13546875483

Committed 26 Feb 2025 03:01PM UTC coverage: 84.16% (-0.02%) from 84.184%

Build # 13546875483

Build Type

push

github

Committed by

web-flow

Commit Message

Feat/notes and narrative (#897)

Resolves issue #642

* Add Notes list view to 'Common' section

* add filterset for notes

* add 'has narrative' filters to Session list view

* remove superfluous calls of filter()

* use regex for filtering narrative

* add 'has_note' filter  to Session list view

* include ContentType with HasNoteFilter / clean-up

* use `\s` instead of ` ` in `HasNarrativeFilter` regex

* flake8

Run Details

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81.31

alyx/misc/admin.py

from pytz import all_timezones

from django import forms
from django.db import models
from django.db.models import Q
from django.contrib import admin
from django.contrib.admin.widgets import AdminFileWidget
from django.contrib.contenttypes.admin import GenericTabularInline
from django.contrib.postgres.fields import JSONField
from django.utils.html import format_html, format_html_join
from django.utils.safestring import mark_safe
from django_admin_listfilter_dropdown.filters import RelatedDropdownFilter
from rest_framework.authtoken.models import TokenProxy
from rangefilter.filters import DateRangeFilter

from misc.models import Note, Lab, LabMembership, LabLocation, CageType, \
    Enrichment, Food, Housing, HousingSubject
from alyx.base import BaseAdmin, DefaultListFilter, get_admin_url


class LabForm(forms.ModelForm):
    def __init__(self, *args, **kwargs):
        super(LabForm, self).__init__(*args, **kwargs)
        # if user has read-only permissions only fields is empty
        if not self.is_bound:
            return
        self.fields['reference_weight_pct'].help_text =\
            'Threshold ratio triggers a warning using the Reference Weight method (0-1)'
        self.fields['reference_weight_pct'].label = 'Reference Weight Ratio'
        self.fields['zscore_weight_pct'].help_text =\
            'Threshold ratio triggers a warning is raised using the Z-Score method (0-1)'
        self.fields['zscore_weight_pct'].label = 'Z-score Weight Ratio'

    def clean_reference_weight_pct(self):
        ref = self.cleaned_data['reference_weight_pct']
        ref = max(ref, 0)
        if ref > 1:
            ref = ref / 100
        return ref

    def clean_zscore_weight_pct(self):
        ref = self.cleaned_data['zscore_weight_pct']
        ref = max(ref, 0)
        if ref > 1:
            ref = ref / 100
        return ref

    def clean_timezone(self):
        ref = self.cleaned_data['timezone']
        if ref not in all_timezones:
            raise forms.ValidationError(
                ("Time Zone is incorrect here is the list (column TZ Database Name):  "
                 "https://en.wikipedia.org/wiki/List_of_tz_database_time_zones"))
        return ref


class LabAdmin(BaseAdmin):
    form = LabForm
    generics = ['name', 'institution', 'address', 'timezone',
                'reference_weight_pct', 'zscore_weight_pct']
    list_display = ['name', 'institution', 'address', 'timezone', 'local', 'server',
                    'reference_weight_pct', 'zscore_weight_pct']
    list_select_related = ['cage_type', 'enrichment', 'food']
    fields = generics + list_select_related + ['cage_cleaning_frequency_days', 'light_cycle',
                                               'repositories']

    def local(self, obj):
        return ','.join([p.name for p in obj.repositories.filter(globus_is_personal=True)])

    def server(self, obj):
        return ','.join([p.name for p in obj.repositories.filter(globus_is_personal=False)])


class LabMembershipAdmin(BaseAdmin):
    fields = ['user', 'lab', 'role', 'start_date', 'end_date']
    list_display = fields


class LabLocationAdmin(BaseAdmin):
    fields = ['name', 'lab']
    list_display = fields
    search_fields = ('lab__name', 'name',)
    ordering = ('lab__name', 'name',)


class AdminImageWidget(AdminFileWidget):

    def render(self, name, value, attrs=None, renderer=None):
        output = []
        if value and getattr(value, "url", None):
            image_url = value.url
            file_name = str(value)
            output.append(f'<a href="{image_url}" target="_blank">'
                          f'<img src="{image_url}" width="400" alt="{file_name}" /></a><br>')
        output.append(super(AdminFileWidget, self).render(name, value, attrs, renderer))
        return mark_safe(''.join(output))


