biosample.tasks.cleanup.get_orphan_samples() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #12..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 066e8b...b9d652 )

by Paolo

created 2023-06-12 09:33 UTC

biosample.tasks.cleanup.get_orphan_samples() B

↳ Parent: biosample.tasks.cleanup

Complexity

Conditions

Size

Total Lines	76
Code Lines	33

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	33
dl	0
loc	76
rs	8.6213
c	0
b	0
f	0
cc	5
nop	1

How to fix Long Method

#!/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
import typing

from yarl import URL
from multidict import MultiDict
from itertools import islice

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, READY
from common.helpers import format_attribute, send_mail_to_admins
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 = 500

# a custom BIOSAMPLE URL with yarl
# ie. https://wwwdev.ebi.ac.uk/biosamples
BIOSAMPLE_BASE_URL = URL(BIOSAMPLE_URL).parent

BIOSAMPLE_SAMPLE_ENDPOINT = BIOSAMPLE_BASE_URL / "samples"
BIOSAMPLE_ACCESSION_ENDPOINT = BIOSAMPLE_BASE_URL / "accessions"

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

# define the orphan queryset once
ORPHAN_QS = OrphanSample.objects.filter(
    ignore=False,
    removed=False,
    status=READY
)


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 parse_json(response, url):
    """Helper function to parse json data"""

    try:
        return await response.json()

    except aiohttp.client_exceptions.ContentTypeError as exc:
        logger.error(repr(exc))
        logger.warning(
            "error while getting data from %s" % url)
        return {}


async def fetch_url(
        session, url, params=BIOSAMPLE_PARAMS, headers=None
        ) -> typing.Awaitable[dict]:
    """
    Fetch a generic url, read data as json and return a promise

    Parameters
    ----------
    session : aiohttp.ClientSession
        an async session object.
    url : str
        the desidered url
    params : MultiDict, optional
        Additional params for request. The default is BIOSAMPLE_PARAMS.
    headers : dict
        Additional HEADER information

    Returns
    -------
    typing.Awaitable[dict]
        json content of the page
    """

    # update URL params with yarl
    url = url.update_query(params)

    logger.debug(url)

    try:
        async with session.get(url, headers=headers) as response:
            # try to read json data
            return await parse_json(response, url)

    except aiohttp.client_exceptions.ServerDisconnectedError as exc:
        logger.error(repr(exc))
        logger.warning(
            "server disconnected during %s" % url)
        return {}


async def fecth_biosample(
        session: aiohttp.ClientSession,
        accession: str,
        base_url: URL = BIOSAMPLE_SAMPLE_ENDPOINT,
        headers: dict = HEADERS) -> typing.Awaitable[dict]:
    """
    Collect a single BioSample object from EBI

    Parameters
    ----------
    session : aiohttp.ClientSession
        an async session object.
    accession : str
        a BioSample accession ID.
    base_url : URL, optional
        DESCRIPTION. The default is BIOSAMPLE_BASE_URL.
    headers : dict, optional
        DESCRIPTION. The default is HEADERS.

    Returns
    -------
    typing.Awaitable[dict]
        A BioSample dictionary object
    """

    # define sample location
    url = base_url / accession

    return await fetch_url(session, url, None, headers)


async def filter_managed_biosamples(
        session: aiohttp.ClientSession,
        data: dict,
        managed_domains: list):
    """
    Parse data from a BioSample results page and yield samples managed
    by InjectTool users.

    Parameters
    ----------
    session : aiohttp.ClientSession
        an async session object.
    data : dict
        biosample data read from BIOSAMPLE_URL.
    managed_domains : list
        A list of AAP domains, as returned from
        :py:meth:`pyUSIrest.auth.Auth.get_domains`.

    Yields
    ------
    sample : dict
        a BioSample record.

