def variable_fav_save(request, variable_fav_id=0):
data = json.loads(request.body)
result = {}
name = data['name']
whitelist = re.compile(WHITELIST_RE, re.UNICODE)
match = whitelist.search(unicode(name))
if match:
# XSS risk, log and fail this cohort save
match = whitelist.findall(unicode(name))
logger.error(
'[ERROR] While saving a variable list, saw a malformed name: ' + name + ', characters: ' + match.__str__())
messages.error(request, "Your variable list's name contains invalid characters; please choose another name.")
result['error'] = "Your variable list's name contains invalid characters; please choose another name."
return HttpResponse(json.dumps(result), status=200)
if variable_fav_id:
try:
variable_model = VariableFavorite.objects.get(id=variable_fav_id)
if variable_model.user == request.user :
variable_model.update(name = data['name'], variables = data['variables'])
result['model'] = { 'id' : variable_model.id, 'name' : variable_model.name }
else :
result['error'] = 'You do not have permission to update this gene favorite list'
messages.error(request, 'You do not have permission to update this gene favorite list')
except ObjectDoesNotExist:
messages.error(request, 'The gene list you want does not exist.')
result['error'] = 'You do not have permission to update this gene favorite list'
else:
variable_model = VariableFavorite.create(name = data['name'],
variables = data['variables'],
user = request.user)
result['model'] = { 'id' : variable_model['id'], 'name' : variable_model['name'] }
return HttpResponse(json.dumps(result), status=200)
def variable_fav_list(request, workbook_id=0, worksheet_id=0, new_workbook=0):
template = 'variables/variable_list.html'
context = {}
variable_list = VariableFavorite.get_list(request.user)
if len(variable_list) == 0:
variable_list = None
context['variable_list']=variable_list
if workbook_id != 0:
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
context['base_url'] = settings.BASE_URL
if variable_list:
template = 'variables/variables_select.html'
else:
return initialize_variable_selection_page(request, workbook_id=workbook_id, worksheet_id=worksheet_id)
except ObjectDoesNotExist:
messages.error(request, 'The workbook and worksheet you were referencing does not exist.')
return redirect('variables')
elif new_workbook :
context['new_workbook'] = True
if variable_list :
template = 'variables/variables_select.html'
else:
return initialize_variable_selection_page(request, new_workbook=True)
return render(request, template, context)
def variable_fav_list(request, workbook_id=0, worksheet_id=0, new_workbook=0):
template = 'variables/variable_list.html'
context = {}
variable_list = VariableFavorite.get_list(request.user)
if len(variable_list) == 0 :
variable_list = None
context['variable_list']=variable_list
if workbook_id != 0 :
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
context['base_url'] = settings.BASE_URL
if variable_list :
template = 'variables/variables_select.html'
else :
return initialize_variable_selection_page(request, workbook_id=workbook_id, worksheet_id=worksheet_id)
except ObjectDoesNotExist:
messages.error(request, 'The workbook and worksheet you were referencing does not exist.')
return redirect('variables')
elif new_workbook :
context['new_workbook'] = True
if variable_list :
template = 'variables/variables_select.html'
else :
return initialize_variable_selection_page(request, new_workbook=True)
return render(request, template, context)
def variable_fav_save(request, variable_fav_id=0):
data = json.loads(request.body)
result = {}
name = data['name']
whitelist = re.compile(WHITELIST_RE, re.UNICODE)
match = whitelist.search(unicode(name))
if match:
# XSS risk, log and fail this cohort save
match = whitelist.findall(unicode(name))
logger.error(
'[ERROR] While saving a variable list, saw a malformed name: ' + name + ', characters: ' + match.__str__())
messages.error(request, "Your variable list's name contains invalid characters; please choose another name.")
result['error'] = "Your variable list's name contains invalid characters; please choose another name."
