uid.admin.SubmissionAdmin.short_message() - Code Metrics - Inspection of ":bookmark: InjectTool release v0.9.3" - cnr-ibba/IMAGE-InjectTool - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Pull Request — master (#91)

by Paolo

created 2020-01-30 16:44 UTC

uid.admin.SubmissionAdmin.short_message() A

↳ Parent: uid.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 django.template.defaultfilters import truncatechars

from .models import (Animal, DictBreed, DictCountry, DictRole, DictSpecie,
                     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')


# 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').filter(animal=animal)


class SampleInline(admin.StackedInline):
    formset = SampleInLineFormSet

    fields = (
        ('name', 'alternative_id', 'biosample_id'),
        ('submission', 'owner', 'status'),
        ('description', 'publication'),
        ('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'),
        'last_submitted',
    )

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

    model = Sample
    extra = 0


class SampleAdmin(admin.ModelAdmin):
    # exclude = ('author',)
    # prepopulated_fields = {'name': ['description']}
    search_fields = ['name', 'biosample_id']
    list_per_page = 25

    list_display = (
        'name', 'biosample_id', 'submission', 'status', 'last_changed',
        'last_submitted', 'alternative_id', 'animal', 'collection_date',
        'collection_place', 'collection_place_latitude',
        'collection_place_longitude', 'collection_place_accuracy',
        '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', 'publication', 'owner'
        )

    # To tell Django we want to perform a join instead of fetching the names of
    # the categories one by one
    # https://medium.com/@hakibenita/things-you-must-know-about-django-admin-as-your-app-gets-bigger-6be0b0ee9614
    list_select_related = (
        'submission', 'submission__gene_bank_country', 'animal',
        'organism_part', 'developmental_stage', 'physiological_stage', 'owner'
    )

    list_filter = ('owner', 'status')

    fields = (
        ('name', 'alternative_id', 'biosample_id'),
        ('submission', 'owner', 'status'),
        ('description', 'publication'),
        ('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'),
        'last_submitted',
    )

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


class AnimalAdmin(admin.ModelAdmin):
    search_fields = ['name', 'biosample_id']

    list_per_page = 25
    list_display = (
        'name', 'biosample_id', 'submission', 'status', 'last_changed',
        'last_submitted', 'alternative_id', 'breed', 'sex', 'father', 'mother',
        'birth_date', 'birth_location', 'birth_location_latitude',
        'birth_location_longitude', 'birth_location_accuracy', 'description',
        'publication', 'owner'
        )

    list_filter = ('owner', 'status')

    # I don't want to change this
    readonly_fields = ("owner",)

    fields = (
        ('name', 'alternative_id', 'biosample_id'),
        ('submission', 'owner', 'status'),
        ('description', 'publication'),
        ('breed', 'sex'),
        ('father', 'mother'),
        ('birth_date', 'birth_location'),
        ('birth_location_latitude',
         'birth_location_longitude', 'birth_location_accuracy'),
        'last_submitted',
    )

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

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

    inlines = [SampleInline]


class SubmissionAdmin(admin.ModelAdmin):
    list_per_page = 25
    list_display = (
        'title', 'owner', 'short_organization', 'created_at', 'updated_at',
        'status', 'gene_bank_name', 'short_country', 'datasource_type',
        'datasource_version', 'short_message'
    )

    def short_organization(self, obj):
        return truncatechars(obj.organization.name, 30)

    # rename column in admin
    short_organization.short_description = "Organization"

    def short_country(self, obj):
        return obj.gene_bank_country.label

    # rename column in admin
    short_country.short_description = "Gene Bank Country"

    def short_message(self, obj):
        return truncatechars(obj.message, 40)