    """
    tasks = []

    # get samples objects
    try:
        accessions = data['_embedded']['accessions']

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

    else:
        for accession in accessions:
            tasks.append(fecth_biosample(session, accession))

        for task in asyncio.as_completed(tasks):
            # read data
            sample = await task

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

            # otherwise return to the caller the sample
            yield sample


async def get_biosamples(
        url=BIOSAMPLE_ACCESSION_ENDPOINT,
        params=BIOSAMPLE_PARAMS,
        managed_domains=[]):
    """
    Get all samples from BioSamples for the IMAGE project. Fecth Biosample
    once, determines how many pages to request and return only accession
    records managed by InjectTool

    Parameters
    ----------
    url : str, optional
        The desidered URL. The default is BIOSAMPLE_ACCESSION_ENDPOINT.
    params : MultiDict, optional
        Additional params for request. The default is BIOSAMPLE_PARAMS.
    managed_domains : list
        A list of AAP domains, as returned from
        :py:meth:`pyUSIrest.auth.Auth.get_domains`.

    Yields
    ------
    sample : dict
        a BioSample record.

    """
    # limiting the number of connections
    # https://docs.aiohttp.org/en/stable/client_advanced.html
    connector = aiohttp.TCPConnector(limit=10, ttl_dns_cache=300)

    # https://stackoverflow.com/a/43857526
    async with aiohttp.ClientSession(connector=connector) as session:
        # get data for the first time to determine how many pages I have
        # to requests
        data = await fetch_url(session, url, params)

        # maybe the request had issues
        if data == {}:
            logger.debug("Got a result with no data")
            raise ConnectionError("Can't fetch biosamples for orphan samples")

        # process data and filter samples I own
        # https://stackoverflow.com/a/47378063
        async for sample in filter_managed_biosamples(
                session, data, managed_domains):
            # return a managed biosample record
            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_url(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

            # maybe the request had issues
            if data == {}:
                logger.debug("Got a result with no data")
                continue

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


async def check_samples():
    """
    Get all records from BioSamples submitted by the InjectTool manager auth
    managed domains, and call check_orphan_sample for each of them

    Returns
    -------
    None.

    """
    # 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_biosamples(managed_domains=managed_domains):
        check_orphan_sample(sample)


def check_orphan_sample(sample):
    """
    Get a BioSample record and check if such BioSampleId is registered into
    InjectTool UID. If Such record is not present, create a new
    :py:class:`biosample.models.OrphanSample` record object in the BioSample
    orphan table

    Parameters
    ----------
    sample : dict
        a BioSample record.

    Returns
    -------
    None.

    """
    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'])

            # set status for new object
            orphan.status = READY
            orphan.save()


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.new_event_loop()

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

        finally:
            # close loop
            loop.close()

        # Ok count orphan samples with a query
        orphan_count = ORPHAN_QS.count()

        if orphan_count > 0:
            email_subject = "Some entries in BioSamples are orphan"
            email_message = (
                "There are %s biosample ids which are not managed by "
                "InjectTool" % orphan_count)

            logger.warning(email_message)

            # Notify admins if I have orphan samples
            send_mail_to_admins(email_subject, email_message)

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

        return "success"


def get_orphan_samples(limit=None):
    """
    Iterate for all BioSample orphaned records which are not yet removed and
    are tracked for removal, get minimal data from BioSample and return a
    dictionary which can be used to patch a BioSample id with a new
    BioSample submission in order to remove a BioSamples record
    (publish the BioSample record after 1000 years from Now).