class ImageWidgetAdmin(BaseAdmin):
    image_fields = []

    def formfield_for_dbfield(self, db_field, **kwargs):
        if db_field.name in self.image_fields:
            request = kwargs.pop("request", None)  # noqa
            kwargs['widget'] = AdminImageWidget
            return db_field.formfield(**kwargs)
        return super(ImageWidgetAdmin, self).formfield_for_dbfield(db_field, **kwargs)


class HasImageFilter(DefaultListFilter):
    title = 'image'
    parameter_name = 'has_image'

    def lookups(self, request, model_admin):
        return (
            (None, 'All'),
            ('image', 'Has image'),
            ('no_image', 'No image'),
        )

    def queryset(self, request, queryset):
        if self.value() == 'image':
            return queryset.exclude(image__exact='')
        if self.value() == 'no_image':
            return queryset.filter(image__exact='')
        elif self.value is None:
            return queryset.all()


class NoteAdmin(ImageWidgetAdmin):
    list_display = ['user', 'date_time', 'content_object', 'text', 'image']
    list_display_links = ['date_time']
    list_filter = [('user', RelatedDropdownFilter),
                   ('date_time', DateRangeFilter),
                   ('content_type', RelatedDropdownFilter),
                   (HasImageFilter),
                   ]
    image_fields = ['image']
    fields = ['user', 'date_time', 'text', 'image', 'content_type', 'object_id']
    ordering = ('-date_time',)
    search_fields = ['text']


class NoteInline(GenericTabularInline):
    model = Note
    extra = 1
    fields = ('user', 'date_time', 'text', 'image')
    image_fields = ('image',)
    ordering = ('-date_time',)

    formfield_overrides = {
        models.TextField: {'widget': forms.Textarea(
                           attrs={'rows': 3,
                                  'cols': 30})},
        JSONField: {'widget': forms.Textarea(
                    attrs={'rows': 3,
                           'cols': 30})},
        models.CharField: {'widget': forms.TextInput(attrs={'size': 16})},
    }

    def formfield_for_foreignkey(self, db_field, request, **kwargs):
        # Logged-in user by default.
        if db_field.name == 'user':
            kwargs['initial'] = request.user
        return super(NoteInline, self).formfield_for_foreignkey(
            db_field, request, **kwargs
        )

    def formfield_for_dbfield(self, db_field, **kwargs):
        if db_field.name in self.image_fields:
            request = kwargs.pop("request", None)  # noqa
            kwargs['widget'] = AdminImageWidget
            return db_field.formfield(**kwargs)
        return super(NoteInline, self).formfield_for_dbfield(db_field, **kwargs)

    def has_delete_permission(self, request, obj=None):
        return False


class CageTypeAdmin(BaseAdmin):
    fields = ('name', 'description',)
    list_display = fields
    search_fields = ('name',)


class EnrichmentAdmin(BaseAdmin):
    fields = ('name', 'description',)
    list_display = fields
    search_fields = ('name',)


class FoodAdmin(BaseAdmin):
    fields = ('name', 'description',)
    list_display = fields
    search_fields = ('name',)


class HousingSubjectAdminInline(admin.TabularInline):
    model = HousingSubject
    extra = 1
    fields = ('subject', 'start_datetime', 'end_datetime')

    def get_queryset(self, request):
        qs = super(HousingSubjectAdminInline, self).get_queryset(request)
        return qs.filter(subject__cull__isnull=True)


class HousingAdminForm(forms.ModelForm):

