def importData(request, species_wid=None):
if request.method == 'POST':
form = ImportDataForm(request.POST or None, request.FILES)
if form.is_valid():
selected_species_wid = form.cleaned_data[
'species'] or form.cleaned_data['new_species']
if selected_species_wid == '' or selected_species_wid is None:
form.species.errors += ['Please select a specices']
else:
#save to temporary file
originalFileName, originalFileExtension = os.path.splitext(
request.FILES['file'].name)
fid = tempfile.NamedTemporaryFile(suffix=originalFileExtension,
delete=False)
filename = fid.name
for chunk in request.FILES['file'].chunks():
fid.write(chunk)
fid.close()
#read file
if originalFileExtension == '.xlsx':
try:
batch_import_from_excel(selected_species_wid, filename,
request.user)
success = True
message = 'Data successfully saved!'
except ValidationError as error:
success = False
message = 'Unable to import data: ' + ' '.join(
error.messages)
elif originalFileExtension == '.fna':
success, message = readFasta(selected_species_wid,
filename, request.user)
else:
raise Http404
#delete file
os.remove(filename)
#render response
return render_queryset_to_response(
species_wid=species_wid,
request=request,
templateFile='public/importDataResult.html',
data={
'success': success,
'message': message,
})
else:
form = ImportDataForm(None)
return render_queryset_to_response(
species_wid=species_wid,
request=request,
templateFile='public/importDataForm.html',
data={'form': form},
)
def importData(request, species_wid=None):
if request.method == 'POST':
form = ImportDataForm(request.POST or None, request.FILES)
if form.is_valid():
selected_species_wid = form.cleaned_data['species'] or form.cleaned_data['new_species']
if selected_species_wid == '' or selected_species_wid is None:
form.species.errors += ['Please select a specices']
else:
#save to temporary file
originalFileName, originalFileExtension = os.path.splitext(request.FILES['file'].name)
fid = tempfile.NamedTemporaryFile(suffix = originalFileExtension, delete = False)
filename = fid.name
for chunk in request.FILES['file'].chunks():
fid.write(chunk)
fid.close()
#read file
if originalFileExtension == '.xlsx':
try:
batch_import_from_excel(selected_species_wid, filename, request.user)
success = True
message = 'Data successfully saved!'
except ValidationError as error:
success = False
message = 'Unable to import data: ' + ' '.join(error.messages)
elif originalFileExtension == '.fna':
success, message = readFasta(selected_species_wid, filename, request.user)
else:
raise Http404
#delete file
os.remove(filename)
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/importDataResult.html',
data = {
'success': success,
'message': message,
})
else:
form = ImportDataForm(None)
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/importDataForm.html',
data = {
'form': form},
)
def about(request, species_wid=None):
return render_queryset_to_response(species_wid=species_wid,
request=request,
templateFile='public/about.html',
data={
'ROOT_URL': settings.ROOT_URL,
})
def sitemap_toplevel(request):
return render_queryset_to_response(
request=request,
templateFile='public/sitemap_toplevel.xml',
data={
'ROOT_URL': settings.ROOT_URL,
})
def sitemap(request):
return render_queryset_to_response(request=request,
templateFile='public/sitemap.xml',
data={
'ROOT_URL': settings.ROOT_URL,
'qs_species': Species.objects.all(),
})
def logout(request, species_wid=None):
auth_logout(request)
return render_queryset_to_response(
species_wid=species_wid,
request=request,
templateFile='public/logout.html',
)
def delete(request, species_wid, wid):
#retrieve object
obj = getEntry(species_wid=species_wid, wid=wid)
if obj is None:
raise Http404
model = obj.__class__
qs = objectToQuerySet(obj, model=model)
#delete
if request.method == 'POST':
obj.delete()
return HttpResponseRedirect(
reverse('public.views.list',
kwargs={
'species_wid': species_wid,
'model_type': model.__name__
}))
#confirmation message
return render_queryset_to_response(
species_wid=species_wid,
request=request,
models=[model],
queryset=qs,
templateFile='public/delete.html',
data={'model_verbose_name': model._meta.verbose_name})
def login(request, species_wid=None):
next = request.REQUEST.get('next', '')
if request.method == "POST":
form = AuthenticationForm(data=request.POST)
if form.is_valid():
auth_login(request, form.get_user())
if request.session.test_cookie_worked():
request.session.delete_test_cookie()
return HttpResponseRedirect(next)
else:
form = AuthenticationForm(request)
request.session.set_test_cookie()
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/login.html',
data = {
'form': form,
'next': next,
})
def logout(request, species_wid=None): auth_logout(request) return render_queryset_to_response( species_wid = species_wid, request = request, templateFile = 'public/logout.html', )
def contributors(request, species_wid=None):
queryset = User.objects.all().filter(is_active=True)
return render_queryset_to_response(species_wid=species_wid,
request=request,
models=[User],
queryset=queryset,
templateFile='public/contributors.html')
def detail(request, species_wid, wid):
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
model = obj.__class__
model_type = model.__name__
fieldsets = deepcopy(model._meta.fieldsets)
#filter out type, metadata
fieldset_names = [x[0] for x in fieldsets]
if 'Type' in fieldset_names:
idx = fieldset_names.index('Type')
del fieldsets[idx]
#filter out empty fields
rmfieldsets = []
for idx in range(len(fieldsets)):
rmfields = []
for idx2 in range(len(fieldsets[idx][1]['fields'])):
if isinstance(fieldsets[idx][1]['fields'][idx2], dict):
field_name = fieldsets[idx][1]['fields'][idx2]['name']
verbose_name = fieldsets[idx][1]['fields'][idx2]['verbose_name']
else:
field_name = fieldsets[idx][1]['fields'][idx2]
field = model._meta.get_field_by_name(field_name)[0]
if isinstance(field, RelatedObject):
verbose_name = capfirst(field.get_accessor_name())
else:
verbose_name = field.verbose_name
data = format_field_detail_view(obj, field_name, request.user.is_anonymous())
if (data is None) or (data == ''):
rmfields = [idx2] + rmfields
fieldsets[idx][1]['fields'][idx2] = {'verbose_name': verbose_name.replace(" ", ' ').replace("-", "‑"), 'data': data}
for idx2 in rmfields:
del fieldsets[idx][1]['fields'][idx2]
if len(fieldsets[idx][1]['fields']) == 0:
rmfieldsets = [idx] + rmfieldsets
for idx in rmfieldsets:
del fieldsets[idx]
#form query set
qs = objectToQuerySet(obj, model = model)
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [model],
queryset = qs,
templateFile = 'public/detail.html',
data = {
'model_type': model_type,
'model': model,
'fieldsets': fieldsets,
'message': request.GET.get('message', ''),
})
def contributor(request, username, species_wid=None):
queryset = objectToQuerySet(get_object_or_404(User, username=username),
model=User)
return render_queryset_to_response(species_wid=species_wid,
request=request,
models=[User],
queryset=queryset,
templateFile='public/contributor.html')
def sitemap_toplevel(request):
return render_queryset_to_response(
request = request,
templateFile = 'public/sitemap_toplevel.xml',
data = {
'ROOT_URL': settings.ROOT_URL,
}
)
def contributors(request, species_wid=None): queryset = User.objects.all().filter(is_active = True) return render_queryset_to_response( species_wid = species_wid, request = request, models = [User], queryset = queryset, templateFile = 'public/contributors.html')