    Yields
    ------
    new_data : dict
        payload to submit to BioSample in order to remove a BioSamples record.
    """

    with requests.Session() as session:
        # get all biosamples candidate for a removal. Pay attention that
        # could be removed from different users
        qs = ORPHAN_QS.order_by('team__name', 'id')

        if limit:
            qs = islice(qs, limit)

        for orphan_sample in qs:
            # 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()

            # check status
            if response.status_code == 403:
                logger.error("Error for %s (%s): %s" % (
                    orphan_sample.biosample_id,
                    data['error'],
                    data['message'])
                )

                # this sample seems already removed
                continue

            # 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()

            new_data['description'] = "Removed by InjectTool"

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

            # return new biosample data
            yield {
                'data': new_data,
                'team': orphan_sample.team,
                'sample': orphan_sample,
            }


# 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			import typing
13
14			from yarl import URL
15			from multidict import MultiDict
16			from itertools import islice
17
18			from datetime import timedelta
19			from celery.utils.log import get_task_logger
20			from django.utils import timezone
21			from django.utils.dateparse import parse_date
22
23			from common.constants import COMPLETED, BIOSAMPLE_URL, READY
24			from common.helpers import format_attribute, send_mail_to_admins
25			from common.tasks import BaseTask, NotifyAdminTaskMixin, exclusive_task
26			from image.celery import app as celery_app
27			from uid.models import Animal as UIDAnimal, Sample as UIDSample, DictSpecie
28
29			from ..helpers import get_manager_auth
30			from ..models import Submission, OrphanSample, ManagedTeam
31
32			# Get an instance of a logger
33			logger = get_task_logger(__name__)
34
35			# defining constants. Clean biosample database data after
36			CLEANUP_DAYS = 30
37
38			# this is the timedelta which I want to add to relaseDate to remove samples
39			RELEASE_TIMEDELTA = timedelta(days=365*1000)
40
41			# Setting page size for biosample requests
42			PAGE_SIZE = 500
43
44			# a custom BIOSAMPLE URL with yarl
45			# ie. https://wwwdev.ebi.ac.uk/biosamples
46			BIOSAMPLE_BASE_URL = URL(BIOSAMPLE_URL).parent
47
48			BIOSAMPLE_SAMPLE_ENDPOINT = BIOSAMPLE_BASE_URL / "samples"
49			BIOSAMPLE_ACCESSION_ENDPOINT = BIOSAMPLE_BASE_URL / "accessions"
50
51			BIOSAMPLE_PARAMS = MultiDict([
52			('size', PAGE_SIZE),
53			('filter', 'attr:project:IMAGE'),
54			])
55			HEADERS = {
56			'Accept': 'application/hal+json',
57			}
58
59			# define the orphan queryset once
60			ORPHAN_QS = OrphanSample.objects.filter(
61			ignore=False,
62			removed=False,
63			status=READY
64			)
65
66
67			class CleanUpTask(NotifyAdminTaskMixin, BaseTask):
68			"""Perform biosample.models cleanup by selecting old completed submission
69			and remove them from database"""
70
71			name = "Clean biosample models"
72			description = """Clean biosample models"""
73
74			@exclusive_task(task_name="Clean biosample models", lock_id="CleanUpTask")
75			def run(self):
76			"""
77			This function is called when delay is called. It will acquire a lock
78			in redis, so those tasks are mutually exclusive
79
80			Returns:
81			str: success if everything is ok. Different messages if task is
82			already running or exception is caught"""
83
84			logger.info("Clean biosample.database started")
85
86			# get an interval starting from now
87			interval = timezone.now() - timedelta(days=CLEANUP_DAYS)
88
89			# select all COMPLETED object older than interval
90			qs = Submission.objects.filter(
91			updated_at__lt=interval,
92			status=COMPLETED)
93
94			logger.info(
95			"Deleting %s biosample.models.Submission objects" % qs.count())
96
97			# delete all old objects
98			qs.delete()