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        request = self.Meta.formfield_callback.keywords['request']
        self.user = request.user
        lab = self.user.lab_id()
        if lab:
            self.fields['cage_type'].initial = lab[0].cage_type
            self.fields['enrichment'].initial = lab[0].enrichment
            self.fields['light_cycle'].initial = lab[0].light_cycle
            self.fields['food'].initial = lab[0].food
            self.fields['cage_cleaning_frequency_days'].initial =\
                lab[0].cage_cleaning_frequency_days

    class Meta():
        model = Housing
        fields = ['cage_type', 'cage_name',
                  'enrichment', 'light_cycle',
                  'food', 'cage_cleaning_frequency_days']


class HousingIsCurrentFilter(DefaultListFilter):
    title = 'Housing Current'
    parameter_name = 'Housing Current'

    def lookups(self, request, model_admin):
        return (
            (None, 'Current'),
            ('All', 'All'),
        )

    def queryset(self, request, queryset):
        if self.value() is None:
            return queryset.exclude(nsubs=0)


class HousingAdmin(BaseAdmin):

    inlines = [HousingSubjectAdminInline]
    form = HousingAdminForm

    fields = ['subjects_l',
              ('cage_type', 'cage_name'),
              ('enrichment', 'light_cycle',),
              ('food', 'cage_cleaning_frequency_days')]
    search_fields = ('housing_subjects__subject__nickname', 'housing_subjects__subject__lab__name')
    list_display = ('cage_l', 'subjects_l', 'subjects_old', 'start',
                    'end', 'subjects_count', 'lab',)
    readonly_fields = ('subjects_l',)
    list_filter = (HousingIsCurrentFilter,)

    def get_queryset(self, request):
        qs = Housing.objects.annotate(
            nsubs=models.Count('housing_subjects',
                               filter=Q(housing_subjects__end_datetime__isnull=True),
                               distinct=True))
        qs = qs.annotate(start_datetime=models.Min('housing_subjects__start_datetime'))
        qs = qs.annotate(end_datetime=models.Case(models.When(
            nsubs=0, then=models.Max('housing_subjects__end_datetime')),
            output_field=models.DateTimeField(),))
        return qs

    def start(self, obj):
        return obj.start_datetime

    def end(self, obj):
        return obj.end_datetime

    def subjects_count(self, obj):
        return obj.nsubs
    subjects_count.short_description = '# active'

    def cage_l(self, obj):
        return format_html('<a href="{url}">{hou}</a>', url=get_admin_url(obj), hou=obj.cage_name)
    cage_l.short_description = 'cage'

    def subjects_l(self, obj):
        out = format_html_join(', ', '<a href="{}">{}</a>',
                               ((get_admin_url(sub), sub) for sub in obj.subjects_current()))
        return format_html(out)
    subjects_l.short_description = 'subjects'

    def subjects_old(self, obj):
        subs = obj.subjects.exclude(pk__in=obj.subjects_current().values_list('pk', flat=True))
        out = format_html_join(', ', '<a href="{}">{}</a>',
                               ((get_admin_url(sub), sub) for sub in subs))
        return format_html(out)
    subjects_old.short_description = 'old subjects'


admin.site.register(Housing, HousingAdmin)
admin.site.register(Lab, LabAdmin)
admin.site.register(LabMembership, LabMembershipAdmin)
admin.site.register(LabLocation, LabLocationAdmin)
admin.site.register(Note, NoteAdmin)
admin.site.register(CageType, CageTypeAdmin)
admin.site.register(Enrichment, EnrichmentAdmin)
admin.site.register(Food, FoodAdmin)
admin.site.unregister(TokenProxy)

