# -*- coding: utf-8 -*- # # Main routing table for GN2 from __future__ import absolute_import, division, print_function import sys import csv import xlsxwriter import StringIO # Todo: Use cStringIO? import gc import cPickle as pickle import uuid import simplejson as json import yaml #Switching from Redis to StrictRedis; might cause some issues import redis Redis = redis.StrictRedis() import flask import base64 import array import sqlalchemy from wqflask import app from flask import g, request, render_template # from flask import (render_template, request, make_response, Response, # Flask, g, config, jsonify, redirect, url_for, # send_from_directory) from wqflask import search_results from wqflask import gsearch from wqflask import update_search_results from wqflask import docs from wqflask import news from base.data_set import DataSet # Used by YAML in marker_regression from base.data_set import create_datasets_list from wqflask.show_trait import show_trait from wqflask.show_trait import export_trait_data from wqflask.heatmap import heatmap from wqflask.marker_regression import marker_regression from wqflask.marker_regression import marker_regression_gn1 from wqflask.correlation import show_corr_results from wqflask.correlation_matrix import show_corr_matrix from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL from base import webqtlFormData from base.webqtlConfig import GENERATED_IMAGE_DIR from utility.benchmark import Bench from pprint import pformat as pf from wqflask import user_manager from wqflask import collect from wqflask.database import db_session import utility.logger logger = utility.logger.getLogger(__name__ ) @app.before_request def connect_db(): db = getattr(g, '_database', None) if db is None: logger.debug("Get new database connector") g.db = g._database = sqlalchemy.create_engine(SQL_URI) logger.debug(g.db) @app.teardown_appcontext def shutdown_session(exception=None): db = getattr(g, '_database', None) if db is not None: logger.debug("remove db_session") db_session.remove() g.db = None #@app.before_request #def trace_it(): # from wqflask import tracer # tracer.turn_on() @app.route("/") def index_page(): logger.info("Sending index_page") if USE_GN_SERVER: # The menu is generated using GN_SERVER return render_template("index_page.html", gn_server_url = GN_SERVER_URL) else: # Old style static menu (OBSOLETE) return render_template("index_page_orig.html") @app.route("/tmp/") def tmp_page(img_path): logger.info("In tmp_page") logger.info("img_path:", img_path) initial_start_vars = request.form logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) return render_template("show_image.html", img_base64 = bytesarray ) #@app.route("/data_sharing") #def data_sharing_page(): # logger.info("In data_sharing") # fd = webqtlFormData.webqtlFormData(request.args) # logger.info("1Have fd") # sharingInfoObject = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) # info, htmlfilelist = sharingInfoObject.getBody(infoupdate="") # logger.info("type(htmlfilelist):", type(htmlfilelist)) # htmlfilelist = htmlfilelist.encode("utf-8") # #template_vars = SharingInfo.SharingInfo(request.args['GN_AccessionId'], None) # logger.info("1 Made it to rendering") # return render_template("data_sharing.html", # info=info, # htmlfilelist=htmlfilelist) @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") if 'info_database' in request.args: logger.info("Going to sharing_info_page") template_vars = sharing_info_page() if template_vars.redirect_url: logger.info("Going to redirect") return flask.redirect(template_vars.redirect_url) else: return render_template("data_sharing.html", **template_vars.__dict__) else: result = None if USE_REDIS: with Bench("Trying Redis cache"): key = "search_results:v1:" + json.dumps(request.args, sort_keys=True) logger.debug("key is:", pf(key)) result = Redis.get(key) if result: logger.info("Redis cache hit on search results!") result = pickle.loads(result) else: logger.info("Skipping Redis cache (USE_REDIS=False)") logger.info("request.args is", request.args) the_search = search_results.SearchResultPage(request.args) result = the_search.__dict__ logger.debugf("result", result) if USE_REDIS: Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL)) Redis.expire(key, 60*60) if result['search_term_exists']: return render_template("search_result_page.html", **result) else: return render_template("search_error.html") @app.route("/gsearch", methods=('GET',)) def gsearchact(): result = gsearch.GSearch(request.args).__dict__ type = request.args['type'] if type == "gene": return render_template("gsearch_gene.html", **result) 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) result = update_search_results.GSearch(request.args).__dict__ return result['results'] # type = request.args['type'] # if type == "gene": # return render_template("gsearch_gene_updating.html", **result) # elif type == "phenotype": # return render_template("gsearch_pheno.html", **result) @app.route("/docedit") def docedit(): doc = docs.Docs(request.args['entry']) return render_template("docedit.html", **doc.