def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/',1)[1]
if request.method == "POST" :
if command == "create" :
workbook_model = Workbook.createDefault(name="Untitled Workbook", description="", user=request.user)
elif command == "edit" :
workbook_model = Workbook.edit(id=workbook_id, name=request.POST.get('name'), description=request.POST.get('description'))
elif command == "copy" :
workbook_model = Workbook.copy(id=workbook_id, user=request.user)
elif command == "delete" :
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET" :
if workbook_id:
try :
ownedWorkbooks = request.user.workbook_set.all().filter(active=True)
sharedWorkbooks = Workbook.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
publicWorkbooks = Workbook.objects.all().filter(is_public=True,active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets()
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'datatypes' : get_gene_datatypes(),
'is_shareable': is_shareable,
'shared' : shared,
'plot_types' : plot_types})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbooks')
return redirect(redirect_url)
def workbook_create_with_program(request):
program_id = request.POST.get('program_id')
program_model = Program.objects.get(id=program_id)
workbook_model = Workbook.create(
name="Untitled Workbook",
description=
"this is an untitled workbook with all variables of program \"" +
program_model.name +
"\" added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
#add every variable within the model
for study in program_model.study_set.filter(active=True):
for var in study.user_feature_definitions_set.all():
work_var = Worksheet_variable.objects.create(
worksheet_id=worksheet_model.id,
name=var.feature_name,
url_code=var.bq_map_id,
feature_id=var.id)
work_var.save()
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_model.id})
return redirect(redirect_url)
def workbook_create_with_variables(request):
json_data = request.POST.get('json_data')
if json_data:
data = json.loads(json_data)
# TODO: Refactor so that user can create using multiple variable lists
var_list_id = data['variable_list_id'][0]
else:
var_list_id = request.POST.get('variable_list_id')
var_list_model = VariableFavorite.objects.get(id=var_list_id)
name = request.POST.get('name', var_list_model.name + ' workbook')
workbook_model = Workbook.create(name=name, description="this is an untitled workbook with all variables of variable favorite list \"" + var_list_model.name + "\" added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
workbook_model.save()
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
worksheet_model.save()
print workbook_model.id
for var in var_list_model.get_variables() :
work_var = Worksheet_variable.objects.create(worksheet_id = worksheet_model.id,
name = var.name,
url_code = var.code,
type = var.type,
feature_id = var.feature_id)
work_var.save()
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
if json_data:
return JsonResponse({'workbook_id': workbook_model.id, 'worksheet_id': worksheet_model.id})
else:
return redirect(redirect_url)
def workbook_create_with_cohort(request):
cohort_id = request.POST.get('cohort_id')
cohort = Cohort.objects.get(id=cohort_id)
workbook_model = Workbook.create(name="Untitled Workbook", description="This workbook was created with cohort \"" + cohort.name + "\" added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
worksheet_model.add_cohort(cohort=cohort)
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
def workbook_create_with_analysis(request):
analysis_type = request.POST.get('analysis')
allowed_types = Analysis.get_types()
redirect_url = reverse('sample_analyses')
for type in allowed_types :
if analysis_type == type['name'] :
workbook_model = Workbook.create(name="Untitled Workbook", description="this is an untitled workbook with a \"" + analysis_type + "\" plot added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
worksheet_model.set_plot(type=analysis_type)
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
break
return redirect(redirect_url)
def workbook_create_with_cohort_list(request):
cohort_ids = json.loads(request.body)['cohorts']
if len(cohort_ids) > 0 :
workbook_model = Workbook.create(name="Untitled Workbook", description="This is a workbook created with cohorts added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
