def get_n2_control_filters(self):
"""
Get the N2 + RNAi controls for this experiment.
It does this by manually setting the strain as N2 and then applying
all the other parameters which are shared by the controls.
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.
N2 controls for this experiment are restricted to those from
the same date, *closest* temperature, same RNAi clone.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'library_stock': self.library_stock,
'worm_strain': WormStrain.get_n2().pk,
}
filters['plate__temperature'] = Experiment.get_closest_temperature(
self.temperature(), filters)
return filters
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 rnai_knockdown(request, clones, temperature=None):
"""
Render the page showing knockdown by RNAi only.
context['data'] is returned in format:
{clone: {
library_stock: [experiments]
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
filters = {
'is_junk': False,
'worm_strain': n2.pk,
'library_stock__intended_clone': clone,
}
if temperature:
filters['plate__temperature'] = temperature
# Do not join manual scores, since N2 not manually scored
experiments = (Experiment.objects.filter(**filters).select_related(
'library_stock',
'plate').prefetch_related('devstarscore_set').order_by(
'-library_stock__plate__screen_stage', 'library_stock',
'-plate__date', 'id'))
data_by_well = OrderedDict()
for experiment in experiments:
library_stock = experiment.library_stock
if library_stock not in data_by_well:
data_by_well[library_stock] = []
data_by_well[library_stock].append(experiment)
if data_by_well:
data[clone] = data_by_well
context = {
'n2': n2,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'rnai_knockdown.html', context)
def rnai_knockdown(request, clones, temperature=None):
"""
Render the page showing knockdown by RNAi only.
context['data'] is returned in format:
{clone: {
library_stock: [experiments]
}}
"""
data = OrderedDict()
n2 = WormStrain.get_n2()
clones = Clone.objects.filter(pk__in=clones.split(','))
for clone in clones:
filters = {
'is_junk': False,
'worm_strain': n2.pk,
'library_stock__intended_clone': clone,
}
if temperature:
filters['plate__temperature'] = temperature
# Do not join manual scores, since N2 not manually scored
experiments = (Experiment.objects.filter(**filters)
.select_related('library_stock', 'plate')
.prefetch_related('devstarscore_set')
.order_by('-library_stock__plate__screen_stage',
'library_stock', '-plate__date', 'id'))
data_by_well = OrderedDict()
for experiment in experiments:
library_stock = experiment.library_stock
if library_stock not in data_by_well:
data_by_well[library_stock] = []
data_by_well[library_stock].append(experiment)
if data_by_well:
data[clone] = data_by_well
context = {
'n2': n2,
'clones': clones,
'temperature': temperature,
'data': data,
}
return render(request, 'rnai_knockdown.html', context)
def get_n2_control_filters(self):
"""
Get the N2 + RNAi 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.
N2 controls for this experiment are restricted to those from
the same date, *closest* temperature, same RNAi clone.
"""
filters = {
'is_junk': False,
'plate__date': self.date(),
'plate__temperature': self.temperature(),
'library_stock': self.library_stock,
'worm_strain': WormStrain.get_n2().pk,
}
filters['plate__temperature'] = Experiment.get_closest_temperature(
self.temperature(), filters)
return filters
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 test_get_n2(self):
n2 = WormStrain.get_n2()
self.assertEquals(n2.id, 'N2')
self.assertIsNone(n2.permissive_temperature)
self.assertIsNone(n2.restrictive_temperature)
