biosample.management.commands.fetch_orphan_biosamples.SubmissionHelper.finalize() - 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 2020-05-30 15:25 UTC

SubmissionHelper.finalize() B

↳ Parent: biosample.management.commands.fetch_orphan_biosamples

Complexity

Conditions

Size

Total Lines	51
Code Lines	24

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	24
dl	0
loc	51
rs	8.8373
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 May 28 16:06:56 2020

@author: Paolo Cozzi <[email protected]>

Fetch the Orphan submissions and track BioSamples removal

"""

import json
import logging

import pyUSIrest.usi

from django.core.management import BaseCommand
from django.utils import timezone

from biosample.helpers import get_manager_auth
from biosample.models import OrphanSubmission
from biosample.tasks.retrieval import FetchStatusHelper
from common.constants import SUBMITTED, NEED_REVISION, COMPLETED


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


class SubmissionHelper(FetchStatusHelper):
    def __init__(self, root, usi_submission, can_finalize=False):
        self.root = root
        self.usi_submission = usi_submission
        self.can_finalize = can_finalize
        self.submission_name = usi_submission.usi_submission_name

        logger.info(
            "Getting info for usi submission '%s'" % (self.submission_name))

        self.submission = root.get_submission_by_name(
            submission_name=self.submission_name)

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

        if not self.can_finalize:
            # skip finalizing a submission
            logger.warning(
                "Ignoring finalization: please call with '--finalize'"
                " argument")
            return

        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:
                if sample.has_errors():
                    logger.error("%s has errors!!!" % sample)

                    # mark this sample since has problems
                    errorMessages = self.sample_has_errors(sample)

                    # 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:
            # TODO: model and test exception in finalization
            self.submission.finalize()

    # override complete method
    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():
            # 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

            orphan_sample = self.usi_submission.submission_data.get(
                biosample_id=sample.accession)
            orphan_sample.status = COMPLETED
            orphan_sample.removed = True
            orphan_sample.removed_at = timezone.now()
            orphan_sample.save()

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

        logger.info(
            "Submission %s is now completed and its samples "
            "removed from BioSamples" % (self.submission_name)
        )

    # custom implementation: here I don't have a record in UID and I
    # can't use the base method of this class
    def sample_has_errors(self, sample):
        """
        Get USI error for sample

        Args:
            sample (pyUSIrest.usi.sample): a USI sample object
        """

        # track status in db like FetchStatusHelper
        orphan_sample = self.usi_submission.submission_data.get(
            biosample_id=sample.accession)
        orphan_sample.status = NEED_REVISION
        orphan_sample.save()

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

        # track errors  in validation tables
        errorMessages = validation_result.errorMessages

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


class Command(BaseCommand):
    help = 'Fetch the Orphan submissions and track BioSamples removal'

    def add_arguments(self, parser):
        parser.add_argument(
            '--finalize',
            default=False,
            action='store_true',
        )

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

        # Ok get all Orphaned BioSample submission in SUBMITTED status
        qs = OrphanSubmission.objects.filter(status=SUBMITTED)

        if qs.count() > 0:
            # ok do stuff
            auth = get_manager_auth()
            root = pyUSIrest.usi.Root(auth)

            for orphan_submission in qs:
                submission_helper = SubmissionHelper(
                    root,
                    orphan_submission,
                    options['finalize'])
                submission_helper.check_submission_status()

