diff options
| -rw-r--r-- | wqflask/other_config/nginx_conf/gn2-lei.conf (renamed from wqflask/other_config/nginx_conf/gn2_lei.conf) | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/corr_scatter_plot.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/css/corr_scatter_plot2.css | 19 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js | 74 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/scatterplot.js | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/corr_scatterplot.html | 57 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 34 |
7 files changed, 178 insertions, 11 deletions
diff --git a/wqflask/other_config/nginx_conf/gn2_lei.conf b/wqflask/other_config/nginx_conf/gn2-lei.conf index 6589d298..893ad435 100644 --- a/wqflask/other_config/nginx_conf/gn2_lei.conf +++ b/wqflask/other_config/nginx_conf/gn2-lei.conf @@ -2,7 +2,7 @@ server { # Modeled after http://flask.pocoo.org/docs/deploying/wsgi-standalone/ listen 80; - server_name gn2_lei.genenetwork.org; + server_name gn2-lei.genenetwork.org; access_log /var/log/nginx/lei_access.log; error_log /var/log/nginx/lei_error.log; diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py index 96afef1e..6a92c501 100644 --- a/wqflask/wqflask/correlation/corr_scatter_plot.py +++ b/wqflask/wqflask/correlation/corr_scatter_plot.py @@ -89,3 +89,4 @@ class CorrScatterPlot(object): line_color = line_color, line_width = line_width ) + self.jsdata = self.js_data diff --git a/wqflask/wqflask/static/new/css/corr_scatter_plot2.css b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css new file mode 100644 index 00000000..92e777c2 --- /dev/null +++ b/wqflask/wqflask/static/new/css/corr_scatter_plot2.css @@ -0,0 +1,19 @@ +.nvd3 .nv-axis.nv-x text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nvd3 .nv-axis.nv-y text { + font-size: 16px; + font-weight: normal; + fill: black; +} + +.nv-y .tick.zero line { + stroke: black; +} + +.nv-y .nv-axis g path.domain { + stroke: black; +} diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js new file mode 100644 index 00000000..7a5a86bd --- /dev/null +++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot-2.js @@ -0,0 +1,74 @@ +var chart; + +nv.addGraph(function() { + // + chart = nv.models.scatterChart(); + // + chart.showLegend(false); + chart.duration(300); + chart.color(d3.scale.category10().range()); + chart.pointRange([200,0]); + // + // chart.showDistX(true); + // chart.showDistY(true); + chart.xAxis.tickFormat(d3.format('.02f')); + chart.yAxis.tickFormat(d3.format('.02f')); + // chart.showXAxis(false); + // chart.showYAxis(false); + chart.xAxis.axisLabel(js_data.trait_1); + chart.yAxis.axisLabel(js_data.trait_2); + // + xmin = d3.min(js_data.data[0]); + xmax = d3.max(js_data.data[0]); + xrange = xmax - xmin; + ymin = d3.min(js_data.data[1]); + ymax = d3.max(js_data.data[1]); + yrange = ymax - ymin; + chart.xDomain([xmin - xrange/10, xmax + xrange/10]); + chart.yDomain([ymin - yrange/10, ymax + yrange/10]); + // + d3.select('#scatterplot2 svg').datum(nv.log(getdata())).call(chart); + nv.utils.windowResize(chart.update); + return chart; +}); + +function getdata () { + var data = []; + data.push({ + values: [], + slope: js_data.slope, + intercept: js_data.intercept + }); + for (j = 0; j < js_data.data[0].length; j++) { + data[0].values.push({ + x: js_data.data[0][j], + y: js_data.data[1][j], + size: 10, + shape: 'circle' + }); + } + return data; +} + +function randomData(groups, points) { + var data = [], + shapes = ['circle'], + random = d3.random.normal(); + for (i = 0; i < groups; i++) { + data.push({ + key: 'Group ' + i, + values: [], + slope: Math.random() - .01, + intercept: Math.random() - .5 + }); + for (j = 0; j < points; j++) { + data[i].values.push({ + x: random(), + y: random(), + size: Math.random(), + shape: shapes[j % shapes.length] + }); + } + } + return data; +} diff --git a/wqflask/wqflask/static/new/javascript/scatterplot.js b/wqflask/wqflask/static/new/javascript/scatterplot.js index de7b7906..d7f2a4a5 100644 --- a/wqflask/wqflask/static/new/javascript/scatterplot.js +++ b/wqflask/wqflask/static/new/javascript/scatterplot.js @@ -166,7 +166,7 @@ scatterplot = function() { maxx = xlim[1]; yticks = yticks != null ? yticks : ys.ticks(nyticks); xticks = xticks != null ? xticks : xs.ticks(nxticks); - titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).style("fill", "black").style("font-size", "28px").text(title); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).style("fill", "black").style("font-size", "24px").text(title); xaxis = g.append("g").attr("class", "x axis"); xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { return xscale(d); diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html index 810f4ca3..4464025e 100644 --- a/wqflask/wqflask/templates/corr_scatterplot.html +++ b/wqflask/wqflask/templates/corr_scatterplot.html @@ -7,6 +7,8 @@ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" /> <link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" /> + <link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css"> + <link rel="stylesheet" type="text/css" href="/static/new/css/corr_scatter_plot2.css" /> {% endblock %} {% block content %} @@ -47,10 +49,48 @@ </tr> </table> </form>--> -<div class="container"> -<div id="chart1" class="qtlcharts"></div> +<div class="container-fluid"> -<div style="margin-left: 80px;"> +<h2>Correlation Scatterplot</h2> + +<table class="table"> + <tbody> + <tr><th class="text-right">num overlap</th> <td>{{jsdata.num_overlap}}</td></tr> + <tr><th class="text-right">slope</th> <td>{{jsdata.slope}}</td></tr> + <tr><th class="text-right">intercept</th> <td>{{jsdata.intercept}}</td></tr> + <tr><th class="text-right">r value</th> <td>{{jsdata.r_value}}</td></tr> + <tr><th class="text-right">p value</th> <td>{{jsdata.p_value}}</td></tr> + </tbody> +</table> + +<!-- +<table class="table"> + <tr> + <td>Correlation Line Width</td> + <td><input type="text" name="lastname" value="2" style="width: 44px;"> px</td> + </tr> + <tr> + <td>Correlation Line Color</td> + <td><input type="color" name="favcolor" value="#000000"></td> + </tr> + <tr> + <td>Dot Stroke</td> + <td><input type="text" name="lastname" value="5" style="width: 44px;"> px</td> + </tr> + <tr> + <td>Dot Color</td> + <td><input type="color" name="favcolor" value="#ff0000"></td> + </tr> +</table> +--> + +<div id="scatterplot2"> + <svg style="width: 1000px; height: 800px;"></svg> +</div> + +<br> + +<div style="margin-left: 75px;"> {% if trait_1.dataset.type == "ProbeSet" %} <div> @@ -103,17 +143,18 @@ {% endif %} </div> + {% endblock %} {% block js %} <script> - js_data = {{ js_data | safe }} + js_data = {{ js_data | safe }}; </script> - <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script> + <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.min.js"></script> + <script language="javascript" type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.js"></script> <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/scatterplot.js"></script> - <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script> -{% endblock %} \ No newline at end of file + <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot-2.js"></script> +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 3882e60a..44ca8de8 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -71,6 +71,8 @@ import werkzeug import utility.logger logger = utility.logger.getLogger(__name__ ) + + @app.before_request def connect_db(): db = getattr(g, '_database', None) @@ -120,6 +122,7 @@ def handle_bad_request(e): @app.route("/") def index_page(): logger.info("Sending index_page") + logger.error(request.url) params = request.args if 'import_collections' in params: import_collections = params['import_collections'] @@ -137,6 +140,7 @@ def index_page(): def tmp_page(img_path): logger.info("In tmp_page") logger.info("img_path:", img_path) + logger.error(request.url) initial_start_vars = request.form logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') @@ -169,6 +173,7 @@ def bd_files(filename): @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") + logger.error(request.url) if 'info_database' in request.args: logger.info("Going to sharing_info_page") template_vars = sharing_info_page() @@ -207,6 +212,7 @@ def search_page(): @app.route("/gsearch", methods=('GET',)) def gsearchact(): + logger.error(request.url) result = gsearch.GSearch(request.args).__dict__ type = request.args['type'] if type == "gene": @@ -217,6 +223,7 @@ def gsearchact(): @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) + logger.error(request.url) result = update_search_results.GSearch(request.args).__dict__ return result['results'] # type = request.args['type'] @@ -227,26 +234,31 @@ def gsearch_updating(): @app.route("/docedit") def docedit(): + logger.error(request.url) doc = docs.Docs(request.args['entry']) return render_template("docedit.html", **doc.__dict__) @app.route('/generated/<filename>') def generated_file(filename): + logger.error(request.url) return send_from_directory(GENERATED_IMAGE_DIR,filename) @app.route("/help") def help(): + logger.error(request.url) 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 + logger.error(request.url) 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) + logger.error(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 @@ -255,11 +267,13 @@ def wcgna_results(): @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 + logger.error(request.url) 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) + logger.error(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 @@ -297,11 +311,13 @@ def environments(): @app.route("/submit_trait") def