uid.mixins.BioSampleMixin.to_biosample() - Code Metrics - Inspection of ":sparkles: "same as" relationship support" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — devel (#71)

by Paolo

created 2020-01-14 16:01 UTC

uid.mixins.BioSampleMixin.to_biosample() B

↳ Parent: uid.mixins

Complexity

Conditions

Size

Total Lines	52
Code Lines	21

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	21
dl	0
loc	52
rs	7.9759
c	0
b	0
f	0
cc	7
nop	2

How to fix Long Method

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 28 14:46:39 2019

@author: Paolo Cozzi <[email protected]>

Define mixins classes for uid.models

"""

import logging

from django.db import connections
from django.utils import timezone

from common.constants import STATUSES
from common.helpers import format_attribute

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


# Adding a classmethod to Category if you want to enable truncate
# https://books.agiliq.com/projects/django-orm-cookbook/en/latest/truncate.html
class BaseMixin(object):
    """Base class for UID tables. It implement common stuff for all UID
    tables::

        from uid.models import BaseMixin

        class Submission(BaseMixin):
            pass

    """

    @classmethod
    def truncate(cls):
        """
        Truncate table data and restart indexes from 0::

            from uid.models import Submission

            Submission.truncate()
        """

        # Django.db.connections is a dictionary-like object that allows you
        # to retrieve a specific connection using its alias
        with connections["default"].cursor() as cursor:
            statement = "TRUNCATE TABLE {0} RESTART IDENTITY CASCADE".format(
                cls._meta.db_table)
            logger.debug(statement)
            cursor.execute(statement)


class BioSampleMixin(BaseMixin):
    """
    Common methods for animal and samples useful in biosample generation
    Need to called with data into biosample or animals::

        from uid.models import Animal

        animal = Animal.objects.get(pk=1)
        biosample_data = animal.to_biosample()

    """

    def __str__(self):
        return str(self.name)

    @property
    def person(self):
        """Retrieve :py:class:`Person` information from owner relationship"""

        return self.owner.person

    @property
    def organization(self):
        """Return :py:class:`Organization` relationship from related
        :py:class:`Submission` object"""

        return self.submission.organization

    @property
    def gene_bank_country(self):
        """Return :py:class:`DictCountry` relationship from related
        :py:class:`Submission` object"""

        return self.submission.gene_bank_country

    @property
    def gene_bank_name(self):
        """Return gene bank name from related :py:class:`Submission` object"""

        return self.submission.gene_bank_name

    @property
    def data_source_id(self):
        """Get Data source id (original animal/sample name)"""

        return self.name

    @property
    def specie(self):
        raise NotImplementedError(
            "You need to define this method in your class")

    def get_attributes(self):
        """Common attribute definition required from Animal and samples. Need
        to be called inside Animal/sample get_atribute method. Keys
        is the name in metadata rules

        Returns:
            dict: a dictionary object
        """

        attributes = {}

        attributes['Data source ID'] = format_attribute(
            value=self.data_source_id)

        attributes['Alternative id'] = format_attribute(
            value=self.alternative_id)

        # HINT: this is a mandatory biosample field: could be removed from
        # attributes?
        attributes['Description'] = format_attribute(
            value=self.description)

        attributes["Project"] = format_attribute(
            value="IMAGE")

        # to retrieve where this sample belongs
        attributes["IMAGE submission id"] = format_attribute(
            value=self.submission.id)

        attributes['Submission title'] = format_attribute(
            value=self.submission.title)

        attributes['Submission description'] = format_attribute(
            value=self.submission.description)

        attributes['Person last name'] = format_attribute(
            value=self.owner.last_name)

        attributes['Person initial'] = format_attribute(
            value=self.person.initials)

        attributes['Person first name'] = format_attribute(
            value=self.owner.first_name)

        attributes['Person email'] = format_attribute(
            value="mailto:%s" % (self.owner.email))

        attributes['Person affiliation'] = format_attribute(
            value=self.person.affiliation.name)

        attributes['Person role'] = self.person.role.format_attribute()

        attributes['Organization name'] = format_attribute(
            value=self.organization.name)

        attributes['Organization address'] = format_attribute(
            value=self.organization.address)

        attributes['Organization uri'] = format_attribute(
            value=self.organization.URI)

        attributes['Organization country'] = \
            self.organization.country.format_attribute()

        attributes[
            'Organization role'] = self.organization.role.format_attribute()

        # this could be present or not
        if self.publication:
            attributes['Publication DOI'] = format_attribute(
                value=self.publication.doi)

        attributes['Gene bank name'] = format_attribute(
            value=self.gene_bank_name)

        attributes[
            'Gene bank country'] = self.gene_bank_country.format_attribute()

        attributes['Data source type'] = format_attribute(
            value=self.submission.get_datasource_type_display())

        attributes['Data source version'] = format_attribute(
            value=self.submission.datasource_version)

        attributes['Species'] = self.specie.format_attribute()

        return attributes

    def to_biosample(self, release_date=None):
        """
        Common stuff to generate a biosample object. Need to be called
        inside Animal/Sample to_biosample method

