diff options
| -rw-r--r-- | etc/default_settings.py | 19 | ||||
| -rw-r--r-- | wqflask/runserver.py | 11 | ||||
| -rw-r--r-- | wqflask/utility/logger.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 13 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/biodalliance.js | 72 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee | 37 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.js | 31 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.coffee | 16 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/create_lodchart.js | 11 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.coffee | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/lod_chart.js | 63 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 209 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 54 |
13 files changed, 395 insertions, 145 deletions
diff --git a/etc/default_settings.py b/etc/default_settings.py index 6acea637..08eae024 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -2,18 +2,22 @@ # webserver running in developer mode with limited console # output. Copy this file and run it from ./bin/genenetwork2 configfile # -# Note that these settings are fetched in ./wqflask/utilities/tools.py +# Note: these settings are fetched in ./wqflask/utilities/tools.py # which has support for overriding them through environment variables, # e.g. # # env LOG_SQL=True USE_REDIS=False ./bin/genenetwork2 # env LOG_LEVEL=DEBUG ./bin/genenetwork2 ~/gn2_settings.py # -# Note also that in the near future we will additionally fetch +# Note: in the near future we will additionally fetch # settings from a JSON file # -# Note that values for False and 0 have to be strings here - otherwise +# Note: values for False and 0 have to be strings here - otherwise # Flask won't pick them up +# +# For GNU Guix deployment also check the paths in +# +# ~/.guix-profile/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg/etc/default_settings.py import os import sys @@ -22,7 +26,7 @@ GN_VERSION = open("../VERSION","r").read() SQL_URI = "mysql://gn2:mysql_password@localhost/db_webqtl_s" SQLALCHEMY_DATABASE_URI = 'mysql://gn2:mysql_password@localhost/db_webqtl_s' SQLALCHEMY_POOL_RECYCLE = 3600 -GN_SERVER_URL = "http://localhost:8880/" +GN_SERVER_URL = "http://test-gn2.genenetwork.org/" # ---- Flask configuration (see website) TRAP_BAD_REQUEST_ERRORS = True @@ -33,7 +37,7 @@ SECURITY_RECOVERABLE = True SECURITY_EMAIL_SENDER = "no-reply@genenetwork.org" SECURITY_POST_LOGIN_VIEW = "/thank_you" -SERVER_PORT = 5003 +SERVER_PORT = 5003 # running on localhost SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' # ---- Behavioural settings (defaults) note that logger and log levels can @@ -41,6 +45,7 @@ SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) WEBSERVER_BRANDING = None # Set the branding (nyi) WEBSERVER_DEPLOY = None # Deployment specifics (nyi) +WEBSERVER_URL = "http://localhost:"+str(SERVER_PORT)+"/" # external URL LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL) LOG_LEVEL_DEBUG = '0' # logger.debugf log level (0-5, 5 = show all) @@ -53,7 +58,8 @@ USE_GN_SERVER = 'False' # Use GN_SERVER SQL calls # Paths to JS libraries -TWITTER_POST_FETCHER_JS_PATH = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" +JS_BIODALLIANCE = os.environ['HOME']+"/genenetwork/biodalliance" +JS_TWITTER_POST_FETCHER = os.environ['HOME']+"/genenetwork/Twitter-Post-Fetcher" # ---- Path overrides for Genenetwork # TMPDIR is normally picked up from the environment @@ -63,6 +69,7 @@ GENENETWORK_FILES = HOME+"/gn2_data" # base dir for all static data files LOCAL_PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files # ---- GN2 Executables +# Paths to invoked binaries PYLMM_COMMAND = str.strip(os.popen("which pylmm_redis").read()) PLINK_COMMAND = str.strip(os.popen("which plink2").read()) GEMMA_COMMAND = str.strip(os.popen("which gemma").read()) diff --git a/wqflask/runserver.py b/wqflask/runserver.py index 0342b7ad..adacc712 100644 --- a/wqflask/runserver.py +++ b/wqflask/runserver.py @@ -19,11 +19,18 @@ ENDC = '\033[0m' import os app.config['SECRET_KEY'] = os.urandom(24) -from utility.tools import WEBSERVER_MODE,get_setting_int +from utility.tools import WEBSERVER_MODE,get_setting_int,get_setting port = get_setting_int("SERVER_PORT") -logger.info("GN2 is running. Visit %shttp://localhost:%s/%s" % (BLUE,port,ENDC)) +print("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]") + +import requests +page = requests.get(get_setting("GN_SERVER_URL")) +if page.status_code != 200: + raise Exception("API server not found!") + +print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))) werkzeug_logger = logging.getLogger('werkzeug') diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py index bacb0aa4..128706df 100644 --- a/wqflask/utility/logger.py +++ b/wqflask/utility/logger.py @@ -72,7 +72,7 @@ LOG_LEVEL_DEBUG (NYI). def warning(self,*args): """Call logging.warning for multiple args""" self.collect(self.logger.warning,*args) - self.logger.warning(self.collect(*args)) + # self.logger.warning(self.collect(*args)) def error(self,*args): """Call logging.error for multiple args""" diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index df032e48..9860f63e 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -121,9 +121,14 @@ def assert_writable_dir(dir): fh.close() os.remove(fn) except IOError: - raise Exception('Unable to write test.txt to directory ' + dir ) + raise Exception('Unable to write test.txt to directory ' + dir) return dir +def assert_file(fn): + if not valid_file(fn): + raise Exception('Unable to find file '+fn) + return fn + def mk_dir(dir): if not valid_path(dir): os.makedirs(dir) @@ -233,4 +238,8 @@ if os.environ.get('WQFLASK_OVERRIDES'): OVERRIDES[k] = cmd logger.debug(OVERRIDES) -assert_dir(get_setting("TWITTER_POST_FETCHER_JS_PATH")) +assert_dir(get_setting("JS_BIODALLIANCE")) +assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") +assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") +assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) +assert_file(get_setting("JS_TWITTER_POST_FETCHER")+"/js/twitterFetcher_min.js") diff --git a/wqflask/wqflask/static/new/javascript/biodalliance.js b/wqflask/wqflask/static/new/javascript/biodalliance.js new file mode 100644 index 00000000..3b9e3b7f --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/biodalliance.js @@ -0,0 +1,72 @@ +"use strict"; + + +var BD = {}; +BD.browser = null; +BD.data = {}; +BD.sources = []; + +var getChrLen = function(chr) { + return js_data[chr * 1]; +}; + +BD.createBrowser = function(chr, start, end, speciesName, sources) { + console.log("creating BD browser"); + var b = new Browser({ + chr: chr, + viewStart: start, + viewEnd: end, + + coordSystem: { + speciesName: speciesName + }, + + sources: sources, + + maxHeight: 1400, + setDocumentTitle: false, + prefix: '/dalliance/', + workerPrefix: 'build/', + noPersist: true, + pageName: 'bd_container' + }); + + console.log("created BD browser"); + return b; +}; + +BD.showButton = function() { + $('#open_bd').show(); + $('#close_bd').hide(); +}; + +BD.hideButton = function() { + $('#close_bd').show(); + $('#open_bd').hide(); +}; + + +BD.putData = function(data) { + for (var key in data) { + BD.data[key] = data[key]; + } +}; + +BD.putSource = function(source) { + BD.sources.push(source); +}; + +BD.openBrowser = function() { + console.log("opening browser"); + if (!BD.browser) { + BD.browser = BD.createBrowser(BD.data.chr, + 0, + BD.data.length * 1000000, + BD.data.species, + BD.sources); + } else { + BD.browser.setLocation(BD.data.chr, 0, BD.data.length * 1000000); + } + + BD.browser.maxViewWidth = BD.data.length * 1000000; +}; diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee index e00694be..8a5a3569 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee @@ -5,7 +5,7 @@ class Chr_Lod_Chart @qtl_results = js_data.qtl_results console.log("qtl_results are:", @qtl_results) console.log("chr is:", @chr) - + @get_max_chr() @filter_qtl_results() @@ -21,16 +21,16 @@ class Chr_Lod_Chart console.log("@x_coords: ", @x_coords) console.log("@y_coords: ", @y_coords) console.timeEnd('Create coordinates') - + # Buffer to allow for the ticks/labels to be drawn @x_buffer = @plot_width/30 @y_buffer = @plot_height/20 - + @x_max = d3.max(@x_coords) @y_max = d3.max(@y_coords) * 1.2 - + @y_threshold = @get_lod_threshold() - + @svg = @create_svg() @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names) @@ -43,14 +43,14 @@ class Chr_Lod_Chart