def view_collection(request, collection_head_id):
collection_head = Collection_Head().GET(collection_head_id)
# get profile id for breadcrumb
profile_id = request.session['profile_id']
request.session['collection_head_id'] = collection_head_id
# ENA Type Handler-----------------------------------
if collection_head['type'].lower() == 'ena submission':
# get template for rendering the UI
ui_template = DataSchemas("ENA").get_ui_template()
if not ui_template:
return render(request,
'copo/error_page.html',
{'message': UI_ERROR_CODES["TEMPLATE_NOT_FOUND"]},
)
return HttpResponseRedirect(reverse('copo:index'))
# get study types
study_types = lkup.DROP_DOWNS['STUDY_TYPES']
if 'collection_details' in collection_head:
request.session['ena_collection_id'] = str(collection_head['collection_details'][0])
profile = Profile().GET(profile_id)
ena_collection = EnaCollection().GET(request.session['ena_collection_id'])
sample_attributes = d_utils.get_sample_attributes()
messages = {}
messages["user_defined_attribute_message"] = lkup.UI_INFO["user_defined_attribute_message"]
messages["system_suggested_attribute_message"] = lkup.UI_INFO["system_suggested_attribute_message"]
data_dict = {'collection_head': collection_head, 'collection_head_id': collection_head_id,
'ena_collection_id': request.session['ena_collection_id'], 'profile_id': profile_id,
'ena_collection': ena_collection,
'profile': profile,
'ui_template': ui_template,
'study_types': study_types,
'sample_attributes': sample_attributes,
'messages': messages,
}
else:
data_dict = {'collection_head': collection_head, 'collection_head_id': collection_head_id,
'profile_id': profile_id}
request.session.delete('collected')
return render(request, 'copo/ena_collection_multi.html', data_dict, context_instance=RequestContext(request))
# Figshare Type Handler -------------------------------------
elif collection_head['type'].lower() == 'figshare':
articles = FigshareCollection().get_articles_in_collection(collection_head_id)
data_dict = {'collection_head': collection_head, 'collection_head_id': collection_head_id,
'profile_id': profile_id,
'articles': articles}
return render(request, 'copo/article.html', data_dict, context_instance=RequestContext(request))
def add_to_collection(request):
return_structure = {}
# get task to be performed
task = request.POST['task']
collection_head_id = request.POST['collection_head_id']
collection = Collection_Head().GET(collection_head_id)
ena_collection_id = str(collection['collection_details'][0])
if task == "add_new_study":
study_fields = request.POST['study_fields']
study_fields = ast.literal_eval(study_fields)
# get studies
st_list = []
for k, v in study_fields.items():
if k.startswith('study_type_select_'):
index_part = k.split("study_type_select_")[1]
# only add if a study reference has been provided
if 'study_type_reference_' + index_part in study_fields:
st_dict = {'study_type': study_fields[k],
'study_type_reference': study_fields['study_type_reference_' + index_part]}
st_list.append(st_dict)
if st_list:
EnaCollection().add_ena_study(ena_collection_id, st_list)
return_structure['study_data'] = htags.generate_study_table2(ena_collection_id)
elif task == "clone_study":
cloned_elements = request.POST['cloned_elements']
cloned_elements = ast.literal_eval(cloned_elements)
EnaCollection().clone_ena_study(ena_collection_id, cloned_elements)
return_structure['study_data'] = htags.generate_study_table2(ena_collection_id)
elif task == "delete_study":
study_id = request.POST['study_id']
EnaCollection().delete_study(ena_collection_id, study_id)
return_structure['study_data'] = htags.generate_study_table2(ena_collection_id)
elif task == "get_tree_study":
return_structure['ena_studies'] = htags.get_studies_tree(ena_collection_id)
elif task == "get_tree_study_sample":
return_structure['ena_studies'] = htags.get_study_sample_tree(ena_collection_id)
elif task == "get_study_sample":
return_structure['sample_data'] = EnaCollection().get_ena_sample(ena_collection_id, request.POST['sample_id'])
return_structure['ena_studies'] = htags.get_study_sample_tree_restrict(ena_collection_id,
request.POST['sample_id'])
messages = {}
messages["edit"] = lkup.UI_LABELS["sample_edit"]
messages["clone"] = lkup.UI_LABELS["sample_clone"]
messages["add"] = lkup.UI_LABELS["sample_add"]
return_structure['messages'] = messages
elif task == "get_sample_attributes":
return_structure['sample_attributes'] = d_utils.get_sample_attributes()
messages = {}
messages["system_suggested_attribute_message"] = lkup.UI_INFO["system_suggested_attribute_message"]
messages["sample_add"] = lkup.UI_LABELS["sample_add"]
return_structure['messages'] = messages
elif task == "add_new_study_sample" or task == "edit_study_sample" or task == "clone_study_sample":
auto_fields = request.POST['auto_fields']
study_type_list = request.POST['study_types']
if study_type_list:
study_type_list = study_type_list.split(",")
else:
study_type_list = []
if task == "edit_study_sample":
sample_id = request.POST['sample_id']
EnaCollection().edit_ena_sample(ena_collection_id, sample_id, study_type_list, auto_fields)
else:
EnaCollection().add_ena_sample(ena_collection_id, study_type_list, auto_fields)
return_structure['sample_data'] = htags.generate_sample_table2(ena_collection_id)
return_structure['study_data'] = htags.generate_study_table2(ena_collection_id)
return_structure['exit_status'] = 'success'
out = jsonpickle.encode(return_structure)
return HttpResponse(out, content_type='json')
