diff options
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 545 |
1 files changed, 268 insertions, 277 deletions
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js index 4dce0705..c0f36eaa 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js +++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -1,307 +1,298 @@ -// Generated by CoffeeScript 1.8.0 -(function() { - var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; +var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; - submit_special = function(url) { - $("#trait_data_form").attr("action", url); - $("#trait_data_form").submit(); - }; - - update_time_remaining = function(percent_complete) { - var minutes_remaining, now, period, total_seconds_remaining; - now = new Date(); - period = now.getTime() - root.start_time; - console.log("period is:", period); - if (period > 8000) { - total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; - minutes_remaining = Math.round(total_seconds_remaining / 60); - if (minutes_remaining < 3) { - return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); - } else { - return $('#time_remaining').text(minutes_remaining + " minutes remaining"); - } +update_time_remaining = function(percent_complete) { + var minutes_remaining, now, period, total_seconds_remaining; + now = new Date(); + period = now.getTime() - root.start_time; + console.log("period is:", period); + if (period > 8000) { + total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; + minutes_remaining = Math.round(total_seconds_remaining / 60); + if (minutes_remaining < 3) { + return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); + } else { + return $('#time_remaining').text(minutes_remaining + " minutes remaining"); } - }; + } +}; - get_progress = function() { - var params, params_str, temp_uuid, url; - console.log("temp_uuid:", $("#temp_uuid").val()); - temp_uuid = $("#temp_uuid").val(); - params = { - key: temp_uuid - }; - params_str = $.param(params); - url = "/get_temp_data?" + params_str; - console.log("url:", url); - $.ajax({ - type: "GET", - url: url, - success: (function(_this) { - return function(progress_data) { - var percent_complete; - percent_complete = progress_data['percent_complete']; - console.log("in get_progress data:", progress_data); - $('#marker_regression_progress').css("width", percent_complete + "%"); - if (root.start_time) { - if (!isNaN(percent_complete)) { - return update_time_remaining(percent_complete); - } - } else { - return root.start_time = new Date().getTime(); - } - }; - })(this) - }); - return false; +get_progress = function() { + var params, params_str, temp_uuid, url; + console.log("temp_uuid:", $("#temp_uuid").val()); + temp_uuid = $("#temp_uuid").val(); + params = { + key: temp_uuid }; - - block_outliers = function() { - return $('.outlier').each((function(_this) { - return function(_index, element) { - return $(element).find('.trait_value_input').val('x'); + params_str = $.param(params); + url = "/get_temp_data?" + params_str; + console.log("url:", url); + $.ajax({ + type: "GET", + url: url, + success: (function(_this) { + return function(progress_data) { + var percent_complete; + percent_complete = progress_data['percent_complete']; + console.log("in get_progress data:", progress_data); + $('#marker_regression_progress').css("width", percent_complete + "%"); + if (root.start_time) { + if (!isNaN(percent_complete)) { + return update_time_remaining(percent_complete); + } + } else { + return root.start_time = new Date().getTime(); + } }; - })(this)); - }; - - do_ajax_post = function(url, form_data) { - $.ajax({ - type: "POST", - url: url, - data: form_data, - error: (function(_this) { - return function(xhr, ajaxOptions, thrownError) { - alert("Sorry, an error occurred"); - console.log(xhr); - clearInterval(_this.my_timer); - $('#progress_bar_container').modal('hide'); - $('#static_progress_bar_container').modal('hide'); - return $("body").html("We got an error."); - }; - })(this), - success: (function(_this) { - return function(data) { - clearInterval(_this.my_timer); - $('#progress_bar_container').modal('hide'); - $('#static_progress_bar_container').modal('hide'); - return open_mapping_results(data); - }; - })(this) - }); - console.log("settingInterval"); - this.my_timer = setInterval(get_progress, 1000); - return false; - }; - - open_mapping_results = function(data) { - return $.colorbox({ - html: data, - href: "#mapping_results_holder", - height: "90%", - width: "90%", - onComplete: (function(_this) { - return function() { - var filename, getSvgXml; - root.create_lod_chart(); - filename = "lod_chart_" + js_data.this_trait; - getSvgXml = function() { - var svg; - svg = $("#topchart").find("svg")[0]; - return (new XMLSerializer).serializeToString(svg); - }; - $("#exportform > #export").click(function() { - var form, svg_xml; - svg_xml = getSvgXml(); - form = $("#exportform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }); - return $("#exportpdfform > #export_pdf").click(function() { - var form, svg_xml; - svg_xml = getSvgXml(); - form = $("#exportpdfform"); - form.find("#data").val(svg_xml); - form.find("#filename").val(filename); - return form.submit(); - }); - }; - })(this) - }); - }; - - outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; - showalert = function(message, alerttype) { - return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); - }; - - $('#suggestive').hide(); + })(this) + }); + return