def expression_boxplot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id,
'expression')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'expression',
'default_gene': 'TP53'
}
return render_to_response('gene_boxplot.html',
context,
context_instance=RequestContext(request))
def feature_matrix_plot(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id,
'feature_matrix')
if file_name is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'feature_matrix'
}
return render_to_response('feature_matrix.html',
context,
context_instance=RequestContext(request))
def features_json(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id, 'feature_matrix')
if file_name is None:
raise Http404
# Compose the path to the .json-file
features_path = os.path.join(settings.DATA_ROOT_PATH, file_name)
if not os.path.isfile(features_path):
raise Http404
f = open(features_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def features_json(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id,
'feature_matrix')
if file_name is None:
raise Http404
# Compose the path to the .json-file
features_path = os.path.join(settings.DATA_ROOT_PATH, file_name)
if not os.path.isfile(features_path):
raise Http404
f = open(features_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def survival_json(request, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'survival')
if path is None:
raise Http404
# Compose the path to the survival data .json-file
platform_root = os.path.join(settings.DATA_ROOT_PATH, path)
gene_path = os.path.join(platform_root, "survival.json")
if not os.path.isfile(gene_path):
raise Http404
f = open(gene_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def platform_gene_list_json(request, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'expression')
if path is None:
raise Http404
# Compose the path to the gene list .json-file
platform_root = os.path.join(settings.DATA_ROOT_PATH, path)
gene_list_path = os.path.join(platform_root, "genes.json")
if not os.path.isfile(gene_list_path):
raise Http404
f = open(gene_list_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def expression_json(request, data_set_id, platform_id, gene):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'expression')
if path is None:
raise Http404
# Compose the path to the expression data .json-file
platform_root = os.path.join(settings.DATA_ROOT_PATH, path)
gene_path = os.path.join(platform_root, gene[0].lower())
gene_path = os.path.join(gene_path, gene.upper() + ".json")
if not os.path.isfile(gene_path):
raise Http404
f = open(gene_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def expression_json(request, data_set_id, platform_id, gene):
path = bdata.get_data_path_if_exists(data_set_id, platform_id,
'expression')
if path is None:
raise Http404
# Compose the path to the expression data .json-file
platform_root = os.path.join(settings.DATA_ROOT_PATH, path)
gene_path = os.path.join(platform_root, gene[0].lower())
gene_path = os.path.join(gene_path, gene.upper() + ".json")
if not os.path.isfile(gene_path):
raise Http404
f = open(gene_path, 'rb')
return HttpResponse(f, mimetype='application/json')
def expression_boxplot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'expression')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'expression',
'default_gene': 'TP53'}
return render_to_response('gene_boxplot.html',
context,
context_instance=RequestContext(request))
def feature_matrix_plot(request, cancer_type, data_set_id, platform_id):
file_name = bdata.get_data_path_if_exists(data_set_id, platform_id, 'feature_matrix')
if file_name is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'feature_matrix'}
return render_to_response('feature_matrix.html',
context,
context_instance=RequestContext(request))
def kaplan_meier_plot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'survival')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {'id': data_set_id, 'meta': bdata.data_sources[data_set_id]},
'cancer_data_sets': cancer_data_sets,
'current_platform': {'id': platform_id, 'name': bdata.platforms[platform_id]},
'current_data_type': 'survival'}
return render_to_response('gene_survival.html',
context,
context_instance=RequestContext(request))
def kaplan_meier_plot(request, cancer_type, data_set_id, platform_id):
path = bdata.get_data_path_if_exists(data_set_id, platform_id, 'survival')
if path is None:
raise Http404
cancer_data_sets = bdata.get_data_sets_by_cancer_type()
context = {
'current_cancer': bdata.make_current_cancer_dict(cancer_type),
'current_data_set': {
'id': data_set_id,
'meta': bdata.data_sources[data_set_id]
},
'cancer_data_sets': cancer_data_sets,
'current_platform': {
'id': platform_id,
'name': bdata.platforms[platform_id]
},
'current_data_type': 'survival'
}
return render_to_response('gene_survival.html',
context,
context_instance=RequestContext(request))
