image_app.admin.DictBreedAdmin.get_term() - Code Metrics - Inspection of ":twisted_rightwards_arrows: Merge pull request #69..." - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — devel ( 3eb06e...2ff9b7 )

by Paolo

created 2019-10-29 14:31 UTC

image_app.admin.DictBreedAdmin.get_term() A

↳ Parent: image_app.admin

Complexity

Conditions

Size

Total Lines	2
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	2
dl	0
loc	2
rs	10
c	0
b	0
f	0
cc	1
nop	2

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov  7 11:54:15 2018

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

from django import forms
from django.contrib import admin
from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
from django.contrib.auth.models import User

from .models import (Animal, DictBreed, DictCountry, DictRole, DictSpecie,
                     Name, Ontology, Organization, Person, Publication, Sample,
                     Submission, DictSex, DictUberon, DictDevelStage,
                     DictPhysioStage)


class DictBreedAdmin(admin.ModelAdmin):
    search_fields = ['supplied_breed']
    list_per_page = 25
    list_display = (
        'supplied_breed', 'get_label', 'get_term', 'mapped_breed',
        'mapped_breed_term', 'confidence', 'country', 'specie')

    # override label and term verbose names
    def get_label(self, instance):
        return instance.label
    get_label.short_description = "label"

    def get_term(self, instance):
        return instance.term
    get_term.short_description = "term"

    list_filter = ('country', 'specie')


class NameAdmin(admin.ModelAdmin):
    """A class to deal with animal names"""

    search_fields = ['name', 'biosample_id']

    list_per_page = 25
    list_display = (
        'name', 'submission', 'biosample_id', 'owner', 'status',
        'last_changed', 'last_submitted')

    list_filter = ('owner', 'status')

    # join immediately name with DataSouce, in order to speed up name rendering
    list_select_related = (
        'submission', 'submission__gene_bank_country', 'owner'
    )


# redefine form to edit Sample. Link animal to names in order to speed up
# name rendering
class SampleAdminForm(forms.ModelForm):
    class Meta:
        model = Sample
        fields = '__all__'

    def __init__(self, *args, **kwargs):
        super(SampleAdminForm, self).__init__(*args, **kwargs)

        # This is the bit that matters:
        self.fields['animal'].queryset = Animal.objects.select_related('name')


# inspired from here:
# https://github.com/geex-arts/django-jet/issues/244#issuecomment-325001298
class SampleInLineFormSet(forms.BaseInlineFormSet):
    ''' Base Inline formset for Sample Model'''

    def __init__(self, *args, **kwargs):
        super(SampleInLineFormSet, self).__init__(*args, **kwargs)

        # Animal will be a Animal object called when editing animal
        animal = kwargs["instance"]

        # get all Sample names from a certain animal with a unique query
        # HINT: all problems related to subquery when displaying names arise
        # from my __str__s methods, which display Sample and Animal name
        # and the relation between table Name. In order to have all sample
        # names for each animal, I need a join with three tables
        self.queryset = Sample.objects.select_related(
            'animal').select_related(
                'name').filter(animal=animal)


class SampleInline(admin.StackedInline):
    formset = SampleInLineFormSet

    fields = (
        ('name', 'alternative_id', 'description', 'owner'),
        ('animal', 'protocol', 'organism_part'),
        ('collection_date', 'collection_place_latitude',
         'collection_place_longitude', 'collection_place'),
        ('developmental_stage', 'physiological_stage',
         'animal_age_at_collection', 'animal_age_at_collection_units',
         'availability'),
        ('storage', 'storage_processing', 'preparation_interval',
         'preparation_interval_units')
    )

    # manage a fields with many FK keys
    # https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
    raw_id_fields = ("name", "animal")

    model = Sample
    extra = 0


class SampleAdmin(admin.ModelAdmin):
    form = SampleAdminForm

    # exclude = ('author',)
    # prepopulated_fields = {'name': ['description']}
    search_fields = ['name__name']
    list_per_page = 25
    list_display = (
        'name', 'alternative_id', 'animal',
        'protocol', 'collection_date', 'collection_place_latitude',
        'collection_place_longitude', 'collection_place', 'organism_part',
        'developmental_stage', 'physiological_stage',
        'animal_age_at_collection', 'animal_age_at_collection_units',
        'availability', 'storage', 'storage_processing',
        'preparation_interval', 'preparation_interval_units', 'description',
        'owner'
    )