99
100			# debug
101			logger.info("Clean biosample.database completed")
102
103			return "success"
104
105
106			async def parse_json(response, url):
107			"""Helper function to parse json data"""
108
109			try:
110			return await response.json()
111
112			except aiohttp.client_exceptions.ContentTypeError as exc:
113			logger.error(repr(exc))
114			logger.warning(
115			"error while getting data from %s" % url)
116			return {}
117
118
119			async def fetch_url(
120			session, url, params=BIOSAMPLE_PARAMS, headers=None
121			) -> typing.Awaitable[dict]:
122			"""
123			Fetch a generic url, read data as json and return a promise
124
125			Parameters
126			----------
127			session : aiohttp.ClientSession
128			an async session object.
129			url : str
130			the desidered url
131			params : MultiDict, optional
132			Additional params for request. The default is BIOSAMPLE_PARAMS.
133			headers : dict
134			Additional HEADER information
135
136			Returns
137			-------
138			typing.Awaitable[dict]
139			json content of the page
140			"""
141
142			# update URL params with yarl
143			url = url.update_query(params)
144
145			logger.debug(url)
146
147			try:
148			async with session.get(url, headers=headers) as response:
149			# try to read json data
150			return await parse_json(response, url)
151
152			except aiohttp.client_exceptions.ServerDisconnectedError as exc:
153			logger.error(repr(exc))
154			logger.warning(
155			"server disconnected during %s" % url)
156			return {}
157
158
159			async def fecth_biosample(
160			session: aiohttp.ClientSession,
161			accession: str,
162			base_url: URL = BIOSAMPLE_SAMPLE_ENDPOINT,
163			headers: dict = HEADERS) -> typing.Awaitable[dict]:
164			"""
165			Collect a single BioSample object from EBI
166
167			Parameters
168			----------
169			session : aiohttp.ClientSession
170			an async session object.
171			accession : str
172			a BioSample accession ID.
173			base_url : URL, optional
174			DESCRIPTION. The default is BIOSAMPLE_BASE_URL.
175			headers : dict, optional
176			DESCRIPTION. The default is HEADERS.
177
178			Returns
179			-------
180			typing.Awaitable[dict]
181			A BioSample dictionary object
182			"""
183
184			# define sample location
185			url = base_url / accession
186
187			return await fetch_url(session, url, None, headers)
188
189
190			async def filter_managed_biosamples(
191			session: aiohttp.ClientSession,
192			data: dict,
193			managed_domains: list):
194			"""
195			Parse data from a BioSample results page and yield samples managed
196			by InjectTool users.
197
198			Parameters
199			----------
200			session : aiohttp.ClientSession
201			an async session object.
202			data : dict
203			biosample data read from BIOSAMPLE_URL.
204			managed_domains : list
205			A list of AAP domains, as returned from
206			:py:meth:`pyUSIrest.auth.Auth.get_domains`.
207
208			Yields
209			------
210			sample : dict
211			a BioSample record.
212
213			"""
214			tasks = []
215
216			# get samples objects
217			try:
218			accessions = data['_embedded']['accessions']
219
220			except KeyError as exc:
221			# logger exception. With repr() the exception name is rendered
222			logger.error(repr(exc))
223			logger.warning("error while parsing accessions")
224			logger.warning(data)
225
226			else:
227			for accession in accessions:
228			tasks.append(fecth_biosample(session, accession))
229
230			for task in asyncio.as_completed(tasks):
231			# read data
232			sample = await task
233
234			# filter out unmanaged records
235			if sample['domain'] not in managed_domains:
236			logger.warning("Ignoring %s (%s)" % (
237			sample['name'], sample['accession']))
238			continue
239
240			# otherwise return to the caller the sample
241			yield sample
242
243
244			async def get_biosamples(
245			url=BIOSAMPLE_ACCESSION_ENDPOINT,
246			params=BIOSAMPLE_PARAMS,
247			managed_domains=[]):
248			"""
249			Get all samples from BioSamples for the IMAGE project. Fecth Biosample
250			once, determines how many pages to request and return only accession
251			records managed by InjectTool
252
253			Parameters