console.time('Create graph') @create_graph() console.timeEnd('Create graph') - + get_max_chr: () -> @max_chr = 0 for key of js_data.chromosomes console.log("key is:", key) if parseInt(key) > @max_chr @max_chr = parseInt(key) - + filter_qtl_results: () -> @these_results = [] this_chr = 100 @@ -59,8 +59,8 @@ class Chr_Lod_Chart this_chr = @max_chr else this_chr = result.chr - console.log("this_chr is:", this_chr) - console.log("@chr[0] is:", parseInt(@chr[0])) + # console.log("this_chr is:", this_chr) + # console.log("@chr[0] is:", parseInt(@chr[0])) if this_chr > parseInt(@chr[0]) break if parseInt(this_chr) == parseInt(@chr[0]) @@ -72,7 +72,7 @@ class Chr_Lod_Chart if result.lod_score > 1 high_qtl_count += 1 console.log("high_qtl_count:", high_qtl_count) - + #if high_qtl_count > 10000 @y_axis_filter = 2 #else if high_qtl_count > 1000 @@ -85,7 +85,7 @@ class Chr_Lod_Chart @x_coords.push(parseFloat(result.Mb)) @y_coords.push(result.lod_score) @marker_names.push(result.name) - + create_svg: () -> svg = d3.select("#topchart") .append("svg") @@ -102,7 +102,7 @@ class Chr_Lod_Chart @y_scale = d3.scale.linear() .domain([0, @y_max]) .range([@plot_height, @y_buffer]) - + get_lod_threshold: () -> if @y_max/2 > 2 return @y_max/2 @@ -125,7 +125,7 @@ class Chr_Lod_Chart [@y_buffer, @plot_height, @plot_width, @plot_width], [@y_buffer, @y_buffer, @x_buffer, @plot_width], [@plot_height, @plot_height, @x_buffer, @plot_width]] - + @svg.selectAll("line") .data(border_coords) .enter() @@ -141,7 +141,7 @@ class Chr_Lod_Chart ) .attr("x2", (d) => return d[3] - ) + ) .style("stroke", "#000") add_x_axis: () -> @@ -166,13 +166,13 @@ class Chr_Lod_Chart .attr("transform", (d) => return "translate(-12,0) rotate(-90)" ) - + add_y_axis: () -> @yAxis = d3.svg.axis() .scale(@y_scale) .orient("left") .ticks(5) - + @svg.append("g") .attr("class", "y_axis") .attr("transform", "translate(" + @x_buffer + ",0)") @@ -200,7 +200,7 @@ class Chr_Lod_Chart .x( (d) => return @x_scale(d[0])) .y( (d) => return @y_scale(d[1])) .interpolate("linear") - + line_graph = @svg.append("path") .attr("d", line_function(@plot_coordinates)) .attr("stroke", "blue") @@ -273,6 +273,9 @@ class Chr_Lod_Chart $("#return_to_full_view").hide() $('#topchart').remove() $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>') + BD.hideButton() + $('#close_bd').hide(); + $('#bd_container').hide() create_lod_chart() show_marker_in_table: (marker_info) -> diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js index c6cbd01b..bae4565d 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js @@ -1,13 +1,12 @@ -// Generated by CoffeeScript 1.9.2 +// Generated by CoffeeScript 1.10.0 var Chr_Lod_Chart; Chr_Lod_Chart = (function() { - function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) { + function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) { this.plot_height = plot_height; this.plot_width = plot_width; this.chr = chr; this.manhattanPlot = manhattanPlot; - this.mappingScale = mappingScale; this.qtl_results = js_data.qtl_results; console.log("qtl_results are:", this.qtl_results); console.log("chr is:", this.chr); @@ -95,18 +94,11 @@ Chr_Lod_Chart = (function() { Chr_Lod_Chart.prototype.create_coordinates = function() { var i, len, ref, result, results; ref = this.these_results; - console.log("THESE_RESULTS:", ref) results = []; for (i = 0, len = ref.length; i < len; i++) { result = ref[i]; this.x_coords.push(parseFloat(result.Mb)); - if (js_data.result_score_type == "LOD") { - this.y_coords.push(result.lod_score); - } - else { - console.log("LRS VALUE:", result['lrs_value']) - this.y_coords.push(result['lrs_value']); - } + this.y_coords.push(result.lod_score); results.push(this.marker_names.push(result.name)); } return results; @@ -119,19 +111,7 @@ Chr_Lod_Chart = (function() { }; Chr_Lod_Chart.prototype.create_scales = function() { - if (this.mappingScale == "morgan") { - max_pos = 0 - for (i = 0, len = this.these_results.length; i < len; i++) { - marker = this.these_results[i] - if (parseFloat(marker['Mb']) > max_pos){ - max_pos = parseFloat(marker.Mb) - } - } - this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]); - } - else { - this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); - } + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); }; @@ -278,6 +258,9 @@ Chr_Lod_Chart = (function() { $("#return_to_full_view").hide(); $('#topchart').remove(); $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + BD.hideButton(); + $('#close_bd').hide(); + $('#bd_container').hide(); return create_lod_chart(); }; diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee index 88003f4e..f6dfd7a3 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee @@ -9,9 +9,9 @@ create_lod_chart = -> additive = js_data.additive else additive = false - + console.log("js_data:", js_data) - + # simplest use #d3.json "data.json", (data) -> mychart = lodchart().lodvarname("lod.hk") @@ -21,13 +21,13 @@ create_lod_chart = -> .ylab(js_data.result_score_type + " score") .manhattanPlot(js_data.manhattan_plot) #.additive(additive) - + data = js_data.json_data - + d3.select("div#topchart") .datum(data) .call(mychart) - + # grab chromosome rectangles; color pink on hover chrrect = mychart.chrSelect() chrrect.on "mouseover", -> @@ -36,7 +36,7 @@ create_lod_chart = -> d3.select(this).attr("fill", -> return "#F1F1F9" if i % 2 "#FBFBFF") - + # animate points at markers on click mychart.markerSelect() .on "click", (d) -> @@ -44,7 +44,3 @@ create_lod_chart = -> d3.select(this) .transition().duration(500).attr("r", r*3) .transition().duration(500).attr("r", r) - -$ -> - root.create_lod_chart = create_lod_chart - diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js index 778eed3a..d2c531f9 100644 --- a/wqflask/wqflask/static/new/javascript/create_lodchart.js +++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js @@ -1,4 +1,5 @@ -//var create_lod_chart; +// Generated by CoffeeScript 1.10.0 +var create_lod_chart; create_lod_chart = function() { var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; @@ -40,11 +41,3 @@ create_lod_chart = function() { return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); }); }; - -create_lod_chart() - -/* -$(function() { - return root.create_lod_chart = create_lod_chart; -}); -*/ \ No newline at end of file diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee index 55ffdce0..a65df84f 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee +++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee @@ -123,6 +123,8 @@ lodchart = () -> .on("click", (d) -> console.log("d is:", d) redraw_plot(d) + BD.putData({chr: d[0], length: d[1]}); + BD.showButton() ) # x-axis labels diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js index 014bf59b..f1df6bd8 100644 --- a/wqflask/wqflask/static/new/javascript/lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/lod_chart.js @@ -1,8 +1,8 @@ -// Generated by CoffeeScript 1.9.2 +// Generated by CoffeeScript 1.10.0 var lodchart; lodchart = function() { - var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; + var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; width = 800; height = 500; margin = { @@ -20,6 +20,7 @@ lodchart = function() { }; titlepos = 20; manhattanPlot = false; + additive = false; ylim = null; additive_ylim = null; nyticks = 5; @@ -29,8 +30,7 @@ lodchart = function() { darkrect = "#F1F1F9"; lightrect = "#FBFBFF"; lodlinecolor = "darkslateblue"; - additivelinecolor_plus = "red"; - additivelinecolor_negative = "green"; + additivelinecolor = "red"; linewidth = 2; suggestivecolor = "gainsboro"; significantcolor = "#EBC7C7"; @@ -70,15 +70,14 @@ lodchart = function() { return results; })(); ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; - - if ('additive' in data) { + if (additive) { data['additive'] = (function() { var j, len, ref, results; ref = data['additive']; results = []; for (j = 0, len = ref.length; j < len; j++) { x = ref[j]; - results.push(x); + results.push(Math.abs(x)); } return results; })(); @@ -92,12 +91,12 @@ lodchart = function() { g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none"); yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]); yticks = yticks != null ? yticks : yscale.ticks(nyticks); - if ('additive' in data) { + if (additive) { additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]); additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); } reorgLodData(data, lodvarname); - data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale); + data = chrscales(data, width, chrGap, margin.left, pad4heatmap); xscale = data.xscale; chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { return "chrrect" + d[0]; @@ -118,7 +117,12 @@ lodchart = function() { return lightrect; }).attr("stroke", "none").on("click", function(d) { console.log("d is:", d); - return redraw_plot(d); + redraw_plot(d); + BD.putData({ + chr: d[0], + length: d[1] + }); + return BD.showButton(); }); xaxis = g.append("g").attr("class", "x axis"); xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) { @@ -133,7 +137,7 @@ lodchart = function() { var chr_plot; $('#topchart').remove(); $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); - return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale); + return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot); }; rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; yaxis = g.append("g").attr("class", "y axis"); @@ -148,7 +152,7 @@ lodchart = function() { return formatAxis(yticks)(d); }); yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue"); - if ('additive' in data) { + if (additive) { rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1; additive_yaxis = g.append("g").attr("class", "y axis"); additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) { @@ -187,19 +191,13 @@ lodchart = function() { return yscale(data.lodByChr[chr][i][lodcolumn]); }); }; - if ('additive' in data) { + if (additive) { additivecurve = function(chr, lodcolumn) { - if (data.additiveByChr[chr][0] < 0) { - pos_neg = "negative" - } - else { - pos_neg = "positive" - } - return [pos_neg, d3.svg.line().x(function(d) { + return d3.svg.line().x(function(d) { return xscale[chr](d); }).y(function(d, i) { - return additive_yscale(Math.abs(data.additiveByChr[chr][i])); - })]; + return additive_yscale(data.additiveByChr[chr][i][lodcolumn]); + }); }; } curves = g.append("g").attr("id", "curves"); @@ -210,17 +208,12 @@ lodchart = function() { curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"); } } - if ('additive' in data) { + if (additive) { ref1 = data.chrnames; for (k = 0, len1 = ref1.length; k < len1; k++) { chr = ref1[k]; if (chr.indexOf(data['chr'])) { - if (additivecurve(chr[0], lodvarnum)[0] == "negative") { - curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); - } - else { - curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); - } + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); } } } @@ -305,13 +298,6 @@ lodchart = function() { manhattanPlot = value; return chart; }; - chart.mappingScale = function(value) { - if (!arguments.length) { - return mappingScale; - } - mappingScale = value; - return chart; - }; chart.ylim = function(value) { if (!arguments.length) { return ylim; @@ -449,6 +435,9 @@ lodchart = function() { chart.yscale = function() { return yscale; }; + chart.additive = function() { + return additive; + }; chart.additive_yscale = function() { return additive_yscale; }; @@ -470,4 +459,4 @@ lodchart = function() { return chrSelect; }; return chart; -}; \ No newline at end of file +}; diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 7454b650..268e3e1c 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -29,7 +29,7 @@ <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}"> <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}"> <input type="hidden" name="pair_scan" value="{{ pair_scan }}"> - + <div class="container"> <div class="col-xs-5"> <h2>Map Viewer: Whole Genome</h2><br> @@ -78,7 +78,7 @@ <tr> <td></td> <td style="padding: 5px;"> - <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span> + <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span> </td> </tr> <tr> @@ -91,14 +91,14 @@ </div> <div class="col-xs-4" style="padding: 0px;"> {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} - <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test + <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank"> <sup style="color:#f00"> ?</sup> </a> <br> {% endif %} {% if mapping_method == "reaper" and nboot > 0 %} - <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test + <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank"> <sup style="color:#f00"> ?