for id in cohort_ids :
cohort = Cohort.objects.get(id=id)
worksheet_model.add_cohort(cohort=cohort)
result = {'workbook_id' : workbook_model.id,
'worksheet_id' : worksheet_model.id}
else :
result = {'error' : 'parameters are not correct'}
return HttpResponse(json.dumps(result), status=200)
def workbook_create_with_cohort(request):
cohort_id = request.POST.get('cohort_id')
cohort = Cohort.objects.get(id=cohort_id)
workbook_model = Workbook.create(
name="Untitled Workbook",
description="This workbook was created with cohort \"" + cohort.name +
"\" added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
worksheet_model.add_cohort(cohort=cohort)
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_model.id})
return redirect(redirect_url)
def worksheet_display(request, workbook_id=0, worksheet_id=0):
template = 'workbooks/workbook.html'
workbook_model = Workbook.deep_get(workbook_id)
workbook_model.mark_viewed(request)
is_shareable = workbook_model.is_shareable(request)
for worksheet in workbook_model.worksheets:
if str(worksheet.id) == worksheet_id:
display_worksheet = worksheet
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'is_shareable' : is_shareable,
'datatypes' : get_gene_datatypes(),
'display_worksheet' : display_worksheet,
'plot_types' : plot_types})
def workbook_create_with_program(request):
program_id = request.POST.get('program_id')
program_model = Program.objects.get(id=program_id)
workbook_model = Workbook.create(name="Untitled Workbook", description="this is an untitled workbook with all variables of program \"" + program_model.name + "\" added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
#add every variable within the model
for study in program_model.study_set.all().filter(active=True) :
for var in study.user_feature_definitions_set.all() :
work_var = Worksheet_variable.objects.create(worksheet_id = worksheet_model.id,
name = var.feature_name,
url_code = var.bq_map_id,
feature_id = var.id)
work_var.save()
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
def workbook_create_with_variables(request):
json_data = request.POST.get('json_data')
if json_data:
data = json.loads(json_data)
# TODO: Refactor so that user can create using multiple variable lists
var_list_id = data['variable_list_id'][0]
else:
var_list_id = request.POST.get('variable_list_id')
var_list_model = VariableFavorite.objects.get(id=var_list_id)
name = request.POST.get('name', var_list_model.name + ' workbook')
workbook_model = Workbook.create(
name=name,
description=
"this is an untitled workbook with all variables of variable favorite list \""
+ var_list_model.name +
"\" added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
workbook_model.save()
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
worksheet_model.save()
print workbook_model.id
for var in var_list_model.get_variables():
work_var = Worksheet_variable.objects.create(
worksheet_id=worksheet_model.id,
name=var.name,
url_code=var.code,
type=var.type,
feature_id=var.feature_id)
work_var.save()
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_model.id})
if json_data:
return JsonResponse({
'workbook_id': workbook_model.id,
'worksheet_id': worksheet_model.id
})
else:
return redirect(redirect_url)
def worksheet_display(request, workbook_id=0, worksheet_id=0):
template = 'workbooks/workbook.html'
workbook_model = Workbook.deep_get(workbook_id)
workbook_model.mark_viewed(request)
is_shareable = workbook_model.is_shareable(request)
for worksheet in workbook_model.worksheets:
if str(worksheet.id) == worksheet_id:
display_worksheet = worksheet
plot_types = Analysis.get_types()
return render(
request, template, {
'workbook': workbook_model,
'is_shareable': is_shareable,
'datatypes': get_gene_datatypes(workbook_model.build),
'display_worksheet': display_worksheet,
'plot_types': plot_types
})
def workbook_create_with_analysis(request):
analysis_type = request.POST.get('analysis')
allowed_types = Analysis.get_types()
redirect_url = reverse('sample_analyses')
for type in allowed_types:
if analysis_type == type['name']:
workbook_model = Workbook.create(
name="Untitled Workbook",
description="this is an untitled workbook with a \"" +
analysis_type +
"\" plot added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
