biosample.management.commands.patch_orphan_biosamples.Command.handle() - Code Metrics - Inspection of ":sparkles: search and track orphaned BioSamples ID..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — devel (#90)

by Paolo

created 2020-06-04 17:30 UTC

Command.handle() B

↳ Parent: biosample.management.commands.patch_orphan_biosamples

Complexity

Conditions

Size

Total Lines	63
Code Lines	35

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	35
dl	0
loc	63
rs	8.5733
c	0
b	0
f	0
cc	5
nop	3

How to fix Long Method

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 26 17:21:28 2020

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

import logging

import pyUSIrest.usi
import pyUSIrest.exceptions

from django.core.management import BaseCommand

from biosample.helpers import get_manager_auth
from biosample.models import OrphanSubmission
from biosample.tasks.cleanup import get_orphan_samples
from common.constants import SUBMITTED, ERROR

# Get an instance of a logger
logger = logging.getLogger(__name__)


def create_biosample_submission(root, team):
    logger.debug("Creating a new submission")

    usi_team = root.get_team_by_name(team.name)
    usi_submission = usi_team.create_submission()

    submission = OrphanSubmission(
        usi_submission_name=usi_submission.name)
    submission.save()

    logger.debug("Created submission '%s' for '%s'" % (submission, team.name))
    return usi_submission, submission


def update_submission_status(submission):
    """Set SUBMITTED status to submission"""

    # update submission status
    if submission:
        submission.status = SUBMITTED
        submission.save()


class Command(BaseCommand):
    help = 'Get a JSON for biosample submission'

    def add_arguments(self, parser):

        parser.add_argument(
            '--limit',
            required=False,
            help="Limit to LIMIT items",
            default=None,
            type=int)

    def handle(self, *args, **options):
        # call commands and fill tables.
        logger.info("Called patch_orphan_samples")

        # get a new auth object
        auth = get_manager_auth()

        # get a new root object
        root = pyUSIrest.usi.Root(auth)

        # some variables
        count = 1
        old_team = None
        usi_submission = None
        submission = None

        # iterate among orphan sample, create a BioSample submission
        # and then add biosample for patch
        for record in get_orphan_samples(limit=options['limit']):
            (data, team, sample) = (
                record['data'], record['team'], record['sample'])

            if count % 100 == 0 or old_team != team:
                update_submission_status(submission)

                # create a new Biosample submission
                usi_submission, submission = create_biosample_submission(
                    root, team)

                # reset count and old_team
                count = 1
                old_team = team

            # add sample to submission
            try:
                logger.info("Submitting '%s'" % data['accession'])
                usi_submission.create_sample(data)

            except pyUSIrest.exceptions.USIDataError as error:
                logger.error(
                    "Can't remove '%s': Error was '%s'" % (
                        data['accession'], str(error)))
                sample.status = ERROR
                sample.save()
                continue

            # update sample status and track submission
            sample.status = SUBMITTED
            sample.submission = submission
            sample.save()

            # update submission count
            submission.samples_count = count
            submission.save()

            # new element
            count += 1

        # update the last submission status
        update_submission_status(submission)

        # end the script
        logger.info("patch_orphan_samples ended")


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Tue May 26 17:21:28 2020
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			import logging
10
11			import pyUSIrest.usi
12			import pyUSIrest.exceptions
13
14			from django.core.management import BaseCommand
15
16			from biosample.helpers import get_manager_auth
17			from biosample.models import OrphanSubmission
18			from biosample.tasks.cleanup import get_orphan_samples
19			from common.constants import SUBMITTED, ERROR
20
21			# Get an instance of a logger
22			logger = logging.getLogger(__name__)
23
24
25			def create_biosample_submission(root, team):
26			logger.debug("Creating a new submission")
27
28			usi_team = root.get_team_by_name(team.name)
29			usi_submission = usi_team.create_submission()
30
31			submission = OrphanSubmission(
32			usi_submission_name=usi_submission.name)
33			submission.save()
34
35			logger.debug("Created submission '%s' for '%s'" % (submission, team.name))
36			return usi_submission, submission
37
38
39			def update_submission_status(submission):
40			"""Set SUBMITTED status to submission"""
41
42			# update submission status
43			if submission:
44			submission.status = SUBMITTED
45			submission.save()
46
47
48			class Command(BaseCommand):
49			help = 'Get a JSON for biosample submission'
50
51			def add_arguments(self, parser):
52
53			parser.add_argument(
54			'--limit',
55			required=False,
56			help="Limit to LIMIT items",
57			default=None,
58			type=int)
59
60			def handle(self, args, *options):
61			# call commands and fill tables.
62			logger.info("Called patch_orphan_samples")
63
64			# get a new auth object
65			auth = get_manager_auth()
66
67			# get a new root object
68			root = pyUSIrest.usi.Root(auth)
69
70			# some variables
71			count = 1
72			old_team = None
73			usi_submission = None
74			submission = None
75
76			# iterate among orphan sample, create a BioSample submission
77			# and then add biosample for patch
78			for record in get_orphan_samples(limit=options['limit']):
79			(data, team, sample) = (
80			record['data'], record['team'], record['sample'])
81
82			if count % 100 == 0 or old_team != team:
83			update_submission_status(submission)
84
85			# create a new Biosample submission
86			usi_submission, submission = create_biosample_submission(
87			root, team)
88
89			# reset count and old_team
90			count = 1
91			old_team = team
92
93			# add sample to submission
94			try:
95			logger.info("Submitting '%s'" % data['accession'])
96			usi_submission.create_sample(data)
97
98			except pyUSIrest.exceptions.USIDataError as error:
99			logger.error(
100			"Can't remove '%s': Error was '%s'" % (
101			data['accession'], str(error)))
102			sample.status = ERROR
103			sample.save()
104			continue
105
106			# update sample status and track submission
107			sample.status = SUBMITTED
108			sample.submission = submission
109			sample.save()
110
111			# update submission count
112			submission.samples_count = count
113			submission.save()
114
115			# new element
116			count += 1
117
118			# update the last submission status
119			update_submission_status(submission)
120
121			# end the script
122			logger.info("patch_orphan_samples ended")
123

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#90)

Command.handle() B

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