</sup> </a> @@ -128,7 +128,7 @@ </div> </div> </div> - + <div class="tabbable" style="margin: 10px;"> <ul class="nav nav-tabs"> <li id="gn1_map_tab"> @@ -160,8 +160,23 @@ </div> {% if mapping_method != "gemma" %} <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map"> - <div id="chart_container"> - <div class="qtlcharts" id="topchart"></div> + <div id="chart_container"> + <ul class="nav nav-tabs"> + <li id="return_to_full_view" class="btn btn-default buttons-html5" style="display:none"> + Return to full view + </li> + <li id="open_bd" class="btn btn-default buttons-html5" style="display:none"> + Open BioDalliance view + </li> + <li id="close_bd" class="btn btn-default buttons-html5" style="display:none"> + Return to vector map + </li> + </ul> + + <div class="qtlcharts" id="topchart"></div> + + <div id="bd_container" class="qtlcharts"> + </div> </div> </div> {% endif %} @@ -262,7 +277,37 @@ {% endblock %} -{% block js %} +{% block js %} + + <script> + /* This section checks for paths to JS libraries by + checking the headers */ + list = [ + /* check for static path */ + "/static/new/javascript/biodalliance.js", + "/static/new/js_external/underscore-min.js", + /* check for dalliance JS (see ./etc/default_settings.py) */ + "/dalliance/build/dalliance-all.js", + /* D3 path (FIXME) */ + "http://d3js.org/d3.v3.min.js", + /* datatables path (FIXME) */ + "https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js" + ]; + for (var i = 0; i < list.length; i++) { + url = list[i]; + $.ajax({ + type: 'HEAD', + url: url, + success: function() { + // page exists + }, + error: function() { + // page does not exist + console.log("Failed to load "+this.url); + alert("Failed to load Javascript for "+this.url); + } + })}; + </script> <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script> @@ -278,19 +323,19 @@ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script> <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script> - <script> - js_data = {{ js_data | safe }} - </script> {% if mapping_method != "gemma" %} <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script> + + <script language="javascript" type="text/javascript" src="/dalliance/build/dalliance-all.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/biodalliance.js"></script> {% endif %} - <script type="text/javascript" charset="utf-8"> - $(document).ready( function () { + <script> + createTable = function() { console.time("Creating table"); $('#qtl_results').DataTable( { "columns": [ @@ -349,15 +394,144 @@ "scrollCollapse": false, "paging": false } ); + }; + + filename = "{{json_filename}}"; + js_data = null; + $.ajax("/generated_text/{{json_filename}}", + {success: + function(data) { + js_data = data; + create_lod_chart(); + createTable(); + } + }); + + BD.putSource({name: 'Genome', + twoBitURI: 'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit', + desc: 'Mouse reference genome build GRCm38', + tier_type: 'sequence', + provides_entrypoints: true + }); + BD.putSource({name: 'Genotype', + controlURI: "{{gn_server_url}}/api_pre1/genotype/mouse/BXD.json", + URIBase: "{{gn_server_url}}/api_pre1/genotype/mouse/", + tier_type: 'rqtl-genotype', + vOffset: 8, + pinned: true, + transposed: true, + style: [ + { type: "default", + method: "U", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "black", + BGCOLOR: "white", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "B", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "blue", + BGCOLOR: "blue", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "H", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "green", + BGCOLOR: "green", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + { type: "default", + method: "D", + style: { glyph: "BOX", + LINE: "0.5", + FGCOLOR: "red", + BGCOLOR: "red", + BGITEM: "true", + HEIGHT: "2", + BUMP: "true", + }}, + ] + }); + BD.putSource({name: 'QTL', + tier_type: 'qtl', + uri: '/generated_text/{{csv_filename}}', + style: [{ + type: 'default', + style: { + glyph: "LINEPLOT", + AUTOMAX: "true", + MIN: 0, + MAX: 3, + HEIGHT: 200, + STEPS: 500, + COLOR1: "blue", + } + }], + }); + BD.putSource({name: 'SNP density', + jbURI: "{{gn_server_url}}/api_pre1/snp", + jbQuery: "", + refetchOnZoom: true, + style: [{ + type: 'default', + style: { + glyph: "HISTOGRAM", + MIN: 0, + MAX: 5000, + AUTOMAX: "true", + HEIGHT: 