1	from pytz import all_timezones	1✔
2
3	from django import forms	1✔
4	from django.db import models	1✔
5	from django.db.models import Q	1✔
6	from django.contrib import admin	1✔
7	from django.contrib.admin.widgets import AdminFileWidget	1✔
8	from django.contrib.contenttypes.admin import GenericTabularInline	1✔
9	from django.contrib.postgres.fields import JSONField	1✔
10	from django.utils.html import format_html, format_html_join	1✔
11	from django.utils.safestring import mark_safe	1✔
12	from django_admin_listfilter_dropdown.filters import RelatedDropdownFilter	1✔
13	from rest_framework.authtoken.models import TokenProxy	1✔
14	from rangefilter.filters import DateRangeFilter	1✔
15
16	from misc.models import Note, Lab, LabMembership, LabLocation, CageType, \	1✔
17	Enrichment, Food, Housing, HousingSubject
18	from alyx.base import BaseAdmin, DefaultListFilter, get_admin_url	1✔
19
20
21	class LabForm(forms.ModelForm):	1✔
22	def __init__(self, args, *kwargs):	1✔
23	super(LabForm, self).__init__(args, *kwargs)	1✔
24	# if user has read-only permissions only fields is empty
25	if not self.is_bound:	1✔
26	return	1✔
27	self.fields['reference_weight_pct'].help_text =\	×
28	'Threshold ratio triggers a warning using the Reference Weight method (0-1)'
29	self.fields['reference_weight_pct'].label = 'Reference Weight Ratio'	×
30	self.fields['zscore_weight_pct'].help_text =\	×
31	'Threshold ratio triggers a warning is raised using the Z-Score method (0-1)'
32	self.fields['zscore_weight_pct'].label = 'Z-score Weight Ratio'	×
33
34	def clean_reference_weight_pct(self):	1✔
35	ref = self.cleaned_data['reference_weight_pct']	×
36	ref = max(ref, 0)	×
37	if ref > 1:	×
38	ref = ref / 100	×
39	return ref	×
40
41	def clean_zscore_weight_pct(self):	1✔
42	ref = self.cleaned_data['zscore_weight_pct']	×
43	ref = max(ref, 0)	×
44	if ref > 1:	×
45	ref = ref / 100	×
46	return ref	×
47
48	def clean_timezone(self):	1✔
49	ref = self.cleaned_data['timezone']	×
50	if ref not in all_timezones:	×
51	raise forms.ValidationError(	×
52	("Time Zone is incorrect here is the list (column TZ Database Name): "
53	"https://en.wikipedia.org/wiki/List_of_tz_database_time_zones"))
54	return ref	×
55
56
57	class LabAdmin(BaseAdmin):	1✔
58	form = LabForm	1✔
59	generics = ['name', 'institution', 'address', 'timezone',	1✔
60	'reference_weight_pct', 'zscore_weight_pct']
61	list_display = ['name', 'institution', 'address', 'timezone', 'local', 'server',	1✔
62	'reference_weight_pct', 'zscore_weight_pct']
63	list_select_related = ['cage_type', 'enrichment', 'food']	1✔
64	fields = generics + list_select_related + ['cage_cleaning_frequency_days', 'light_cycle',	1✔
65	'repositories']
66
67	def local(self, obj):	1✔
68	return ','.join([p.name for p in obj.repositories.filter(globus_is_personal=True)])	1✔
69
70	def server(self, obj):	1✔
71	return ','.join([p.name for p in obj.repositories.filter(globus_is_personal=False)])	1✔
72
73
74	class LabMembershipAdmin(BaseAdmin):	1✔
75	fields = ['user', 'lab', 'role', 'start_date', 'end_date']	1✔
76	list_display = fields	1✔
77
78
79	class LabLocationAdmin(BaseAdmin):	1✔
80	fields = ['name', 'lab']	1✔
81	list_display = fields	1✔
82	search_fields = ('lab__name', 'name',)	1✔
83	ordering = ('lab__name', 'name',)	1✔
84
85
86	class AdminImageWidget(AdminFileWidget):	1✔
87
88	def render(self, name, value, attrs=None, renderer=None):	1✔
89	output = []	1✔
90	if value and getattr(value, "url", None):	1✔
91	image_url = value.url	×
92	file_name = str(value)	×
93	output.append(f'<a href="{image_url}" target="_blank">'	×
94	f'<img src="{image_url}" width="400" alt="{file_name}" /></a><br>')