def contributor(request, username, species_wid=None): queryset = objectToQuerySet(get_object_or_404(User, username = username), model = User) return render_queryset_to_response( species_wid = species_wid, request = request, models = [User], queryset = queryset, templateFile = 'public/contributor.html')
def search_google(request, species_wid, query):
return render_queryset_to_response(species_wid=species_wid,
request=request,
templateFile='public/googleSearch.html',
data={
'query': query,
'engine': 'google',
})
def sitemap(request):
return render_queryset_to_response(
request = request,
templateFile = 'public/sitemap.xml',
data = {
'ROOT_URL': settings.ROOT_URL,
'qs_species': Species.objects.all(),
}
)
def about(request, species_wid=None):
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/about.html',
data = {
'ROOT_URL': settings.ROOT_URL,
}
)
def search_google(request, species_wid, query):
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/googleSearch.html',
data = {
'query': query,
'engine': 'google',
})
def sitemap_species(request, species_wid):
species = Species.objects.get(wid=species_wid)
return render_queryset_to_response(
request=request,
templateFile='public/sitemap_species.xml',
data={
'ROOT_URL': settings.ROOT_URL,
'species': species,
'entries': SpeciesComponent.objects.filter(species__id=species.id),
})
def validate(request, species_wid):
errors = get_invalid_objects(
Species.objects.values('id').get(wid=species_wid)['id'])
return render_queryset_to_response(
species_wid=species_wid,
request=request,
templateFile='public/validate.html',
data={'errors': errors},
)
def validate(request, species_wid):
errors = get_invalid_objects(Species.objects.values('id').get(wid=species_wid)['id'])
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/validate.html',
data = {
'errors': errors
},
)
def sitemap_species(request, species_wid):
species = Species.objects.get(wid=species_wid)
return render_queryset_to_response(
request = request,
templateFile = 'public/sitemap_species.xml',
data = {
'ROOT_URL': settings.ROOT_URL,
'species': species,
'entries': SpeciesComponent.objects.filter(species__id = species.id),
}
)
def exportData(request, species_wid=None):
getDict = request.GET.copy()
if getDict.get('format', ''):
getDict.__setitem__('species', getDict.get('species', species_wid))
form = ExportDataForm(getDict or None)
if not form.is_valid():
return render_queryset_to_response(
species_wid=species_wid,
request=request,
templateFile='public/exportDataForm.html',
data={'form': form})
else:
species = Species.objects.get(wid=form.cleaned_data['species'])
queryset = EmptyQuerySet()
models = []
if form.cleaned_data['all_model_types'] == 'True':
model_types = getObjectTypes()
else:
model_types = form.cleaned_data['model_type']
for model_type in model_types:
model = getModel(model_type)
if issubclass(model, SpeciesComponent):
queryset = chain(
queryset,
model.objects.filter(
species__id=species.id).select_related(depth=2).all())
else:
queryset = chain(
queryset,
model.objects.select_related(depth=2).filter(
id=species.id))
models.append(getModel(model_type))
return render_queryset_to_response(
species_wid=species_wid,
request=request,
queryset=queryset,
templateFile='public/exportDataResult.html',
models=models)
def exportData(request, species_wid=None):
getDict = request.GET.copy()
if getDict.get('format', ''):
getDict.__setitem__('species', getDict.get('species', species_wid))
form = ExportDataForm(getDict or None)
if not form.is_valid():
return render_queryset_to_response(
species_wid=species_wid,
request = request,
templateFile = 'public/exportDataForm.html',
data = {
'form': form
}
)
else:
species = Species.objects.get(wid = form.cleaned_data['species'])
queryset = EmptyQuerySet()
models = []
if form.cleaned_data['all_model_types'] == 'True':
model_types = getObjectTypes()
else:
model_types = form.cleaned_data['model_type']
for model_type in model_types:
model = getModel(model_type)
if issubclass(model, SpeciesComponent):
queryset = chain(queryset, model.objects.filter(species__id=species.id).select_related(depth=2).all())
else:
queryset = chain(queryset, model.objects.select_related(depth=2).filter(id=species.id))
models.append(getModel(model_type))
return render_queryset_to_response(
species_wid = species_wid,
request = request,
queryset = queryset,
templateFile = 'public/exportDataResult.html',
models = models)
def search_haystack(request, species_wid, query):
#search
if species_wid is None:
species_wid = Species.objects.all()[0].wid
results = SearchQuerySet().filter(species_wid=species_wid).filter(
content=query)
#calculate facets
facets = results.facet('model_type')
tmp = facets.facet_counts()['fields']['model_type']
modelNameFacet = []
objectTypes = getObjectTypes()
models = []
for tmp2 in tmp:
modelName = objectTypes[objectTypes.index(tmp2[0])]
modelNameFacet.append({
'name': modelName,
'verbose_name': getModel(modelName)._meta.verbose_name,
'count': tmp2[1],
})
models.append(getModel(modelName))
modelNameFacet.sort(lambda x, y: cmp(x['verbose_name'], y['verbose_name']))
#narrow search by facets
model_type = request.GET.get('model_type', '')
if model_type:
results = results.models(getModel(model_type))
#order results
results = results.order_by('wid')
#convert results to query set
queryset = EmptyQuerySet()
for object in results:
tmp = object.model.objects.none()
tmp._result_cache.append(object.object)
queryset = chain(queryset, tmp)
#form response
return render_queryset_to_response(species_wid=species_wid,
request=request,
models=models,
queryset=queryset,
templateFile='public/search.html',
data={
'query': query,
'engine': 'haystack',
'model_type': model_type,
'modelNameFacet': modelNameFacet,
})
def search_haystack(request, species_wid, query):
#search
if species_wid is None:
species_wid = Species.objects.all()[0].wid
results = SearchQuerySet().filter(species_wid=species_wid).filter(content=query)
#calculate facets
facets = results.facet('model_type')
tmp = facets.facet_counts()['fields']['model_type']
modelNameFacet = []
objectTypes = getObjectTypes()
models = []
for tmp2 in tmp:
modelName = objectTypes[objectTypes.index(tmp2[0])]
modelNameFacet.append({
'name':modelName,
'verbose_name': getModel(modelName)._meta.verbose_name,
'count':tmp2[1],
})
models.append(getModel(modelName))
modelNameFacet.sort(lambda x, y:cmp(x['verbose_name'], y['verbose_name']))
#narrow search by facets
model_type = request.GET.get('model_type', '')
if model_type:
results = results.models(getModel(model_type))
#order results
results = results.order_by('wid')
#convert results to query set
queryset = EmptyQuerySet()
for object in results:
tmp = object.model.objects.none()
tmp._result_cache.append(object.object)
queryset = chain(queryset, tmp)
#form response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = models,
queryset = queryset,
templateFile = 'public/search.html',
data = {
'query': query,
'engine': 'haystack',
'model_type': model_type,
'modelNameFacet': modelNameFacet,
})
def viewParameterInSimulation(request, species_wid, wid):
#get associated simulation property
qs = Parameter.objects.filter(species__wid = species_wid, wid=wid)
if not qs[0].state is None:
sim_class_name = 'edu.stanford.covert.cell.sim.state.%s' % qs[0].state.wid.replace('State_', '')
verbose_class_name = '%s: %s' % (wid, qs[0].state.name)
else:
sim_class_name = 'edu.stanford.covert.cell.sim.process.%s' % qs[0].process.wid.replace('Process_', '')
verbose_class_name = '%s: %s' % (wid, qs[0].process.name)
sim_property_name = qs[0].name
verbose_property_name = qs[0].name
#highlight code for simulation class
pathParts = sim_class_name.split('.')