        Args:
            release_date (str): data will no be published before this day
                (YYYY-MM-DD)

        Returns:
            dict: a dictionary object
        """

        result = {}

        # define mandatory fields
        result['alias'] = self.biosample_alias
        result['title'] = self.name

        # in case of update, I need to provide the old accession in payload
        if self.biosample_id and self.biosample_id != '':
            result['accession'] = self.biosample_id

        if release_date:
            result['releaseDate'] = release_date

        else:
            now = timezone.now()
            result['releaseDate'] = str(now.date())

        result['taxonId'] = self.specie.taxon_id

        result['taxon'] = self.specie.label

        # define optinal fields
        if self.description:
            result['description'] = self.description

        # define attributes that will be customized in Animal and sample
        result['attributes'] = self.get_attributes()

        # define an empty relationship array
        result['sampleRelationships'] = []

        # test for same as relationship
        if self.same_as and self.same_as != '':
            result['sampleRelationships'].append({
                "relationshipNature": "same as",
                "accession": self.same_as
            })

        return result

    def __can_I(self, statuses):
        """
        Return True id self.status in statuses

        Args:
            statuses (list): a list of :py:class:`common.constants.STATUSES`

        Returns:
            bool
        """

        statuses = [x.value[0] for x in STATUSES if x.name in statuses]

        if self.submission.status not in statuses:
            return True

        else:
            return False

    def can_edit(self):
        """Returns True if I can edit a sample/animal according to submission
        status

        Returns:
            bool
        """

        statuses = ['waiting', 'submitted']

        return self.__can_I(statuses)

    def can_delete(self):
        """Returns True if I can delete a sample/animal according to submission
        status

        Returns:
            bool
        """

        statuses = ['waiting', 'submitted']