    # To tell Django we want to perform a join instead of fetching the names of
    # the categories one by one
    list_select_related = ('name', 'animal__name', 'owner', 'organism_part')

    list_filter = ('owner', 'name__status')

    fields = (
        ('name', 'alternative_id', 'description', 'owner'),
        ('animal', 'protocol', 'organism_part'),
        ('collection_date', 'collection_place', 'collection_place_latitude',
         'collection_place_longitude', 'collection_place_accuracy'),
        ('developmental_stage',
         'physiological_stage', 'animal_age_at_collection',
         'animal_age_at_collection_units', 'availability'),
        ('storage', 'storage_processing', 'preparation_interval',
         'preparation_interval_units')
    )

    # manage a fields with many FK keys
    # https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
    raw_id_fields = ("name", "animal")


class AnimalAdmin(admin.ModelAdmin):
    search_fields = ['name__name']

    list_per_page = 25
    list_display = (
        'name', 'alternative_id', 'breed', 'sex',
        'father', 'mother', 'birth_location', 'birth_location_latitude',
        'birth_location_longitude', 'description', 'owner'
        )

    list_filter = ('owner', 'name__status')

    fields = (
        'name', 'alternative_id', 'breed', 'sex', 'father',
        'mother', ('birth_location', 'birth_location_latitude',
                   'birth_location_longitude'),
        'description', 'owner'
        )

    # I can add manually an item if it is a readonly field
    # readonly_fields = ("name",)

    # manage a fields with many FK keys
    # https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
    raw_id_fields = ("name", "father", "mother", "breed")

    # https://medium.com/@hakibenita/things-you-must-know-about-django-admin-as-your-app-gets-bigger-6be0b0ee9614
    list_select_related = (
        'name', 'breed', 'breed__specie', 'sex', 'father', 'mother', 'owner')

    inlines = [SampleInline]


class SubmissionAdmin(admin.ModelAdmin):
    list_per_page = 25
    list_display = (
        'title', 'description', 'gene_bank_name', 'gene_bank_country',
        'datasource_type', 'datasource_version', 'organization', 'created_at',
        'updated_at', 'status', 'owner'
    )

    # I cannot edit a auto_add_now field
    readonly_fields = ('created_at', 'updated_at')

    list_filter = ('owner', 'status')


class PersonAdmin(admin.ModelAdmin):
    list_per_page = 25
    list_display = (
        'user_name', 'full_name', 'initials', 'affiliation', 'role',
    )

    def user_name(self, obj):
        return obj.user.username

    # rename column in admin
    user_name.short_description = "User Name"

    def full_name(self, obj):
        return "%s %s" % (obj.user.first_name, obj.user.last_name)

    full_name.short_description = "Full Name"


# https://simpleisbetterthancomplex.com/tutorial/2016/11/23/how-to-add-user-profile-to-django-admin.html
class PersonInLine(admin.StackedInline):
    model = Person
    can_delete = False
    verbose_name_plural = 'Person'
    fk_name = 'user'


class UserAdmin(BaseUserAdmin):
    inlines = (PersonInLine, )
    list_display = ('username', 'email', 'first_name', 'last_name', 'is_staff',
                    'get_role')
    list_select_related = ('person', )

    # this will display a column Role in User admin
    def get_role(self, instance):
        return instance.person.role
    get_role.short_description = 'Role'

