diff options
| -rw-r--r-- | wqflask/wqflask/views.py | 222 |
1 files changed, 154 insertions, 68 deletions
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index a33c64f1..319f1270 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -91,9 +91,11 @@ def connect_db(): logger.info("@app.before_request connect_db") db = getattr(g, '_database', None) if db is None: - g.db = g._database = sqlalchemy.create_engine(SQL_URI, encoding="latin1") + g.db = g._database = sqlalchemy.create_engine( + SQL_URI, encoding="latin1") logger.debug(g.db) + @app.before_request def check_access_permissions(): logger.debug("@app.before_request check_access_permissions") @@ -105,7 +107,8 @@ def check_access_permissions(): if dataset.type == "Temp": permissions = DEFAULT_PRIVILEGES elif 'trait_id' in request.args: - permissions = check_resource_availability(dataset, request.args['trait_id']) + permissions = check_resource_availability( + dataset, request.args['trait_id']) elif dataset.type != "Publish": permissions = check_resource_availability(dataset) @@ -116,6 +119,7 @@ def check_access_permissions(): if permissions['data'] == 'no-access': return redirect(url_for("no_access_page")) + @app.teardown_appcontext def shutdown_session(exception=None): db = getattr(g, '_database', None) @@ -124,6 +128,7 @@ def shutdown_session(exception=None): db_session.remove() g.db = None + @app.errorhandler(Exception) def handle_bad_request(e): err_msg = str(e) @@ -134,25 +139,30 @@ def handle_bad_request(e): logger.error(traceback.format_exc()) now = datetime.datetime.utcnow() time_str = now.strftime('%l:%M%p UTC %b %d, %Y') - formatted_lines = [request.url + " ("+time_str+")"]+traceback.format_exc().splitlines() + formatted_lines = [request.url + + " ("+time_str+")"]+traceback.format_exc().splitlines() # Handle random animations # Use a cookie to have one animation on refresh animation = request.cookies.get(err_msg[:32]) if not animation: - list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ] + list = [fn for fn in os.listdir( + "./wqflask/static/gif/error") if fn.endswith(".gif")] animation = random.choice(list) - resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION)) + resp = make_response(render_template("error.html", message=err_msg, + stack=formatted_lines, error_image=animation, version=GN_VERSION)) # logger.error("Set cookie %s with %s" % (err_msg, animation)) resp.set_cookie(err_msg[:32], animation) return resp + @app.route("/authentication_needed") def no_access_page(): return render_template("new_security/not_authenticated.html") + @app.route("/") def index_page(): logger.info("Sending index_page") @@ -177,7 +187,7 @@ def tmp_page(img_path): imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) return render_template("show_image.html", - img_base64 = bytesarray ) + img_base64=bytesarray) @app.route("/js/<path:filename>") @@ -189,6 +199,7 @@ def js(filename): name = name.replace('js_alt/', '') return send_from_directory(js_path, name) + @app.route("/css/<path:filename>") def css(filename): js_path = JS_GUIX_PATH @@ -198,10 +209,12 @@ def css(filename): name = name.replace('js_alt/', '') return send_from_directory(js_path, name) + @app.route("/twitter/<path:filename>") def twitter(filename): return send_from_directory(JS_TWITTER_POST_FETCHER_PATH, filename) + @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") @@ -209,7 +222,8 @@ def search_page(): result = None if USE_REDIS: with Bench("Trying Redis cache"): - key = "search_results:v1:" + json.dumps(request.args, sort_keys=True) + key = "search_results:v1:" + \ + json.dumps(request.args, sort_keys=True) logger.debug("key is:", pf(key)) result = Redis.get(key) if result: @@ -232,6 +246,7 @@ def search_page(): else: return render_template("search_error.html") + @app.route("/search_table", methods=('GET',)) def search_page_table(): logger.info("in search_page table") @@ -242,7 +257,7 @@ def search_page_table(): logger.info(type(the_search.trait_list)) logger.info(the_search.trait_list) - + current_page = server_side.ServerSideTable( len(the_search.trait_list), the_search.trait_list, @@ -252,6 +267,7 @@ def search_page_table(): return flask.jsonify(current_page) + @app.route("/gsearch", methods=('GET',)) def gsearchact(): logger.info(request.url) @@ -262,6 +278,7 @@ def gsearchact(): elif type == "phenotype": return render_template("gsearch_pheno.html", **result) + @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) @@ -292,41 +309,59 @@ def generated_file(filename): logger.info(request.url) return send_from_directory(GENERATED_IMAGE_DIR, filename) + @app.route("/help") def help(): logger.info(request.url) doc = Docs("help", request.args) return render_template("docs.html", **doc.