLETED, BIOSAMPLE_URL
from common.helpers import format_attribute
from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task
from image.celery import app as celery_app
from uid.models import Animal as UIDAnimal, Sample as UIDSample, DictSpecie

from ..helpers import get_manager_auth
from ..models import Submission, OrphanSample, ManagedTeam

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

# defining constants. Clean biosample database data after
CLEANUP_DAYS = 30

# this is the timedelta which I want to add to relaseDate to remove samples
RELEASE_TIMEDELTA = timedelta(days=365*1000)

# Setting page size for biosample requests
PAGE_SIZE = 20

PARAMS = MultiDict([
    ('size', PAGE_SIZE),
    ('filter', 'attr:project:IMAGE'),
    ])
HEADERS = {
        'Accept': 'application/hal+json',
    }


class CleanUpTask(NotifyAdminTaskMixin, BaseTask):
    """Perform biosample.models cleanup by selecting old completed submission
    and remove them from database"""

    name = "Clean biosample models"
    description = """Clean biosample models"""

    @exclusive_task(task_name="Clean biosample models", lock_id="CleanUpTask")
    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"""

        logger.info("Clean biosample.database started")

        # get an interval starting from now
        interval = timezone.now() - timedelta(days=CLEANUP_DAYS)

        # select all COMPLETED object older than interval
        qs = Submission.objects.filter(
            updated_at__lt=interval,
            status=COMPLETED)

        logger.info(
            "Deleting %s biosample.models.Submission objects" % qs.count())

        # delete all old objects
        qs.delete()

        # debug
        logger.info("Clean biosample.database completed")

        return "success"


async def fetch(session, url=BIOSAMPLE_URL, params=PARAMS):
    """Get a page from biosamples"""

    # define a URL with yarl
    url = URL(url)
    url = url.update_query(params)

    async with session.get(url, headers=HEADERS) as response:
        return await response.json()


async def parse_samples_data(data, managed_domains):
    # get samples objects
    try:
        samples = data['_embedded']['samples']

        for sample in samples:
            # filter out unmanaged records
            if sample['domain'] not in managed_domains:
                logger.warning("Ignoring %s" % (sample['name']))
                continue

            # otherwise return to the caller the sample
            yield sample

    except KeyError as exc:
        # logger exception. With repr() the exception name is rendered
        logger.error(repr(exc))
        logger.warning("error while parsing samples")
        logger.warning(data)


async def get_samples(
        url=BIOSAMPLE_URL,
        params=PARAMS,
        managed_domains=[]):
    async with aiohttp.ClientSession() as session:
        data = await fetch(session, url, params)

        # process data and filter samples I own
        # https://stackoverflow.com/a/47378063
        async for sample in parse_samples_data(data, managed_domains):
            yield sample

        tasks = []

        # get pages
        totalPages = data['page']['totalPages']

        # generate new awaitable objects
        for page in range(1, totalPages):
            # get a new param object to edit
            my_params = params.copy()

            # edit a multidict object
            my_params.update(page=page)

            # track the new awaitable object
            tasks.append(fetch(session, url, my_params))

        # Run awaitable objects in the aws set concurrently.
        # Return an iterator of Future objects.
        for task in asyncio.as_completed(tasks):
            # read data
            data = await task

            # process data and filter samples I own
            # https://stackoverflow.com/a/47378063
            async for sample in parse_samples_data(data, managed_domains):
                yield sample


async def check_samples():
    # I need an pyUSIrest.auth.Auth object to filter out records that don't
    # belong to me
    auth = get_manager_auth()
    managed_domains = auth.get_domains()

    async for sample in get_samples(managed_domains=managed_domains):
        check_orphan_sample(sample)


def check_orphan_sample(sample):
    animal_qs = UIDAnimal.objects.filter(
        biosample_id=sample['accession'])

    sample_qs = UIDSample.objects.filter(
        biosample_id=sample['accession'])

    if animal_qs.exists() or sample_qs.exists():
        logger.debug("Sample %s is tracked in UID" % (sample['accession']))

    else:
        # get a managed team
        team = ManagedTeam.objects.get(name=sample["domain"])

        # Create an orphan sample
        orphan, created = OrphanSample.objects.get_or_create(
            biosample_id=sample['accession'],
            name=sample['name'],
            team=team)

        if created:
            logger.warning("Add %s to orphan samples" % sample['accession'])


class SearchOrphanTask(NotifyAdminTaskMixin, BaseTask):
    """Search accross biosamples for objects not present in UID"""

    name = "Search Orphan BioSamples IDs"
    description = """Track BioSamples IDs not present in UID"""

    @exclusive_task(
        task_name=name, lock_id="SearchOrphanTask")
    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"""

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

        # create a loop object
        loop = asyncio.get_event_loop()

        # execute stuff
        try:
            loop.run_until_complete(check_samples())

        finally:
            # close loop
            loop.close()