__dict__) @app.route('/generated/') def generated_file(filename): return send_from_directory(GENERATED_IMAGE_DIR,filename) @app.route("/help") def help(): doc = docs.Docs("help") 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 return render_template("wgcna_setup.html", **request.form) # Display them using the template @app.route("/wgcna_results", methods=('POST',)) def wcgna_results(): logger.info("In wgcna, request.form is:", request.form) 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 @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 return render_template("ctl_setup.html", **request.form) # Display them using the template @app.route("/ctl_results", methods=('POST',)) def ctl_results(): logger.info("In ctl, request.form is:", request.form) 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 @app.route("/news") def news_route(): newsobject = news.News() return render_template("news.html", **newsobject.__dict__) @app.route("/references") def references(): doc = docs.Docs("references") return render_template("docs.html", **doc.__dict__) @app.route("/intro") def intro(): doc = docs.Docs("intro") return render_template("docs.html", **doc.__dict__) @app.route("/policies") def policies(): doc = docs.Docs("policies") return render_template("docs.html", **doc.__dict__) @app.route("/links") def links(): doc = docs.Docs("links") return render_template("docs.html", **doc.__dict__) @app.route("/environments") def environments(): doc = docs.Docs("environments") return render_template("docs.html", **doc.__dict__) @app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" logger.info("In export_trait_excel") logger.info("request.form:", request.form) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) worksheet = workbook.add_worksheet() for i, row in enumerate(sample_data): worksheet.write(i, 0, row[0]) worksheet.write(i, 1, row[1]) if len(row) > 2: worksheet.write(i, 2, row[2]) workbook.close() excel_data = buff.getvalue() buff.close() return Response(excel_data, mimetype='application/vnd.ms-excel', headers={"Content-Disposition":"attachment;filename=sample_data.xlsx"}) @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): """CSV file consisting of the sample data from the trait data and analysis page""" logger.info("In export_trait_csv") logger.info("request.form:", request.form) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() writer = csv.writer(buff) for row in sample_data: writer.writerow(row) csv_data = buff.getvalue() buff.close() return Response(csv_data, mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=sample_data.csv"}) @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): """CSV file consisting of the permutation data for the mapping results""" num_perm = float(request.form['num_perm']) perm_data = json.loads(request.form['perm_results']) buff = StringIO.StringIO() writer = csv.writer(buff) writer.writerow(["Suggestive LRS (p=0.63) = " + str(perm_data[int(num_perm*0.37-1)])]) writer.writerow(["Significant LRS (p=0.05) = " + str(perm_data[int(num_perm*0.95-1)])]) writer.writerow(["Highly Significant LRS (p=0.01) = " + str(perm_data[int(num_perm*0.99-1)])]) writer.writerow("") writer.writerow([str(num_perm) + " Permutations"]) writer.writerow("") for item in perm_data: writer.writerow([item]) csv_data = buff.getvalue() buff.close() return Response(csv_data, mimetype='text/csv', headers={"Content-Disposition":"attachment;filename=perm_data.csv"}) @app.route("/show_trait") def show_trait_page(): # Here it's currently too complicated not to use an fd that is a webqtlFormData #fd = webqtlFormData.webqtlFormData(request.args) #logger.info("stp y1:", pf(vars(fd))) template_vars = show_trait.ShowTrait(request.args) #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") # Sorting the keys messes up the ordered dictionary, so don't do that #sort_keys=True) #logger.info("js_data after dump:", template_vars.js_data) #logger.info("show_trait template_vars:", pf(template_vars.__dict__)) return render_template("show_trait.html", **template_vars.__dict__) @app.route("/heatmap", methods=('POST',)) def heatmap_page(): logger.info("In heatmap, request.form is:", pf(request.form)) start_vars = request.form temp_uuid = uuid.uuid4() 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) logger.info("key is:", pf(key)) with Bench("Loading cache"): result = Redis.get(key) if result: logger.info("Cache hit!!!") with Bench("Loading results"): result = pickle.loads(result) else: logger.info("Cache miss!!!") template_vars = heatmap.Heatmap(request.form, temp_uuid) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") result = template_vars.__dict__ for item in template_vars.