worksheet_model.set_plot(type=analysis_type)
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_model.id})
break
return redirect(redirect_url)
def workbook_create_with_cohort_list(request):
cohort_ids = json.loads(request.body)['cohorts']
if len(cohort_ids) > 0:
workbook_model = Workbook.create(
name="Untitled Workbook",
description=
"This is a workbook created with cohorts added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1",
description="",
workbook=workbook_model)
for id in cohort_ids:
cohort = Cohort.objects.get(id=id)
worksheet_model.add_cohort(cohort=cohort)
result = {
'workbook_id': workbook_model.id,
'worksheet_id': worksheet_model.id
}
else:
result = {'error': 'parameters are not correct'}
return HttpResponse(json.dumps(result), status=200)
def worksheet_variables(request, workbook_id=0, worksheet_id=0, variable_id=0):
command = request.path.rsplit('/', 1)[1]
json_response = False
workbook_name = "Untitled Workbook"
result = {}
if request.method == "POST":
if command == "delete":
Worksheet_variable.destroy(workbook_id=workbook_id,
worksheet_id=worksheet_id,
id=variable_id,
user=request.user)
result['message'] = "variables have been deleted from workbook"
else:
variables = []
#from Edit Page
if "variables" in request.body:
json_response = True
name = json.loads(request.body)['name']
variable_list = json.loads(request.body)['variables']
variable_favorite_result = VariableFavorite.create(
name=name, variables=variable_list, user=request.user)
model = VariableFavorite.objects.get(
id=variable_favorite_result['id'])
messages.info(
request,
'The variable favorite list \"' + escape(model.name) +
'\" was created and added to your worksheet')
variables = model.get_variables()
#from Details Page or list page
if request.POST.get("variable_list_id"):
workbook_name = request.POST.get("name")
variable_id = request.POST.get("variable_list_id")
try:
variable_fav = VariableFavorite.objects.get(id=variable_id)
variables = variable_fav.get_variables()
except ObjectDoesNotExist:
result['error'] = "variable favorite does not exist"
#from Select Page
if "var_favorites" in request.body:
variable_fav_list = json.loads(request.body)['var_favorites']
json_response = True
for fav in variable_fav_list:
try:
fav = VariableFavorite.objects.get(id=fav['id'])
variables = fav.get_variables()
except ObjectDoesNotExist:
result['error'] = "variable favorite does not exist"
if len(variables) > 0:
if workbook_id == 0:
workbook_model = Workbook.create(
name=workbook_name,
description=
"This workbook was created with variables added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(
name="worksheet 1",
description="",
workbook=workbook_model)
else:
workbook_model = Workbook.objects.get(id=workbook_id)
workbook_model.save()
worksheet_model = Worksheet.objects.get(id=worksheet_id)
Worksheet_variable.edit_list(workbook_id=workbook_model.id,
worksheet_id=worksheet_model.id,
variable_list=variables,
user=request.user)
result['workbook_id'] = workbook_model.id
result['worksheet_id'] = worksheet_model.id
else:
result['error'] = "no variables to add"
else:
result['error'] = "method not correct"
if json_response:
return HttpResponse(json.dumps(result), status=200)
else:
redirect_url = reverse('worksheet_display',
kwargs={
'workbook_id': workbook_model.id,
'worksheet_id': worksheet_model.id
})
return redirect(redirect_url)
def worksheet_genes(request, workbook_id=0, worksheet_id=0, genes_id=0):
command = request.path.rsplit('/',1)[1];
json_response = False
result = {}
if request.method == "POST" :
if command == "delete" :
Worksheet_gene.destroy(workbook_id=workbook_id, worksheet_id=worksheet_id, id=genes_id, user=request.user)
result['message'] = "genes have been deleted from workbook"
else :
genes = []
workbook_name = 'Untitled Workbook'
#from Gene Edit Page
if request.POST.get("genes-list") :
# Get workbook name
if request.POST.get('name'):
workbook_name = request.POST.get('name')
name = request.POST.get("genes-name")
gene_list = request.POST.get("genes-list")
gene_list = [x.strip() for x in gene_list.split(' ')]
gene_list = list(set(gene_list))
GeneFavorite.create(name=name, gene_list=gene_list, user=request.user)
messages.info(request, 'The gene favorite list \"' + name + '\" was created and added to your worksheet')
for g in gene_list:
genes.append(g)
#from Gene Details Page
if request.POST.get("gene_list_id") :
# Get workbook name
if request.POST.get('name'):
workbook_name = request.POST.get('name')
gene_id = request.POST.get("gene_list_id")
try :
gene_fav = GeneFavorite.objects.get(id=gene_id)
names = gene_fav.get_gene_name_list()
for g in names:
if g not in genes:
genes.append(g)
except ObjectDoesNotExist:
None
#from Gene List Page
if "gene_fav_list" in request.body :
json_response = True
gene_fav_list = json.loads(request.body)['gene_fav_list']
for id in gene_fav_list:
try:
fav = GeneFavorite.objects.get(id=id)
names = fav.get_gene_name_list()
for g in names:
if g not in genes:
genes.append(g)
except ObjectDoesNotExist:
None
if len(genes) > 0:
if workbook_id is 0:
workbook_model = Workbook.create(name=workbook_name, description="This workbook was created with genes added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
else :
workbook_model = Workbook.objects.get(id=workbook_id)
workbook_model.save()
worksheet_model = Worksheet.objects.get(id=worksheet_id)
Worksheet_gene.edit_list(workbook_id=workbook_model.id, worksheet_id=worksheet_model.id, gene_list=genes, user=request.user)
result['genes'] = genes
else :
result['error'] = "no genes to add"
else :
result['error'] = "method not correct"
if json_response :
return HttpResponse(json.dumps(result), status=200)
else :
redirect_url = reverse('worksheet_display', kwargs={'workbook_id':workbook_model.id, 'worksheet_id': worksheet_model.id})
return redirect(redirect_url)
def worksheet_variables(request, workbook_id=0, worksheet_id=0, variable_id=0):
command = request.path.rsplit('/',1)[1];
json_response = False
workbook_name = "Untitled Workbook"
result = {}
if request.method == "POST" :
if command == "delete" :
Worksheet_variable.destroy(workbook_id=workbook_id, worksheet_id=worksheet_id, id=variable_id, user=request.user)
result['message'] = "variables have been deleted from workbook"
else :
variables = []
#from Edit Page
if "variables" in request.body :
json_response = True
name = json.loads(request.body)['name']
variable_list = json.loads(request.body)['variables']
variable_favorite_result = VariableFavorite.create(name = name,
variables = variable_list,
user = request.user)
model = VariableFavorite.objects.get(id=variable_favorite_result['id'])
messages.info(request, 'The variable favorite list \"' + model.name + '\" was created and added to your worksheet')
variables = model.get_variables()
#from Details Page or list page
if request.POST.get("variable_list_id") :
workbook_name = request.POST.get("name")
variable_id = request.POST.get("variable_list_id")
try :
variable_fav = VariableFavorite.objects.get(id=variable_id)
variables = variable_fav.get_variables()
except ObjectDoesNotExist:
result['error'] = "variable favorite does not exist"
#from Select Page
if "var_favorites" in request.body :
variable_fav_list = json.loads(request.body)['var_favorites']
json_response = True
for fav in variable_fav_list:
try:
fav = VariableFavorite.objects.get(id=fav['id'])
variables = fav.get_variables()
except ObjectDoesNotExist:
result['error'] = "variable favorite does not exist"
if len(variables) > 0:
if workbook_id == 0:
workbook_model = Workbook.create(name=workbook_name, description="This workbook was created with variables added to the first worksheet. Click Edit Details to change your workbook title and description.", user=request.user)
worksheet_model = Worksheet.objects.create(name="worksheet 1", description="", workbook=workbook_model)
else :
workbook_model = Workbook.objects.get(id=workbook_id)
workbook_model.save()
worksheet_model = Worksheet.objects.get(id=worksheet_id)
Worksheet_variable.edit_list(workbook_id=workbook_model.id, worksheet_id=worksheet_model.id, variable_list=variables, user=request.user)
result['workbook_id'] = workbook_model.id
result['worksheet_id'] = worksheet_model.id
else :
result['error'] = "no variables to add"
else :
result['error'] = "method not correct"
if json_response :
return HttpResponse(json.dumps(result), status=200)
else :
redirect_url = reverse('worksheet_display', kwargs={'workbook_id':workbook_model.id, 'worksheet_id': worksheet_model.id})
return redirect(redirect_url)
def worksheet_genes(request, workbook_id=0, worksheet_id=0, genes_id=0):
command = request.path.rsplit('/', 1)[1]