false; +}; - $('input[name=display_all]').change((function(_this) { - return function() { - console.log("check"); - if ($('input[name=display_all]:checked').val() === "False") { - return $('#suggestive').show(); - } else { - return $('#suggestive').hide(); - } +block_outliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait_value_input').val('x'); }; })(this)); +}; - //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping - var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', - 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', - 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', - 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', - 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] - - $(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ - var form_data, url; - url = "/loading"; - $('input[name=method]').val("rqtl_geno"); - $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); - $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); - $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); - $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); - $('input[name=categorical_vars]').val(js_data.categorical_vars) - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); - $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); - $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val()); - $('input[name=tool_used]').val("Mapping"); - $('input[name=form_url]').val("/run_mapping"); - $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); - return submit_special(url); - } else { - return true - } - }; - })(this)); - - $(".gemma_tab, #gemma_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ - var form_data, url; - console.log("RUNNING GEMMA"); - url = "/loading"; - $('input[name=method]').val("gemma"); - $('input[name=selected_chr]').val($('#chr_gemma').val()); - $('input[name=num_perm]').val(0); - $('input[name=genofile]').val($('#genofile_gemma').val()); - $('input[name=maf]').val($('input[name=maf_gemma]').val()); - $('input[name=tool_used]').val("Mapping"); - $('input[name=form_url]').val("/run_mapping"); - $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); - return submit_special(url); - } else { - return true - } - }; - })(this)); +do_ajax_post = function(url, form_data) { + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: (function(_this) { + return function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }; + })(this), + success: (function(_this) { + return function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return open_mapping_results(data); + }; + })(this) + }); + console.log("settingInterval"); + this.my_timer = setInterval(get_progress, 1000); + return false; +}; - $(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) { - return function() { - if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ - var form_data, url; - console.log("In interval mapping"); - url = "/loading"; - $('input[name=method]').val("reaper"); - $('input[name=selected_chr]').val($('#chr_reaper').val()); - $('input[name=mapping_scale]').val($('#scale_reaper').val()); - $('input[name=genofile]').val($('#genofile_reaper').val()); - $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); - $('input[name=control_marker]').val($('input[name=control_reaper]').val()); - $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); - $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); - $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); - $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); - $('input[name=tool_used]').val("Mapping"); - $('input[name=form_url]').val("/run_mapping"); - $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); - return submit_special(url); - } else { - return true - } - }; - })(this)); +open_mapping_results = function(data) { + return $.colorbox({ + html: data, + href: "#mapping_results_holder", + height: "90%", + width: "90%", + onComplete: (function(_this) { + return function() { + var filename, getSvgXml; + root.create_lod_chart(); + filename = "lod_chart_" + js_data.this_trait; + getSvgXml = function() { + var svg; + svg = $("#topchart").find("svg")[0]; + return (new XMLSerializer).serializeToString(svg); + }; + $("#exportform > #export").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + return $("#exportpdfform > #export_pdf").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + }; + })(this) + }); +}; - $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { - return function() { - if ($(".outlier").length && $(".outlier-alert").length < 1) { - return showalert(outlier_text, "alert-success outlier-alert"); - } - }; - })(this)); +outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; +showalert = function(message, alerttype) { + return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); +}; - composite_mapping_fields = function() { - return $(".composite_fields").toggle(); - }; +$('#suggestive').hide(); - mapping_method_fields = function() { - return $(".mapping_method_fields").toggle(); +$('input[name=display_all]').change((function(_this) { + return function() { + console.log("check"); + if ($('input[name=display_all]:checked').val() === "False") { + return $('#suggestive').show(); + } else { + return $('#suggestive').hide(); + } }; +})(this)); - $("#use_composite_choice").change(composite_mapping_fields); - - $("#mapping_method_choice").change(mapping_method_fields); +//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results', + 'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', + 