__dict__.keys(): 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)) Redis.set(key, pickled_result) Redis.expire(key, 60*60) with Bench("Rendering template"): rendered_template = render_template("heatmap.html", **result) else: rendered_template = render_template("empty_collection.html", **{'tool':'Heatmap'}) return rendered_template @app.route("/mapping_results_container") def mapping_results_container_page(): return render_template("mapping_results_container.html") @app.route("/marker_regression", methods=('POST',)) def marker_regression_page(): initial_start_vars = request.form temp_uuid = initial_start_vars['temp_uuid'] wanted = ( 'trait_id', 'dataset', 'method', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'maf', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno' ) logger.info("Marker regression called with initial_start_vars:", initial_start_vars) start_vars = {} for key, value in initial_start_vars.iteritems(): if key in wanted or key.startswith(('value:')): start_vars[key] = value version = "v3" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) logger.info("key is:", pf(key)) with Bench("Loading cache"): result = None # Just for testing #result = Redis.get(key) #logger.info("************************ Starting result *****************") #logger.info("result is [{}]: {}".format(type(result), result)) #logger.info("************************ Ending result ********************") if result: logger.info("Cache hit!!!") with Bench("Loading results"): result = pickle.loads(result) else: logger.info("Cache miss!!!") with Bench("Total time in MarkerRegression"): template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") result = template_vars.__dict__ if result['pair_scan']: with Bench("Rendering template"): img_path = result['pair_scan_filename'] logger.info("img_path:", img_path) initial_start_vars = request.form logger.info("initial_start_vars:", initial_start_vars) imgfile = open(TEMPDIR + img_path, 'rb') imgdata = imgfile.read() imgB64 = imgdata.encode("base64") bytesarray = array.array('B', imgB64) result['pair_scan_array'] = bytesarray rendered_template = render_template("pair_scan_results.html", **result) else: #for item in template_vars.__dict__.keys(): # logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) Redis.expire(key, 1*60) with Bench("Rendering template"): rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) # with Bench("Rendering template"): # if result['pair_scan'] == True: # img_path = result['pair_scan_filename'] # logger.info("img_path:", img_path) # initial_start_vars = request.form # logger.info("initial_start_vars:", initial_start_vars) # imgfile = open(TEMPDIR + '/' + img_path, 'rb') # imgdata = imgfile.read() # imgB64 = imgdata.encode("base64") # bytesarray = array.array('B', imgB64) # result['pair_scan_array'] = bytesarray # rendered_template = render_template("pair_scan_results.html", **result) # else: # rendered_template = render_template("marker_regression.html", **result) # rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) return rendered_template @app.route("/export", methods = ('POST',)) def export(): logger.info("request.form:", request.form) 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 return response @app.route("/export_pdf", methods = ('POST',)) def export_pdf(): import cairosvg logger.info("request.form:", request.form) svg_xml = request.form.get("data", "Invalid data") logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") filepath = GENERATED_IMAGE_DIR+filename pdf_file = cairosvg.svg2pdf(bytestring=svg_xml) response = Response(pdf_file, mimetype="application/pdf") response.headers["Content-Disposition"] = "attachment; filename=%s"%filename return response @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) #fd = webqtlFormData.webqtlFormData(request.form) 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)) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": template_vars = show_corr_matrix.CorrelationMatrix(start_vars) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") return render_template("correlation_matrix.html", **template_vars.__dict__) else: return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): template_vars = corr_scatter_plot.CorrScatterPlot(request.args) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") return render_template("corr_scatterplot.html", **template_vars.__dict__) # Todo: Can we simplify this? -Sam def sharing_info_page(): """Info page displayed when the user clicks the "Info" button next to the dataset selection""" logger.info("In sharing_info_page") fd = webqtlFormData.webqtlFormData(request.args) template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars # Take this out or secure it before putting into production @app.route("/get_temp_data") def get_temp_data(): temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) ########################################################################## def json_default_handler(obj): '''Based on http://stackoverflow.com/a/2680060/1175849''' # Handle datestamps if hasattr(obj, 'isoformat'): return obj.isoformat() # Handle integer keys for dictionaries elif isinstance(obj, int): return str(int) # Handle custom objects if hasattr(obj, '__dict__'): return obj.__dict__ #elif type(obj) == "Dataset": # logger.info("Not going to serialize Dataset") # return None else: raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % ( type(obj), repr(obj))