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

        return "success"


def purge_orphan_samples():
    """A function to remove objects from OrphanSample table"""

    with requests.Session() as session:
        for orphan_sample in OrphanSample.objects.filter(
                ignore=False, removed=False):

            # define the url I need to check
            url = "/".join([BIOSAMPLE_URL, orphan_sample.biosample_id])

            # read data from url
            response = session.get(url)
            data = response.json()

            # I need a new data dictionary to submit
            new_data = dict()

            # I suppose the accession exists, since I found this sample
            # using accession [biosample.id]
            new_data['accession'] = data.get(
                'accession', orphan_sample.biosample_id)

            new_data['alias'] = data['name']

            new_data['title'] = data['characteristics']['title'][0]['text']

            # this will be the most important attribute
            new_data['releaseDate'] = str(
                parse_date(data['releaseDate']) + RELEASE_TIMEDELTA)

            new_data['taxonId'] = data['taxId']

            # need to determine taxon as
            new_data['taxon'] = DictSpecie.objects.get(
                term__endswith=data['taxId']).label

            new_data['attributes'] = dict()

            # set project again
            new_data['attributes']["Project"] = format_attribute(
                value="IMAGE")

            # return new biosample data
            yield new_data


# register explicitly tasks
# https://github.com/celery/celery/issues/3744#issuecomment-271366923
celery_app.tasks.register(CleanUpTask)
celery_app.tasks.register(SearchOrphanTask)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Thu Nov 14 16:06:10 2019
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import asyncio
10			import aiohttp
11			import requests
12
13			from yarl import URL
14			from multidict import MultiDict
15
16			from datetime import timedelta
17			from celery.utils.log import get_task_logger
18			from django.utils import timezone
19			from django.utils.dateparse import parse_date
20
21			from common.constants import COMPLETED, BIOSAMPLE_URL
22			from common.helpers import format_attribute
23			from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task
24			from image.celery import app as celery_app
25			from uid.models import Animal as UIDAnimal, Sample as UIDSample, DictSpecie
26
27			from ..helpers import get_manager_auth
28			from ..models import Submission, OrphanSample, ManagedTeam
29
30			# Get an instance of a logger
31			logger = get_task_logger(__name__)
32
33			# defining constants. Clean biosample database data after
34			CLEANUP_DAYS = 30
35
36			# this is the timedelta which I want to add to relaseDate to remove samples
37			RELEASE_TIMEDELTA = timedelta(days=365*1000)
38
39			# Setting page size for biosample requests
40			PAGE_SIZE = 20
41
42			PARAMS = MultiDict([
43			('size', PAGE_SIZE),
44			('filter', 'attr:project:IMAGE'),
45			])
46			HEADERS = {
47			'Accept': 'application/hal+json',
48			}
49
50
51			class CleanUpTask(NotifyAdminTaskMixin, BaseTask):
52			"""Perform biosample.models cleanup by selecting old completed submission
53			and remove them from database"""
54
55			name = "Clean biosample models"
56			description = """Clean biosample models"""
57
58			@exclusive_task(task_name="Clean biosample models", lock_id="CleanUpTask")
59			def run(self):
60			"""
61			This function is called when delay is called. It will acquire a lock
62			in redis, so those tasks are mutually exclusive
63
64			Returns:
65			str: success if everything is ok. Different messages if task is
66			already running or exception is caught"""
67
68			logger.info("Clean biosample.database started")
69
70			# get an interval starting from now
71			interval = timezone.now() - timedelta(days=CLEANUP_DAYS)
72
73			# select all COMPLETED object older than interval
74			qs = Submission.objects.filter(
75			updated_at__lt=interval,
76			status=COMPLETED)
77
78			logger.info(
79			"Deleting %s biosample.models.Submission objects" % qs.count())
80
81			# delete all old objects
82			qs.delete()
83
84			# debug
85			logger.info("Clean biosample.database completed")
86
87			return "success"
88
89
90			async def fetch(session, url=BIOSAMPLE_URL, params=PARAMS):
91			"""Get a page from biosamples"""
92
93			# define a URL with yarl
94			url = URL(url)
95			url = url.update_query(params)
96
97			async with session.get(url, headers=HEADERS) as response:
98			return await response.json()
99
100
101			async def parse_samples_data(data, managed_domains):
102			# get samples objects
103			try:
104			samples = data['_embedded']['samples']
105
106			for sample in samples:
107			# filter out unmanaged records
108			if sample['domain'] not in managed_domains:
109			logger.warning("Ignoring %s" % (sample['name']))
110			continue
111
112			# otherwise return to the caller the sample
113			yield sample
114
115			except KeyError as exc:
116			# logger exception. With repr() the exception name is rendered
117			logger.error(repr(exc))
118			logger.warning("error while parsing samples")
119			logger.warning(data)
120
121
122			async def get_samples(
123			url=BIOSAMPLE_URL,
124			params=PARAMS,
125			managed_domains=[]):
126			async with aiohttp.ClientSession() as session:
127			data = await fetch(session, url, params)
128
129			# process data and filter samples I own
130			# https://stackoverflow.com/a/47378063
131			async for sample in parse_samples_data(data, managed_domains):
132			yield sample
133
134			tasks = []
135
136			# get pages
137			totalPages = data['page']['totalPages']
138
139			# generate new awaitable objects
140			for page in range(1, totalPages):
141			# get a new param object to edit
142			my_params = params.copy()
143
144			# edit a multidict object
145			my_params.update(page=page)
146
147			# track the new awaitable object
148			tasks.append(fetch(session, url, my_params))
149
150			# Run awaitable objects in the aws set concurrently.
151			# Return an iterator of Future objects.
152			for task in asyncio.as_completed(tasks):
153			# read data
154			data = await task
155
156			# process data and filter samples I own
157			# https://stackoverflow.com/a/47378063
158			async for sample in parse_samples_data(data, managed_domains):
159			yield sample
160
161
162			async def check_samples():
163			# I need an pyUSIrest.auth.Auth object to filter out records that don't
164			# belong to me
165			auth = get_manager_auth()
166			managed_domains = auth.get_domains()
167
168			async for sample in get_samples(managed_domains=managed_domains):
169			check_orphan_sample(sample)
170
171
172			def check_orphan_sample(sample):
173			animal_qs = UIDAnimal.objects.filter(
174			biosample_id=sample['accession'])
175
176			sample_qs = UIDSample.objects.filter(
177			biosample_id=sample['accession'])
178
179			if animal_qs.exists() or sample_qs.exists():
180			logger.debug("Sample %s is tracked in UID" % (sample['accession']))
181
182			else:
183			# get a managed team
184			team = ManagedTeam.objects.get(name=sample["domain"])
185
186			# Create an orphan sample
187			orphan, created = OrphanSample.objects.get_or_create(
188			biosample_id=sample['accession'],
189			name=sample['name'],
190			team=team)
191
192			if created:
193			logger.warning("Add %s to orphan samples" % sample['accession'])
194
195
196			class SearchOrphanTask(NotifyAdminTaskMixin, BaseTask):
197			"""Search accross biosamples for objects not present in UID"""
198
199			name = "Search Orphan BioSamples IDs"
200			description = """Track BioSamples IDs not present in UID"""
201
202			@exclusive_task(
203			task_name=name, lock_id="SearchOrphanTask")
204			def run(self):
205			"""
206			This function is called when delay is called. It will acquire a lock
207			in redis, so those tasks are mutually exclusive
208
209			Returns:
210			str: success if everything is ok. Different messages if task is
211			already running or exception is caught"""
212
213			logger.info("%s started" % (self.name))
214
215			# create a loop object
216			loop = asyncio.get_event_loop()
217
218			# execute stuff
219			try:
220			loop.run_until_complete(check_samples())
221
222			finally:
223			# close loop
224			loop.close()
225
226			# debug
227			logger.info("%s completed" % (self.name))
228
229			return "success"
230
231
232			def purge_orphan_samples():
233			"""A function to remove objects from OrphanSample table"""
234
235			with requests.Session() as session:
236			for orphan_sample in OrphanSample.objects.filter(
237			ignore=False, removed=False):
238
239			# define the url I need to check
240			url = "/".join([BIOSAMPLE_URL, orphan_sample.biosample_id])
241
242			# read data from url
243			response = session.get(url)
244			data = response.json()
245
246			# I need a new data dictionary to submit
247			new_data = dict()
248
249			# I suppose the accession exists, since I found this sample
250			# using accession [biosample.id]
251			new_data['accession'] = data.get(
252			'accession', orphan_sample.biosample_id)
253
254			new_data['alias'] = data['name']
255
256			new_data['title'] = data['characteristics']['title'][0]['text']
257
258			# this will be the most important attribute
259			new_data['releaseDate'] = str(
260			parse_date(data['releaseDate']) + RELEASE_TIMEDELTA)
261
262			new_data['taxonId'] = data['taxId']
263
264			# need to determine taxon as
265			new_data['taxon'] = DictSpecie.objects.get(
266			term__endswith=data['taxId']).label
267
268			new_data['attributes'] = dict()
269
270			# set project again
271			new_data['attributes']["Project"] = format_attribute(
272			value="IMAGE")
273
274			# return new biosample data
275			yield new_data
276
277
278			# register explicitly tasks
279			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
280			celery_app.tasks.register(CleanUpTask)
281			celery_app.tasks.register(SearchOrphanTask)
282

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#90)

biosample.tasks.cleanup.check_orphan_sample() A

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