60, + STEPS: 100, + COLOR1: "red", + COLOR2: "red", + COLOR3: "red", + AXISCENTER: "true", + } + }] + }); + </script> + + <script type="text/javascript" charset="utf-8"> + $(document).ready( function () { + BD.putData({species: "{{ dataset.group.species }}" }); + $('#vector_map_tab').click(function(){ $('div#gn1_map_options').hide(); }); $('#gn1_map_tab').click(function(){ - $('div#gn1_map_options').show(); + $('#gn1_map_options').show(); + $('div#bd_container').hide(); }); + $('#close_bd').click(function() { + $('#open_bd').show(); + $('#close_bd').hide(); + + $('#bd_container').hide(); + $('#topchart').show(); + }); + + $('#open_bd').click(function() { + $('#close_bd').show(); + $('#open_bd').hide() + + $('#topchart').hide(); + $('#bd_container').show(); + + BD.openBrowser(); + }) }); chrView = function(this_chr, chr_mb_list) { @@ -376,9 +550,9 @@ return $('#marker_regression_form').submit(); }; - remap = function() { + remap = function() { $('input[name=selected_chr]').val($('select[name=chromosomes]').val()); - return $('#marker_regression_form').submit(); + return $('#marker_regression_form').submit(); }; export_perm_data = function() { @@ -394,4 +568,3 @@ </script> {% endblock %} - diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index fb52165a..9fdaabf3 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -21,6 +21,7 @@ import uuid import simplejson as json import yaml +import csv #Switching from Redis to StrictRedis; might cause some issues import redis @@ -50,11 +51,12 @@ from wqflask.correlation import corr_scatter_plot from wqflask.wgcna import wgcna_analysis from wqflask.ctl import ctl_analysis +from utility import webqtlUtil from utility import temp_data from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION from base import webqtlFormData -from base.webqtlConfig import GENERATED_IMAGE_DIR +from base.webqtlConfig import GENERATED_IMAGE_DIR, GENERATED_TEXT_DIR from utility.benchmark import Bench from pprint import pformat as pf @@ -144,10 +146,16 @@ def tmp_page(img_path): img_base64 = bytesarray ) @app.route("/twitter/<path:filename>") -def bd_files(filename): - bd_path = app.config['TWITTER_POST_FETCHER_JS_PATH'] +def twitter_js(filename): + bd_path = app.config['JS_TWITTER_POST_FETCHER'] + return send_from_directory(bd_path, filename) + +@app.route("/dalliance/<path:filename>") +def biodalliance_js(filename): + bd_path = app.config['JS_BIODALLIANCE'] return send_from_directory(bd_path, filename) + #@app.route("/data_sharing") #def data_sharing_page(): # logger.info("In data_sharing") @@ -232,6 +240,10 @@ def docedit(): def generated_file(filename): return send_from_directory(GENERATED_IMAGE_DIR,filename) +@app.route('/generated_text/<filename>') +def generated_text(filename): + return send_from_directory(GENERATED_TEXT_DIR, filename) + @app.route("/help") def help(): doc = docs.Docs("help") @@ -495,10 +507,27 @@ def marker_regression_page(): with Bench("Total time in MarkerRegression"): template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) + + qtl_results = template_vars.js_data['qtl_results'] + template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") + + json_filename = webqtlUtil.genRandStr("") + ".json" + with open(GENERATED_TEXT_DIR + "/" + json_filename, "wb") as json_file: + json_file.write(template_vars.js_data) + + csv_filename = webqtlUtil.genRandStr("") + ".csv" + with open(GENERATED_TEXT_DIR + "/" + csv_filename, "wb") as csv_file: + writer = csv.writer(csv_file) + writer.writerow(("Locus", "Chr", "Mb", "LOD")) + for (row) in qtl_results: + score = row["lod_score"] if "lod_score" in row else row["lrs_value"] + writer.writerow((row["name"], row["chr"], row["Mb"], score)) + + result = template_vars.__dict__ if result['pair_scan']: @@ -518,6 +547,9 @@ def marker_regression_page(): # logger.info(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ + gn1_template_vars['json_filename'] = json_filename; + gn1_template_vars['csv_filename'] = csv_filename; + gn1_template_vars['gn_server_url'] = GN_SERVER_URL; pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) logger.info("pickled result length:", len(pickled_result)) @@ -527,22 +559,6 @@ def marker_regression_page(): 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 |