    # display the inlines only in the edit form
    def get_inline_instances(self, request, obj=None):
        if not obj:
            return list()
        return super(UserAdmin, self).get_inline_instances(request, obj)


class OrganizationAdmin(admin.ModelAdmin):
    list_per_page = 25
    search_fields = ['name']
    list_display = (
        'name', 'address', 'country', 'URI', 'role',
    )


class OntologyAdmin(admin.ModelAdmin):
    list_per_page = 25
    search_fields = ['library_name']
    list_display = (
        'library_name', 'library_uri', 'comment',
    )


class DictCountryAdmin(admin.ModelAdmin):
    list_per_page = 25
    list_display = ('label', 'term', 'confidence')


class DictSpecieAdmin(admin.ModelAdmin):
    list_per_page = 25
    list_display = (
        'label', 'term', 'confidence', 'general_breed_label',
        'general_breed_term')


# --- registering applications

# default admin class
admin.site.register(DictRole, admin.ModelAdmin)
admin.site.register(DictSex, admin.ModelAdmin)
admin.site.register(DictUberon, admin.ModelAdmin)
admin.site.register(DictDevelStage, admin.ModelAdmin)
admin.site.register(DictPhysioStage, admin.ModelAdmin)

# Custom admin class
admin.site.register(DictSpecie, DictSpecieAdmin)
admin.site.register(DictCountry, DictCountryAdmin)
admin.site.register(Submission, SubmissionAdmin)
admin.site.register(Animal, AnimalAdmin)
admin.site.register(Sample, SampleAdmin)
admin.site.register(Name, NameAdmin)
admin.site.register(DictBreed, DictBreedAdmin)
admin.site.register(Person, PersonAdmin)
admin.site.register(Organization, OrganizationAdmin)
admin.site.register(Publication, admin.ModelAdmin)
admin.site.register(Ontology, OntologyAdmin)

