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 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 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 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 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 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 = 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', ''),
})