def test_disorderapilist(self):
disorder = Disorder()
response = self.client.get(reverse('disorder_api_list'))
count = disorder.count()
content = json.loads(response.content.decode('utf-8'))
self.assertEqual(len(content), count)
self.assertEqual(response.status_code, 200)
def test_view_disorder(self):
disorder = Disorder()
dis = disorder.create("test_view_disorder", {"prop": "prop"})
uid = dis.properties['id']
response = self.client.get(reverse('disorder', kwargs={'uid': uid}))
self.assertEqual(response.status_code, 200)
self.assertEqual(response.context['disorder']['id'], uid)
dis.delete()
def update_disorder(request, uid):
if request.method == "POST":
definition = request.POST.get('disorder_definition', '')
name = request.POST.get('disorder_name', '')
updates = add_update("name", name)
updates = add_update("definition", definition, updates)
Disorder.update(uid, updates=updates)
return view_disorder(request, uid)
def __init__(self, name=None, *args, **kwargs):
super(DisorderDisorderForm, self).__init__(*args, **kwargs)
name = (name if name is not None else '')
disorders = Disorder()
type_choices = [
('parent', '{} is a kind of <selected disorder>'.format(name)),
('child', '<selected disorder> is a kind of {}'.format(name))
]
dis_choices = [(x['id'], x['name']) for x in disorders.all()]
self.fields['type'] = forms.ChoiceField(choices=type_choices)
self.fields['disorders'] = forms.ChoiceField(choices=dis_choices)
self.helper = FormHelper()
self.helper.form_tag = False
self.helper.add_input(Submit('submit', 'Submit'))
self.helper.add_input(Reset('disorder-disorder-cancel', 'Cancel'))
def test_disorderapidetail_by_name(self):
disorder = Disorder()
response = self.client.get(reverse('disorder_api_list'),
{'name': self.disorder.properties['name']})
content = json.loads(response.content.decode('utf-8'))
self.assertEqual(content['id'], self.disorder.properties['id'])
self.assertEqual(response.status_code, 200)
def test_update_disorder(self):
self.assertTrue(
self.client.login(username=self.user.username,
password=self.password))
disorder = Disorder()
dis = disorder.create('test_update_disorder', {'prop': 'prop'})
response = self.client.post(
reverse('update_disorder', kwargs={'uid': dis.properties['id']}), {
'disorder_name': 'disorder_name',
'disorder_definition': 'disorder_definition'
})
self.assertEqual(response.status_code, 200)
self.assertEqual('disorder_name', response.context['disorder']['name'])
self.assertEqual('disorder_definition',
response.context['disorder']['definition'])
dis.delete()
def __init__(self, task_id, *args, **kwargs):
super(TaskDisorderForm, self).__init__(*args, **kwargs)
disorders = Disorder()
behaviors = query.Behavior()
traits = query.Trait()
tasks = Task()
contrasts = tasks.get_relation(task_id, "HASCONTRAST")
cont_choices = [(x['id'], x['name']) for x in contrasts]
self.fields['contrasts'] = forms.ChoiceField(choices=cont_choices)
pheno_choices = []
pheno_choices.extend([(x['id'], ''.join([x['name'], " (Disorder)"]))
for x in disorders.all()])
pheno_choices.extend([(x['id'], ''.join([x['name'], " (Behavior)"]))
for x in behaviors.all()])
pheno_choices.extend([(x['id'], ''.join([x['name'], " (Trait)"]))
for x in traits.all()])
self.fields['disorders'] = forms.ChoiceField(choices=pheno_choices)
self.helper = FormHelper()
self.helper.form_tag = False
self.helper.add_input(Submit('submit', 'Submit'))
self.helper.add_input(Reset('task-disorder-cancel', 'Cancel'))
def all_disorders(request):
'''all_disorders returns page with list of all disorders'''
disorders = Disorder.all(order_by="name")
for d in range(len(disorders)):
disorder = disorders[d]
if disorder["classification"] == None:
disorder["classification"] = "None"
disorders[d] = disorder
context = {
'appname': "The Cognitive Atlas",
'active': "disorders",
'nodes': disorders
}
return render(request, "atlas/all_disorders.html", context)
def base(request):
# We only need id and name for the home page
fields = ["id","name"]
concepts = Concept.all(limit=10,order_by="last_updated",fields=fields)
tasks = Task.all(limit=10,order_by="last_updated",fields=fields)
disorders = Disorder.all(limit=10,order_by="last_updated",fields=fields)
theories = Theory.all(limit=7,order_by="last_updated",fields=fields)
appname = "The Cognitive Atlas"
context = {'appname': appname,
'active':'homepage',
'concepts':concepts,
'tasks':tasks,
'theories':theories,
'disorders':disorders}
return context
def setUp(self):
disorder = Disorder()
self.disorder = disorder.create("test_view_disorder", {
"prop": "prop",
"definition": "definition"
})
from cognitive.apps.atlas.query import Concept, Task, Disorder, Theory, Battery
from django.shortcuts import render, render_to_response
from django.template import RequestContext
from cognitive.settings import DOMAIN
from django.shortcuts import render
from django.template import loader
Concept = Concept()
Task = Task()
Disorder = Disorder()
Theory = Theory()
Battery = Battery()
def base(request):
# We only need id and name for the home page
fields = ["id","name"]
concepts = Concept.all(limit=10,order_by="last_updated",fields=fields)
tasks = Task.all(limit=10,order_by="last_updated",fields=fields)
disorders = Disorder.all(limit=10,order_by="last_updated",fields=fields)
theories = Theory.all(limit=7,order_by="last_updated",fields=fields)
appname = "The Cognitive Atlas"
context = {'appname': appname,
'active':'homepage',
'concepts':concepts,
'tasks':tasks,
'theories':theories,
'disorders':disorders}
def view_disorder(request, uid):
disorder = Disorder.get(uid)[0]
context = {"disorder": disorder}
return render(request, 'atlas/view_disorder.html', context)
from cognitive.apps.atlas.query import Concept, Task, Disorder, \
Contrast, Battery, Theory, Condition, search
from cognitive.apps.atlas.utils import clean_html, update_lookup, add_update
from django.http import JsonResponse, HttpResponse
from cognitive.settings import DOMAIN
from django.shortcuts import render
from django.template import loader
import pickle
import json
import numpy
Concept = Concept()
Task = Task()
Disorder = Disorder()
Contrast = Contrast()
Battery = Battery()
Theory = Theory()
Condition = Condition()
# Needed on all pages
counts = {
"disorders": Disorder.count(),
"tasks": Task.count(),
"contrasts": Contrast.count(),
"concepts": Concept.count(),
"batteries": Battery.count(),
"theories": Theory.count()
}
# VIEWS FOR ALL NODES #############################################################
from cognitive.apps.atlas.query import Concept, Task, Disorder, Theory, Battery
Concept = Concept()
Task = Task()
Disorder = Disorder()
Theory = Theory()
Battery = Battery()
# Needed on all pages
counts = {"disorders":Disorder.count(),
"tasks":Task.count(),
"concepts":Concept.count(),
"theories":Theory.count(),
"batteries":Battery.count()}
def counts_processor(request):
return {'counts': counts}