95	output.append(super(AdminFileWidget, self).render(name, value, attrs, renderer))	1✔
96	return mark_safe(''.join(output))	1✔
97
98
99	class ImageWidgetAdmin(BaseAdmin):	1✔
100	image_fields = []	1✔
101
102	def formfield_for_dbfield(self, db_field, **kwargs):	1✔
103	if db_field.name in self.image_fields:	1✔
104	request = kwargs.pop("request", None) # noqa	1✔
105	kwargs['widget'] = AdminImageWidget	1✔
106	return db_field.formfield(**kwargs)	1✔
107	return super(ImageWidgetAdmin, self).formfield_for_dbfield(db_field, **kwargs)	1✔
108
109
110	class HasImageFilter(DefaultListFilter):	1✔
111	title = 'image'	1✔
112	parameter_name = 'has_image'	1✔
113
114	def lookups(self, request, model_admin):	1✔
115	return (	1✔
116	(None, 'All'),
117	('image', 'Has image'),
118	('no_image', 'No image'),
119	)
120
121	def queryset(self, request, queryset):	1✔
122	if self.value() == 'image':	1✔
123	return queryset.exclude(image__exact='')	×
124	if self.value() == 'no_image':	1✔
125	return queryset.filter(image__exact='')	×
126	elif self.value is None:	1✔
127	return queryset.all()	×
128
129
130	class NoteAdmin(ImageWidgetAdmin):	1✔
131	list_display = ['user', 'date_time', 'content_object', 'text', 'image']	1✔
132	list_display_links = ['date_time']	1✔
133	list_filter = [('user', RelatedDropdownFilter),	1✔
134	('date_time', DateRangeFilter),
135	('content_type', RelatedDropdownFilter),
136	(HasImageFilter),
137	]
138	image_fields = ['image']	1✔
139	fields = ['user', 'date_time', 'text', 'image', 'content_type', 'object_id']	1✔
140	ordering = ('-date_time',)	1✔
141	search_fields = ['text']	1✔
142
143
144	class NoteInline(GenericTabularInline):	1✔
145	model = Note	1✔
146	extra = 1	1✔
147	fields = ('user', 'date_time', 'text', 'image')	1✔
148	image_fields = ('image',)	1✔
149	ordering = ('-date_time',)	1✔
150
151	formfield_overrides = {	1✔
152	models.TextField: {'widget': forms.Textarea(
153	attrs={'rows': 3,
154	'cols': 30})},
155	JSONField: {'widget': forms.Textarea(
156	attrs={'rows': 3,
157	'cols': 30})},
158	models.CharField: {'widget': forms.TextInput(attrs={'size': 16})},
159	}
160
161	def formfield_for_foreignkey(self, db_field, request, **kwargs):	1✔
162	# Logged-in user by default.
163	if db_field.name == 'user':	1✔
164	kwargs['initial'] = request.user	1✔
165	return super(NoteInline, self).formfield_for_foreignkey(	1✔
166	db_field, request, **kwargs
167	)
168
169	def formfield_for_dbfield(self, db_field, **kwargs):	1✔
170	if db_field.name in self.image_fields:	1✔
171	request = kwargs.pop("request", None) # noqa	1✔
172	kwargs['widget'] = AdminImageWidget	1✔
173	return db_field.formfield(**kwargs)	1✔
174	return super(NoteInline, self).formfield_for_dbfield(db_field, **kwargs)	1✔
175
176	def has_delete_permission(self, request, obj=None):	1✔
177	return False	1✔
178
179
180	class CageTypeAdmin(BaseAdmin):	1✔
181	fields = ('name', 'description',)	1✔
182	list_display = fields	1✔
183	search_fields = ('name',)	1✔
184
185
186	class EnrichmentAdmin(BaseAdmin):	1✔
187	fields = ('name', 'description',)	1✔
188	list_display = fields	1✔
189	search_fields = ('name',)	1✔
190
191
192	class FoodAdmin(BaseAdmin):	1✔
193	fields = ('name', 'description',)	1✔
194	list_display = fields	1✔
195	search_fields = ('name',)	1✔
196
197
198	class HousingSubjectAdminInline(admin.TabularInline):	1✔
199	model = HousingSubject	1✔
200	extra = 1	1✔
201	fields = ('subject', 'start_datetime', 'end_datetime')	1✔
202
203	def get_queryset(self, request):	1✔
204	qs = super(HousingSubjectAdminInline, self).get_queryset(request)	1✔
205	return qs.filter(subject__cull__isnull=True)	1✔
206
207
208	class HousingAdminForm(forms.ModelForm):	1✔
209
210	def __init__(self, args, *kwargs):	1✔
