image_app.mixins.BioSampleMixin.data_source_id() - Code Metrics - Inspection of "Checking UID fields and minor refactoring" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#39)

by Paolo

created 2019-06-28 14:18 UTC

image_app.mixins.BioSampleMixin.data_source_id() A

↳ Parent: image_app.mixins

Complexity

Conditions

Size

Total Lines	6
Code Lines	3

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	3
dl	0
loc	6
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 .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
19			from .helpers import format_attribute
20
21			# Get an instance of a logger
22			logger = logging.getLogger(__name__)
23
24
25			# Adding a classmethod to Category if you want to enable truncate
26			# https://books.agiliq.com/projects/django-orm-cookbook/en/latest/truncate.html
27			class BaseMixin(object):
28			"""Base class for UID tables. It implement common stuff for all UID
29			tables::
30
31			from image_app.models import BaseMixin
32
33			class Submission(BaseMixin):
34			pass
35
36			"""
37
38			@classmethod
39			def truncate(cls):
40			"""
41			Truncate table data and restart indexes from 0::
42
43			from image_app.models import Submission
44
45			Submission.truncate()
46			"""
47
48			# Django.db.connections is a dictionary-like object that allows you
49			# to retrieve a specific connection using its alias
50			with connections["default"].cursor() as cursor:
51			statement = "TRUNCATE TABLE {0} RESTART IDENTITY CASCADE".format(
52			cls._meta.db_table)
53			logger.debug(statement)
54			cursor.execute(statement)
55
56
57			class BioSampleMixin(BaseMixin):
58			"""
59			Common methods for animal and samples useful in biosample generation
60			Need to called with data into biosample or animals::
61
62			from image_app.models import Animal
63
64			animal = Animal.objects.get(pk=1)
65			biosample_data = animal.to_biosample()
66
67			"""
68
69			def __str__(self):
70			return str(self.name)
71
72			@property
73			def person(self):
74			"""Retrieve :py:class:`Person` information from owner relationship"""
75
76			return self.owner.person
77
78			@property
79			def organization(self):
80			"""Return :py:class:`Organization` relationship from related
81			:py:class:`Submission` object"""
82
83			return self.name.submission.organization
84
85			@property
86			def gene_bank_country(self):
87			"""Return :py:class:`DictCountry` relationship from related
88			:py:class:`Submission` object"""
89
90			return self.name.submission.gene_bank_country
91
92			@property
93			def gene_bank_name(self):
94			"""Return gene bank name from related :py:class:`Submission` object"""
95
96			return self.name.submission.gene_bank_name
97
98			@property
99			def data_source_id(self):
100			"""Get Data source id (original animal/sample name) from related
101			:py:class:`Name` object"""
102
103			return self.name.name
104
105			@property
106			def submission(self):
107			"""Get related :py:class:`Submission` object throgh :py:class:`Name`
108			"""
109			return self.name.submission
110
111			@property
112			def specie(self):
113			raise NotImplementedError(
114			"You need to define this method in your class")
115
116			@property
117			def biosample_id(self):
118			"""Get the biosample_id of an object (need to be submitted and
119			retrieved sing USI)"""
120
121			return self.name.biosample_id
122
123			def get_attributes(self):
124			"""Common attribute definition required from Animal and samples. Need
125			to be called inside Animal/sample get_atribute method. Keys
126			is the name in metadata rules
127
128			Returns:
129			dict: a dictionary object
130			"""
131
132			attributes = {}
133
134			attributes['Data source ID'] = format_attribute(
135			value=self.data_source_id)
136
137			attributes['Alternative id'] = format_attribute(
138			value=self.alternative_id)
139
140			# HINT: this is a mandatory biosample field: could be removed from
141			# attributes?
142			attributes['Description'] = format_attribute(
143			value=self.description)
144
145			attributes["Project"] = format_attribute(
146			value="IMAGE")
147
148			attributes['Submission title'] = format_attribute(
149			value=self.submission.title)
150
151			attributes['Submission description'] = format_attribute(
152			value=self.submission.description)
153
154			attributes['Person last name'] = format_attribute(
155			value=self.owner.last_name)
156
157			attributes['Person initial'] = format_attribute(
158			value=self.person.initials)
159
160			attributes['Person first name'] = format_attribute(
161			value=self.owner.first_name)
162
163			attributes['Person email'] = format_attribute(
164			value="mailto:%s" % (self.owner.email))
165
166			attributes['Person affiliation'] = format_attribute(
167			value=self.person.affiliation.name)
168
169			attributes['Person role'] = self.person.role.format_attribute()
170
171			attributes['Organization name'] = format_attribute(
172			value=self.organization.name)
173
174			attributes['Organization address'] = format_attribute(
175			value=self.organization.address)
176
177			attributes['Organization uri'] = format_attribute(
178			value=self.organization.URI)
179
180			attributes['Organization country'] = \
181			self.organization.country.format_attribute()
182
183			attributes[
184			'Organization role'] = self.organization.role.format_attribute()
185
186			# this could be present or not
187			if self.name.publication:
188			attributes['Publication DOI'] = format_attribute(
189			value=self.name.publication.doi)
190
191			attributes['Gene bank name'] = format_attribute(
192			value=self.gene_bank_name)
193
194			attributes[
195			'Gene bank country'] = self.gene_bank_country.format_attribute()
196
197			attributes['Data source type'] = format_attribute(
198			value=self.submission.get_datasource_type_display())
199
200			attributes['Data source version'] = format_attribute(
201			value=self.submission.datasource_version)
202
203			attributes['Species'] = self.specie.format_attribute()
204
205			return attributes
206
207			def to_biosample(self, release_date=None):
208			"""
209			Common stuff to generate a biosample object. Need to be called
210			inside Animal/Sample to_biosample method
211
212			Args:
213			release_date (str): data will no be published before this day
214			(YYYY-MM-DD)
215
216			Returns:
217			dict: a dictionary object
218			"""
219
220			result = {}
221
222			# define mandatory fields
223			result['alias'] = self.biosample_alias
224			result['title'] = self.name.name
225
226			# in case of update, I need to provide the old accession in payload
227			if self.biosample_id and self.biosample_id != '':
228			result['accession'] = self.biosample_id
229
230			if release_date:
231			result['releaseDate'] = release_date
232
233			else:
234			now = timezone.now()
235			result['releaseDate'] = str(now.date())
236
237			result['taxonId'] = self.specie.taxon_id
238
239			result['taxon'] = self.specie.label
240
241			# define optinal fields
242			if self.description:
243			result['description'] = self.description
244
245			# define attributes that will be customized in Animal and sample
246			result['attributes'] = self.get_attributes()
247
248			return result
249
250			def __can_I(self, names):
251			"""
252			Return True id self.status in statuses
253
254			Args:
255			names (list): a list of :py:class:`common.constants.STATUSES`
256
257			Returns:
258			bool
259			"""
260
261			statuses = [x.value[0] for x in STATUSES if x.name in names]
262
263			if self.submission.status not in statuses:
264			return True
265
266			else:
267			return False
268
269			def can_edit(self):
270			"""Returns True if I can edit a sample/animal according to submission
271			status
272
273			Returns:
274			bool
275			"""
276
277			names = ['waiting', 'submitted']
278
279			return self.__can_I(names)
280
281			def can_delete(self):
282			"""Returns True if I can delete a sample/animal according to submission
283			status
284
285			Returns:
286			bool
287			"""
288
289			names = ['waiting', 'submitted']
290
291			return self.__can_I(names)
292

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#39)

image_app.mixins.BioSampleMixin.data_source_id() A

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