def image_category(request, category):
tuples = []
f = open(settings.BASE_DIR_IMAGE_CATEGORIES + '/' + category, 'r')
rows = f.readlines()
for row in rows:
experiment_plate_id, tile = row.split('_')
tile = tile.split('.')[0]
well = tile_to_well(tile)
experiment = get_object_or_404(Experiment,
plate=experiment_plate_id,
well=well)
tuples.append((experiment, tile))
f.close()
display_tuples = get_paginated(request, tuples, IMAGES_PER_PAGE)
context = {
'category': category,
'tuples': tuples,
'display_tuples': display_tuples,
}
return render(request, 'image_category.html', context)
def change_experiment_plates(request, pks):
"""
Render the page to update bulk experiment plates.
When bulk updating experiment plates, the corresponding experiment
wells might change too.
"""
split_pks = pks.split(',')
experiment_plates = ExperimentPlate.objects.filter(pk__in=split_pks)
display_plates = get_paginated(request, experiment_plates,
EXPERIMENT_PLATES_PER_PAGE)
if request.POST:
form = ChangeExperimentPlatesForm(request.POST)
if form.is_valid():
for plate in experiment_plates:
process_ChangeExperimentPlatesForm_data(plate,
form.cleaned_data)
return redirect('change_experiment_plates_url', pks)
else:
form = ChangeExperimentPlatesForm()
context = {
'experiment_plates': experiment_plates,
'display_plates': display_plates,
'form': form,
}
return render(request, 'change_experiment_plates.html', context)
def change_experiment_plates(request, pks):
"""
Render the page to update bulk experiment plates.
When bulk updating experiment plates, the corresponding experiment
wells might change too.
"""
split_pks = pks.split(',')
experiment_plates = ExperimentPlate.objects.filter(pk__in=split_pks)
display_plates = get_paginated(request, experiment_plates,
EXPERIMENT_PLATES_PER_PAGE)
if request.POST:
form = ChangeExperimentPlatesForm(request.POST)
if form.is_valid():
for plate in experiment_plates:
process_ChangeExperimentPlatesForm_data(
plate, form.cleaned_data)
return redirect('change_experiment_plates_url', pks)
else:
form = ChangeExperimentPlatesForm()
context = {
'experiment_plates': experiment_plates,
'display_plates': display_plates,
'form': form,
}
return render(request, 'change_experiment_plates.html', context)
def library_plates(request):
"""Render the page listing all library plates."""
screen_stage = request.GET.get('screen_stage')
library_plates = LibraryPlate.get_screening_plates(
screen_stage=screen_stage)
display_plates = get_paginated(request, library_plates, PLATES_PER_PAGE)
context = {
'library_plates': library_plates,
'display_plates': display_plates,
}
return render(request, 'library_plates.html', context)
def get_context_data(self, **kwargs):
context_ = super().get_context_data(**kwargs)
empe_filter, empr_filter = self.request.GET.get(
'empe_srch'), self.request.GET.get('empr_srch')
vac_filters = (self.request.GET.get('vac_srch'),
self.request.GET.get('vac_pos'))
employees = Employee.objects.order_by('user__created', 'name')
if empe_filter:
employees = employees.filter(name__icontains=empe_filter)
employers = Employer.objects.order_by('user__created', 'name')
if empr_filter:
employers = employers.filter(name__icontains=empr_filter)
vacancies = Vacancy.objects.filter(is_active=True).order_by(
'employer__user__created', 'title')
if any(vac_filters):
if vac_filters[0]:
vacancies = vacancies.filter(title__icontains=vac_filters[0])
if vac_filters[1] and vac_filters[1] != '*':
vacancies = vacancies.filter(position_id__exact=vac_filters[1])
context_['employees'] = get_paginated(self.request,
employees,
page_query='page_empe')
context_['employers'] = get_paginated(self.request,
employers,
page_query='page_empr')
context_['vacancies'] = get_paginated(self.request,
vacancies,
page_query='page_vac')
context_['positions'] = Position.objects.all()
context_.update({'vac_filterss': vac_filters})
return context_
def library_plates(request):
"""Render the page listing all library plates."""
screen_stage = request.GET.get('screen_stage')
library_plates = LibraryPlate.get_screening_plates(
screen_stage=screen_stage)
display_plates = get_paginated(request, library_plates,
PLATES_PER_PAGE)
context = {
'library_plates': library_plates,
'display_plates': display_plates,
}
return render(request, 'library_plates.html', context)
def clones(request):
"""Render the page listing all RNAi clones."""
if "clone_query" in request.GET:
form = CloneSearchForm(request.GET)
if form.is_valid():
data = form.cleaned_data
clones = data["clone_query"]
else:
clones = []
else:
form = CloneSearchForm()
clones = Clone.objects.all()
display_clones = get_paginated(request, clones, CLONES_PER_PAGE)
context = {"clones": clones, "display_clones": display_clones, "form": form}
return render(request, "clones.html", context)
def find_experiment_wells(request):
"""Render the page to find experiment wells based on filters."""
experiments = None
display_experiments = None
if request.GET:
form = FilterExperimentWellsForm(request.GET)
if form.is_valid():
experiments = form.process()
display_experiments = get_paginated(request, experiments,
EXPERIMENT_WELLS_PER_PAGE)
else:
form = FilterExperimentWellsForm()
context = {
'form': form,
'experiments': experiments,
'display_experiments': display_experiments,
}
return render(request, 'find_experiment_wells.html', context)
def find_experiment_wells(request):
"""Render the page to find experiment wells based on filters."""
experiments = None
display_experiments = None
if request.GET:
form = FilterExperimentWellsForm(request.GET)
if form.is_valid():
experiments = form.process()
display_experiments = get_paginated(request, experiments,
EXPERIMENT_WELLS_PER_PAGE)
else:
form = FilterExperimentWellsForm()
context = {
'form': form,
'experiments': experiments,
'display_experiments': display_experiments,
}
return render(request, 'find_experiment_wells.html', context)
def clones(request):
"""Render the page listing all RNAi clones."""
if 'clone_query' in request.GET:
form = CloneSearchForm(request.GET)
if form.is_valid():
data = form.cleaned_data
clones = data['clone_query']
else:
clones = []
else:
form = CloneSearchForm()
clones = Clone.objects.all()
display_clones = get_paginated(request, clones, CLONES_PER_PAGE)
context = {
'clones': clones,
'display_clones': display_clones,
'form': form,
}
return render(request, 'clones.html', context)
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 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)