codePath = "%s/src/+%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1])
if not os.path.isfile(codePath):
codePath = "%s/src/+%s/@%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1], pathParts[-1])
if os.path.isfile(codePath):
with open (codePath, "r") as codeFile:
code = codeFile.read()
lexer = MatlabLexer()
lexer.add_filter(PropertyDefinitionFilter(property_names = [sim_property_name], tokentype=Token.Name.Variable))
tokens = lexer.get_tokens(code)
object = {
'class_name': sim_class_name,
'property_names': [sim_property_name],
'code': pygments.format(tokens, PygmentsFormatter(linenos='inline', linenostep=1, style=PygmentsStyle, noclasses=True)),
}
else:
raise Http404
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [Parameter],
queryset = qs,
templateFile = 'public/viewPropertyInSimulation.html',
data = {
'object_list': [object],
'verbose_class_name': verbose_class_name,
'verbose_property_name': verbose_property_name,
})
def delete(request, species_wid, wid):
#retrieve object
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
model = obj.__class__
qs = objectToQuerySet(obj, model = model)
#delete
if request.method == 'POST':
obj.delete()
return HttpResponseRedirect(reverse('public.views.list', kwargs={'species_wid':species_wid, 'model_type': model.__name__}))
#confirmation message
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [model],
queryset = qs,
templateFile = 'public/delete.html',
data = {
'model_verbose_name': model._meta.verbose_name
}
)
def login(request, species_wid=None):
next = request.REQUEST.get('next', '')
if request.method == "POST":
form = AuthenticationForm(data=request.POST)
if form.is_valid():
auth_login(request, form.get_user())
if request.session.test_cookie_worked():
request.session.delete_test_cookie()
return HttpResponseRedirect(next)
else:
form = AuthenticationForm(request)
request.session.set_test_cookie()
return render_queryset_to_response(species_wid=species_wid,
request=request,
templateFile='public/login.html',
data={
'form': form,
'next': next,
})
def detail(request, species_wid, wid):
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
model = obj.__class__
model_type = model.__name__
fieldsets = deepcopy(model._meta.fieldsets)
#filter out type, metadata
fieldset_names = [x[0] for x in fieldsets]
if 'Type' in fieldset_names:
idx = fieldset_names.index('Type')
del fieldsets[idx]
#filter out empty fields
rmfieldsets = []
for idx in range(len(fieldsets)):
rmfields = []
for idx2 in range(len(fieldsets[idx][1]['fields'])):
if isinstance(fieldsets[idx][1]['fields'][idx2], dict):
field = fieldsets[idx][1]['fields'][idx2]
field_name = field['name']
verbose_name = field['verbose_name']
else:
field_name = fieldsets[idx][1]['fields'][idx2]
field = model._meta.get_field_by_name(field_name)[0]
if isinstance(field, RelatedObject):
verbose_name = capfirst(field.get_accessor_name())
else:
verbose_name = field.verbose_name
data = format_field_detail_view(obj, field_name, request.user.is_anonymous())
if (data is None) or (data == ''):
rmfields = [idx2] + rmfields
if issubclass(model, Parameter) and field_name == 'value':
is_modeled_url = reverse('public.views.viewParameterInSimulation', kwargs = {
'species_wid':species_wid,
'wid': wid,
})
elif (isinstance(field, (ForeignKey, ManyToManyField)) and issubclass(field.rel.to, Parameter)) or \
(isinstance(field, (RelatedObject)) and issubclass(field.model, Parameter)):
is_modeled_url = reverse('public.views.viewParametersInSimulation', kwargs = {
'species_wid':species_wid,
'wid': wid,
})
else:
try:
if ModelProperty.objects.get(species__wid = species_wid, class_name = model_type, property_name = field_name).simulation_properties.exists():
is_modeled_url = reverse('public.views.viewPropertyInSimulation', kwargs = {
'species_wid':species_wid,
'class_name': model_type,
'property_name': field_name,
})
except ObjectDoesNotExist:
is_modeled_url = ''
fieldsets[idx][1]['fields'][idx2] = {
'name': field_name,
'verbose_name': verbose_name.replace(" ", ' ').replace("-", "‑"),
'data': data,
'is_modeled_url': is_modeled_url,
}
for idx2 in rmfields:
del fieldsets[idx][1]['fields'][idx2]
if len(fieldsets[idx][1]['fields']) == 0:
rmfieldsets = [idx] + rmfieldsets
for idx in rmfieldsets:
del fieldsets[idx]
#form query set
qs = objectToQuerySet(obj, model = model)
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [model],
queryset = qs,
templateFile = 'public/detail.html',
data = {
'model_type': model_type,
'model': model,
'fieldsets': fieldsets,
'message': request.GET.get('message', ''),
})
def viewParametersInSimulation(request, species_wid, wid):
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
model = obj.__class__
verbose_class_name = model._meta.verbose_name
verbose_property_name = '%s parameters' % obj.name
#get associated simulation property
qs = EmptyQuerySet()
for field in model._meta.get_all_related_objects() + model._meta.get_all_related_many_to_many_objects():
accessor_name = field.get_accessor_name()
if accessor_name == '+':
continue
if isinstance(field, ForeignKey) and issubclass(field.rel.to, Parameter):
qs._result_cache.append(getattr(obj, accessor_name))
if (isinstance(field, ManyToManyField) and issubclass(field.rel.to, Parameter)) or \
(isinstance(field, RelatedObject) and issubclass(field.model, Parameter)):
qs2 = getattr(obj, accessor_name).all()
if len(qs2) > 0:
qs._result_cache.extend(qs2._result_cache)
classes = {}
for o in qs:
if not o.state is None:
sim_class_name = 'edu.stanford.covert.cell.sim.state.%s' % o.state.wid.replace('State_', '')
else:
sim_class_name = 'edu.stanford.covert.cell.sim.process.%s' % o.process.wid.replace('Process_', '')
if not classes.has_key(sim_class_name):
classes[sim_class_name] = []
classes[sim_class_name].append(o.name)
#highlight code for simulation class
objects = []
for sim_class_name in classes:
sim_property_names = classes[sim_class_name]
sim_property_names.sort()
pathParts = sim_class_name.split('.')
codePath = "%s/src/+%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1])
if not os.path.isfile(codePath):
codePath = "%s/src/+%s/@%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1], pathParts[-1])
if not os.path.isfile(codePath):
continue
with open (codePath, "r") as codeFile:
code = codeFile.read()
lexer = MatlabLexer()
lexer.add_filter(PropertyDefinitionFilter(property_names = sim_property_names, tokentype=Token.Name.Variable))
tokens = lexer.get_tokens(code)
objects.append({
'class_name': sim_class_name,
'property_names': sim_property_names,
'code': pygments.format(tokens, PygmentsFormatter(linenos='inline', linenostep=1, style=PygmentsStyle, noclasses=True)),
})
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [Parameter],
queryset = qs,
templateFile = 'public/viewPropertyInSimulation.html',
data = {
'object_list': objects,
'verbose_class_name': verbose_class_name,
'verbose_property_name': verbose_property_name,
})
def detail(request, species_wid, wid):
obj = getEntry(species_wid=species_wid, wid=wid)
if obj is None:
raise Http404
model = obj.__class__
model_type = model.__name__
fieldsets = deepcopy(model._meta.fieldsets)
#filter out type, metadata
fieldset_names = [x[0] for x in fieldsets]
if 'Type' in fieldset_names:
idx = fieldset_names.index('Type')
del fieldsets[idx]
#filter out empty fields
rmfieldsets = []
for idx in range(len(fieldsets)):
rmfields = []
for idx2 in range(len(fieldsets[idx][1]['fields'])):
if isinstance(fieldsets[idx][1]['fields'][idx2], dict):
field_name = fieldsets[idx][1]['fields'][idx2]['name']
verbose_name = fieldsets[idx][1]['fields'][idx2][
'verbose_name']
else:
field_name = fieldsets[idx][1]['fields'][idx2]
field = model._meta.get_field_by_name(field_name)[0]
if isinstance(field, RelatedObject):
verbose_name = capfirst(field.get_accessor_name())
else:
verbose_name = field.verbose_name
data = format_field_detail_view(obj, field_name,
request.user.is_anonymous())
if (data is None) or (data == ''):
rmfields = [idx2] + rmfields
fieldsets[idx][1]['fields'][idx2] = {
'verbose_name':
verbose_name.replace(" ", ' ').replace("-", "‑"),
'data':
data
}
for idx2 in rmfields:
del fieldsets[idx][1]['fields'][idx2]
if len(fieldsets[idx][1]['fields']) == 0:
rmfieldsets = [idx] + rmfieldsets
for idx in rmfieldsets:
del fieldsets[idx]
#form query set
qs = objectToQuerySet(obj, model=model)
#render response
return render_queryset_to_response(species_wid=species_wid,
request=request,
models=[model],
queryset=qs,
templateFile='public/detail.html',
data={
'model_type':
model_type,
'model':
model,
'fieldsets':
fieldsets,
'message':
request.GET.get('message', ''),
})
def edit(request, wid=None, model_type=None, species_wid=None, action='edit'):
#retrieve object
if action == 'edit':
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
model = obj.__class__
else:
model = getModel(model_type)
obj = model()
#save object
error_messages = {}
if request.method == 'POST':
submitted_data = get_edit_form_data(model, request.POST)
data = submitted_data
data['id'] = obj.id
data['species'] = species_wid
data['model_type'] = model.__name__
try:
#validate is WID unique
if issubclass(model, SpeciesComponent):
qs = SpeciesComponent.objects.values('wid', 'model_type').filter(species__wid=species_wid)
else:
qs = model.objects.values('wid', 'model_type').all()
if action == 'edit':
