def _create_inner_dictionary(filters, join_devstar=True, join_manual=False):
experiments = Experiment.objects.filter(**filters).select_related('plate')
if join_devstar:
experiments = experiments.prefetch_related('devstarscore_set')
if join_manual:
experiments = experiments.prefetch_related('manualscore_set')
d = {}
d['experiments'] = experiments
d['link_to_all'] = build_url('find_experiment_wells_url', get=filters)
return d
def _create_inner_dictionary(filters, join_devstar=True, join_manual=False):
experiments = Experiment.objects.filter(**filters).select_related('plate')
if join_devstar:
experiments = experiments.prefetch_related('devstarscore_set')
if join_manual:
experiments = experiments.prefetch_related('manualscore_set')
d = {}
d['experiments'] = experiments
d['link_to_all'] = build_url('find_experiment_wells_url', get=filters)
return d
def mutant_knockdown(request, mutant, temperature):
"""
Render the page showing knockdown by mutation only.
context['data'] is returned in format:
{date: {
'experiments': [experiments], 'link_to_all': url,
}}
"""
data = OrderedDict()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
filters = {
'is_junk': False,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
# Do not join manual scores, since L4440 not manually scored
experiments = (Experiment.objects.filter(**filters).select_related(
'library_stock',
'plate').prefetch_related('devstarscore_set').order_by(
'-plate__date', 'id'))
for experiment in experiments:
date = experiment.plate.date
if date not in data:
data[date] = {'experiments': []}
data[date]['experiments'].append(experiment)
inner_filters = copy(filters)
inner_filters['plate__date'] = date
data[date]['link_to_all'] = build_url('find_experiment_wells_url',
get=inner_filters)
context = {
'mutant': mutant,
'l4440': l4440,
'temperature': temperature,
'data': data,
}
return render(request, 'mutant_knockdown.html', context)
def mutant_knockdown(request, mutant, temperature):
"""
Render the page showing knockdown by mutation only.
context['data'] is returned in format:
{date: {
'experiments': [experiments], 'link_to_all': url,
}}
"""
data = OrderedDict()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
filters = {
'is_junk': False,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
# Do not join manual scores, since L4440 not manually scored
experiments = (Experiment.objects.filter(**filters)
.select_related('library_stock', 'plate')
.prefetch_related('devstarscore_set')
.order_by('-plate__date', 'id'))
for experiment in experiments:
date = experiment.plate.date
if date not in data:
data[date] = {'experiments': []}
data[date]['experiments'].append(experiment)
inner_filters = copy(filters)
inner_filters['plate__date'] = date
data[date]['link_to_all'] = build_url(
'find_experiment_wells_url', get=inner_filters)
context = {
'mutant': mutant,
'l4440': l4440,
'temperature': temperature,
'data': data,
}
return render(request, 'mutant_knockdown.html', context)
def get_link_to_n2_controls(self):
filters = self.get_n2_control_filters()
return build_url('find_experiment_wells_url', get=filters)
def score_experiment_wells(request):
"""
Render the page to score experiment wells.
