def get_l4440_control_filters(self):
"""
Get the filters for the L4440 controls for this experiment.
To get the actual control experiments from the returned filters,
simply do Experiment.objects.filter(**filters). Returning
the filters is more flexible for customization, or for inserting
into a URL without performing the query.
L4440 controls for this experiment are restricted to those from
the same date, same temperature, same worm.
If this experiment is itself an L4440 clone, the function works
the same way, returning all L4440 experiments from the same
date, same worm, same temperature.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'worm_strain': self.worm_strain.pk,
'library_stock__intended_clone': Clone.get_l4440(),
}
return filters
def to_python(self, value):
if value == 'L4440':
raise forms.ValidationError('RNAi query cannot be L4440')
elif not value:
return None
else:
return Clone.get_clones_from_search_term(value)
def to_python(self, value):
if value == 'L4440':
raise forms.ValidationError('RNAi query cannot be L4440')
elif not value:
return None
else:
return Clone.get_clones_from_search_term(value)
def get_n2_l4440_control_filters(self):
"""
Get the filters for the L4440 controls for this experiment.
To get the actual control experiments from the returned filters,
simply do Experiment.objects.filter(**filters). Returning
the filters is more flexible for customization, or for inserting
into a URL without performing the query.
L4440 controls for this experiment are restricted to those from
the same date, same temperature, same worm.
If this experiment is itself an L4440 clone, the function works
the same way, returning all L4440 experiments from the same
date, same worm, same temperature.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'worm_strain': WormStrain.get_n2().pk,
'library_stock__intended_clone': Clone.get_l4440(),
}
return filters
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 double_knockdown(request, mutant, clones, temperature):
"""
Render the page showing knockdown by both mutation and RNAi.
context['data'] is returned in format:
{clone: {
library_stock: {
date: {
'mutant_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'n2_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'mutant_l4440': {
'experiments': [experiments], 'link_to_all': url
},
'n2_l4440': {
'experiments': [experiments], 'link_to_all': url
},
}
}
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
data_per_clone = OrderedDict()
library_stocks = (LibraryStock.objects.filter(
intended_clone=clone).order_by('-plate__screen_stage', 'id'))
for library_stock in library_stocks:
data_per_well = OrderedDict()
dates = Experiment.get_distinct_dates({
'is_junk':
False,
'worm_strain':
mutant,
'library_stock':
library_stock,
'plate__temperature':
temperature,
})
for date in dates:
# Add double knockdowns
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock': library_stock,
'plate__temperature': temperature,
}
mutant_rnai = _create_inner_dictionary(filters,
join_manual=True)
# Add mutant + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
mutant_l4440 = _create_inner_dictionary(filters)
# Add N2 + RNAi controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock': library_stock,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_rnai = _create_inner_dictionary(filters)
# Add N2 + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock__intended_clone': l4440,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_l4440 = _create_inner_dictionary(filters)
data_per_well[date] = {
'mutant_rnai': mutant_rnai,
'mutant_l4440': mutant_l4440,
'n2_rnai': n2_rnai,
'n2_l4440': n2_l4440,
}
if data_per_well:
data_per_clone[library_stock] = data_per_well
data[clone] = data_per_clone
context = {
'mutant': mutant,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'double_knockdown.html', context)
def double_knockdown(request, mutant, clones, temperature):
"""
Render the page showing knockdown by both mutation and RNAi.
context['data'] is returned in format:
{clone: {
library_stock: {
date: {
'mutant_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'n2_rnai': {
'experiments': [experiments], 'link_to_all': url
},
'mutant_l4440': {
'experiments': [experiments], 'link_to_all': url
},
'n2_l4440': {
'experiments': [experiments], 'link_to_all': url
},
}
}
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
l4440 = Clone.get_l4440()
mutant = get_object_or_404(WormStrain, pk=mutant)
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
data_per_clone = OrderedDict()
library_stocks = (LibraryStock.objects.filter(intended_clone=clone)
.order_by('-plate__screen_stage', 'id'))
for library_stock in library_stocks:
data_per_well = OrderedDict()
dates = Experiment.get_distinct_dates({
'is_junk': False,
'worm_strain': mutant,
'library_stock': library_stock,
'plate__temperature': temperature,
})
for date in dates:
# Add double knockdowns
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock': library_stock,
'plate__temperature': temperature,
}
mutant_rnai = _create_inner_dictionary(
filters, join_manual=True)
# Add mutant + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': mutant.pk,
'library_stock__intended_clone': l4440,
'plate__temperature': temperature,
}
mutant_l4440 = _create_inner_dictionary(filters)
# Add N2 + RNAi controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock': library_stock,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_rnai = _create_inner_dictionary(filters)
# Add N2 + L4440 controls
filters = {
'is_junk': False,
'plate__date': date,
'worm_strain': n2.pk,
'library_stock__intended_clone': l4440,
}
t = Experiment.get_closest_temperature(temperature, filters)
filters['plate__temperature'] = t
n2_l4440 = _create_inner_dictionary(filters)
data_per_well[date] = {
'mutant_rnai': mutant_rnai,
'mutant_l4440': mutant_l4440,
'n2_rnai': n2_rnai,
'n2_l4440': n2_l4440,
}
if data_per_well:
data_per_clone[library_stock] = data_per_well
data[clone] = data_per_clone
context = {
'mutant': mutant,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'double_knockdown.html', context)
def get_l4440_stocks(self):
return self.librarystock_set.filter(intended_clone=Clone.get_l4440())
def to_python(self, value):
if not value:
return Clone.objects.all()
else:
return Clone.get_clones_from_search_term(value)
def sync_clone_row_vidal(legacy_row):
vidal_clone_name = generate_vidal_clone_name(legacy_row[0],
legacy_row[1])
new_clone = Clone(id=vidal_clone_name)
return update_or_save_object(command, new_clone, recorded_clones,
fields_to_compare)
def sync_clone_row(legacy_row):
new_clone = Clone(id=legacy_row[0])
return update_or_save_object(command, new_clone, recorded_clones,
fields_to_compare)
def to_python(self, value):
if not value:
return Clone.objects.all()
else:
return Clone.get_clones_from_search_term(value)
def get_l4440_stocks(self):
return self.librarystock_set.filter(intended_clone=Clone.get_l4440())