diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/wqflask/show_trait/SampleList.py | 8 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 1 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait.coffee | 17 | ||||
| -rwxr-xr-x | wqflask/wqflask/static/new/javascript/show_trait.js | 888 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 20 |
5 files changed, 470 insertions, 464 deletions
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py index d196e722..060cb519 100755 --- a/wqflask/wqflask/show_trait/SampleList.py +++ b/wqflask/wqflask/show_trait/SampleList.py @@ -25,7 +25,11 @@ class SampleList(object): self.sample_list = [] # The actual list - self.get_attributes() + try: + self.get_attributes() + except Exception: + print("failed to get attributes") + self.attributes = {} print("camera: attributes are:", pf(self.attributes)) @@ -243,4 +247,4 @@ def natural_sort_key(x): x = int(x) except ValueError: pass - return x
\ No newline at end of file + return x diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 836a0be5..b28c9b76 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -123,6 +123,7 @@ class ShowTrait(object): hddn['control_marker'] = "" hddn['maf'] = 0.01 hddn['compare_traits'] = [] + hddn['export_data'] = "" # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self self.hddn = hddn diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee index d05ccbf7..ee57831f 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.coffee +++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee @@ -377,11 +377,9 @@ $ -> ##Get Sample Data From Table Code - get_sample_table_data = -> - samples = {} - primary_samples = [] - other_samples = [] - $('#sortable1').find('.value_se').each (_index, element) => + get_sample_table_data = (table_name) -> + samples = [] + $('#' + table_name).find('.value_se').each (_index, element) => row_data = {} row_data.name = $.trim($(element).find('.column_name-Sample').text()) row_data.value = $(element).find('.edit_sample_value').val() @@ -391,10 +389,7 @@ $ -> row_data[attribute_info.name] = $.trim($(element).find( '.column_name-'+attribute_info.name.replace(" ", "_")).text()) console.log("row_data is:", row_data) - primary_samples.push(row_data) - console.log("primary_samples is:", primary_samples) - samples.primary_samples = primary_samples - samples.other_samples = other_samples + samples.push(row_data) return samples ##End Get Sample Data from Table Code @@ -402,7 +397,9 @@ $ -> ##Export Sample Table Data Code export_sample_table_data = -> - sample_data = get_sample_table_data() + sample_data = {} + sample_data.primary_samples = get_sample_table_data('samples_primary') + sample_data.other_samples = get_sample_table_data('samples_other') console.log("sample_data is:", sample_data) json_sample_data = JSON.stringify(sample_data) console.log("json_sample_data is:", json_sample_data) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 159dafcb..c2dc07ee 100755 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -1,469 +1,469 @@ -// Generated by CoffeeScript 1.8.0 -var Stat_Table_Rows, is_number, - __hasProp = {}.hasOwnProperty, - __slice = [].slice; +// Generated by CoffeeScript 1.9.2 +(function() { + var Stat_Table_Rows, is_number, + hasProp = {}.hasOwnProperty, + slice = [].slice; -console.log("start_b"); + console.log("start_b"); -is_number = function(o) { - return !isNaN((o - 0) && o !== null); -}; - -Stat_Table_Rows = [ - { - vn: "n_of_samples", - pretty: "N of Samples", - digits: 0 - }, { - vn: "mean", - pretty: "Mean", - digits: 2 - }, { - vn: "median", - pretty: "Median", - digits: 2 - }, { - vn: "std_error", - pretty: "Standard Error (SE)", - digits: 2 - }, { - vn: "std_dev", - pretty: "Standard Deviation (SD)", - digits: 2 - }, { - vn: "min", - pretty: "Minimum", - digits: 2 - }, { - vn: "max", - pretty: "Maximum", - digits: 2 - }, { - vn: "range", - pretty: "Range (log2)", - digits: 2 - }, { - vn: "range_fold", - pretty: "Range (fold)", - digits: 2 - }, { - vn: "interquartile", - pretty: "Interquartile Range", - url: "/glossary.html#Interquartile", - digits: 2 - } -]; + is_number = function(o) { + return !isNaN((o - 0) && o !