# Re-register UserAdmin (to see related person data)
admin.site.unregister(User)
admin.site.register(User, UserAdmin)


1			#!/usr/bin/env python3
2			# -- coding: utf-8 --
3			"""
4			Created on Wed Nov 7 11:54:15 2018
5
6			@author: Paolo Cozzi <[email protected]>
7			"""
8
9			from django import forms
10			from django.contrib import admin
11			from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
12			from django.contrib.auth.models import User
13
14			from .models import (Animal, DictBreed, DictCountry, DictRole, DictSpecie,
15			Name, Ontology, Organization, Person, Publication, Sample,
16			Submission, DictSex, DictUberon, DictDevelStage,
17			DictPhysioStage)
18
19
20			class DictBreedAdmin(admin.ModelAdmin):
21			search_fields = ['supplied_breed']
22			list_per_page = 25
23			list_display = (
24			'supplied_breed', 'get_label', 'get_term', 'mapped_breed',
25			'mapped_breed_term', 'confidence', 'country', 'specie')
26
27			# override label and term verbose names
28			def get_label(self, instance):
29			return instance.label
30			get_label.short_description = "label"
31
32			def get_term(self, instance):
33			return instance.term
34			get_term.short_description = "term"
35
36			list_filter = ('country', 'specie')
37
38
39			class NameAdmin(admin.ModelAdmin):
40			"""A class to deal with animal names"""
41
42			search_fields = ['name', 'biosample_id']
43
44			list_per_page = 25
45			list_display = (
46			'name', 'submission', 'biosample_id', 'owner', 'status',
47			'last_changed', 'last_submitted')
48
49			list_filter = ('owner', 'status')
50
51			# join immediately name with DataSouce, in order to speed up name rendering
52			list_select_related = (
53			'submission', 'submission__gene_bank_country', 'owner'
54			)
55
56
57			# redefine form to edit Sample. Link animal to names in order to speed up
58			# name rendering
59			class SampleAdminForm(forms.ModelForm):
60			class Meta:
61			model = Sample
62			fields = '__all__'
63
64			def __init__(self, args, *kwargs):
65			super(SampleAdminForm, self).__init__(args, *kwargs)
66
67			# This is the bit that matters:
68			self.fields['animal'].queryset = Animal.objects.select_related('name')
69
70
71			# inspired from here:
72			# https://github.com/geex-arts/django-jet/issues/244#issuecomment-325001298
73			class SampleInLineFormSet(forms.BaseInlineFormSet):
74			''' Base Inline formset for Sample Model'''
75
76			def __init__(self, args, *kwargs):
77			super(SampleInLineFormSet, self).__init__(args, *kwargs)
78
79			# Animal will be a Animal object called when editing animal
80			animal = kwargs["instance"]
81
82			# get all Sample names from a certain animal with a unique query
83			# HINT: all problems related to subquery when displaying names arise
84			# from my __str__s methods, which display Sample and Animal name
85			# and the relation between table Name. In order to have all sample
86			# names for each animal, I need a join with three tables
87			self.queryset = Sample.objects.select_related(
88			'animal').select_related(
89			'name').filter(animal=animal)
90
91
92			class SampleInline(admin.StackedInline):
93			formset = SampleInLineFormSet
94
95			fields = (
96			('name', 'alternative_id', 'description', 'owner'),
97			('animal', 'protocol', 'organism_part'),
98			('collection_date', 'collection_place_latitude',
99			'collection_place_longitude', 'collection_place'),
100			('developmental_stage', 'physiological_stage',
101			'animal_age_at_collection', 'animal_age_at_collection_units',
102			'availability'),
103			('storage', 'storage_processing', 'preparation_interval',
104			'preparation_interval_units')
105			)
106
107			# manage a fields with many FK keys
108			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
109			raw_id_fields = ("name", "animal")
110
111			model = Sample
112			extra = 0
113
114
115			class SampleAdmin(admin.ModelAdmin):
116			form = SampleAdminForm
117
118			# exclude = ('author',)
119			# prepopulated_fields = {'name': ['description']}
120			search_fields = ['name__name']
121			list_per_page = 25
122			list_display = (
123			'name', 'alternative_id', 'animal',
124			'protocol', 'collection_date', 'collection_place_latitude',
125			'collection_place_longitude', 'collection_place', 'organism_part',
126			'developmental_stage', 'physiological_stage',
127			'animal_age_at_collection', 'animal_age_at_collection_units',
128			'availability', 'storage', 'storage_processing',
129			'preparation_interval', 'preparation_interval_units', 'description',
130			'owner'
131			)
132
133			# To tell Django we want to perform a join instead of fetching the names of
134			# the categories one by one
135			list_select_related = ('name', 'animal__name', 'owner', 'organism_part')
136
137			list_filter = ('owner', 'name__status')
138
139			fields = (
140			('name', 'alternative_id', 'description', 'owner'),
141			('animal', 'protocol', 'organism_part'),
142			('collection_date', 'collection_place', 'collection_place_latitude',
143			'collection_place_longitude', 'collection_place_accuracy'),
144			('developmental_stage',
145			'physiological_stage', 'animal_age_at_collection',
146			'animal_age_at_collection_units', 'availability'),