qs = qs.exclude(id=obj.id)
wids = {}
for x in qs:
wids[x['wid']] = x['model_type']
if data['wid'] in wids.keys():
raise ValidationError({'wid': 'Value must be unique'})
wids[data['wid']] = model.__name__
#validate
data = validate_object_fields(model, data, wids, species_wid, data['wid'])
validate_model_objects(model, data)
validate_model_unique(model, [data])
#save
obj = save_object_data(species_wid, obj, data, {}, request.user, save=False, save_m2m=False)
obj = save_object_data(species_wid, obj, data, {data['wid']: obj}, request.user, save=True, save_m2m=False)
obj = save_object_data(species_wid, obj, data, {data['wid']: obj}, request.user, save=True, save_m2m=True)
#redirect to details page
return HttpResponseRedirect(obj.get_absolute_url())
except ValidationError as error:
error_messages = error.message_dict
#form query set
if action == 'edit':
obj = getEntry(species_wid = species_wid, wid = wid)
if obj is None:
raise Http404
qs = objectToQuerySet(obj, model = model)
else:
obj = None
qs = model.objects.none()
#display form
fields, initial_values = get_edit_form_fields(species_wid, model, obj=obj)
if request.method == 'POST':
initial_values = submitted_data
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [model],
queryset = qs,
templateFile = 'public/edit.html',
data = {
'model_verbose_name': model._meta.verbose_name,
'action': action,
'fields': fields,
'references_choices': Reference.objects.filter(species__wid = species_wid).values_list('wid'),
'initial_values': initial_values,
'error_messages': error_messages,
}
)
def edit(request, wid=None, model_type=None, species_wid=None, action='edit'):
#retrieve object
if action == 'edit':
obj = getEntry(species_wid=species_wid, wid=wid)
if obj is None:
raise Http404
model = obj.__class__
else:
model = getModel(model_type)
obj = model()
#save object
error_messages = {}
if request.method == 'POST':
submitted_data = get_edit_form_data(model, request.POST)
data = submitted_data
data['id'] = obj.id
data['species'] = species_wid
data['model_type'] = model.__name__
try:
#validate is WID unique
if issubclass(model, SpeciesComponent):
qs = SpeciesComponent.objects.values(
'wid', 'model_type').filter(species__wid=species_wid)
else:
qs = model.objects.values('wid', 'model_type').all()
if action == 'edit':
qs = qs.exclude(id=obj.id)
wids = {}
for x in qs:
wids[x['wid']] = x['model_type']
if data['wid'] in wids.keys():
raise ValidationError({'wid': 'Value must be unique'})
wids[data['wid']] = model.__name__
#validate
data = validate_object_fields(model, data, wids, species_wid,
data['wid'])
validate_model_objects(model, data)
validate_model_unique(model, [data])
#save
obj = save_object_data(species_wid,
obj,
data, {},
request.user,
save=False,
save_m2m=False)
obj = save_object_data(species_wid,
obj,
data, {data['wid']: obj},
request.user,
save=True,
save_m2m=False)
obj = save_object_data(species_wid,
obj,
data, {data['wid']: obj},
request.user,
save=True,
save_m2m=True)
#redirect to details page
return HttpResponseRedirect(obj.get_absolute_url())
except ValidationError as error:
error_messages = error.message_dict
#form query set
if action == 'edit':
obj = getEntry(species_wid=species_wid, wid=wid)
if obj is None:
raise Http404
qs = objectToQuerySet(obj, model=model)
else:
obj = None
qs = model.objects.none()
#display form
fields, initial_values = get_edit_form_fields(species_wid, model, obj=obj)
if request.method == 'POST':
initial_values = submitted_data
return render_queryset_to_response(
species_wid=species_wid,
request=request,
models=[model],
queryset=qs,
templateFile='public/edit.html',
data={
'model_verbose_name':
model._meta.verbose_name,
'action':
action,
'fields':
fields,
'references_choices':
Reference.objects.filter(
species__wid=species_wid).values_list('wid'),
'initial_values':
initial_values,
'error_messages':
error_messages,
})
def list(request, species_wid, model_type):
try:
getObjectTypes().index(model_type)
except ValueError:
raise Http404
species = Species.objects.get(wid=species_wid)
model = getModel(model_type)
objects = model.objects.all().filter(species__id=species.id)
facet_fields = []
for field_full_name in model._meta.facet_fields:
#facet
field_names = str(field_full_name).split('__')
tmp_model = model
field_verbose_name = []
for field_name in field_names:
field = tmp_model._meta.get_field_by_name(field_name)[0]
field_verbose_name.append(field.verbose_name)
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp_model = field.rel.to
field_verbose_name = ' › '.join(field_verbose_name)
if isinstance(field, (ForeignKey, ManyToManyField)) and not issubclass(field.rel.to, Entry):
continue
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp = model.objects.filter(species__id=species.id).order_by(field_full_name + '__name').values(field_full_name).annotate(count=Count(field_full_name))
else:
tmp = model.objects.filter(species__id=species.id).order_by(field_full_name).values(field_full_name).annotate(count=Count(field_full_name))
facets = []
for facet in tmp:
value = facet[field_full_name]
if value is None or unicode(value) == '':
continue
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp2 = tmp_model.objects.values('wid', 'name').get(id=value)
id = tmp2['wid']
name = capfirst(tmp2['name'])
elif (field.choices is not None) and (len(field.choices) > 0) and (not isinstance(field, (BooleanField, NullBooleanField))):
id = value
choices = [x[0] for x in field.choices]
if id in choices:
name = field.choices[choices.index(id)][1]
else:
name = capfirst(value)
else:
id = value
name = capfirst(value)
if value is not None and unicode(value) != '':
facets.append({
'id': unicode(id),
'name': unicode(name),
'count': facet['count']})
if len(facets) > 1:
facet_fields.append({
'name': field_full_name,
'verbose_name': field_verbose_name,
'facets': facets,
})
#filter
val = request.GET.get(field_full_name)
if val:
if isinstance(field, (ForeignKey, ManyToManyField)):
kwargs = {field_full_name + '__wid': val}
elif isinstance(field, (BooleanField, NullBooleanField)):
kwargs = {field_full_name: val == 'True'}
elif isinstance(field, (AutoField, BigIntegerField, DecimalField, FloatField, IntegerField, PositiveIntegerField, PositiveSmallIntegerField, SmallIntegerField)):
kwargs = {field_full_name: float(val)}
else:
kwargs = {field_full_name: val}
objects = objects.filter(**kwargs)
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [model],
queryset = objects,
templateFile = 'public/list.html',
data = {
'model_type': model_type,
'model_verbose_name': model._meta.verbose_name,
'model_verbose_name_plural': model._meta.verbose_name_plural,
'facet_fields': facet_fields,
})
def tutorial(request, species_wid=None): return render_queryset_to_response( species_wid = species_wid, request = request, templateFile = 'public/tutorial.html')
def index(request, species_wid=None):
if species_wid is not None and species_wid != '':
species = Species.objects.get(wid=species_wid)
else:
species = Species.objects.all()
if len(species) > 0:
species = species[0]
else:
species = None
content = []
if species is not None:
content.append([
[
0, 'Compartments',
models.Compartment.objects.filter(
species__id=species.id).count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Compartment'
})
],
])
chrs = models.Chromosome.objects.filter(species__id=species.id)
chrcontent = chrs.aggregate(length=Sum('length'))
gc_content = sum([chr.get_gc_content() * chr.length
for chr in chrs]) / chrcontent['length']
content.append([
[
0, 'Chromosomes',
chrs.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Chromosome'
})
],
[1, 'Length', chrcontent['length'], 'nt'],
[1, 'GC-content', ('%0.1f' % (gc_content * 100)), '%'],
])
tus = models.TranscriptionUnit.objects.filter(
species__id=species.id).annotate(num_genes=Count('genes'))
mons = tus.filter(num_genes__lte=1)
nPolys = tus.filter(num_genes__gt=1).count()
content.append([
[
0, 'Transcription units',
tus.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'TranscriptionUnit'
})
],
[1, 'Monocistrons', tus.count() - nPolys],
[1, 'Polycistrons', nPolys],
])
content.append([
[
0, 'Genes',
models.Gene.objects.filter(species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Gene'
})
],
[
1, 'mRNA',
models.Gene.objects.filter(species__id=species.id,
type__wid='mRNA').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Gene'
}) + '?type=mRNA'
],
[
1, 'rRNA',
models.Gene.objects.filter(species__id=species.id,
type__wid='rRNA').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Gene'
}) + '?type=rRNA'
],
[
1, 'sRNA',
models.Gene.objects.filter(species__id=species.id,
type__wid='sRNA').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Gene'
}) + '?type=sRNA'
],
[
1, 'tRNA',
models.Gene.objects.filter(species__id=species.id,
type__wid='tRNA').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Gene'
}) + '?type=tRNA'
],
])
content.append([
[
0,
'Chromosome features',
models.ChromosomeFeature.objects.filter(
species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'ChromosomeFeature'
}),
],
[
1,
'DnaA boxes',
models.ChromosomeFeature.objects.filter(
species__id=species.id,
type__parent__wid='ChromosomeFeature-DnaA_box').count(),
],
[
1,
'Short tandem repeats',
models.ChromosomeFeature.objects.filter(
species__id=species.id,
type__parent__wid='ChromosomeFeature-Short_Tandem_Repeat').