== null); + }; -$(function() { - var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; - sample_lists = js_data.sample_lists; - sample_group_types = js_data.sample_group_types; - root.bar_chart = new Bar_Chart(sample_lists[0]); - root.histogram = new Histogram(sample_lists[0]); - new Box_Plot(sample_lists[0]); - $('.bar_chart_samples_group').change(function() { - var all_samples, group; - $('#bar_chart').remove(); - $('#bar_chart_container').append('<div id="bar_chart"></div>'); - group = $(this).val(); - if (group === "samples_primary") { - return root.bar_chart = new Bar_Chart(sample_lists[0]); - } else if (group === "samples_other") { - return root.bar_chart = new Bar_Chart(sample_lists[1]); - } else if (group === "samples_all") { - all_samples = sample_lists[0].concat(sample_lists[1]); - return root.bar_chart = new Bar_Chart(all_samples); - } - }); - $('.box_plot_samples_group').change(function() { - var all_samples, group; - $('#box_plot').remove(); - $('#box_plot_container').append('<div id="box_plot"></div>'); - group = $(this).val(); - if (group === "samples_primary") { - return new Box_Plot(sample_lists[0]); - } else if (group === "samples_other") { - return new Box_Plot(sample_lists[1]); - } else if (group === "samples_all") { - all_samples = sample_lists[0].concat(sample_lists[1]); - return new Box_Plot(all_samples); + Stat_Table_Rows = [ + { + vn: "n_of_samples", + pretty: "N of Samples", + digits: 0 + }, { + vn: "mean", + pretty: "Mean", + digits: 2 + }, { + vn: "median", + pretty: "Median", + digits: 2 + }, { + vn: "std_error", + pretty: "Standard Error (SE)", + digits: 2 + }, { + vn: "std_dev", + pretty: "Standard Deviation (SD)", + digits: 2 + }, { + vn: "min", + pretty: "Minimum", + digits: 2 + }, { + vn: "max", + pretty: "Maximum", + digits: 2 + }, { + vn: "range", + pretty: "Range (log2)", + digits: 2 + }, { + vn: "range_fold", + pretty: "Range (fold)", + digits: 2 + }, { + vn: "interquartile", + pretty: "Interquartile Range", + url: "/glossary.html#Interquartile", + digits: 2 } - }); - d3.select("#select_compare_trait").on("click", (function(_this) { - return function() { - $('.scatter-matrix-container').remove(); - return open_trait_selection(); - }; - })(this)); - d3.select("#clear_compare_trait").on("click", (function(_this) { - return function() { - return $('.scatter-matrix-container').remove(); - }; - })(this)); - open_trait_selection = function() { - return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { + ]; + + $(function() { + var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; + sample_lists = js_data.sample_lists; + sample_group_types = js_data.sample_group_types; + root.bar_chart = new Bar_Chart(sample_lists[0]); + root.histogram = new Histogram(sample_lists[0]); + new Box_Plot(sample_lists[0]); + $('.bar_chart_samples_group').change(function() { + var all_samples, group; + $('#bar_chart').remove(); + $('#bar_chart_container').append('<div id="bar_chart"></div>'); + group = $(this).val(); + if (group === "samples_primary") { + return root.bar_chart = new Bar_Chart(sample_lists[0]); + } else if (group === "samples_other") { + return root.bar_chart = new Bar_Chart(sample_lists[1]); + } else if (group === "samples_all") { + all_samples = sample_lists[0].concat(sample_lists[1]); + return root.bar_chart = new Bar_Chart(all_samples); + } + }); + $('.box_plot_samples_group').change(function() { + var all_samples, group; + $('#box_plot').remove(); + $('#box_plot_container').append('<div id="box_plot"></div>'); + group = $(this).val(); + if (group === "samples_primary") { + return new Box_Plot(sample_lists[0]); + } else if (group === "samples_other") { + return new Box_Plot(sample_lists[1]); + } else if (group === "samples_all") { + all_samples = sample_lists[0].concat(sample_lists[1]); + return new Box_Plot(all_samples); + } + }); + d3.select("#select_compare_trait").on("click", (function(_this) { return