147			('storage', 'storage_processing', 'preparation_interval',
148			'preparation_interval_units')
149			)
150
151			# manage a fields with many FK keys
152			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
153			raw_id_fields = ("name", "animal")
154
155
156			class AnimalAdmin(admin.ModelAdmin):
157			search_fields = ['name__name']
158
159			list_per_page = 25
160			list_display = (
161			'name', 'alternative_id', 'breed', 'sex',
162			'father', 'mother', 'birth_location', 'birth_location_latitude',
163			'birth_location_longitude', 'description', 'owner'
164			)
165
166			list_filter = ('owner', 'name__status')
167
168			fields = (
169			'name', 'alternative_id', 'breed', 'sex', 'father',
170			'mother', ('birth_location', 'birth_location_latitude',
171			'birth_location_longitude'),
172			'description', 'owner'
173			)
174
175			# I can add manually an item if it is a readonly field
176			# readonly_fields = ("name",)
177
178			# manage a fields with many FK keys
179			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
180			raw_id_fields = ("name", "father", "mother", "breed")
181
182			# https://medium.com/@hakibenita/things-you-must-know-about-django-admin-as-your-app-gets-bigger-6be0b0ee9614
183			list_select_related = (
184			'name', 'breed', 'breed__specie', 'sex', 'father', 'mother', 'owner')
185
186			inlines = [SampleInline]
187
188
189			class SubmissionAdmin(admin.ModelAdmin):
190			list_per_page = 25
191			list_display = (
192			'title', 'description', 'gene_bank_name', 'gene_bank_country',
193			'datasource_type', 'datasource_version', 'organization', 'created_at',
194			'updated_at', 'status', 'owner'
195			)
196
197			# I cannot edit a auto_add_now field
198			readonly_fields = ('created_at', 'updated_at')
199
200			list_filter = ('owner', 'status')
201
202
203			class PersonAdmin(admin.ModelAdmin):
204			list_per_page = 25
205			list_display = (
206			'user_name', 'full_name', 'initials', 'affiliation', 'role',
207			)
208
209			def user_name(self, obj):
210			return obj.user.username
211
212			# rename column in admin
213			user_name.short_description = "User Name"
214
215			def full_name(self, obj):
216			return "%s %s" % (obj.user.first_name, obj.user.last_name)
217
218			full_name.short_description = "Full Name"
219
220
221			# https://simpleisbetterthancomplex.com/tutorial/2016/11/23/how-to-add-user-profile-to-django-admin.html
222			class PersonInLine(admin.StackedInline):
223			model = Person
224			can_delete = False
225			verbose_name_plural = 'Person'
226			fk_name = 'user'
227
228
229			class UserAdmin(BaseUserAdmin):
230			inlines = (PersonInLine, )
231			list_display = ('username', 'email', 'first_name', 'last_name', 'is_staff',
232			'get_role')
233			list_select_related = ('person', )
234
235			# this will display a column Role in User admin
236			def get_role(self, instance):
237			return instance.person.role
238			get_role.short_description = 'Role'
239
240			# display the inlines only in the edit form
241			def get_inline_instances(self, request, obj=None):
242			if not obj:
243			return list()
244			return super(UserAdmin, self).get_inline_instances(request, obj)
245
246
247			class OrganizationAdmin(admin.ModelAdmin):
248			list_per_page = 25
249			search_fields = ['name']
250			list_display = (
251			'name', 'address', 'country', 'URI', 'role',
252			)
253
254
255			class OntologyAdmin(admin.ModelAdmin):
256			list_per_page = 25
257			search_fields = ['library_name']
258			list_display = (
259			'library_name', 'library_uri', 'comment',
260			)
261
262
263			class DictCountryAdmin(admin.ModelAdmin):
264			list_per_page = 25
265			list_display = ('label', 'term', 'confidence')
266
267
268			class DictSpecieAdmin(admin.ModelAdmin):
269			list_per_page = 25
270			list_display = (
271			'label', 'term', 'confidence', 'general_breed_label',
272			'general_breed_term')
273
274
275			# --- registering applications
276
277			# default admin class
278			admin.site.register(DictRole, admin.ModelAdmin)
279			admin.site.register(DictSex, admin.ModelAdmin)
280			admin.site.register(DictUberon, admin.ModelAdmin)
281			admin.site.register(DictDevelStage, admin.ModelAdmin)
282			admin.site.register(DictPhysioStage, admin.ModelAdmin)
283
284			# Custom admin class
285			admin.site.register(DictSpecie, DictSpecieAdmin)
286			admin.site.register(DictCountry, DictCountryAdmin)
287			admin.site.register(Submission, SubmissionAdmin)
288			admin.site.register(Animal, AnimalAdmin)
289			admin.site.register(Sample, SampleAdmin)
290			admin.site.register(Name, NameAdmin)
291			admin.site.register(DictBreed, DictBreedAdmin)
292			admin.site.register(Person, PersonAdmin)
293			admin.site.register(Organization, OrganizationAdmin)
294			admin.site.register(Publication, admin.ModelAdmin)
295			admin.site.register(Ontology, OntologyAdmin)
296
297			# Re-register UserAdmin (to see related person data)
298			admin.site.unregister(User)
299			admin.site.register(User, UserAdmin)
300

cnr-ibba / IMAGE-InjectTool

Push — devel ( 3eb06e...2ff9b7 )

image_app.admin.DictBreedAdmin.get_term() A

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