image_app.mixins.BioSampleMixin.specie() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #39..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

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by Paolo

created 2019-07-01 14:44 UTC

image_app.mixins.BioSampleMixin.specie() A

↳ Parent: image_app.mixins

Complexity

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Total Lines	4
Code Lines	4

Duplication

Lines	0
Ratio	0 %

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eloc	4
dl	0
loc	4
rs	10
c	0
b	0
f	0
cc	1
nop	1

#!/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 image_app.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 image_app.models import BaseMixin

        class Submission(BaseMixin):
            pass

    """

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

            from image_app.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 image_app.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.name.submission.organization

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

        return self.name.submission.gene_bank_country

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

        return self.name.submission.gene_bank_name

    @property
    def data_source_id(self):
        """Get Data source id (original animal/sample name) from related
        :py:class:`Name` object"""

        return self.name.name

    @property
    def submission(self):
        """Get related :py:class:`Submission` object throgh :py:class:`Name`
        """
        return self.name.submission

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

    @property
    def biosample_id(self):
        """Get the biosample_id of an object (need to be submitted and
        retrieved sing USI)"""

        return self.name.biosample_id

    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")

        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.name.publication:
            attributes['Publication DOI'] = format_attribute(
                value=self.name.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.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()

        return result

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

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

        Returns:
            bool
        """

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

        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
        """

        names = ['waiting', 'submitted']

        return self.__can_I(names)

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

        Returns:
            bool
        """

        names = ['waiting', 'submitted']

        return self.__can_I(names)


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 image_app.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 image_app.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 image_app.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 image_app.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.name.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.name.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.name.submission.gene_bank_name
96
97			@property
98			def data_source_id(self):
99			"""Get Data source id (original animal/sample name) from related
100			:py:class:`Name` object"""
101
102			return self.name.name
103
104			@property
105			def submission(self):
106			"""Get related :py:class:`Submission` object throgh :py:class:`Name`
107			"""
108			return self.name.submission
109
110			@property
111			def specie(self):
112			raise NotImplementedError(
113			"You need to define this method in your class")
114
115			@property
116			def biosample_id(self):
117			"""Get the biosample_id of an object (need to be submitted and
118			retrieved sing USI)"""
119
120			return self.name.biosample_id
121
122			def get_attributes(self):
123			"""Common attribute definition required from Animal and samples. Need
124			to be called inside Animal/sample get_atribute method. Keys
125			is the name in metadata rules
126
127			Returns:
128			dict: a dictionary object
129			"""
130
131			attributes = {}
132
133			attributes['Data source ID'] = format_attribute(
134			value=self.data_source_id)
135
136			attributes['Alternative id'] = format_attribute(
137			value=self.alternative_id)
138
139			# HINT: this is a mandatory biosample field: could be removed from
140			# attributes?
141			attributes['Description'] = format_attribute(
142			value=self.description)
143
144			attributes["Project"] = format_attribute(
145			value="IMAGE")
146
147			attributes['Submission title'] = format_attribute(
148			value=self.submission.title)
149
150			attributes['Submission description'] = format_attribute(
151			value=self.submission.description)
152
153			attributes['Person last name'] = format_attribute(
154			value=self.owner.last_name)
155
156			attributes['Person initial'] = format_attribute(
157			value=self.person.initials)
158
159			attributes['Person first name'] = format_attribute(
160			value=self.owner.first_name)
161
162			attributes['Person email'] = format_attribute(
163			value="mailto:%s" % (self.owner.email))
164
165			attributes['Person affiliation'] = format_attribute(
166			value=self.person.affiliation.name)
167
168			attributes['Person role'] = self.person.role.format_attribute()
169
170			attributes['Organization name'] = format_attribute(
171			value=self.organization.name)
172
173			attributes['Organization address'] = format_attribute(
174			value=self.organization.address)
175
176			attributes['Organization uri'] = format_attribute(
177			value=self.organization.URI)
178
179			attributes['Organization country'] = \
180			self.organization.country.format_attribute()
181
182			attributes[
183			'Organization role'] = self.organization.role.format_attribute()
184
185			# this could be present or not
186			if self.name.publication:
187			attributes['Publication DOI'] = format_attribute(
188			value=self.name.publication.doi)
189
190			attributes['Gene bank name'] = format_attribute(
191			value=self.gene_bank_name)
192
193			attributes[
194			'Gene bank country'] = self.gene_bank_country.format_attribute()
195
196			attributes['Data source type'] = format_attribute(
197			value=self.submission.get_datasource_type_display())
198
199			attributes['Data source version'] = format_attribute(
200			value=self.submission.datasource_version)
201
202			attributes['Species'] = self.specie.format_attribute()
203
204			return attributes
205
206			def to_biosample(self, release_date=None):
207			"""
208			Common stuff to generate a biosample object. Need to be called
209			inside Animal/Sample to_biosample method
210
211			Args:
212			release_date (str): data will no be published before this day
213			(YYYY-MM-DD)
214
215			Returns:
216			dict: a dictionary object
217			"""
218
219			result = {}
220
221			# define mandatory fields
222			result['alias'] = self.biosample_alias
223			result['title'] = self.name.name
224
225			# in case of update, I need to provide the old accession in payload
226			if self.biosample_id and self.biosample_id != '':
227			result['accession'] = self.biosample_id
228
229			if release_date:
230			result['releaseDate'] = release_date
231
232			else:
233			now = timezone.now()
234			result['releaseDate'] = str(now.date())
235
236			result['taxonId'] = self.specie.taxon_id
237
238			result['taxon'] = self.specie.label
239
240			# define optinal fields
241			if self.description:
242			result['description'] = self.description
243
244			# define attributes that will be customized in Animal and sample
245			result['attributes'] = self.get_attributes()
246
247			return result
248
249			def __can_I(self, names):
250			"""
251			Return True id self.status in statuses
252
253			Args:
254			names (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 names]
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			names = ['waiting', 'submitted']
277
278			return self.__can_I(names)
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			names = ['waiting', 'submitted']
289
290			return self.__can_I(names)
291

cnr-ibba / IMAGE-InjectTool

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image_app.mixins.BioSampleMixin.specie() A

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