__dict__) + @app.route("/wgcna_setup", methods=('POST',)) def wcgna_setup(): - logger.info("In wgcna, request.form is:", request.form) # We are going to get additional user input for the analysis + # We are going to get additional user input for the analysis + logger.info("In wgcna, request.form is:", request.form) logger.info(request.url) - return render_template("wgcna_setup.html", **request.form) # Display them using the template + # Display them using the template + return render_template("wgcna_setup.html", **request.form) + @app.route("/wgcna_results", methods=('POST',)) def wcgna_results(): logger.info("In wgcna, request.form is:", request.form) logger.info(request.url) - wgcna = wgcna_analysis.WGCNA() # Start R, load the package and pointers and create the analysis - wgcnaA = wgcna.run_analysis(request.form) # Start the analysis, a wgcnaA object should be a separate long running thread - result = wgcna.process_results(wgcnaA) # After the analysis is finished store the result - return render_template("wgcna_results.html", **result) # Display them using the template + # Start R, load the package and pointers and create the analysis + wgcna = wgcna_analysis.WGCNA() + # Start the analysis, a wgcnaA object should be a separate long running thread + wgcnaA = wgcna.run_analysis(request.form) + # After the analysis is finished store the result + result = wgcna.process_results(wgcnaA) + # Display them using the template + return render_template("wgcna_results.html", **result) + @app.route("/ctl_setup", methods=('POST',)) def ctl_setup(): - logger.info("In ctl, request.form is:", request.form) # We are going to get additional user input for the analysis + # We are going to get additional user input for the analysis + logger.info("In ctl, request.form is:", request.form) logger.info(request.url) - return render_template("ctl_setup.html", **request.form) # Display them using the template + # Display them using the template + return render_template("ctl_setup.html", **request.form) + @app.route("/ctl_results", methods=('POST',)) def ctl_results(): logger.info("In ctl, request.form is:", request.form) logger.info(request.url) - ctl = ctl_analysis.CTL() # Start R, load the package and pointers and create the analysis - ctlA = ctl.run_analysis(request.form) # Start the analysis, a ctlA object should be a separate long running thread - result = ctl.process_results(ctlA) # After the analysis is finished store the result - return render_template("ctl_results.html", **result) # Display them using the template + # Start R, load the package and pointers and create the analysis + ctl = ctl_analysis.CTL() + # Start the analysis, a ctlA object should be a separate long running thread + ctlA = ctl.run_analysis(request.form) + # After the analysis is finished store the result + result = ctl.process_results(ctlA) + # Display them using the template + return render_template("ctl_results.html", **result) + @app.route("/news") def news(): @@ -381,9 +416,11 @@ def export_trait_excel(): logger.info("In export_trait_excel") logger.info("request.form:", request.form) logger.info(request.url) - trait_name, sample_data = export_trait_data.export_sample_table(request.form) + trait_name, sample_data = export_trait_data.export_sample_table( + request.form) - logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % + (type(sample_data), len(sample_data))) buff = io.BytesIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) @@ -397,7 +434,8 @@ def export_trait_excel(): return Response(excel_data, mimetype='application/vnd.ms-excel', - headers={"Content-Disposition":"attachment;filename="+ trait_name + ".xlsx"}) + headers={"Content-Disposition": "attachment;filename=" + trait_name + ".xlsx"}) + @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): @@ -405,9 +443,11 @@ def export_trait_csv(): logger.info("In export_trait_csv") logger.info("request.form:", request.form) logger.info(request.url) - trait_name, sample_data = export_trait_data.export_sample_table(request.form) + trait_name, sample_data = export_trait_data.export_sample_table( + request.form) - logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) + logger.info("sample_data - type: %s -- size: %s" % + (type(sample_data), len(sample_data))) buff = io.StringIO() writer = csv.writer(buff) @@ -418,7 +458,8 @@ def export_trait_csv(): return Response(csv_data, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename="+ trait_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + trait_name + ".csv"}) + @app.route('/export_traits_csv', methods=('POST',)) def export_traits_csv(): @@ -443,7 +484,8 @@ def export_traits_csv(): else: return Response(file_list[0][1], mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_list[0][0]}) + headers={"Content-Disposition": "attachment;filename=" + file_list[0][0]}) + @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): @@ -454,7 +496,8 @@ def export_perm_data(): now = datetime.datetime.now() time_str = now.strftime('%H:%M_%d%B%Y') - file_name = "Permutation_" + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str + file_name = "Permutation_" + \ + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str the_rows = [ ["#Permutation Test"], @@ -468,10 +511,14 @@ def export_perm_data(): ["#N_genotypes: " + str(perm_info['n_genotypes'])], ["#Genotype_file: " + perm_info['genofile']], ["#Units_linkage: " + perm_info['units_linkage']], - ["#Permutation_stratified_by: " + ", ".join([ str(cofactor) for cofactor in perm_info['strat_cofactors']])], - ["#RESULTS_1: Suggestive LRS(p=0.63) = " + str(np.percentile(np.array(perm_info['perm_data']), 67))], - ["#RESULTS_2: Significant LRS(p=0.05) = " + str(np.percentile(np.array(perm_info['perm_data']), 95))], - ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(np.percentile(np.array(perm_info['perm_data']), 99))], + ["#Permutation_stratified_by: " + + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])], + ["#RESULTS_1: Suggestive LRS(p=0.63) = " + + str(np.percentile(np.array(perm_info['perm_data']), 67))], + ["#RESULTS_2: Significant LRS(p=0.05) = " + str( + np.percentile(np.array(perm_info['perm_data']), 95))], + ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str( + np.percentile(np.array(perm_info['perm_data']), 99))], ["#Comment: Results sorted from low to high peak linkage"] ] @@ -485,7 +532,7 @@ def export_perm_data(): return Response(csv_data, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"}) @app.route("/show_temp_trait", methods=('POST',)) @@ -519,7 +566,8 @@ def heatmap_page(): traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": version = "v5" - key = "heatmap:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + key = "heatmap:{}:".format( + version) + json.dumps(start_vars, sort_keys=True) logger.info("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) @@ -540,7 +588,8 @@ def heatmap_page(): result = template_vars.__dict__ for item in list(template_vars.__dict__.keys()): - logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) + logger.info( + " ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) @@ -551,10 +600,12 @@ def heatmap_page(): rendered_template = render_template("heatmap.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'Heatmap'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'Heatmap'}) return rendered_template + @app.route("/bnw_page", methods=('POST',)) def bnw_page(): logger.info("In run BNW, request.form is:", pf(request.form)) @@ -569,10 +620,12 @@ def bnw_page(): result = template_vars.__dict__ rendered_template = render_template("bnw_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'BNW'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'BNW'}) return rendered_template + @app.route("/webgestalt_page", methods=('POST',)) def webgestalt_page(): logger.info("In run WebGestalt, request.form is:", pf(request.form)) @@ -587,10 +640,12 @@ def webgestalt_page(): result = template_vars.__dict__ rendered_template = render_template("webgestalt_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'WebGestalt'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'WebGestalt'}) return rendered_template + @app.route("/geneweaver_page", methods=('POST',)) def geneweaver_page(): logger.info("In run WebGestalt, request.form is:", pf(request.form)) @@ -605,10 +660,12 @@ def geneweaver_page(): result = template_vars.__dict__ rendered_template = render_template("geneweaver_page.