count(),
],
[
1, 'Other',
models.ChromosomeFeature.objects.filter(
species__id=species.id).exclude(
type__parent__wid='ChromosomeFeature-DnaA_box').
exclude(
type__parent__wid='ChromosomeFeature-Short_Tandem_Repeat').
count()
],
])
content.append([
[
0, 'Metabolites',
models.Metabolite.objects.filter(
species__id=species.id).count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Metabolite'
})
],
[
1, 'Amino acids',
models.Metabolite.objects.filter(
species__id=species.id, type__wid='amino_acid').count() +
models.Metabolite.objects.filter(
species__id=species.id,
type__wid='modified_amino_acid').count() +
models.Metabolite.objects.filter(
species__id=species.id,
type__wid='non-standard_amino_acid').count() +
models.Metabolite.objects.filter(
species__id=species.id,
type__wid='vitamin_non-standard_amino_acid').count()
],
[
1, 'Antibiotic',
models.Metabolite.objects.filter(
species__id=species.id, type__wid='antibiotic').count() +
models.Metabolite.objects.filter(
species__id=species.id,
type__parent__wid='antibiotic').count()
],
[
1, 'Gases',
models.Metabolite.objects.filter(species__id=species.id,
type__wid='gas').count() +
models.Metabolite.objects.filter(
species__id=species.id, type__parent__wid='gas').count()
],
[
1, 'Ions',
models.Metabolite.objects.filter(species__id=species.id,
type__wid='ion').count() +
models.Metabolite.objects.filter(
species__id=species.id, type__parent__wid='ion').count()
],
[
1, 'Lipids',
models.Metabolite.objects.filter(species__id=species.id,
type__wid='lipid').count() +
models.Metabolite.objects.filter(
species__id=species.id, type__parent__wid='lipid').count()
+ models.Metabolite.objects.filter(
species__id=species.id,
type__parent__parent__wid='lipid').count()
],
[
1, 'Vitamins',
models.Metabolite.objects.filter(species__id=species.id,
type__wid='vitamin').count() +
models.Metabolite.objects.filter(
species__id=species.id,
type__parent__wid='vitamin').count()
],
])
mons = models.ProteinMonomer.objects.filter(species__id=species.id)
cpxs = models.ProteinComplex.objects.filter(species__id=species.id)
monDNABind = mons.filter(dna_footprint__length__gt=0).count()
monIntMem = mons.filter(localization__wid='m').exclude(
signal_sequence__type='lipoprotein').count() + mons.filter(
localization__wid='tm').exclude(
signal_sequence__type='lipoprotein').count()
monLipo = mons.filter(signal_sequence__type='lipoprotein').count()
monSecreted = mons.filter(signal_sequence__type='secretory').count()
monTermOrg = mons.filter(localization__wid='tc').count() + mons.filter(
localization__wid='tm').count()
cpxDNABind = cpxs.filter(dna_footprint__length__gt=0).count()
content.append([
[0, 'Proteins', mons.count() + cpxs.count()],
[
1, 'Monomers',
mons.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'ProteinMonomer'
})
],
[2, 'DNA-binding', monDNABind],
[2, 'Integral membrane', monIntMem],
[
2, 'Lipoprotein', monLipo, None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'ProteinMonomer'
}) + '?signal_sequence__type=lipoprotein'
],
[
2, 'Secreted', monSecreted, None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'ProteinMonomer'
}) + '?signal_sequence__type=secretory'
],
[2, 'Terminal organelle', monTermOrg],
[
1, 'Complexes',
cpxs.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'ProteinComplex'
})
],
[2, 'DNA-binding', cpxDNABind],
])
rxns = models.Reaction.objects.filter(species__id=species.id)
content.append([
[
0, 'Reactions',
rxns.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
})
],
[
1, 'DNA damage',
rxns.filter(processes__wid='Process_DNADamage').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_DNADamage'
],
[
1, 'DNA repair',
rxns.filter(processes__wid='Process_DNARepair').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_DNARepair'
],
[
1, 'Metabolic',
rxns.filter(processes__wid='Process_Metabolism').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_Metabolism'
],
[
1, 'Protein decay',
rxns.filter(processes__wid='Process_ProteinDecay').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_ProteinDecay'
],
[
1, 'Protein modification',
rxns.filter(
processes__wid='Process_ProteinModification').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_ProteinModification'
],
[
1, 'Replication Initiation',
rxns.filter(
processes__wid='Process_ReplicationInitiation').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_ReplicationInitiation'
],
[
1, 'RNA decay',
rxns.filter(processes__wid='Process_RNADecay').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_RNADecay'
],
[
1, 'RNA modification',
rxns.filter(processes__wid='Process_RNAModification').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_RNAModification'
],
[
1, 'RNA processing',
rxns.filter(processes__wid='Process_RNAProcessing').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_RNAProcessing'
],
[
1, 'Transcription',
rxns.filter(processes__wid='Process_Transcription').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_Transcription'
],
[
1, 'Translation',
rxns.filter(processes__wid='Process_Translation').count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_Translation'
],
[
1, 'tRNA aminoacylation',
rxns.filter(
processes__wid='Process_tRNAAminoacylation').count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Reaction'
}) + '?processes=Process_tRNAAminoacylation'
],
[
1, 'Other',
rxns.exclude(processes__wid='Process_DNADamage').exclude(
processes__wid='Process_DNARepair').exclude(
processes__wid='Process_Metabolism').exclude(
processes__wid='Process_ProteinDecay').
exclude(processes__wid='Process_ProteinModification').exclude(
processes__wid='Process_ReplicationInitiation').exclude(
processes__wid='Process_RNADecay').exclude(
processes__wid='Process_RNAModification').exclude(
processes__wid='Process_RNAProcessing').