function() { - $.colorbox({ - inline: true, - href: "#collections_holder" - }); - return $('a.collection_name').attr('onClick', 'return false'); + $('.scatter-matrix-container').remove(); + return open_trait_selection(); }; })(this)); - }; - hide_tabs = function(start) { - var x, _i, _results; - _results = []; - for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) { - _results.push($("#stats_tabs" + x).hide()); - } - return _results; - }; - stats_mdp_change = function() { - var selected; - selected = $(this).val(); - hide_tabs(0); - return $("#stats_tabs" + selected).show(); - }; - change_stats_value = function(sample_sets, category, value_type, decimal_places) { - var current_value, id, in_box, the_value, title_value; - id = "#" + process_id(category, value_type); - console.log("the_id:", id); - in_box = $(id).html; - current_value = parseFloat($(in_box)).toFixed(decimal_places); - the_value = sample_sets[category][value_type](); - console.log("After running sample_sets, the_value is:", the_value); - if (decimal_places > 0) { - title_value = the_value.toFixed(decimal_places * 2); - the_value = the_value.toFixed(decimal_places); - } else { - title_value = null; - } - console.log("*-* the_value:", the_value); - console.log("*-* current_value:", current_value); - if (the_value !== current_value) { - console.log("object:", $(id).html(the_value)); - $(id).html(the_value).effect("highlight"); - } - if (title_value) { - return $(id).attr('title', title_value); - } - }; - update_stat_values = function(sample_sets) { - var category, row, _i, _len, _ref, _results; - _ref = ['samples_primary', 'samples_other', 'samples_all']; - _results = []; - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - category = _ref[_i]; - _results.push((function() { - var _j, _len1, _results1; - _results1 = []; - for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) { - row = Stat_Table_Rows[_j]; - console.log("Calling change_stats_value"); - _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits)); - } - return _results1; - })()); - } - return _results; - }; - make_table = function() { - var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1; - header = "<thead><tr><th> </th>"; - console.log("js_data.sample_group_types:", js_data.sample_group_types); - _ref = js_data.sample_group_types; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - value = _ref[key]; - console.log("aa key:", key); - console.log("aa value:", value); - the_id = process_id("column", key); - header += "<th id=\"" + the_id + "\">" + value + "</th>"; - } - header += "</thead>"; - console.log("windex header is:", header); - the_rows = "<tbody>"; - for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { - row = Stat_Table_Rows[_i]; - console.log("rowing"); - row_line = "<tr>"; - if (row.url != null) { - row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>"; + d3.select("#clear_compare_trait").on("click", (function(_this) { + return function() { + return $('.scatter-matrix-container').remove(); + }; + })(this)); + open_trait_selection = function() { + return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder" + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); + }; + hide_tabs = function(start) { + var i, ref, results, x; + results = []; + for (x = i = ref = start; ref <= 10 ? i <= 10 : i >= 10; x = ref <= 10 ? ++i : --i) { + results.push($("#stats_tabs" + x).hide()); + } + return results; + }; + stats_mdp_change = function() { + var selected; + selected = $(this).val(); + hide_tabs(0); + return $("#stats_tabs" + selected).show(); + }; + change_stats_value = function(sample_sets, category, value_type, decimal_places) { + var current_value, id, in_box, the_value, title_value; + id = "#" + process_id(category, value_type); + console.log("the_id:", id); + in_box = $(id).html; + current_value = parseFloat($(in_box)).toFixed(decimal_places); + the_value = sample_sets[category][value_type](); + console.log("After running sample_sets, the_value is:", the_value); + if (decimal_places > 0) { + title_value = the_value.toFixed(decimal_places * 2); + the_value = the_value.toFixed(decimal_places); } else { - row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>"; + title_value = null; } - console.log("box - js_data.sample_group_types:", js_data.sample_group_types); - _ref1 = js_data.sample_group_types; - for (key in _ref1) { - if (!