submit_trait_form(): + logger.error(request.url) species_and_groups = get_species_groups() return render_template("submit_trait.html", **{'species_and_groups' : species_and_groups, 'gn_server_url' : GN_SERVER_URL, 'version' : GN_VERSION}) @app.route("/create_temp_trait", methods=('POST',)) def create_temp_trait(): + logger.error(request.url) print("REQUEST.FORM:", request.form) #template_vars = submit_trait.SubmitTrait(request.form) @@ -314,6 +330,7 @@ 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) + logger.error(request.url) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) @@ -339,6 +356,7 @@ 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) + logger.error(request.url) sample_data = export_trait_data.export_sample_table(request.form) logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) @@ -359,6 +377,7 @@ def export_traits_csv(): """CSV file consisting of the traits from the search result page""" logger.info("In export_traits_csv") logger.info("request.form:", request.form) + logger.error(request.url) csv_data = export_traits.export_search_results_csv(request.form) return Response(csv_data, @@ -368,6 +387,7 @@ def export_traits_csv(): @app.route('/export_perm_data', methods=('POST',)) def export_perm_data(): """CSV file consisting of the permutation data for the mapping results""" + logger.error(request.url) num_perm = float(request.form['num_perm']) perm_data = json.loads(request.form['perm_results']) @@ -390,6 +410,7 @@ def export_perm_data(): @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): + logger.error(request.url) template_vars = show_trait.ShowTrait(request.form) #logger.info("js_data before dump:", template_vars.js_data) template_vars.js_data = json.dumps(template_vars.js_data, @@ -404,6 +425,7 @@ def show_temp_trait_page(): @app.route("/show_trait") def show_trait_page(): + logger.error(request.url) 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, @@ -419,6 +441,7 @@ def show_trait_page(): @app.route("/heatmap", methods=('POST',)) def heatmap_page(): logger.info("In heatmap, request.form is:", pf(request.form)) + logger.error(request.url) start_vars = request.form temp_uuid = uuid.uuid4() @@ -468,6 +491,7 @@ def mapping_results_container_page(): @app.route("/loading", methods=('POST',)) def loading_page(): + logger.error(request.url) initial_start_vars = request.form logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) #temp_uuid = initial_start_vars['temp_uuid'] @@ -524,6 +548,7 @@ def loading_page(): def marker_regression_page(): initial_start_vars = request.form logger.debug("Marker regression called with initial_start_vars:", initial_start_vars.items()) + logger.error(request.url) temp_uuid = initial_start_vars['temp_uuid'] wanted = ( 'trait_id', @@ -645,6 +670,7 @@ def marker_regression_page(): @app.route("/export", methods = ('POST',)) def export(): logger.info("request.form:", request.form) + logger.error(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") @@ -655,6 +681,7 @@ def export(): def export_pdf(): import cairosvg logger.info("request.form:", request.form) + logger.error(request.url) svg_xml = request.form.get("data", "Invalid data") logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") @@ -667,7 +694,7 @@ def export_pdf(): @app.route("/network_graph", methods=('POST',)) def network_graph_page(): logger.info("In network_graph, request.form is:", pf(request.form)) - + logger.error(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": @@ -683,6 +710,7 @@ def network_graph_page(): @app.route("/corr_compute", methods=('POST',)) def corr_compute_page(): logger.info("In corr_compute, request.form is:", pf(request.form)) + logger.error(request.url) #fd = webqtlFormData.webqtlFormData(request.form) template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) @@ -690,6 +718,7 @@ def corr_compute_page(): @app.route("/corr_matrix", methods=('POST',)) def corr_matrix_page(): logger.info("In corr_matrix, request.form is:", pf(request.form)) + logger.error(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] @@ -705,6 +734,7 @@ def corr_matrix_page(): @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): + logger.error(request.url) template_vars = corr_scatter_plot.CorrScatterPlot(request.args) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, @@ -716,6 +746,7 @@ def corr_scatter_plot_page(): 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") + logger.error(request.url) fd = webqtlFormData.webqtlFormData(request.args) template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars @@ -723,6 +754,7 @@ def sharing_info_page(): # Take this out or secure it before putting into production @app.route("/get_temp_data") def get_temp_data(): + logger.error(request.url) temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) |