        return self.__can_I(statuses)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Fri Jun 28 14:46:39 2019
5
6			@author: Paolo Cozzi <[email protected]>
7
8			Define mixins classes for uid.models
9
10			"""
11
12			import logging
13
14			from django.db import connections
15			from django.utils import timezone
16
17			from common.constants import STATUSES
18			from common.helpers import format_attribute
19
20			# Get an instance of a logger
21			logger = logging.getLogger(__name__)
22
23
24			# Adding a classmethod to Category if you want to enable truncate
25			# https://books.agiliq.com/projects/django-orm-cookbook/en/latest/truncate.html
26			class BaseMixin(object):
27			"""Base class for UID tables. It implement common stuff for all UID
28			tables::
29
30			from uid.models import BaseMixin
31
32			class Submission(BaseMixin):
33			pass
34
35			"""
36
37			@classmethod
38			def truncate(cls):
39			"""
40			Truncate table data and restart indexes from 0::
41
42			from uid.models import Submission
43
44			Submission.truncate()
45			"""
46
47			# Django.db.connections is a dictionary-like object that allows you
48			# to retrieve a specific connection using its alias
49			with connections["default"].cursor() as cursor:
50			statement = "TRUNCATE TABLE {0} RESTART IDENTITY CASCADE".format(
51			cls._meta.db_table)
52			logger.debug(statement)
53			cursor.execute(statement)
54
55
56			class BioSampleMixin(BaseMixin):
57			"""
58			Common methods for animal and samples useful in biosample generation
59			Need to called with data into biosample or animals::
60
61			from uid.models import Animal
62
63			animal = Animal.objects.get(pk=1)
64			biosample_data = animal.to_biosample()
65
66			"""
67
68			def __str__(self):
69			return str(self.name)
70
71			@property
72			def person(self):
73			"""Retrieve :py:class:`Person` information from owner relationship"""
74
75			return self.owner.person
76
77			@property
78			def organization(self):
79			"""Return :py:class:`Organization` relationship from related
80			:py:class:`Submission` object"""
81
82			return self.submission.organization
83
84			@property
85			def gene_bank_country(self):
86			"""Return :py:class:`DictCountry` relationship from related
87			:py:class:`Submission` object"""
88
89			return self.submission.gene_bank_country
90
91			@property
92			def gene_bank_name(self):
93			"""Return gene bank name from related :py:class:`Submission` object"""
94
95			return self.submission.gene_bank_name
96
97			@property
98			def data_source_id(self):
99			"""Get Data source id (original animal/sample name)"""
100
101			return self.name
102
103			@property
104			def specie(self):
105			raise NotImplementedError(
106			"You need to define this method in your class")
107
108			def get_attributes(self):
109			"""Common attribute definition required from Animal and samples. Need
110			to be called inside Animal/sample get_atribute method. Keys
111			is the name in metadata rules
112
113			Returns:
114			dict: a dictionary object
115			"""
116
117			attributes = {}
118
119			attributes['Data source ID'] = format_attribute(
120			value=self.data_source_id)
121
122			attributes['Alternative id'] = format_attribute(
123			value=self.alternative_id)
124
125			# HINT: this is a mandatory biosample field: could be removed from
126			# attributes?
127			attributes['Description'] = format_attribute(
128			value=self.description)
129
130			attributes["Project"] = format_attribute(
131			value="IMAGE")
132
133			# to retrieve where this sample belongs
134			attributes["IMAGE submission id"] = format_attribute(
135			value=self.submission.id)
136
137			attributes['Submission title'] = format_attribute(
138			value=self.submission.title)
139
140			attributes['Submission description'] = format_attribute(
141			value=self.submission.description)
142
143			attributes['Person last name'] = format_attribute(
144			value=self.owner.last_name)
145
146			attributes['Person initial'] = format_attribute(
147			value=self.person.initials)
148
149			attributes['Person first name'] = format_attribute(
150			value=self.owner.first_name)
151
152			attributes['Person email'] = format_attribute(
153			value="mailto:%s" % (self.owner.email))
154
155			attributes['Person affiliation'] = format_attribute(
156			value=self.person.affiliation.name)
157
158			attributes['Person role'] = self.person.role.format_attribute()
159
160			attributes['Organization name'] = format_attribute(
161			value=self.organization.name)
162
163			attributes['Organization address'] = format_attribute(
164			value=self.organization.address)
165
166			attributes['Organization uri'] = format_attribute(
167			value=self.organization.URI)
168
169			attributes['Organization country'] = \
170			self.organization.country.format_attribute()
171
172			attributes[
173			'Organization role'] = self.organization.role.format_attribute()
174
175			# this could be present or not
176			if self.publication:
177			attributes['Publication DOI'] = format_attribute(
178			value=self.publication.doi)
179
180			attributes['Gene bank name'] = format_attribute(
181			value=self.gene_bank_name)
182
183			attributes[
184			'Gene bank country'] = self.gene_bank_country.format_attribute()
185
186			attributes['Data source type'] = format_attribute(
187			value=self.submission.get_datasource_type_display())
188
189			attributes['Data source version'] = format_attribute(
190			value=self.submission.datasource_version)
191
192			attributes['Species'] = self.specie.format_attribute()
193
194			return attributes
195
196			def to_biosample(self, release_date=None):
197			"""
198			Common stuff to generate a biosample object. Need to be called
199			inside Animal/Sample to_biosample method
200
201			Args:
202			release_date (str): data will no be published before this day
203			(YYYY-MM-DD)
204
205			Returns:
206			dict: a dictionary object
207			"""
208
209			result = {}
210
211			# define mandatory fields
212			result['alias'] = self.biosample_alias
213			result['title'] = self.name
214
215			# in case of update, I need to provide the old accession in payload
216			if self.biosample_id and self.biosample_id != '':
217			result['accession'] = self.biosample_id
218
219			if release_date:
220			result['releaseDate'] = release_date
221
222			else:
223			now = timezone.now()
224			result['releaseDate'] = str(now.date())
225
226			result['taxonId'] = self.specie.taxon_id
227
228			result['taxon'] = self.specie.label
229
230			# define optinal fields
231			if self.description:
232			result['description'] = self.description
233
234			# define attributes that will be customized in Animal and sample
235			result['attributes'] = self.get_attributes()
236
237			# define an empty relationship array
238			result['sampleRelationships'] = []
239
240			# test for same as relationship
241			if self.same_as and self.same_as != '':
242			result['sampleRelationships'].append({
243			"relationshipNature": "same as",
244			"accession": self.same_as
245			})
246
247			return result
248
249			def __can_I(self, statuses):
250			"""
251			Return True id self.status in statuses
252
253			Args:
254			statuses (list): a list of :py:class:`common.constants.STATUSES`
255
256			Returns:
257			bool
258			"""
259
260			statuses = [x.value[0] for x in STATUSES if x.name in statuses]
261
262			if self.submission.status not in statuses:
263			return True
264
265			else:
266			return False
267
268			def can_edit(self):
269			"""Returns True if I can edit a sample/animal according to submission
270			status
271
272			Returns:
273			bool
274			"""
275
276			statuses = ['waiting', 'submitted']
277
278			return self.__can_I(statuses)
279
280			def can_delete(self):
281			"""Returns True if I can delete a sample/animal according to submission
282			status
283
284			Returns:
285			bool
286			"""
287
288			statuses = ['waiting', 'submitted']
289
290			return self.__can_I(statuses)
291

cnr-ibba / IMAGE-InjectTool

Pull Request — devel (#71)

uid.mixins.BioSampleMixin.to_biosample() B

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