__hasProp.call(_ref1, key)) continue; - value = _ref1[key]; - console.log("apple key:", key); - the_id = process_id(key, row.vn); - console.log("the_id:", the_id); - row_line += "<td id=\"" + the_id + "\">foo</td>"; + console.log("*-* the_value:", the_value); + console.log("*-* current_value:", current_value); + if (the_value !== current_value) { + console.log("object:", $(id).html(the_value)); + $(id).html(the_value).effect("highlight"); } - row_line += "</tr>"; - console.log("row line:", row_line); - the_rows += row_line; - } - the_rows += "</tbody>"; - table = header + the_rows; - console.log("table is:", table); - return $("#stats_table").append(table); - }; - process_id = function() { - var processed, value, values, _i, _len; - values = 1 <= arguments.length ? __slice.call(arguments, 0) : []; - - /* Make an id or a class valid javascript by, for example, eliminating spaces */ - processed = ""; - for (_i = 0, _len = values.length; _i < _len; _i++) { - value = values[_i]; - console.log("value:", value); - value = value.replace(" ", "_"); - if (processed.length) { - processed += "-"; + if (title_value) { + return $(id).attr('title', title_value); } - processed += value; - } - return processed; - }; - edit_data_change = function() { - var already_seen, checkbox, checked, name, real_value, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; - already_seen = {}; - sample_sets = { - samples_primary: new Stats([]), - samples_other: new Stats([]), - samples_all: new Stats([]) }; - console.log("at beginning:", sample_sets); - tables = ['samples_primary', 'samples_other']; - for (_i = 0, _len = tables.length; _i < _len; _i++) { - table = tables[_i]; - rows = $("#" + table).find('tr'); - for (_j = 0, _len1 = rows.length; _j < _len1; _j++) { - row = rows[_j]; - name = $(row).find('.edit_sample_sample_name').html(); - name = $.trim(name); - real_value = $(row).find('.edit_sample_value').val(); - console.log("real_value:", real_value); - checkbox = $(row).find(".edit_sample_checkbox"); - checked = $(checkbox).attr('checked'); - if (checked && is_number(real_value) && real_value !== "") { - console.log("in the iffy if"); - real_value = parseFloat(real_value); - sample_sets[table].add_value(real_value); - console.log("checking name of:", name); - if (!(name in already_seen)) { - console.log("haven't seen"); - sample_sets['samples_all'].add_value(real_value); - already_seen[name] = true; + update_stat_values = function(sample_sets) { + var category, i, len, ref, results, row; + ref = ['samples_primary', 'samples_other', 'samples_all']; + results = []; + for (i = 0, len = ref.length; i < len; i++) { + category = ref[i]; + results.push((function() { + var j, len1, results1; + results1 = []; + for (j = 0, len1 = Stat_Table_Rows.length; j < len1; j++) { + row = Stat_Table_Rows[j]; + console.log("Calling change_stats_value"); + results1.push(change_stats_value(sample_sets, category, row.vn, row.digits)); } + return results1; + })()); + } + return results; + }; + make_table = function() { + var header, i, key, len, ref, ref1, row, row_line, table, the_id, the_rows, value; + header = "<thead><tr><th> </th>"; + console.log("js_data.sample_group_types:", js_data.sample_group_types); + ref = js_data.sample_group_types; + for (key in ref) { + if (!hasProp.call(ref, key)) continue; + value = ref[key]; + console.log("aa key:", key); + console.log("aa value:", value); + the_id = process_id("column", key); + header += "<th id=\"" + the_id + "\">" + value + "</th>"; + } + header += "</thead>"; + console.log("windex header is:", header); + the_rows = "<tbody>"; + for (i = 0, len = Stat_Table_Rows.length; i < len; i++) { + row = Stat_Table_Rows[i]; + console.log("rowing"); + row_line = "<tr>"; + if (row.url != null) { + row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>"; + } else { + row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>"; } + console.log("box - js_data.sample_group_types:", js_data.sample_group_types); + ref1 = js_data.sample_group_types; + for (key in ref1) { + if (!hasProp.call(ref1, key)) continue; + value = ref1[key]; + console.log("apple key:", key); + the_id = process_id(key, row.vn); + console.log("the_id:", the_id); + row_line += "<td id=\"" + the_id + "\">foo</td>"; + } + row_line += "</tr>"; + console.log("row line:", row_line); + the_rows += row_line; } - } - console.log("towards end:", sample_sets); - return update_stat_values(sample_sets); - }; - show_hide_outliers = function() { - var label; - console.log("FOOBAR in beginning of show_hide_outliers"); - label = $('#show_hide_outliers').val(); - console.log("lable is:", label); - if (label === "Hide Outliers") { - return $('#show_hide_outliers').val("Show Outliers"); - } else if (label === "Show Outliers") { - console.log("Found Show Outliers"); - $('#show_hide_outliers').val("Hide Outliers"); - return console.log("Should be now Hide Outliers"); - } - }; - on_corr_method_change = function() { - var corr_method; - console.log("in beginning of on_corr_method_change"); - corr_method = $('select[name=corr_method]').val(); - console.log("corr_method is:", corr_method); - $('.correlation_desc').hide(); - $('#' + corr_method + "_r_desc").show().effect("highlight"); - if (corr_method === "lit") { - return $("#corr_sample_method_options").hide(); - } else { - return $("#corr_sample_method_options").show(); - } - }; - $('select[name=corr_method]').change(on_corr_method_change); - create_value_dropdown = function(value) { - return "<option val=" + value + ">" + value + "</option>"; - }; - populate_sample_attributes_values_dropdown = function() { - var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; - console.log("in beginning of psavd"); - $('#attribute_values').empty(); - sample_attributes = {}; - _ref = js_data.attribute_names; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - attribute_info = _ref[key]; - sample_attributes[attribute_info.name] = attribute_info.distinct_values; - } - console.log("[visa] attributes is:", sample_attributes); - selected_attribute = $('#exclude_menu').val().replace("_", " "); - console.log("selected_attribute is:", selected_attribute); - _ref1 = sample_attributes[selected_attribute]; - _results = []; - for (_i = 0, _len = _ref1.length; _i < _len; _i++) { - value = _ref1[_i]; - _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); - } - return _results; - }; - if (js_data.attribute_names.length > 0) { - populate_sample_attributes_values_dropdown(); - } - $('#exclude_menu').change(populate_sample_attributes_values_dropdown); - block_by_attribute_value = function() { - var attribute_name, cell_class, exclude_by_value; - attribute_name = $('#exclude_menu').val(); - exclude_by_value = $('#attribute_values').val(); - cell_class = ".column_name-" + attribute_name; - return $(cell_class).each((function(_this) { - return function(index, element) { - var row; - if ($.trim($(element).text()) === exclude_by_value) { - row = $(element).parent('tr'); - return $(row).find(".trait_value_input").val("x"); + the_rows += "</tbody>"; + table = header + the_rows; + console.log("table is:", table); + return $("#stats_table").append(table); + }; + process_id = function() { + var i, len, processed, value, values; + values = 1 <= arguments.length ? slice.call(arguments, 0) : []; + + /* Make an id or a class valid javascript by, for example, eliminating spaces */ + processed = ""; + for (i = 0, len = values.length; i < len; i++) { + value = values[i]; + console.log("value:", value); + value = value.replace(" ", "_"); + if (processed.length) { + processed += "-"; } + processed += value; + } + return processed; + }; + edit_data_change = function() { + var already_seen, checkbox, checked, i, j, len, len1, name, real_value, row, rows, sample_sets, table, tables; + already_seen = {}; + sample_sets = { + samples_primary: new Stats([]), + samples_other: new Stats([]), + samples_all: new Stats([]) }; - })(this)); - }; - $('#exclude_group').click(block_by_attribute_value); - block_by_index = function() { - var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref, _results; - index_string = $('#remove_samples_field').val(); - index_list = []; - _ref = index_string.split(","); - for (_i = 0, _len = _ref.length; _i < _len; _i++) { - index_set = _ref[_i]; - if (index_set.indexOf('-') !