return HttpResponse(json.dumps(result), status=200)
if variable_fav_id:
try:
variable_model = VariableFavorite.objects.get(id=variable_fav_id)
if variable_model.user == request.user :
variable_model.update(name = data['name'], variables = data['variables'])
result['model'] = { 'id' : variable_model.id, 'name' : variable_model.name }
else :
result['error'] = 'You do not have permission to update this gene favorite list'
messages.error(request, 'You do not have permission to update this gene favorite list')
except ObjectDoesNotExist:
messages.error(request, 'The gene list you want does not exist.')
result['error'] = 'You do not have permission to update this gene favorite list'
else :
variable_model = VariableFavorite.create(name = data['name'],
variables = data['variables'],
user = request.user)
result['model'] = { 'id' : variable_model['id'], 'name' : variable_model['name'] }
return HttpResponse(json.dumps(result), status=200)
def variable_fav_detail(request,
variable_fav_id,
workbook_id=0,
worksheet_id=0,
new_workbook=0):
template = 'variables/variable_detail.html'
context = {}
if new_workbook:
context['new_workbook'] = True
if workbook_id:
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
except ObjectDoesNotExist:
messages.error(
request, 'The workbook you were referencing does not exist.')
return redirect('variables')
try:
variable_fav = VariableFavorite.get_deep(id=variable_fav_id,
user=request.user)
context['variables'] = variable_fav
variable_fav.mark_viewed(request)
except ObjectDoesNotExist:
messages.error(
request,
'The variable favorite you were looking for does not exist.')
return redirect('variables')
return render(request, template, context)
def variable_fav_save(request, variable_fav_id=0):
data = json.loads(request.body)
result = {}
if variable_fav_id :
try:
variable_model = VariableFavorite.objects.get(id=variable_fav_id)
if variable_model.user == request.user :
variable_model.update(name = data['name'], variables = data['variables'])
result['model'] = { 'id' : variable_model.id, 'name' : variable_model.name }
else :
result['error'] = 'You do not have permission to update this gene favorite list'
messages.error(request, 'You do not have permission to update this gene favorite list')
except ObjectDoesNotExist:
messages.error(request, 'The gene list you want does not exist.')
result['error'] = 'You do not have permission to update this gene favorite list'
else :
variable_model = VariableFavorite.create(name = data['name'],
variables = data['variables'],
user = request.user)
result['model'] = { 'id' : variable_model['id'], 'name' : variable_model['name'] }
return HttpResponse(json.dumps(result), status=200)
def variable_fav_detail(request, variable_fav_id, workbook_id=0, worksheet_id=0, new_workbook=0):
template = 'variables/variable_detail.html'
context = {}
if new_workbook :
context['new_workbook'] = True
if workbook_id :
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
except ObjectDoesNotExist:
messages.error(request, 'The workbook you were referencing does not exist.')
return redirect('variables')
try:
variable_fav = VariableFavorite.get_deep(variable_fav_id)
context['variables'] = variable_fav
variable_fav.mark_viewed(request)
except ObjectDoesNotExist:
messages.error(request, 'The variable favorite you were looking for does not exist.')
return redirect('variables')
return render(request, template, context)
def initialize_variable_selection_page(request,
variable_list_id=0,
workbook_id=0,
worksheet_id=0,
new_workbook=False):
template = 'variables/variable_edit.html'
context = {'variables' : [] }
workbook_model = None
worksheet_model = None
existing_variable_list = None
if workbook_id != 0:
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
except ObjectDoesNotExist:
messages.error(request, 'The workbook you were referencing does not exist.')
return redirect('variables')
if variable_list_id != 0:
try:
existing_variable_list = request.user.variablefavorite_set.get(id=variable_list_id)
if existing_variable_list.version != 'v2':
messages.warning(request, 'Version 1 Variable lists cannot be edited due to changes in available variables.')
return redirect('variables')
except ObjectDoesNotExist:
messages.error(request, 'The variable favorite you were looking for does not exist.')