json_response = False
result = {}
if request.method == "POST":
if command == "delete":
Worksheet_gene.destroy(workbook_id=workbook_id,
worksheet_id=worksheet_id,
id=genes_id,
user=request.user)
result['message'] = "genes have been deleted from workbook"
else:
genes = []
workbook_name = 'Untitled Workbook'
#from Gene Edit Page
if request.POST.get("genes-list"):
# Get workbook name
if request.POST.get('name'):
workbook_name = request.POST.get('name')
name = request.POST.get("genes-name")
gene_list = request.POST.get("genes-list")
gene_list = [x.strip() for x in gene_list.split(' ')]
gene_list = list(set(gene_list))
GeneFave = GeneFavorite.create(name=name,
gene_list=gene_list,
user=request.user)
messages.info(
request, 'The gene favorite list \"' + name +
'\" was created and added to your worksheet')
# Refetch the created gene list, because it will have the names correctly formatted
for g in GeneFavorite.objects.get(
id=GeneFave['id']).get_genes_list():
genes.append(g)
#from Gene Details Page
if request.POST.get("gene_list_id"):
# Get workbook name
if request.POST.get('name'):
workbook_name = request.POST.get('name')
gene_id = request.POST.get("gene_list_id")
try:
gene_fav = GeneFavorite.objects.get(id=gene_id)
names = gene_fav.get_gene_name_list()
for g in names:
if g not in genes:
genes.append(g)
except ObjectDoesNotExist:
None
#from Gene List Page
if "gene_fav_list" in request.body:
json_response = True
gene_fav_list = json.loads(request.body)['gene_fav_list']
for id in gene_fav_list:
try:
fav = GeneFavorite.objects.get(id=id)
names = fav.get_gene_name_list()
for g in names:
if g not in genes:
genes.append(g)
except ObjectDoesNotExist:
None
if len(genes) > 0:
if workbook_id is 0:
workbook_model = Workbook.create(
name=workbook_name,
description=
"This workbook was created with genes added to the first worksheet. Click Edit Details to change your workbook title and description.",
user=request.user)
worksheet_model = Worksheet.objects.create(
name="worksheet 1",
description="",
workbook=workbook_model)
else:
workbook_model = Workbook.objects.get(id=workbook_id)
workbook_model.save()
worksheet_model = Worksheet.objects.get(id=worksheet_id)
Worksheet_gene.edit_list(workbook_id=workbook_model.id,
worksheet_id=worksheet_model.id,
gene_list=genes,
user=request.user)
result['genes'] = genes
else:
result['error'] = "no genes to add"
else:
result['error'] = "method not correct"
if json_response:
return HttpResponse(json.dumps(result), status=200)
else:
redirect_url = reverse('worksheet_display',
kwargs={
'workbook_id': workbook_model.id,
'worksheet_id': worksheet_model.id
})
return redirect(redirect_url)
def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/',1)[1]
if request.method == "POST":
if command == "create":
workbook_model = Workbook.createDefault(name="Untitled Workbook", description="", user=request.user)
elif command == "edit":
workbook_name = request.POST.get('name')
workbook_desc = request.POST.get('description')
whitelist = re.compile(WHITELIST_RE, re.UNICODE)
match_name = whitelist.search(unicode(workbook_name))
match_desc = whitelist.search(unicode(workbook_desc))
if match_name or match_desc:
# XSS risk, log and fail this cohort save
matches = ""
fields = ""
if match_name:
match_name = whitelist.findall(unicode(workbook_name))
logger.error('[ERROR] While saving a workbook, saw a malformed name: ' + workbook_name + ', characters: ' + match_name.__str__())
matches = "name contains"
fields = "name"
if match_desc:
match_desc = whitelist.findall(unicode(workbook_desc))
logger.error('[ERROR] While saving a workbook, saw a malformed description: ' + workbook_desc + ', characters: ' + match_desc.__str__())
matches = "name and description contain" if match_name else "description contains"
fields += (" and description" if match_name else "description")
err_msg = "Your workbook's %s invalid characters; please choose another %s." % (matches, fields,)
messages.error(request, err_msg)
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_id})
return redirect(redirect_url)
workbook_model = Workbook.edit(id=workbook_id, name=workbook_name, description=workbook_desc)
elif command == "copy":
workbook_model = Workbook.copy(id=workbook_id, user=request.user)
elif command == "delete":
