diff options
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 43 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 176 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 66 |
4 files changed, 180 insertions, 106 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 9b048346..12f76b7d 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -236,28 +236,29 @@ class CorrelationResults(object): self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait]) elif self.corr_type == "sample": - if self.dataset.type == "ProbeSet" and cache_available: - dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') - - #XZ, 01/08/2009: read the first line - line = dataset_file.readline() - dataset_strains = webqtlUtil.readLineCSV(line)[1:] - - self.this_trait_vals = [] - for item in dataset_strains: - if item in self.sample_data: - self.this_trait_vals.append(self.sample_data[item]) - else: - self.this_trait_vals.append("None") - num_overlap = len(self.this_trait_vals) - logger.debug("DOING PARALLEL") - self.do_parallel_correlation(db_filename, num_overlap) - else: - for trait, values in self.target_dataset.trait_data.iteritems(): - self.get_sample_r_and_p_values(trait, values) + #ZS: Commented out since parallel correlation has issues with gunicorn + # if self.dataset.type == "ProbeSet" and cache_available: + # dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') + + ##XZ, 01/08/2009: read the first line + # line = dataset_file.readline() + # dataset_strains = webqtlUtil.readLineCSV(line)[1:] + + # self.this_trait_vals = [] + # for item in dataset_strains: + # if item in self.sample_data: + # self.this_trait_vals.append(self.sample_data[item]) + # else: + # self.this_trait_vals.append("None") + # num_overlap = len(self.this_trait_vals) + # logger.debug("DOING PARALLEL") + # self.do_parallel_correlation(db_filename, num_overlap) + # else: + for trait, values in self.target_dataset.trait_data.iteritems(): + self.get_sample_r_and_p_values(trait, values) - self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), - key=lambda t: -abs(t[1][0]))) + self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(), + key=lambda t: -abs(t[1][0]))) if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py index e1df1e63..17625474 100644 --- a/wqflask/wqflask/do_search.py +++ b/wqflask/wqflask/do_search.py @@ -989,3 +989,4 @@ if __name__ == "__main__": #results = GoSearch("0045202", dataset, cursor, db_conn).run() logger.debug("results are:", pf(results)) + db_conn.close() diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index df10c060..117d8f12 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -250,15 +250,29 @@ }; redraw_box_plot = function() { - var x; - var _i, _len, _ref, data; - _ref = _.values(root.selected_samples[root.stats_group]); - trait_vals = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - x = _ref[_i]; - trait_vals.push(x.value); + var y_value_list = [] + for (var sample_group in root.selected_samples){ + var trait_sample_data = _.values(root.selected_samples[sample_group]) + var trait_vals = []; + for (i = 0, len = trait_sample_data.length; i < len; i++) { + this_sample_data = trait_sample_data[i]; + trait_vals.push(this_sample_data.value); + } + y_value_list.push(trait_vals) + } + + if (Object.keys(js_data.sample_group_types).length > 1) { + var update = { + y: y_value_list + } + console.log("REDRAW UPDATE:", update) + Plotly.restyle('box_plot', update, [0, 1, 2]) + } else { + var update = { + y: y_value_list + } + Plotly.restyle('box_plot', update) } - Plotly.restyle('box_plot', 'y', [trait_vals]) } redraw_prob_plot = function() { @@ -640,6 +654,108 @@ }; root.stats_group = 'samples_primary'; + + if (Object.keys(js_data.sample_group_types).length > 1) { + full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])] + sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] + } else { + full_sample_lists = [sample_lists[0]] + sample_group_list = [js_data.sample_group_types['samples_primary']] + } + + if (full_sample_lists.length > 1) { + var box_layout = { + width: 1200, + height: 500, + margin: { + l: 50, + r: 30, + t: 30, + b: 80 + } + }; + var trace1 = { + y: get_sample_vals(full_sample_lists[0]), + type: 'box', + name: sample_group_list[0], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + var trace2 = { + y: get_sample_vals(full_sample_lists[1]), + type: 'box', + name: sample_group_list[1], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + var trace3 = { + y: get_sample_vals(full_sample_lists[2]), + type: 'box', + name: sample_group_list[2], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + box_data = [trace1, trace2, trace3] + } else { + var box_layout = { + width: 500, + height: 500, + margin: { + l: 50, + r: 30, + t: 30, + b: 80 + } + }; + box_data = [ + { + type: 'box', + y: get_sample_vals(full_sample_lists[0]), + name: sample_group_list[0], + boxpoints: 'all', + jitter: 0.5, + whiskerwidth: 0.2, + fillcolor: 'cls', + marker: { + size: 2 + }, + line: { + width: 1 + } + } + ] + } + + obj = { + data: box_data, + layout: box_layout + } + Plotly.newPlot('box_plot', obj); + // Histogram var hist_trace = { x: get_sample_vals(sample_lists[0]), @@ -686,50 +802,6 @@ root.bar_layout = layout Plotly.newPlot('bar_chart', root.bar_data, layout) - if (Object.keys(js_data.sample_group_types).length > 1) { - full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])] - sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] - } else { - full_sample_lists = [sample_lists[0]] - sample_group_list = [js_data.sample_group_types['samples_primary']] - } - - data = [] - for ( var i = 0; i < full_sample_lists.length; i ++ ) { - var box_trace = { - type: 'box', - y: get_sample_vals(full_sample_lists[i]), - name: sample_group_list[i], - boxpoints: 'all', - jitter: 0.5, - whiskerwidth: 0.2, - fillcolor: 'cls', - marker: { - size: 2 - }, - line: { - width: 1 - } - }; - data.push(box_trace) - }; - layout = { - title: 'Box Plot', - yaxis: { - autorange: true, - showgrid: true, - zeroline: true - }, - margin: { - l: 50, - r: 30, - t: 80, - b: 80 - } - }; - - Plotly.newPlot('box_plot', data, layout); - $('.histogram_samples_group').val(root.stats_group); $('.histogram_samples_group').change(function() { root.stats_group = $(this).val(); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 17a2d762..998e5302 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -123,7 +123,7 @@ def handle_bad_request(e): @app.route("/") def index_page(): logger.info("Sending index_page") - logger.error(request.url) + logger.debug(request.url) params = request.args if 'import_collections' in params: import_collections = params['import_collections'] @@ -141,7 +141,7 @@ def index_page(): def tmp_page(img_path): logger.info("In tmp_page") logger.info("img_path:", img_path) - logger.error(request.url) + logger.debug(request.url) initial_start_vars = request.form logger.info("initial_start_vars:", initial_start_vars) imgfile = open(GENERATED_IMAGE_DIR + img_path, 'rb') @@ -174,7 +174,7 @@ def twitter(filename): @app.route("/search", methods=('GET',)) def search_page(): logger.info("in search_page") - logger.error(request.url) + logger.debug(request.url) if 'info_database' in request.args: logger.info("Going to sharing_info_page") template_vars = sharing_info_page() @@ -213,7 +213,7 @@ def search_page(): @app.route("/gsearch", methods=('GET',)) def gsearchact(): - logger.error(request.url) + logger.debug(request.url) result = gsearch.GSearch(request.args).__dict__ type = request.args['type'] if type == "gene": @@ -224,7 +224,7 @@ def gsearchact(): @app.route("/gsearch_updating", methods=('POST',)) def gsearch_updating(): logger.info("REQUEST ARGS:", request.values) - logger.error(request.url) + logger.debug(request.url) result = update_search_results.GSearch(request.args).__dict__ return result['results'] # type = request.args['type'] @@ -235,31 +235,31 @@ def gsearch_updating(): @app.route("/docedit") def docedit(): - logger.error(request.url) + logger.debug(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) + logger.debug(request.url) return send_from_directory(GENERATED_IMAGE_DIR,filename) @app.route("/help") def help(): - logger.error(request.url) + logger.debug(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) + logger.debug(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) + logger.debug(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 @@ -268,13 +268,13 @@ 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) + logger.debug(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) + logger.debug(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 @@ -313,13 +313,13 @@ def environments(): @app.route("/submit_trait") def