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'GeneWeaver'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'GeneWeaver'}) return rendered_template + @app.route("/comparison_bar_chart", methods=('POST',)) def comp_bar_chart_page(): logger.info("In comp bar chart, request.form is:", pf(request.form)) @@ -620,26 +677,30 @@ def comp_bar_chart_page(): if traits[0] != "": template_vars = comparison_bar_chart.ComparisonBarChart(request.form) template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") + default=json_default_handler, + indent=" ") result = template_vars.__dict__ - rendered_template = render_template("comparison_bar_chart.html", **result) + rendered_template = render_template( + "comparison_bar_chart.html", **result) else: - rendered_template = render_template("empty_collection.html", **{'tool':'Comparison Bar Chart'}) + rendered_template = render_template( + "empty_collection.html", **{'tool': 'Comparison Bar Chart'}) return rendered_template + @app.route("/mapping_results_container") def mapping_results_container_page(): return render_template("mapping_results_container.html") + @app.route("/loading", methods=('POST',)) def loading_page(): logger.info(request.url) initial_start_vars = request.form start_vars_container = {} - n_samples = 0 #ZS: So it can be displayed on loading page + n_samples = 0 # ZS: So it can be displayed on loading page if 'wanted_inputs' in initial_start_vars: wanted = initial_start_vars['wanted_inputs'].split(",") start_vars = {} @@ -652,7 +713,8 @@ def loading_page(): else: sample_vals_dict = json.loads(start_vars['sample_vals']) if 'group' in start_vars: - dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group']) + dataset = create_dataset( + start_vars['dataset'], group_name=start_vars['group']) else: dataset = create_dataset(start_vars['dataset']) samples = start_vars['primary_samples'].split(",") @@ -660,7 +722,8 @@ def loading_page(): if start_vars['genofile'] != "": genofile_string = start_vars['genofile'] dataset.group.genofile = genofile_string.split(":")[0] - genofile_samples = run_mapping.get_genofile_samplelist(dataset) + genofile_samples = run_mapping.get_genofile_samplelist( + dataset) if len(genofile_samples) > 1: samples = genofile_samples @@ -680,6 +743,7 @@ def loading_page(): return rendered_template + @app.route("/run_mapping", methods=('POST',)) def mapping_results_page(): initial_start_vars = request.form @@ -750,9 +814,10 @@ def mapping_results_page(): start_vars[key] = value version = "v3" - key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True) + key = "mapping_results:{}:".format( + version) + json.dumps(start_vars, sort_keys=True) with Bench("Loading cache"): - result = None # Just for testing + result = None # Just for testing #result = Redis.get(key) #logger.info("************************ Starting result *****************") @@ -772,12 +837,12 @@ def mapping_results_page(): rendered_template = render_template("mapping_error.html") return rendered_template except: - rendered_template = render_template("mapping_error.html") - return rendered_template + rendered_template = render_template("mapping_error.html") + return rendered_template template_vars.js_data = json.dumps(template_vars.js_data, - default=json_default_handler, - indent=" ") + default=json_default_handler, + indent=" ") result = template_vars.__dict__ @@ -792,18 +857,22 @@ def mapping_results_page(): imgB64 = base64.b64encode(imgdata) bytesarray = array.array('B', imgB64) result['pair_scan_array'] = bytesarray - rendered_template = render_template("pair_scan_results.html", **result) + rendered_template = render_template( + "pair_scan_results.html", **result) else: - gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__ + gn1_template_vars = display_mapping_results.DisplayMappingResults( + result).__dict__ with Bench("Rendering template"): #if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"): #gn1_template_vars.pop('qtlresults', None) - rendered_template = render_template("mapping_results.html", **gn1_template_vars) + rendered_template = render_template( + "mapping_results.html", **gn1_template_vars) return rendered_template -@app.route("/export_mapping_results", methods = ('POST',)) + +@app.route("/export_mapping_results", methods=('POST',)) def export_mapping_results(): logger.info("request.form:", request.form) logger.info(request.url) @@ -811,32 +880,35 @@ def export_mapping_results(): results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=mapping_results.csv"}) + headers={"Content-Disposition": "attachment;filename=mapping_results.csv"}) return response -@app.route("/export_corr_matrix", methods = ('POST',)) + +@app.route("/export_corr_matrix", methods=('POST',)) def export_corr_matrix(): file_path = request.form.get("export_filepath") file_name = request.form.get("export_filename") results_csv = open(file_path, "r").read() response = Response(results_csv, mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"}) + headers={"Content-Disposition": "attachment;filename=" + file_name + ".csv"}) return response -@app.route("/export", methods = ('POST',)) + +@app.route("/export", methods=('POST',)) def export(): logger.info("request.form:", request.form) logger.info(request.url) svg_xml = request.form.get("data", "Invalid data") filename = request.form.get("filename", "manhattan_plot_snp") response = Response(svg_xml, mimetype="image/svg+xml") - response.headers["Content-Disposition"] = "attachment; filename=%s"%filename + response.headers["Content-Disposition"] = "attachment; filename=%s" % filename return response -@app.route("/export_pdf", methods = ('POST',)) + +@app.route("/export_pdf", methods=('POST',)) def export_pdf(): import cairosvg logger.info("request.form:", request.form) @@ -846,9 +918,10 @@ def export_pdf(): filename = request.form.get("filename", "interval_map_pdf") pdf_file = cairosvg.svg2pdf(bytestring=svg_xml) response = Response(pdf_file, mimetype="application/pdf") - response.headers["Content-Disposition"] = "attachment; filename=%s"%filename + response.headers["Content-Disposition"] = "attachment; filename=%s" % filename return response + @app.route("/network_graph", methods=('POST',)) def network_graph_page(): logger.info("In network_graph, request.form is:", pf(request.form)) @@ -863,7 +936,8 @@ def network_graph_page(): return render_template("network_graph.html", **template_vars.__dict__) else: - return render_template("empty_collection.html", **{'tool':'Network Graph'}) + return render_template("empty_collection.html", **{'tool': 'Network Graph'}) + @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): @@ -872,6 +946,7 @@ def corr_compute_page(): template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) + @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): logger.info("In corr_matrix, request.form is:", pf(request.form)) @@ -887,7 +962,8 @@ def corr_matrix_page(): return render_template("correlation_matrix.html", **template_vars.__dict__) else: - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'}) + @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): @@ -898,6 +974,7 @@ def corr_scatter_plot_page(): indent=" ") return render_template("corr_scatterplot.html", **template_vars.__dict__) + @app.route("/snp_browser", methods=('GET',)) def snp_browser_page(): logger.info(request.url) @@ -905,12 +982,14 @@ def snp_browser_page(): return render_template("snp_browser.html", **template_vars.__dict__) + @app.route("/db_info", methods=('GET',)) def db_info_page(): template_vars = InfoPage(request.args) return render_template("info_page.html", **template_vars.__dict__) + @app.route("/snp_browser_table", methods=('GET',)) def snp_browser_table(): logger.info(request.url) @@ -924,30 +1003,36 @@ def snp_browser_table(): return flask.jsonify(current_page) + @app.route("/tutorial/WebQTLTour", methods=('GET',)) def tutorial_page(): - #ZS: Currently just links to GN1 + # ZS: Currently just links to GN1 logger.info(request.url) return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/") + @app.route("/tutorial/security", methods=('GET',)) def security_tutorial_page(): - #ZS: Currently just links to GN1 + # ZS: Currently just links to GN1 logger.info(request.url) return render_template("admin/security_help.html") + @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): logger.info(request.url) - return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) + return render_template("empty_collection.html", **{'tool': 'Correlation Matrix'}) # Take this out or secure it before putting into production + + @app.route("/get_temp_data") def get_temp_data(): logger.info(request.url) temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) + @app.route("/browser_input", methods=('GET',)) def browser_inputs(): """ Returns JSON from tmp directory for the purescript genome browser""" @@ -961,6 +1046,7 @@ def browser_inputs(): ########################################################################## + def json_default_handler(obj): """Based on http://stackoverflow.com/a/2680060/1175849""" # Handle datestamps |