exclude(processes__wid='Process_Transcription').exclude(
processes__wid='Process_Translation').exclude(
processes__wid='Process_tRNAAminoacylation').count()
],
])
tr = models.TranscriptionalRegulation.objects.filter(
species__id=species.id)
nTus = len(set([x[0] for x in tr.values_list('transcription_unit')]))
nTfs = len(set([x[0] for x in tr.values_list('transcription_factor')]))
content.append([
[0, 'Transcriptional regulation'],
[
1, 'Interactions',
tr.count(), None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'TranscriptionalRegulation'
})
],
[1, 'Transcriptional regulators', nTfs],
[1, 'Regulated promoters', nTus],
])
content.append([
[
0, 'Pathways',
models.Pathway.objects.filter(species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Pathway'
})
],
])
content.append([
[
0, 'Stimuli',
models.Stimulus.objects.filter(species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Stimulus'
})
],
])
nCellComp = models.Metabolite.objects.filter(
species__id=species.id,
biomass_composition__concentration__isnull=False).count()
nMediaComp = models.Metabolite.objects.filter(
species__id=species.id,
media_composition__concentration__isnull=False).count()
nKineticsKeq = models.Reaction.objects.filter(
species__id=species.id, keq__isnull=False).count()
nKineticsKm = \
models.Reaction.objects.filter(species__id = species.id, kinetics_forward__km__isnull=False).count() + \
models.Reaction.objects.filter(species__id = species.id, kinetics_backward__km__isnull=False).count()
nKineticsVmax = \
models.Reaction.objects.filter(species__id = species.id, kinetics_forward__vmax__isnull=False).count() + \
models.Reaction.objects.filter(species__id = species.id, kinetics_backward__vmax__isnull=False).count()
nRnaExp = models.Gene.objects.filter(species__id=species.id,
expression__isnull=False).count()
nRnaHl = models.Gene.objects.filter(species__id=species.id,
half_life__isnull=False).count()
nStimuli = models.Stimulus.objects.filter(species__id=species.id,
value__isnull=False).count()
nTrAffinity = models.TranscriptionalRegulation.objects.filter(
species__id=species.id, affinity__isnull=False).count()
nTrActivity = models.TranscriptionalRegulation.objects.filter(
species__id=species.id, activity__isnull=False).count()
nOther = models.Parameter.objects.filter(
species__id=species.id).count()
nTotParameters = nCellComp + nMediaComp + nKineticsVmax + nRnaExp + nRnaHl + nStimuli + nTrAffinity + nTrActivity + nOther
content.append([
[0, 'Quantitative parameters', nTotParameters],
[1, 'Cell composition', nCellComp],
[1, 'Media composition', nMediaComp],
[1, 'Reaction K<sub>eq</sub>', nKineticsKeq],
[1, 'Reaction K<sub>m</sub>', nKineticsKm],
[1, 'Reaction V<sub>max</sub>', nKineticsVmax],
[1, 'RNA expression', nRnaExp],
[1, 'RNA half-lives', nRnaHl],
[1, 'Stimulus values', nStimuli],
[1, 'Transcr. reg. activity', nTrAffinity],
[1, 'Transcr. reg. affinity', nTrActivity],
[
1, 'Other', nOther, None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Parameter'
})
],
])
content.append([
[
0, 'Processes',
models.Process.objects.filter(species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'Process'
})
],
])
content.append([
[
0, 'States',
models.State.objects.filter(species__id=species.id).count(),
None,
reverse('public.views.list',
kwargs={
'species_wid': species.wid,
'model_type': 'State'
})
],
])
nContent = [len(x) for x in content]
totContent = sum(nContent)
cum = 0
idx = 0
breakIdxs = [0, 0]
for x in nContent:
cum += x
idx += 1
if cum > totContent * 1 / 3 and breakIdxs[0] == 0:
breakIdxs[0] = idx
if cum > totContent * 2 / 3 and breakIdxs[1] == 0:
breakIdxs[1] = idx
contentCol1 = []
contentCol2 = []
contentCol3 = []
i = 0
for x in content[:breakIdxs[0]]:
i += 1
for y in x:
contentCol1.append([i] + y)
i = 0
for x in content[breakIdxs[0]:breakIdxs[1]]:
i += 1
for y in x:
contentCol2.append([i] + y)
i = 0
for x in content[breakIdxs[1]:]:
i += 1
for y in x:
contentCol3.append([i] + y)
sources = {
'total': 0,
'types': [],
'dates': [],
'evidence_parameters': [],
'evidence_species': [],
'evidence_media': [],
'evidence_pH': [],
'evidence_temperature': [],
}
if species is not None:
refs = models.Reference.objects.filter(species__id=species.id)
sources['total'] = refs.count()
sources['types'] = [
{
'type':
'Articles',
'count':
refs.filter(species__id=species.id,
type__wid='article').count()
},
{
'type':
'Books',
'count':
refs.filter(species__id=species.id, type__wid='book').count()
},
{
'type':
'Thesis',
'count':
refs.filter(species__id=species.id,
type__wid='thesis').count()
},
{
'type':
'Other',
'count':
refs.filter(species__id=species.id, type__wid='misc').count()
},
]
sources['dates'] = refs.filter(
year__isnull=False).order_by('year').values('year').annotate(
count=Count('year'))
nEstimated = models.Parameter.objects.filter(
species__id=species.id,
value__evidence__is_experimentally_constrained=False).count()
nExpConstrained = nTotParameters - nEstimated
sources['evidence_parameters'] = [
{
'type': 'Experimentally constrained',
'count': nExpConstrained
},
{
'type': 'Computationally estimated',
'count': nEstimated
},
]
sources['evidence_species'] = models.Evidence.objects.filter(
species_component__species__id=species.id).values(
'species').annotate(count=Count('id'))
sources['evidence_media'] = models.Evidence.objects.filter(
species_component__species__id=species.id).values(
'media').annotate(count=Count('id'))
sources['evidence_pH'] = models.Evidence.objects.filter(
species_component__species__id=species.id).values('pH').annotate(
count=Count('id'))
sources['evidence_temperature'] = models.Evidence.objects.filter(
species_component__species__id=species.id).values(
'temperature').annotate(count=Count('id'))
return render_queryset_to_response(
species_wid=species_wid,
data={
'content': [contentCol1, contentCol2, contentCol3],
'contentRows':
range(max(len(contentCol1), len(contentCol2), len(contentCol3))),
'sources':
sources,
},
request=request,
templateFile='public/index.html')
def viewPropertyInSimulation(request, species_wid, class_name, property_name):
#get model
model = getModel(class_name)
#get verbose class name
verbose_class_name = model._meta.verbose_name
#get verbose property name
verbose_property_name = property_name
for fieldset in model._meta.fieldsets:
for field in fieldset[1]['fields']:
if isinstance(field, (str, unicode)) and field == property_name:
tmp = model._meta.get_field_by_name(property_name)
if len(tmp) > 0:
verbose_property_name = tmp[0].verbose_name
if isinstance(field, dict) and field['name'] == property_name:
verbose_property_name = field['verbose_name']
#get associated simulation code properties
qs = ModelProperty.objects.get(
species__wid = species_wid,
class_name = class_name,
property_name = property_name
).simulation_properties.all().order_by('class_name', 'property_name')
#organize simulation code properties by class
classes = {}
for object in qs:
if not classes.has_key(object.class_name):
classes[object.class_name] = []
classes[object.class_name].append(object.property_name)
#highlight code for each simulation class
object_list = []
for sim_class_name in classes:
sim_property_names = classes[sim_class_name]
sim_property_names.sort()
pathParts = sim_class_name.split('.')
