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 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_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))