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples'] - $("#mapmodel_rqtl_geno").change(function() { - if ($(this).val() == "np"){ - $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); - $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); - $("#missing_geno").attr('disabled', 'disabled'); - $("#missing_geno").css('background-color', '#CCC'); +$(".rqtl_tab, #rqtl_geno_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); + $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); + $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); + $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); } else { - $("#mapmethod_rqtl_geno").removeAttr('disabled'); - $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); - $("#missing_geno").removeAttr('disabled'); - $("#missing_geno").css('background-color', '#FFF'); + return true } - }); + }; +})(this)); - $("#mapmethod_rqtl_geno").change(function() { - if ($(this).val() == "mr"){ - $("#missing_geno_div").css('display', 'block'); +$(".gemma_tab, #gemma_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ + var form_data, url; + console.log("RUNNING GEMMA"); + url = "/loading"; + $('input[name=method]').val("gemma"); + $('input[name=selected_chr]').val($('#chr_gemma').val()); + $('input[name=num_perm]').val(0); + $('input[name=genofile]').val($('#genofile_gemma').val()); + $('input[name=maf]').val($('input[name=maf_gemma]').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); } else { - $("#missing_geno_div").css('display', 'none'); + return true } - }); + }; +})(this)); - $("li.mapping_tab").click(function() { - if ($(this).hasClass("rqtl")){ - $(".rqtl_description").css("display", "block"); +$(".reaper_tab, #interval_mapping_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ + var form_data, url; + console.log("In interval mapping"); + url = "/loading"; + $('input[name=method]').val("reaper"); + $('input[name=selected_chr]').val($('#chr_reaper').val()); + $('input[name=mapping_scale]').val($('#scale_reaper').val()); + $('input[name=genofile]').val($('#genofile_reaper').val()); + $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); + $('input[name=control_marker]').val($('input[name=control_reaper]').val()); + $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); } else { - $(".rqtl_description").css("display", "none"); + return true } - }); + }; +})(this)); - toggle_enable_disable = function(elem) { - return $(elem).prop("disabled", !$(elem).prop("disabled")); +$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { + return function() { + if ($(".outlier").length && $(".outlier-alert").length < 1) { + return showalert(outlier_text, "alert-success outlier-alert"); + } }; +})(this)); - $("#choose_closet_control").change(function() { - return toggle_enable_disable("#control_locus"); - }); +composite_mapping_fields = function() { + return $(".composite_fields").toggle(); +}; - $("#display_all_lrs").change(function() { - return toggle_enable_disable("#suggestive_lrs"); - }); +mapping_method_fields = function() { + return $(".mapping_method_fields").toggle(); +}; - $('#genofile_rqtl_geno').change(function() { - geno_location = $(this).children("option:selected").val().split(":")[0] - $('#scale_rqtl_geno').empty() - the_scales = js_data.scales_in_geno[geno_location] - for (var i = 0; i < the_scales.length; i++){ - $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); - } - }); - $('#genofile_reaper').change(function() { - geno_location = $(this).children("option:selected").val().split(":")[0] - $('#scale_reaper').empty() - the_scales = js_data.scales_in_geno[geno_location] - for (var i = 0; i < the_scales.length; i++){ - $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); - } - }); +$("#use_composite_choice").change(composite_mapping_fields); + +$("#mapping_method_choice").change(mapping_method_fields); + +$("#mapmodel_rqtl_geno").change(function() { + if ($(this).val() == "np"){ + $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); + $("#missing_geno").attr('disabled', 'disabled'); + $("#missing_geno").css('background-color', '#CCC'); + } else { + $("#mapmethod_rqtl_geno").removeAttr('disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); + $("#missing_geno").removeAttr('disabled'); + $("#missing_geno").css('background-color', '#FFF'); + } +}); + +$("#mapmethod_rqtl_geno").change(function() { + if ($(this).val() == "mr"){ + $("#missing_geno_div").css('display', 'block'); + } else { + $("#missing_geno_div").css('display', 'none'); + } +}); + +$("li.mapping_tab").click(function() { + if ($(this).hasClass("rqtl")){ + $(".rqtl_description").css("display", "block"); + } else { + $(".rqtl_description").css("display", "none"); + } +}); + +toggle_enable_disable = function(elem) { + return $(elem).prop("disabled", !$(elem).prop("disabled")); +}; + +$("#choose_closet_control").change(function() { + return toggle_enable_disable("#control_locus"); +}); + +$("#display_all_lrs").change(function() { + return toggle_enable_disable("#suggestive_lrs"); +}); -}).call(this); +$('#genofile_rqtl_geno').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_rqtl_geno').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); +$('#genofile_reaper').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_reaper').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); |