    # rename column in admin
    short_message.short_description = "Message"

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

    # I cannot edit a auto_add_now field
    readonly_fields = ('owner', '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			from django.template.defaultfilters import truncatechars
14
15			from .models import (Animal, DictBreed, DictCountry, DictRole, DictSpecie,
16			Ontology, Organization, Person, Publication, Sample,
17			Submission, DictSex, DictUberon, DictDevelStage,
18			DictPhysioStage)
19
20
21			class DictBreedAdmin(admin.ModelAdmin):
22			search_fields = ['supplied_breed']
23			list_per_page = 25
24			list_display = (
25			'supplied_breed', 'get_label', 'get_term', 'mapped_breed',
26			'mapped_breed_term', 'confidence', 'country', 'specie')
27
28			# override label and term verbose names
29			def get_label(self, instance):
30			return instance.label
31			get_label.short_description = "label"
32
33			def get_term(self, instance):
34			return instance.term
35			get_term.short_description = "term"
36
37			list_filter = ('country', 'specie')
38
39
40			# inspired from here:
41			# https://github.com/geex-arts/django-jet/issues/244#issuecomment-325001298
42			class SampleInLineFormSet(forms.BaseInlineFormSet):
43			''' Base Inline formset for Sample Model'''
44
45			def __init__(self, args, *kwargs):
46			super(SampleInLineFormSet, self).__init__(args, *kwargs)
47
48			# Animal will be a Animal object called when editing animal
49			animal = kwargs["instance"]
50
51			# get all Sample names from a certain animal with a unique query
52			# HINT: all problems related to subquery when displaying names arise
53			# from my __str__s methods, which display Sample and Animal name
54			# and the relation between table Name. In order to have all sample
55			# names for each animal, I need a join with three tables
56			self.queryset = Sample.objects.select_related(
57			'animal').filter(animal=animal)
58
59
60			class SampleInline(admin.StackedInline):
61			formset = SampleInLineFormSet
62
63			fields = (
64			('name', 'alternative_id', 'biosample_id'),
65			('submission', 'owner', 'status'),
66			('description', 'publication'),
67			('animal', 'protocol', 'organism_part'),
68			('collection_date', 'collection_place', 'collection_place_latitude',
69			'collection_place_longitude', 'collection_place_accuracy'),
70			('developmental_stage',
71			'physiological_stage', 'animal_age_at_collection',
72			'animal_age_at_collection_units', 'availability'),
73			('storage', 'storage_processing', 'preparation_interval',
74			'preparation_interval_units'),
75			'last_submitted',
76			)
77
78			# manage a fields with many FK keys
79			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
80			raw_id_fields = ("animal", "submission", "publication")
81
82			model = Sample
83			extra = 0
84
85
86			class SampleAdmin(admin.ModelAdmin):
87			# exclude = ('author',)
88			# prepopulated_fields = {'name': ['description']}
89			search_fields = ['name', 'biosample_id']
90			list_per_page = 25
91
92			list_display = (
93			'name', 'biosample_id', 'submission', 'status', 'last_changed',
94			'last_submitted', 'alternative_id', 'animal', 'collection_date',
95			'collection_place', 'collection_place_latitude',
96			'collection_place_longitude', 'collection_place_accuracy',
97			'organism_part', 'developmental_stage', 'physiological_stage',
98			'animal_age_at_collection', 'animal_age_at_collection_units',
99			'availability', 'storage', 'storage_processing',
100			'preparation_interval', 'preparation_interval_units',
101			'description', 'publication', 'owner'
102			)
103
104			# To tell Django we want to perform a join instead of fetching the names of
105			# the categories one by one
106			# https://medium.com/@hakibenita/things-you-must-know-about-django-admin-as-your-app-gets-bigger-6be0b0ee9614
107			list_select_related = (
108			'submission', 'submission__gene_bank_country', 'animal',
109			'organism_part', 'developmental_stage', 'physiological_stage', 'owner'
110			)
111
112			list_filter = ('owner', 'status')
113
114			fields = (
115			('name', 'alternative_id', 'biosample_id'),
116			('submission', 'owner', 'status'),
117			('description', 'publication'),
118			('animal', 'protocol', 'organism_part'),
119			('collection_date', 'collection_place', 'collection_place_latitude',
120			'collection_place_longitude', 'collection_place_accuracy'),
121			('developmental_stage',
122			'physiological_stage', 'animal_age_at_collection',
123			'animal_age_at_collection_units', 'availability'),
124			('storage', 'storage_processing', 'preparation_interval',
125			'preparation_interval_units'),
126			'last_submitted',
127			)
128
129			# manage a fields with many FK keys
130			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
131			raw_id_fields = ("animal", "submission", "publication")
132
133
134			class AnimalAdmin(admin.ModelAdmin):
135			search_fields = ['name', 'biosample_id']
136
137			list_per_page = 25
138			list_display = (
139			'name', 'biosample_id', 'submission', 'status', 'last_changed',
140			'last_submitted', 'alternative_id', 'breed', 'sex', 'father', 'mother',
141			'birth_date', 'birth_location', 'birth_location_latitude',
142			'birth_location_longitude', 'birth_location_accuracy', 'description',
143			'publication', 'owner'
144			)
145
146			list_filter = ('owner', 'status')
147
148			# I don't want to change this