return redirect('variables')
data_attr = [
'DNA_sequencing',
'RNA_sequencing',
'miRNA_sequencing',
'Protein',
'SNP_CN',
'DNA_methylation'
]
# This is a list of specific data classifications which require additional filtering in order to
# Gather categorical or numercial variables for use in the plot
# Filter Options
datatype_labels = {'CLIN' : 'Clinical',
'GEXP' : 'Gene Expression',
'MIRN' : 'miRNA',
'METH' : 'Methylation',
'CNVR' : 'Copy Number',
'RPPA' : 'Protein',
'GNAB' : 'Mutation'}
datatype_list = SearchableFieldHelper.get_fields_for_all_datatypes()
for type in datatype_list:
type['label'] = datatype_labels[type['datatype']]
#remove gene in fields
for index, field in enumerate(type['fields']):
if field['label'] == "Gene":
del type['fields'][index]
# Public programs
isb_user = Django_User.objects.filter(username='******').first()
public_programs = Program.objects.filter(active=True, is_public=True, owner=isb_user)
# User programs
ownedPrograms = request.user.program_set.all().filter(active=True)
sharedPrograms = Program.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
programs = ownedPrograms | sharedPrograms
user_programs = programs.distinct()
# User favorites
favorite_list = VariableFavorite.get_list(user=request.user, version='v2')
for fav in favorite_list:
fav.variables = fav.get_variables()
full_fave_count = len(VariableFavorite.get_list(user=request.user))
program_attrs = {}
for prog in public_programs:
program_attrs[prog.id] = fetch_program_attr(prog.id)
attr_codes = ClinicalColumnFeatureSupport.get_features_ids_for_column_names(program_attrs[prog.id].keys())
if 'not_found_columns' in attr_codes:
new_keys = [x for x in program_attrs[prog.id].keys() if x not in attr_codes['not_found_columns']]
attr_codes = ClinicalColumnFeatureSupport.get_features_ids_for_column_names(new_keys)
for attr in program_attrs[prog.id]:
if attr in attr_codes['clinical_feature_ids']:
program_attrs[prog.id][attr]['data_code'] = attr_codes['clinical_feature_ids'][attr]
else:
program_attrs[prog.id][attr]['data_code'] = 'v2:CLIN:'+attr
# users can select from their saved variable favorites
variable_favorites = VariableFavorite.get_list(request.user)
context = {
'favorite_list' : favorite_list,
'full_favorite_list_count': full_fave_count,
'datatype_list' : datatype_list,
'data_attr' : data_attr,
'public_programs' : public_programs,
'user_programs' : programs,
'base_url' : settings.BASE_URL,
'base_api_url' : settings.BASE_API_URL,
'variable_favorites' : variable_favorites,
'workbook' : workbook_model,
'worksheet' : worksheet_model,
'existing_variable_list' : existing_variable_list,
'new_workbook' : new_workbook,
'program_attrs' : program_attrs
}
return render(request, template, context)
def initialize_variable_selection_page(request,
variable_list_id=0,
workbook_id=0,
worksheet_id=0,
new_workbook=False):
template = 'variables/variable_edit.html'
context = {'variables' : [] }
workbook_model = None
worksheet_model = None
existing_variable_list = None
if workbook_id != 0 :
try:
workbook_model = Workbook.objects.get(id=workbook_id)
context['workbook'] = workbook_model
worksheet_model = Worksheet.objects.get(id=worksheet_id)
context['worksheet'] = worksheet_model
except ObjectDoesNotExist:
messages.error(request, 'The workbook you were referencing does not exist.')
return redirect('variables')
if variable_list_id != 0:
try:
existing_variable_list = request.user.variablefavorite_set.get(id=variable_list_id)
except ObjectDoesNotExist:
messages.error(request, 'The variable favorite you were looking for does not exist.')