TODO: create base class to capture commonality between this and
find_experiment_wells
TODO: better handle case of invalid filter_form
"""
post_experiments = []
redo_post = False
# If there was a previous submit
if request.POST:
exp = '^[0-9]+_[A-H][0-1][0-9]-.*_scores?$'
pattern = re.compile(exp)
pks = [k.split('-')[0] for k in request.POST if pattern.match(k)]
# Check if all POSTs are valid
for experiment in Experiment.objects.filter(pk__in=pks):
f = get_score_form(request.GET.get('score_form_key'))
experiment.score_form = f(request.POST, user=request.user,
prefix=experiment.pk)
post_experiments.append(experiment)
if not experiment.score_form.is_valid():
redo_post = True
# If all POSTs valid, process and redirect
if not redo_post:
for experiment in post_experiments:
# This actually submits the scores to the database
experiment.score_form.process()
url = build_url('score_experiment_wells_url', get=request.GET)
return HttpResponseRedirect(url)
# Bind filter form with GET params
if request.GET:
filter_form = FilterExperimentWellsToScoreForm(
request.GET, user=request.user)
else:
filter_form = FilterExperimentWellsToScoreForm()
if (not request.GET or not filter_form.is_valid()):
return render(request, 'score_experiment_wells_setup.html', {
'filter_form': filter_form
})
# At this point, filter form is valid and cleaned
filter_data = filter_form.process()
experiments = filter_data['experiments']
unscored_by_user = filter_data['unscored_by_user']
if redo_post:
# These already have attached and bound score forms
display_experiments = post_experiments
else:
per_page = filter_data['images_per_page']
if unscored_by_user:
display_experiments = experiments[:per_page]
else:
display_experiments = get_paginated(request, experiments, per_page)
# Attach a score form to each experiment
score_form = filter_data['score_form']
for experiment in display_experiments:
experiment.score_form = score_form(prefix=experiment.pk)
context = {
'experiments': experiments,
'display_experiments': display_experiments,
'unscored_by_user': filter_data['unscored_by_user'],
'do_not_display': ['images_per_page', 'score_form_key', 'is_junk']
}
return render(request, 'score_experiment_wells.html', context)
def get_link_to_n2_controls(self):
filters = self.get_n2_control_filters()
return build_url('find_experiment_wells_url', get=filters)
def score_experiment_wells(request):
"""
Render the page to score experiment wells.
TODO: create base class to capture commonality between this and
find_experiment_wells
TODO: better handle case of invalid filter_form
"""
post_experiments = [] # list that stores all submitted scores per exp
redo_post = False
# If there was a previous submit
# post is submitting the database
# This is passing through all the same get paramters (the filtering params)
# keeping him on the same page
# GET and POST both happen every time
if request.POST:
exp = '^[0-9]+_[A-H][0-1][0-9]-.*_scores?$'
pattern = re.compile(exp)
pks = [k.split('-')[0] for k in request.POST if pattern.match(k)]
# Check if all POSTs are valid
for experiment in Experiment.objects.filter(pk__in=pks):
# gets the form from either enhancer or Suppressor
f = get_score_form(request.GET.get('score_form_key'))
experiment.score_form = f(request.POST,
user=request.user,
prefix=experiment.pk)
post_experiments.append(experiment)
if not experiment.score_form.is_valid():
redo_post = True
# If all POSTs valid, process and redirect
# this saves scores and brings back to the same page and
# resets the POST data so that there's not a double submit
if not redo_post:
for experiment in post_experiments:
# This actually submits the scores to the database
experiment.score_form.process()
url = build_url('score_experiment_wells_url', get=request.GET)
return HttpResponseRedirect(url)
# Bind filter form with GET params
# If there's stuff to limit on
# .GET parameters is taken from the input form
if request.GET:
filter_form = FilterExperimentWellsToScoreForm(request.GET,
user=request.user)
else:
filter_form = FilterExperimentWellsToScoreForm()
if (not request.GET or not filter_form.is_valid()):
return render(request, 'score_experiment_wells_setup.html',
{'filter_form': filter_form})
# At this point, filter form is valid and cleaned
filter_data = filter_form.process()
experiments = filter_data['experiments']
unscored_by_user = filter_data['unscored_by_user']
if redo_post:
# These already have attached and bound score forms
display_experiments = post_experiments
else:
per_page = filter_data['images_per_page']
if unscored_by_user:
display_experiments = experiments[:per_page]
else:
display_experiments = get_paginated(request, experiments, per_page)
# Attach a score form to each experiment
# the prefix attaches the experiment's pk to each form field which makes it queryable
# when posting
# This sets the class attribute 'score_form' to the secondary enhacer score forms
# which is then called and rendered in the template
score_form = filter_data['score_form']
for experiment in display_experiments:
experiment.score_form = score_form(prefix=experiment.pk)
context = {
'experiments': experiments,
'display_experiments': display_experiments,
'unscored_by_user': filter_data['unscored_by_user'],
# 'do_not_display': ['images_per_page', 'score_form_key', 'is_junk']
'do_not_display': ['images_per_page', 'score_form_key']
}
return render(request, 'score_experiment_wells.html', context)