149			readonly_fields = ("owner",)
150
151			fields = (
152			('name', 'alternative_id', 'biosample_id'),
153			('submission', 'owner', 'status'),
154			('description', 'publication'),
155			('breed', 'sex'),
156			('father', 'mother'),
157			('birth_date', 'birth_location'),
158			('birth_location_latitude',
159			'birth_location_longitude', 'birth_location_accuracy'),
160			'last_submitted',
161			)
162
163			# manage a fields with many FK keys
164			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
165			raw_id_fields = ("father", "mother", "breed", "submission", "publication")
166
167			# https://medium.com/@hakibenita/things-you-must-know-about-django-admin-as-your-app-gets-bigger-6be0b0ee9614
168			list_select_related = (
169			'submission', 'submission__gene_bank_country', 'breed',
170			'breed__specie', 'breed__country', 'sex', 'father', 'mother', 'owner')
171
172			inlines = [SampleInline]
173
174
175			class SubmissionAdmin(admin.ModelAdmin):
176			list_per_page = 25
177			list_display = (
178			'title', 'owner', 'short_organization', 'created_at', 'updated_at',
179			'status', 'gene_bank_name', 'short_country', 'datasource_type',
180			'datasource_version', 'short_message'
181			)
182
183			def short_organization(self, obj):
184			return truncatechars(obj.organization.name, 30)
185
186			# rename column in admin
187			short_organization.short_description = "Organization"
188
189			def short_country(self, obj):
190			return obj.gene_bank_country.label
191
192			# rename column in admin
193			short_country.short_description = "Gene Bank Country"
194
195			def short_message(self, obj):
196			return truncatechars(obj.message, 40)
197
198			# rename column in admin
199			short_message.short_description = "Message"
200
201			# manage a fields with many FK keys
202			# https://books.agiliq.com/projects/django-admin-cookbook/en/latest/many_fks.html
203			raw_id_fields = ("gene_bank_country", "organization")
204
205			# I cannot edit a auto_add_now field
206			readonly_fields = ('owner', 'created_at', 'updated_at')
207
208			list_filter = ('owner', 'status')
209
210
211			class PersonAdmin(admin.ModelAdmin):
212			list_per_page = 25
213			list_display = (
214			'user_name', 'full_name', 'initials', 'affiliation', 'role',
215			)
216
217			def user_name(self, obj):
218			return obj.user.username
219
220			# rename column in admin
221			user_name.short_description = "User Name"
222
223			def full_name(self, obj):
224			return "%s %s" % (obj.user.first_name, obj.user.last_name)
225
226			full_name.short_description = "Full Name"
227
228
229			# https://simpleisbetterthancomplex.com/tutorial/2016/11/23/how-to-add-user-profile-to-django-admin.html
230			class PersonInLine(admin.StackedInline):
231			model = Person
232			can_delete = False
233			verbose_name_plural = 'Person'
234			fk_name = 'user'
235
236
237			class UserAdmin(BaseUserAdmin):
238			inlines = (PersonInLine, )
239			list_display = ('username', 'email', 'first_name', 'last_name', 'is_staff',
240			'get_role')
241			list_select_related = ('person', )
242
243			# this will display a column Role in User admin
244			def get_role(self, instance):
245			return instance.person.role
246			get_role.short_description = 'Role'
247
248			# display the inlines only in the edit form
249			def get_inline_instances(self, request, obj=None):
250			if not obj:
251			return list()
252			return super(UserAdmin, self).get_inline_instances(request, obj)
253
254
255			class OrganizationAdmin(admin.ModelAdmin):
256			list_per_page = 25
257			search_fields = ['name']
258			list_display = (
259			'name', 'address', 'country', 'URI', 'role',
260			)
261
262
263			class OntologyAdmin(admin.ModelAdmin):
264			list_per_page = 25
265			search_fields = ['library_name']
266			list_display = (
267			'library_name', 'library_uri', 'comment',
268			)
269
270
271			class DictCountryAdmin(admin.ModelAdmin):
272			list_per_page = 25
273			list_display = ('label', 'term', 'confidence')
274
275
276			class DictSpecieAdmin(admin.ModelAdmin):
277			list_per_page = 25
278			list_display = (
279			'label', 'term', 'confidence', 'general_breed_label',
280			'general_breed_term')
281
282
283			# --- registering applications
284
285			# default admin class
286			admin.site.register(DictRole, admin.ModelAdmin)
287			admin.site.register(DictSex, admin.ModelAdmin)
288			admin.site.register(DictUberon, admin.ModelAdmin)
289			admin.site.register(DictDevelStage, admin.ModelAdmin)
290			admin.site.register(DictPhysioStage, admin.ModelAdmin)
291
292			# Custom admin class
293			admin.site.register(DictSpecie, DictSpecieAdmin)
294			admin.site.register(DictCountry, DictCountryAdmin)
295			admin.site.register(Submission, SubmissionAdmin)
296			admin.site.register(Animal, AnimalAdmin)
297			admin.site.register(Sample, SampleAdmin)
298			# admin.site.register(Name, NameAdmin)
299			admin.site.register(DictBreed, DictBreedAdmin)
300			admin.site.register(Person, PersonAdmin)
301			admin.site.register(Organization, OrganizationAdmin)
302			admin.site.register(Publication, admin.ModelAdmin)
303			admin.site.register(Ontology, OntologyAdmin)
304
305			# Re-register UserAdmin (to see related person data)
306			admin.site.unregister(User)
307			admin.site.register(User, UserAdmin)
308

cnr-ibba / IMAGE-InjectTool

Pull Request — master (#91)

uid.admin.SubmissionAdmin.short_message() A

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