        # call commands and fill tables.
        logger.info("fetch_orphan_biosamples finished")


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Thu May 28 16:06:56 2020
5
6			@author: Paolo Cozzi <[email protected]>
7
8			Fetch the Orphan submissions and track BioSamples removal
9
10			"""
11
12			import json
13			import logging
14
15			import pyUSIrest.usi
16
17			from django.core.management import BaseCommand
18			from django.utils import timezone
19
20			from biosample.helpers import get_manager_auth
21			from biosample.models import OrphanSubmission
22			from biosample.tasks.retrieval import FetchStatusHelper
23			from common.constants import SUBMITTED, NEED_REVISION, COMPLETED
24
25
26			# Get an instance of a logger
27			logger = logging.getLogger(__name__)
28
29
30			class SubmissionHelper(FetchStatusHelper):
31			def __init__(self, root, usi_submission, can_finalize=False):
32			self.root = root
33			self.usi_submission = usi_submission
34			self.can_finalize = can_finalize
35			self.submission_name = usi_submission.usi_submission_name
36
37			logger.info(
38			"Getting info for usi submission '%s'" % (self.submission_name))
39
40			self.submission = root.get_submission_by_name(
41			submission_name=self.submission_name)
42
43			# override finalize method
44			def finalize(self):
45			"""Finalize a submission by closing document and send it to
46			biosample"""
47
48			if not self.can_finalize:
49			# skip finalizing a submission
50			logger.warning(
51			"Ignoring finalization: please call with '--finalize'"
52			" argument")
53			return
54
55			logger.info("Finalizing submission '%s'" % (
56			self.submission_name))
57
58			# get errors for a submission
59			errors = self.submission.has_errors()
60
61			# collect all error messages in a list
62			messages = []
63
64			if True in errors:
65			# get sample with errors then update database
66			samples = self.submission.get_samples(has_errors=True)
67
68			for sample in samples:
69			if sample.has_errors():
70			logger.error("%s has errors!!!" % sample)
71
72			# mark this sample since has problems
73			errorMessages = self.sample_has_errors(sample)
74
75			# append this into error messages list
76			messages.append(errorMessages)
77
78			# if a sample has no errors, status will be the same
79
80			logger.error(
81			"Errors for submission: '%s'" % (self.submission_name))
82			logger.error("Fix them, then finalize")
83
84			# report error
85			message = json.dumps(messages, indent=2)
86
87			# Update status for biosample.models.Submission
88			self.usi_submission.status = NEED_REVISION
89			self.usi_submission.message = message
90			self.usi_submission.save()
91
92			else:
93			# TODO: model and test exception in finalization
94			self.submission.finalize()
95
96			# override complete method
97			def complete(self):
98			"""Complete a submission and fetch biosample names"""
99
100			logger.info("Completing submission '%s'" % (
101			self.submission_name))
102
103			for sample in self.submission.get_samples():
104			# if no accession, return without doing anything
105			if sample.accession is None:
106			logger.error("No accession found for sample '%s'" % (sample))
107			logger.error("Ignoring submission '%s'" % (self.submission))
108			return
109
110			orphan_sample = self.usi_submission.submission_data.get(
111			biosample_id=sample.accession)
112			orphan_sample.status = COMPLETED
113			orphan_sample.removed = True
114			orphan_sample.removed_at = timezone.now()
115			orphan_sample.save()
116
117			# update submission
118			self.usi_submission.status = COMPLETED
119			self.usi_submission.message = "Successful removal from biosample"
120			self.usi_submission.save()
121
122			logger.info(
123			"Submission %s is now completed and its samples "
124			"removed from BioSamples" % (self.submission_name)
125			)
126
127			# custom implementation: here I don't have a record in UID and I
128			# can't use the base method of this class
129			def sample_has_errors(self, sample):
130			"""
131			Get USI error for sample
132
133			Args:
134			sample (pyUSIrest.usi.sample): a USI sample object
135			"""
136
137			# track status in db like FetchStatusHelper
138			orphan_sample = self.usi_submission.submission_data.get(
139			biosample_id=sample.accession)
140			orphan_sample.status = NEED_REVISION
141			orphan_sample.save()
142
143			# get a USI validation result
144			validation_result = sample.get_validation_result()
145
146			# track errors in validation tables
147			errorMessages = validation_result.errorMessages
148
149			# return an error for each object
150			return {str(sample): errorMessages}
151
152
153			class Command(BaseCommand):
154			help = 'Fetch the Orphan submissions and track BioSamples removal'
155
156			def add_arguments(self, parser):
157			parser.add_argument(
158			'--finalize',
159			default=False,
160			action='store_true',
161			)
162
163			def handle(self, args, *options):
164			# call commands and fill tables.
165			logger.info("Called fetch_orphan_biosamples")
166
167			# Ok get all Orphaned BioSample submission in SUBMITTED status
168			qs = OrphanSubmission.objects.filter(status=SUBMITTED)
169
170			if qs.count() > 0:
171			# ok do stuff
172			auth = get_manager_auth()
173			root = pyUSIrest.usi.Root(auth)
174
175			for orphan_submission in qs:
176			submission_helper = SubmissionHelper(
177			root,
178			orphan_submission,
179			options['finalize'])
180			submission_helper.check_submission_status()
181
182			# call commands and fill tables.
183			logger.info("fetch_orphan_biosamples finished")
184

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#90)

SubmissionHelper.finalize() B

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