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
else:
redirect_url = reverse('workbook_detail', kwargs={'workbook_id':workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET" :
if workbook_id:
try :
ownedWorkbooks = request.user.workbook_set.all().filter(active=True)
sharedWorkbooks = Workbook.objects.filter(shared__matched_user=request.user, shared__active=True, active=True)
publicWorkbooks = Workbook.objects.all().filter(is_public=True,active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets()
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(request, template, {'workbook' : workbook_model,
'datatypes' : get_gene_datatypes(),
'is_shareable': is_shareable,
'shared' : shared,
'plot_types' : plot_types})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else :
redirect_url = reverse('workbooks')
return redirect(redirect_url)
def workbook(request, workbook_id=0):
template = 'workbooks/workbook.html'
command = request.path.rsplit('/', 1)[1]
workbook_model = None
try:
if request.method == "POST":
if command == "create":
workbook_model = Workbook.createDefault(
name="Untitled Workbook",
description="",
user=request.user)
elif command == "edit":
# Truncate incoming name and desc fields in case someone tried to send ones which were too long
workbook_name = request.POST.get('name')[0:2000]
workbook_desc = request.POST.get('description')[0:2000]
workbook_build = request.POST.get('build')
blacklist = re.compile(BLACKLIST_RE, re.UNICODE)
match_name = blacklist.search(unicode(workbook_name))
match_desc = blacklist.search(unicode(workbook_desc))
if match_name or match_desc:
# XSS risk, log and fail this cohort save
matches = ""
fields = ""
if match_name:
match_name = blacklist.findall(unicode(workbook_name))
logger.error(
'[ERROR] While saving a workbook, saw a malformed name: '
+ workbook_name + ', characters: ' +
str(match_name))
matches = "name contains"
fields = "name"
if match_desc:
match_desc = blacklist.findall(unicode(workbook_desc))
logger.error(
'[ERROR] While saving a workbook, saw a malformed description: '
+ workbook_desc + ', characters: ' +
str(match_desc))
matches = "name and description contain" if match_name else "description contains"
fields += (" and description"
if match_name else "description")
err_msg = "Your workbook's %s invalid characters; please choose another %s." % (
matches,
fields,
)
messages.error(request, err_msg)
redirect_url = reverse('workbook_detail',
kwargs={'workbook_id': workbook_id})
return redirect(redirect_url)
workbook_model = Workbook.edit(id=workbook_id,
name=workbook_name,
description=workbook_desc,
build=workbook_build)
elif command == "copy":
workbook_model = Workbook.copy(id=workbook_id,
user=request.user)
elif command == "delete":
Workbook.destroy(id=workbook_id)
if command == "delete":
redirect_url = reverse('workbooks')
else:
redirect_url = reverse(
'workbook_detail',
kwargs={'workbook_id': workbook_model.id})
return redirect(redirect_url)
elif request.method == "GET":
if workbook_id:
try:
ownedWorkbooks = request.user.workbook_set.filter(
active=True)
sharedWorkbooks = Workbook.objects.filter(
shared__matched_user=request.user,
shared__active=True,
active=True)
publicWorkbooks = Workbook.objects.filter(is_public=True,
active=True)
workbooks = ownedWorkbooks | sharedWorkbooks | publicWorkbooks
workbooks = workbooks.distinct()
workbook_model = workbooks.get(id=workbook_id)
workbook_model.worksheets = workbook_model.get_deep_worksheets(
)
is_shareable = workbook_model.is_shareable(request)
shared = None
if workbook_model.owner.id != request.user.id and not workbook_model.is_public:
shared = request.user.shared_resource_set.get(
workbook__id=workbook_id)
plot_types = Analysis.get_types()
return render(
request, template, {
'workbook': workbook_model,
'datatypes': get_gene_datatypes(
workbook_model.build),
'is_shareable': is_shareable,
'shared': shared,
'plot_types': plot_types
})
except ObjectDoesNotExist:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
else:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
except Exception as e:
logger.error("[ERROR] Exception when viewing a workbook: ")
logger.exception(e)
messages.error(
request,
"An error was encountered while trying to view this workbook.")
finally:
redirect_url = reverse('workbooks')
return redirect(redirect_url)