codePath = "%s/src/+%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1])
if not os.path.isfile(codePath):
codePath = "%s/src/+%s/@%s/%s.m" % (MODEL_CODE_BASE_DIR, '/+'.join(pathParts[0:-1]), pathParts[-1], pathParts[-1])
if not os.path.isfile(codePath):
continue
with open (codePath, "r") as codeFile:
code = codeFile.read()
lexer = MatlabLexer()
lexer.add_filter(PropertyDefinitionFilter(property_names = sim_property_names, tokentype=Token.Name.Variable))
tokens = lexer.get_tokens(code)
object_list.append({
'class_name': sim_class_name,
'property_names': sim_property_names,
'code': pygments.format(tokens, PygmentsFormatter(linenos='inline', linenostep=1, style=PygmentsStyle, noclasses=True)),
})
#render response
return render_queryset_to_response(
species_wid = species_wid,
request = request,
models = [SimulationProperty],
queryset = qs,
templateFile = 'public/viewPropertyInSimulation.html',
data = {
'object_list': object_list,
'verbose_class_name': verbose_class_name,
'verbose_property_name': verbose_property_name,
})
def index(request, species_wid=None):
if species_wid is not None and species_wid != '':
species = Species.objects.get(wid=species_wid)
else:
species = Species.objects.all()
if len(species) > 0:
species = species[0]
else:
species = None
content = []
if species is not None:
content.append([
[0, 'Compartments', models.Compartment.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Compartment'})],
])
chrs = models.Chromosome.objects.filter(species__id = species.id)
chrcontent = chrs.aggregate(length=Sum('length'));
gc_content = sum([chr.get_gc_content() * chr.length for chr in chrs]) / chrcontent['length']
content.append([
[0, 'Chromosomes', chrs.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Chromosome'})],
[1, 'Length', chrcontent['length'], 'nt'],
[1, 'GC-content', ('%0.1f' % (gc_content * 100)), '%'],
])
tus = models.TranscriptionUnit.objects.filter(species__id = species.id).annotate(num_genes = Count('genes'))
mons = tus.filter(num_genes__lte = 1)
nPolys = tus.filter(num_genes__gt = 1).count()
content.append([
[0, 'Transcription units', tus.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'TranscriptionUnit'})],
[1, 'Monocistrons', tus.count() - nPolys],
[1, 'Polycistrons', nPolys],
])
content.append([
[0, 'Genes', models.Gene.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Gene'})],
[1, 'mRNA', models.Gene.objects.filter(species__id = species.id, type__wid='mRNA').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Gene'}) + '?type=mRNA'],
[1, 'rRNA', models.Gene.objects.filter(species__id = species.id, type__wid='rRNA').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Gene'}) + '?type=rRNA'],
[1, 'sRNA', models.Gene.objects.filter(species__id = species.id, type__wid='sRNA').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Gene'}) + '?type=sRNA'],
[1, 'tRNA', models.Gene.objects.filter(species__id = species.id, type__wid='tRNA').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Gene'}) + '?type=tRNA'],
])
content.append([
[0, 'Chromosome features',
models.ChromosomeFeature.objects.filter(species__id = species.id).count(),
None,
reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'ChromosomeFeature'}),
],
[1, 'DnaA boxes',
models.ChromosomeFeature.objects.filter(species__id = species.id, type__parent__wid='ChromosomeFeature-DnaA_box').count(),
],
[1, 'Short tandem repeats',
models.ChromosomeFeature.objects.filter(species__id = species.id, type__parent__wid='ChromosomeFeature-Short_Tandem_Repeat').count(),
],
[1, 'Other',
models.ChromosomeFeature.objects.filter(species__id = species.id).exclude(type__parent__wid='ChromosomeFeature-DnaA_box').exclude(type__parent__wid='ChromosomeFeature-Short_Tandem_Repeat').count()],
])
content.append([
[0, 'Metabolites', models.Metabolite.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Metabolite'})],
[1, 'Amino acids',
models.Metabolite.objects.filter(species__id = species.id, type__wid='amino_acid').count() +
models.Metabolite.objects.filter(species__id = species.id, type__wid='modified_amino_acid').count() +
models.Metabolite.objects.filter(species__id = species.id, type__wid='non-standard_amino_acid').count() +
models.Metabolite.objects.filter(species__id = species.id, type__wid='vitamin_non-standard_amino_acid').count()
],
[1, 'Antibiotic',
models.Metabolite.objects.filter(species__id = species.id, type__wid='antibiotic').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__wid='antibiotic').count()
],
[1, 'Gases',
models.Metabolite.objects.filter(species__id = species.id, type__wid='gas').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__wid='gas').count()
],
[1, 'Ions',
models.Metabolite.objects.filter(species__id = species.id, type__wid='ion').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__wid='ion').count()
],
[1, 'Lipids',
models.Metabolite.objects.filter(species__id = species.id, type__wid='lipid').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__wid='lipid').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__parent__wid='lipid').count()
],
[1, 'Vitamins',
models.Metabolite.objects.filter(species__id = species.id, type__wid='vitamin').count() +
models.Metabolite.objects.filter(species__id = species.id, type__parent__wid='vitamin').count()
],
])
mons = models.ProteinMonomer.objects.filter(species__id = species.id)
cpxs = models.ProteinComplex.objects.filter(species__id = species.id)
monDNABind = mons.filter(dna_footprint__length__gt=0).count()
monIntMem = mons.filter(localization__wid = 'm').exclude(signal_sequence__type = 'lipoprotein').count() + mons.filter(localization__wid = 'tm').exclude(signal_sequence__type = 'lipoprotein').count()
monLipo = mons.filter(signal_sequence__type = 'lipoprotein').count()
monSecreted = mons.filter(signal_sequence__type = 'secretory').count()
monTermOrg = mons.filter(localization__wid = 'tc').count() + mons.filter(localization__wid = 'tm').count()
cpxDNABind = cpxs.filter(dna_footprint__length__gt=0).count()
content.append([
[0, 'Proteins', mons.count() + cpxs.count()],
[1, 'Monomers', mons.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'ProteinMonomer'})],
[2, 'DNA-binding', monDNABind],
[2, 'Integral membrane', monIntMem],
[2, 'Lipoprotein', monLipo, None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'ProteinMonomer'}) + '?signal_sequence__type=lipoprotein'],
[2, 'Secreted', monSecreted, None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'ProteinMonomer'}) + '?signal_sequence__type=secretory'],
[2, 'Terminal organelle', monTermOrg],
[1, 'Complexes', cpxs.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'ProteinComplex'})],
[2, 'DNA-binding', cpxDNABind],
])
rxns = models.Reaction.objects.filter(species__id = species.id)
content.append([
[0, 'Reactions', rxns.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'})],
[1, 'DNA damage', rxns.filter(processes__wid='Process_DNADamage').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_DNADamage'],
[1, 'DNA repair', rxns.filter(processes__wid='Process_DNARepair').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_DNARepair'],
[1, 'Metabolic', rxns.filter(processes__wid='Process_Metabolism').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_Metabolism'],
[1, 'Protein decay', rxns.filter(processes__wid='Process_ProteinDecay').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_ProteinDecay'],
[1, 'Protein modification', rxns.filter(processes__wid='Process_ProteinModification').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_ProteinModification'],
[1, 'Replication Initiation', rxns.filter(processes__wid='Process_ReplicationInitiation').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_ReplicationInitiation'],
[1, 'RNA decay', rxns.filter(processes__wid='Process_RNADecay').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_RNADecay'],
[1, 'RNA modification', rxns.filter(processes__wid='Process_RNAModification').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_RNAModification'],
[1, 'RNA processing', rxns.filter(processes__wid='Process_RNAProcessing').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_RNAProcessing'],
[1, 'Transcription', rxns.filter(processes__wid='Process_Transcription').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_Transcription'],
[1, 'Translation', rxns.filter(processes__wid='Process_Translation').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_Translation'],
[1, 'tRNA aminoacylation', rxns.filter(processes__wid='Process_tRNAAminoacylation').count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Reaction'}) + '?processes=Process_tRNAAminoacylation'],
[1, 'Other', rxns.exclude(processes__wid='Process_DNADamage')
.exclude(processes__wid='Process_DNARepair')
.exclude(processes__wid='Process_Metabolism')
.exclude(processes__wid='Process_ProteinDecay')
.exclude(processes__wid='Process_ProteinModification')
.exclude(processes__wid='Process_ReplicationInitiation')
.exclude(processes__wid='Process_RNADecay')
.exclude(processes__wid='Process_RNAModification')
.exclude(processes__wid='Process_RNAProcessing')
.exclude(processes__wid='Process_Transcription')
.exclude(processes__wid='Process_Translation')
.exclude(processes__wid='Process_tRNAAminoacylation')
.count()],
])
tr = models.TranscriptionalRegulation.objects.filter(species__id = species.id)
nTus = len(set([x[0] for x in tr.values_list('transcription_unit')]))
nTfs = len(set([x[0] for x in tr.values_list('transcription_factor')]))
content.append([
[0, 'Transcriptional regulation'],