211	super().__init__(args, *kwargs)	1✔
212	request = self.Meta.formfield_callback.keywords['request']	1✔
213	self.user = request.user	1✔
214	lab = self.user.lab_id()	1✔
215	if lab:	1✔
216	self.fields['cage_type'].initial = lab[0].cage_type	×
217	self.fields['enrichment'].initial = lab[0].enrichment	×
218	self.fields['light_cycle'].initial = lab[0].light_cycle	×
219	self.fields['food'].initial = lab[0].food	×
220	self.fields['cage_cleaning_frequency_days'].initial =\	×
221	lab[0].cage_cleaning_frequency_days
222
223	class Meta():	1✔
224	model = Housing	1✔
225	fields = ['cage_type', 'cage_name',	1✔
226	'enrichment', 'light_cycle',
227	'food', 'cage_cleaning_frequency_days']
228
229
230	class HousingIsCurrentFilter(DefaultListFilter):	1✔
231	title = 'Housing Current'	1✔
232	parameter_name = 'Housing Current'	1✔
233
234	def lookups(self, request, model_admin):	1✔
235	return (	1✔
236	(None, 'Current'),
237	('All', 'All'),
238	)
239
240	def queryset(self, request, queryset):	1✔
241	if self.value() is None:	1✔
242	return queryset.exclude(nsubs=0)	1✔
243
244
245	class HousingAdmin(BaseAdmin):	1✔
246
247	inlines = [HousingSubjectAdminInline]	1✔
248	form = HousingAdminForm	1✔
249
250	fields = ['subjects_l',	1✔
251	('cage_type', 'cage_name'),
252	('enrichment', 'light_cycle',),
253	('food', 'cage_cleaning_frequency_days')]
254	search_fields = ('housing_subjects__subject__nickname', 'housing_subjects__subject__lab__name')	1✔
255	list_display = ('cage_l', 'subjects_l', 'subjects_old', 'start',	1✔
256	'end', 'subjects_count', 'lab',)
257	readonly_fields = ('subjects_l',)	1✔
258	list_filter = (HousingIsCurrentFilter,)	1✔
259
260	def get_queryset(self, request):	1✔
261	qs = Housing.objects.annotate(	1✔
262	nsubs=models.Count('housing_subjects',
263	filter=Q(housing_subjects__end_datetime__isnull=True),
264	distinct=True))
265	qs = qs.annotate(start_datetime=models.Min('housing_subjects__start_datetime'))	1✔
266	qs = qs.annotate(end_datetime=models.Case(models.When(	1✔
267	nsubs=0, then=models.Max('housing_subjects__end_datetime')),
268	output_field=models.DateTimeField(),))
269	return qs	1✔
270
271	def start(self, obj):	1✔
272	return obj.start_datetime	×
273
274	def end(self, obj):	1✔
275	return obj.end_datetime	×
276
277	def subjects_count(self, obj):	1✔
278	return obj.nsubs	×
279	subjects_count.short_description = '# active'	1✔
280
281	def cage_l(self, obj):	1✔
282	return format_html('<a href="{url}">{hou}</a>', url=get_admin_url(obj), hou=obj.cage_name)	×
283	cage_l.short_description = 'cage'	1✔
284
285	def subjects_l(self, obj):	1✔
286	out = format_html_join(', ', '<a href="{}">{}</a>',	1✔
287	((get_admin_url(sub), sub) for sub in obj.subjects_current()))
288	return format_html(out)	×
289	subjects_l.short_description = 'subjects'	1✔
290
291	def subjects_old(self, obj):	1✔
292	subs = obj.subjects.exclude(pk__in=obj.subjects_current().values_list('pk', flat=True))	×
293	out = format_html_join(', ', '<a href="{}">{}</a>',	×
294	((get_admin_url(sub), sub) for sub in subs))
295	return format_html(out)	×
296	subjects_old.short_description = 'old subjects'	1✔
297
298
299	admin.site.register(Housing, HousingAdmin)	1✔
300	admin.site.register(Lab, LabAdmin)	1✔
301	admin.site.register(LabMembership, LabMembershipAdmin)	1✔
302	admin.site.register(LabLocation, LabLocationAdmin)	1✔
303	admin.site.register(Note, NoteAdmin)	1✔
304	admin.site.register(CageType, CageTypeAdmin)	1✔
305	admin.site.register(Enrichment, EnrichmentAdmin)	1✔
306	admin.site.register(Food, FoodAdmin)	1✔
307	admin.site.unregister(TokenProxy)	1✔

cortex-lab / alyx / 13546875483

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