254			----------
255			url : str, optional
256			The desidered URL. The default is BIOSAMPLE_ACCESSION_ENDPOINT.
257			params : MultiDict, optional
258			Additional params for request. The default is BIOSAMPLE_PARAMS.
259			managed_domains : list
260			A list of AAP domains, as returned from
261			:py:meth:`pyUSIrest.auth.Auth.get_domains`.
262
263			Yields
264			------
265			sample : dict
266			a BioSample record.
267
268			"""
269			# limiting the number of connections
270			# https://docs.aiohttp.org/en/stable/client_advanced.html
271			connector = aiohttp.TCPConnector(limit=10, ttl_dns_cache=300)
272
273			# https://stackoverflow.com/a/43857526
274			async with aiohttp.ClientSession(connector=connector) as session:
275			# get data for the first time to determine how many pages I have
276			# to requests
277			data = await fetch_url(session, url, params)
278
279			# maybe the request had issues
280			if data == {}:
281			logger.debug("Got a result with no data")
282			raise ConnectionError("Can't fetch biosamples for orphan samples")
283
284			# process data and filter samples I own
285			# https://stackoverflow.com/a/47378063
286			async for sample in filter_managed_biosamples(
287			session, data, managed_domains):
288			# return a managed biosample record
289			yield sample
290
291			tasks = []
292
293			# get pages
294			totalPages = data['page']['totalPages']
295
296			# generate new awaitable objects
297			for page in range(1, totalPages):
298			# get a new param object to edit
299			my_params = params.copy()
300
301			# edit a multidict object
302			my_params.update(page=page)
303
304			# track the new awaitable object
305			tasks.append(fetch_url(session, url, my_params))
306
307			# Run awaitable objects in the aws set concurrently.
308			# Return an iterator of Future objects.
309			for task in asyncio.as_completed(tasks):
310			# read data
311			data = await task
312
313			# maybe the request had issues
314			if data == {}:
315			logger.debug("Got a result with no data")
316			continue
317
318			# process data and filter samples I own
319			# https://stackoverflow.com/a/47378063
320			async for sample in filter_managed_biosamples(
321			session, data, managed_domains):
322			yield sample
323
324
325			async def check_samples():
326			"""
327			Get all records from BioSamples submitted by the InjectTool manager auth
328			managed domains, and call check_orphan_sample for each of them
329
330			Returns
331			-------
332			None.
333
334			"""
335			# I need an pyUSIrest.auth.Auth object to filter out records that don't
336			# belong to me
337			auth = get_manager_auth()
338			managed_domains = auth.get_domains()
339
340			async for sample in get_biosamples(managed_domains=managed_domains):
341			check_orphan_sample(sample)
342
343
344			def check_orphan_sample(sample):
345			"""
346			Get a BioSample record and check if such BioSampleId is registered into
347			InjectTool UID. If Such record is not present, create a new
348			:py:class:`biosample.models.OrphanSample` record object in the BioSample
349			orphan table
350
351			Parameters
352			----------
353			sample : dict
354			a BioSample record.
355
356			Returns
357			-------
358			None.
359
360			"""
361			animal_qs = UIDAnimal.objects.filter(
362			biosample_id=sample['accession'])
363
364			sample_qs = UIDSample.objects.filter(
365			biosample_id=sample['accession'])
366
367			if animal_qs.exists() or sample_qs.exists():
368			logger.debug("Sample %s is tracked in UID" % (sample['accession']))
369
370			else:
371			# get a managed team
372			team = ManagedTeam.objects.get(name=sample["domain"])
373
374			# Create an orphan sample
375			orphan, created = OrphanSample.objects.get_or_create(
376			biosample_id=sample['accession'],
377			name=sample['name'],
378			team=team,
379			)
380
381			if created:
382			logger.warning("Add %s to orphan samples" % sample['accession'])
383
384			# set status for new object
385			orphan.status = READY
386			orphan.save()
387
388
389			class SearchOrphanTask(NotifyAdminTaskMixin, BaseTask):
390			"""Search accross biosamples for objects not present in UID"""