return redirect('variables')
data_attr = [
'DNA_sequencing',
'RNA_sequencing',
'miRNA_sequencing',
'Protein',
'SNP_CN',
'DNA_methylation'
]
# This is a list of specific data classifications which require additional filtering in order to
# Gather categorical or numercial variables for use in the plot
# Filter Options
datatype_labels = {'CLIN' : 'Clinical',
'GEXP' : 'Gene Expression',
'MIRN' : 'miRNA',
'METH' : 'Methylation',
'CNVR' : 'Copy Number',
'RPPA' : 'Protein',
'GNAB' : 'Mutation'}
datatype_list = SearchableFieldHelper.get_fields_for_all_datatypes()
for type in datatype_list:
type['label'] = datatype_labels[type['datatype']]
#remove gene in fields
for index, field in enumerate(type['fields']):
if field['label'] == "Gene":
del type['fields'][index]
#get user programs and variables
ownedPrograms = request.user.program_set.all().filter(active=True)
sharedPrograms = Program.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
programs = ownedPrograms | sharedPrograms
programs = programs.distinct()
#get user favorites
favorite_list = VariableFavorite.get_list(user=request.user)
for fav in favorite_list :
fav.variables = fav.get_variables()
#TODO common variables need to be refactored into an adaptive list based on common used
displayed_common_variables = [
{'name' : "vital_status", 'code' : 'CLIN:vital_status', 'type' : 'C'},
{'name' : "gender", 'code' : 'CLIN:gender', 'type' : 'C'},
{'name' : "age_at_initial_pathologic_diagnosis", 'code' : 'CLIN:age_at_initial_pathologic_diagnosis', 'type' : 'N'},
{'name' : "tumor_tissue_site", 'code' : 'CLIN:tumor_tissue_site', 'type' : 'C'},
{'name' : "histological_type", 'code' : 'CLIN:histological_type', 'type' : 'C'},
{'name' : "other_diagnosis", 'code' : 'CLIN:other_dx', 'type' : 'C'},
{'name' : "tumor_status", 'code' : 'CLIN:person_neoplasm_cancer_status', 'type' : 'C'},
{'name' : "new_tumor_event_after_initial_treatment", 'code' : 'CLIN:new_tumor_event_after_initial_treatment', 'type' : 'C'},
{'name' : "histological_grade", 'code' : 'CLIN:neoplasm_histologic_grade', 'type' : 'C'},
{'name' : "residual_tumor", 'code' : 'CLIN:residual_tumor', 'type' : 'C'},
{'name' : "tobacco_smoking_history", 'code' : 'CLIN:tobacco_smoking_history', 'type' : 'C'},
{'name' : "icd-10", 'code' : 'CLIN:icd_10', 'type' : 'C'},
{'name' : "icd-o-3_site", 'code' : 'CLIN:icd_o_3_site', 'type' : 'C'},
{'name' : "icd-o-3_histology", 'code' : 'CLIN:icd_o_3_histology', 'type' : 'C'}
]
common_variables = displayed_common_variables
TCGA_program = {"id" : -1, "study" : {"id" :-1, "name" : ""}, "name" : "TCGA"}
common_program = {"id" : -1, "study" : {"id" :-1, "name" : ""}, "name" : "Common", "variables" : common_variables}
# users can select from their saved variable favorites
variable_favorites = VariableFavorite.get_list(request.user)
context = {
'favorite_list' : favorite_list,
'datatype_list' : datatype_list,
'programs' : programs,
'data_attr' : data_attr,
'base_url' : settings.BASE_URL,
'base_api_url' : settings.BASE_API_URL,
'TCGA_program' : TCGA_program,
'common_program' : common_program,
'variable_favorites' : variable_favorites,
'workbook' : workbook_model,
'worksheet' : worksheet_model,
'existing_variable_list' : existing_variable_list,
'new_workbook' : new_workbook
}
return render(request, template, context)