submit_trait_form(): - logger.error(request.url) + logger.debug(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) + logger.debug(request.url) print("REQUEST.FORM:", request.form) #template_vars = submit_trait.SubmitTrait(request.form) @@ -332,7 +332,7 @@ 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) + logger.debug(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))) @@ -358,7 +358,7 @@ 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) + logger.debug(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))) @@ -379,7 +379,7 @@ 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) + logger.debug(request.url) csv_data = export_traits.export_search_results_csv(request.form) return Response(csv_data, @@ -389,7 +389,7 @@ 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) + logger.debug(request.url) num_perm = float(request.form['num_perm']) perm_data = json.loads(request.form['perm_results']) @@ -412,7 +412,7 @@ def export_perm_data(): @app.route("/show_temp_trait", methods=('POST',)) def show_temp_trait_page(): - logger.error(request.url) + logger.debug(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, @@ -427,7 +427,7 @@ def show_temp_trait_page(): @app.route("/show_trait") def show_trait_page(): - logger.error(request.url) + logger.debug(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, @@ -443,7 +443,7 @@ 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) + logger.debug(request.url) start_vars = request.form temp_uuid = uuid.uuid4() @@ -493,7 +493,7 @@ def mapping_results_container_page(): @app.route("/loading", methods=('POST',)) def loading_page(): - logger.error(request.url) + logger.debug(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'] @@ -552,7 +552,7 @@ 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) + logger.debug(request.url) temp_uuid = initial_start_vars['temp_uuid'] wanted = ( 'trait_id', @@ -678,7 +678,7 @@ def marker_regression_page(): @app.route("/export_mapping_results", methods = ('POST',)) def export_mapping_results(): logger.info("request.form:", request.form) - logger.error(request.url) + logger.debug(request.url) file_path = request.form.get("results_path") results_csv = open(file_path, "r").read() response = Response(results_csv, @@ -691,7 +691,7 @@ def export_mapping_results(): @app.route("/export", methods = ('POST',)) def export(): logger.info("request.form:", request.form) - logger.error(request.url) + logger.debug(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") @@ -702,7 +702,7 @@ def export(): def export_pdf(): import cairosvg logger.info("request.form:", request.form) - logger.error(request.url) + logger.debug(request.url) svg_xml = request.form.get("data", "Invalid data") logger.info("svg_xml:", svg_xml) filename = request.form.get("filename", "interval_map_pdf") @@ -715,7 +715,7 @@ 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) + logger.debug(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] if traits[0] != "": @@ -731,7 +731,7 @@ 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) + logger.debug(request.url) #fd = webqtlFormData.webqtlFormData(request.form) template_vars = show_corr_results.CorrelationResults(request.form) return render_template("correlation_page.html", **template_vars.__dict__) @@ -739,7 +739,7 @@ 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) + logger.debug(request.url) start_vars = request.form traits = [trait.strip() for trait in start_vars['trait_list'].split(',')] @@ -755,7 +755,7 @@ def corr_matrix_page(): @app.route("/corr_scatter_plot") def corr_scatter_plot_page(): - logger.error(request.url) + logger.debug(request.url) template_vars = corr_scatter_plot.CorrScatterPlot(request.args) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, @@ -764,7 +764,7 @@ def corr_scatter_plot_page(): @app.route("/submit_bnw", methods=('POST',)) def submit_bnw(): - logger.error(request.url) + logger.debug(request.url) template_vars = get_bnw_input(request.form) return render_template("empty_collection.html", **{'tool':'Correlation Matrix'}) @@ -772,7 +772,7 @@ def submit_bnw(): 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) + logger.debug(request.url) fd = webqtlFormData.webqtlFormData(request.args) template_vars = SharingInfoPage.SharingInfoPage(fd) return template_vars @@ -780,7 +780,7 @@ 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) + logger.debug(request.url) temp_uuid = request.args['key'] return flask.jsonify(temp_data.TempData(temp_uuid).get_all()) |