[1, 'Interactions', tr.count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'TranscriptionalRegulation'})],
[1, 'Transcriptional regulators', nTfs],
[1, 'Regulated promoters', nTus],
])
content.append([
[0, 'Pathways', models.Pathway.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Pathway'})],
])
content.append([
[0, 'Stimuli', models.Stimulus.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Stimulus'})],
])
nCellComp = models.Metabolite.objects.filter(species__id = species.id, biomass_composition__concentration__isnull=False).count()
nMediaComp = models.Metabolite.objects.filter(species__id = species.id, media_composition__concentration__isnull=False).count()
nKineticsKeq = models.Reaction.objects.filter(species__id = species.id, keq__isnull=False).count()
nKineticsKm = \
models.Reaction.objects.filter(species__id = species.id, kinetics_forward__km__isnull=False).count() + \
models.Reaction.objects.filter(species__id = species.id, kinetics_backward__km__isnull=False).count()
nKineticsVmax = \
models.Reaction.objects.filter(species__id = species.id, kinetics_forward__vmax__isnull=False).count() + \
models.Reaction.objects.filter(species__id = species.id, kinetics_backward__vmax__isnull=False).count()
nRnaExp = models.Gene.objects.filter(species__id = species.id, expression__isnull=False).count()
nRnaHl = models.Gene.objects.filter(species__id = species.id, half_life__isnull=False).count()
nStimuli = models.Stimulus.objects.filter(species__id = species.id, value__isnull=False).count()
nTrAffinity = models.TranscriptionalRegulation.objects.filter(species__id = species.id, affinity__isnull=False).count()
nTrActivity = models.TranscriptionalRegulation.objects.filter(species__id = species.id, activity__isnull=False).count()
nOther = models.Parameter.objects.filter(species__id = species.id).count()
nTotParameters = nCellComp + nMediaComp + nKineticsVmax + nRnaExp + nRnaHl + nStimuli + nTrAffinity + nTrActivity + nOther
content.append([
[0, 'Quantitative parameters', nTotParameters],
[1, 'Cell composition', nCellComp],
[1, 'Media composition', nMediaComp],
[1, 'Reaction K<sub>eq</sub>', nKineticsKeq],
[1, 'Reaction K<sub>m</sub>', nKineticsKm],
[1, 'Reaction V<sub>max</sub>', nKineticsVmax],
[1, 'RNA expression', nRnaExp],
[1, 'RNA half-lives', nRnaHl],
[1, 'Stimulus values', nStimuli],
[1, 'Transcr. reg. activity', nTrAffinity],
[1, 'Transcr. reg. affinity', nTrActivity],
[1, 'Other', nOther, None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Parameter'})],
])
content.append([
[0, 'Processes', models.Process.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'Process'})],
])
content.append([
[0, 'States', models.State.objects.filter(species__id = species.id).count(), None, reverse('public.views.list', kwargs={'species_wid': species.wid, 'model_type': 'State'})],
])
nContent = [len(x) for x in content]
totContent = sum(nContent)
cum = 0
idx = 0
breakIdxs = [0, 0]
for x in nContent:
cum += x
idx += 1
if cum > totContent * 1/ 3 and breakIdxs[0] == 0:
breakIdxs[0] = idx
if cum > totContent * 2 / 3 and breakIdxs[1] == 0:
breakIdxs[1] = idx
contentCol1 = []
contentCol2 = []
contentCol3 = []
i = 0
for x in content[:breakIdxs[0]]:
i += 1
for y in x:
contentCol1.append([i] + y)
i = 0
for x in content[breakIdxs[0]:breakIdxs[1]]:
i += 1
for y in x:
contentCol2.append([i] + y)
i = 0
for x in content[breakIdxs[1]:]:
i += 1
for y in x:
contentCol3.append([i] + y)
sources = {
'total': 0,
'types': [],
'dates': [],
'evidence_parameters': [],
'evidence_species': [],
'evidence_media': [],
'evidence_pH': [],
'evidence_temperature': [],
}
if species is not None:
refs = models.Reference.objects.filter(species__id = species.id)
sources['total'] = refs.count()
sources['types'] = [
{'type': 'Articles', 'count': refs.filter(species__id = species.id, type__wid='article').count()},
{'type': 'Books', 'count': refs.filter(species__id = species.id, type__wid='book').count()},
{'type': 'Thesis', 'count': refs.filter(species__id = species.id, type__wid='thesis').count()},
{'type': 'Other', 'count': refs.filter(species__id = species.id, type__wid='misc').count()},
]
sources['dates'] = refs.filter(year__isnull=False).order_by('year').values('year').annotate(count=Count('year'))
nEstimated = models.Parameter.objects.filter(species__id = species.id, value__evidence__is_experimentally_constrained=False).count()
nExpConstrained = nTotParameters - nEstimated
sources['evidence_parameters'] = [
{'type': 'Experimentally constrained', 'count': nExpConstrained},
{'type': 'Computationally estimated', 'count': nEstimated},
]
sources['evidence_species'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('species').annotate(count = Count('id'))
sources['evidence_media'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('media').annotate(count = Count('id'))
sources['evidence_pH'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('pH').annotate(count = Count('id'))
sources['evidence_temperature'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('temperature').annotate(count = Count('id'))
return render_queryset_to_response(
species_wid = species_wid,
data = {
'content': [contentCol1, contentCol2, contentCol3],
'contentRows': range(max(len(contentCol1), len(contentCol2), len(contentCol3))),
'sources': sources,
},
request = request,
templateFile = 'public/index.html')
def tutorial(request, species_wid=None):
return render_queryset_to_response(species_wid=species_wid,
request=request,
templateFile='public/tutorial.html')
def list(request, species_wid, model_type):
try:
getObjectTypes().index(model_type)
except ValueError:
raise Http404
species = Species.objects.get(wid=species_wid)
model = getModel(model_type)
objects = model.objects.all().filter(species__id=species.id)
facet_fields = []
for field_full_name in model._meta.facet_fields:
#facet
field_names = str(field_full_name).split('__')
tmp_model = model
field_verbose_name = []
for field_name in field_names:
field = tmp_model._meta.get_field_by_name(field_name)[0]
field_verbose_name.append(field.verbose_name)
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp_model = field.rel.to
field_verbose_name = ' › '.join(field_verbose_name)
if isinstance(field, (ForeignKey, ManyToManyField)) and not issubclass(
field.rel.to, Entry):
continue
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp = model.objects.filter(species__id=species.id).order_by(
field_full_name + '__name').values(field_full_name).annotate(
count=Count(field_full_name))
else:
tmp = model.objects.filter(species__id=species.id).order_by(
field_full_name).values(field_full_name).annotate(
count=Count(field_full_name))
facets = []
for facet in tmp:
value = facet[field_full_name]
if value is None or unicode(value) == '':
continue
if isinstance(field, (ForeignKey, ManyToManyField)):
tmp2 = tmp_model.objects.values('wid', 'name').get(id=value)
id = tmp2['wid']
name = capfirst(tmp2['name'])
elif (field.choices is not None) and (len(field.choices) > 0) and (
not isinstance(field, (BooleanField, NullBooleanField))):
id = value
choices = [x[0] for x in field.choices]
if id in choices:
name = field.choices[choices.index(id)][1]
else:
name = capfirst(value)
else:
id = value
name = capfirst(value)
if value is not None and unicode(value) != '':
facets.append({
'id': unicode(id),
'name': unicode(name),
'count': facet['count']
})
if len(facets) > 1:
facet_fields.append({
'name': field_full_name,
'verbose_name': field_verbose_name,
'facets': facets,
})
#filter
val = request.GET.get(field_full_name)
if val:
if isinstance(field, (ForeignKey, ManyToManyField)):
kwargs = {field_full_name + '__wid': val}
elif isinstance(field, (BooleanField, NullBooleanField)):
kwargs = {field_full_name: val == 'True'}
elif isinstance(field,
(AutoField, BigIntegerField, DecimalField,
FloatField, IntegerField, PositiveIntegerField,
PositiveSmallIntegerField, SmallIntegerField)):
kwargs = {field_full_name: float(val)}
else:
kwargs = {field_full_name: val}
objects = objects.filter(**kwargs)
return render_queryset_to_response(species_wid=species_wid,
request=request,
models=[model],
queryset=objects,
templateFile='public/list.html',
data={
'model_type':
model_type,
'model_verbose_name':
model._meta.verbose_name,
'model_verbose_name_plural':
model._meta.verbose_name_plural,
'facet_fields':
facet_fields,
})
sources['evidence_parameters'] = [
{'type': 'Experimentally constrained', 'count': nExpConstrained},
{'type': 'Computationally estimated', 'count': nEstimated},
]
sources['evidence_species'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('species').annotate(count = Count('id'))
sources['evidence_media'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('media').annotate(count = Count('id'))
sources['evidence_pH'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('pH').annotate(count = Count('id'))
sources['evidence_temperature'] = models.Evidence.objects.filter(species_component__species__id = species.id).values('temperature').annotate(count = Count('id'))
return render_queryset_to_response(
request = request,
species_wid = species_wid,
data = {
'content': [contentCol1, contentCol2, contentCol3],
'contentRows': range(max(len(contentCol1), len(contentCol2), len(contentCol3))),
'sources': sources,
},
templateFile = 'public/index.html')
def about(request, species_wid=None):
return render_queryset_to_response(
species_wid = species_wid,
request = request,
templateFile = 'public/about.html',
data = {
'ROOT_URL': settings.ROOT_URL,
}
)