391
392			name = "Search Orphan BioSamples IDs"
393			description = """Track BioSamples IDs not present in UID"""
394
395			@exclusive_task(
396			task_name=name, lock_id="SearchOrphanTask")
397			def run(self):
398			"""
399			This function is called when delay is called. It will acquire a lock
400			in redis, so those tasks are mutually exclusive
401
402			Returns:
403			str: success if everything is ok. Different messages if task is
404			already running or exception is caught"""
405
406			logger.info("%s started" % (self.name))
407
408			# create a loop object
409			loop = asyncio.new_event_loop()
410
411			# execute stuff
412			try:
413			loop.run_until_complete(check_samples())
414
415			finally:
416			# close loop
417			loop.close()
418
419			# Ok count orphan samples with a query
420			orphan_count = ORPHAN_QS.count()
421
422			if orphan_count > 0:
423			email_subject = "Some entries in BioSamples are orphan"
424			email_message = (
425			"There are %s biosample ids which are not managed by "
426			"InjectTool" % orphan_count)
427
428			logger.warning(email_message)
429
430			# Notify admins if I have orphan samples
431			send_mail_to_admins(email_subject, email_message)
432
433			# debug
434			logger.info("%s completed" % (self.name))
435
436			return "success"
437
438
439			def get_orphan_samples(limit=None):
440			"""
441			Iterate for all BioSample orphaned records which are not yet removed and
442			are tracked for removal, get minimal data from BioSample and return a
443			dictionary which can be used to patch a BioSample id with a new
444			BioSample submission in order to remove a BioSamples record
445			(publish the BioSample record after 1000 years from Now).
446
447			Yields
448			------
449			new_data : dict
450			payload to submit to BioSample in order to remove a BioSamples record.
451			"""
452
453			with requests.Session() as session:
454			# get all biosamples candidate for a removal. Pay attention that
455			# could be removed from different users
456			qs = ORPHAN_QS.order_by('team__name', 'id')
457
458			if limit:
459			qs = islice(qs, limit)
460
461			for orphan_sample in qs:
462			# define the url I need to check
463			url = "/".join([BIOSAMPLE_URL, orphan_sample.biosample_id])
464
465			# read data from url
466			response = session.get(url)
467			data = response.json()
468
469			# check status
470			if response.status_code == 403:
471			logger.error("Error for %s (%s): %s" % (
472			orphan_sample.biosample_id,
473			data['error'],
474			data['message'])
475			)
476
477			# this sample seems already removed
478			continue
479
480			# I need a new data dictionary to submit
481			new_data = dict()
482
483			# I suppose the accession exists, since I found this sample
484			# using accession [biosample.id]
485			new_data['accession'] = data.get(
486			'accession', orphan_sample.biosample_id)
487
488			new_data['alias'] = data['name']
489
490			new_data['title'] = data['characteristics']['title'][0]['text']
491
492			# this will be the most important attribute
493			new_data['releaseDate'] = str(
494			parse_date(data['releaseDate']) + RELEASE_TIMEDELTA)
495
496			new_data['taxonId'] = data['taxId']
497
498			# need to determine taxon as
499			new_data['taxon'] = DictSpecie.objects.get(
500			term__endswith=data['taxId']).label
501
502			new_data['attributes'] = dict()
503
504			new_data['description'] = "Removed by InjectTool"
505
506			# set project again
507			new_data['attributes']["Project"] = format_attribute(
508			value="IMAGE")
509
510			# return new biosample data
511			yield {
512			'data': new_data,
513			'team': orphan_sample.team,
514			'sample': orphan_sample,
515			}
516
517
518			# register explicitly tasks
519			# https://github.com/celery/celery/issues/3744#issuecomment-271366923
520			celery_app.tasks.register(CleanUpTask)
521			celery_app.tasks.register(SearchOrphanTask)
522

cnr-ibba / IMAGE-InjectTool

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biosample.tasks.cleanup.get_orphan_samples() B

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