== -1) { - try { - start_index = parseInt(index_set.split("-")[0]); - end_index = parseInt(index_set.split("-")[1]); - for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) { - index_list.push(index); + console.log("at beginning:", sample_sets); + tables = ['samples_primary', 'samples_other']; + for (i = 0, len = tables.length; i < len; i++) { + table = tables[i]; + rows = $("#" + table).find('tr'); + for (j = 0, len1 = rows.length; j < len1; j++) { + row = rows[j]; + name = $(row).find('.edit_sample_sample_name').html(); + name = $.trim(name); + real_value = $(row).find('.edit_sample_value').val(); + console.log("real_value:", real_value); + checkbox = $(row).find(".edit_sample_checkbox"); + checked = $(checkbox).attr('checked'); + if (checked && is_number(real_value) && real_value !== "") { + console.log("in the iffy if"); + real_value = parseFloat(real_value); + sample_sets[table].add_value(real_value); + console.log("checking name of:", name); + if (!(name in already_seen)) { + console.log("haven't seen"); + sample_sets['samples_all'].add_value(real_value); + already_seen[name] = true; + } } - } catch (_error) { - error = _error; - alert("Syntax error"); } - } else { - index = parseInt(index_set); - console.log("index:", index); - index_list.push(index); } - } - console.log("index_list:", index_list); - _results = []; - for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { - index = index_list[_k]; - if ($('#block_group').val() === "primary") { - console.log("block_group:", $('#block_group').val()); - console.log("row:", $('#Primary_' + index.toString())); - _results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x")); - } else if ($('#block_group').val() === "other") { - console.log("block_group:", $('#block_group').val()); - console.log("row:", $('#Other_' + index.toString())); - _results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x")); + console.log("towards end:", sample_sets); + return update_stat_values(sample_sets); + }; + show_hide_outliers = function() { + var label; + console.log("FOOBAR in beginning of show_hide_outliers"); + label = $('#show_hide_outliers').val(); + console.log("lable is:", label); + if (label === "Hide Outliers") { + return $('#show_hide_outliers').val("Show Outliers"); + } else if (label === "Show Outliers") { + console.log("Found Show Outliers"); + $('#show_hide_outliers').val("Hide Outliers"); + return console.log("Should be now Hide Outliers"); + } + }; + on_corr_method_change = function() { + var corr_method; + console.log("in beginning of on_corr_method_change"); + corr_method = $('select[name=corr_method]').val(); + console.log("corr_method is:", corr_method); + $('.correlation_desc').hide(); + $('#' + corr_method + "_r_desc").show().effect("highlight"); + if (corr_method === "lit") { + return $("#corr_sample_method_options").hide(); } else { - _results.push(void 0); + return $("#corr_sample_method_options").show(); + } + }; + $('select[name=corr_method]').change(on_corr_method_change); + create_value_dropdown = function(value) { + return "<option val=" + value + ">" + value + "</option>"; + }; + populate_sample_attributes_values_dropdown = function() { + var attribute_info, i, key, len, ref, ref1, results, sample_attributes, selected_attribute, value; + console.log("in beginning of psavd"); + $('#attribute_values').empty(); + sample_attributes = {}; + ref = js_data.attribute_names; + for (key in ref) { + if (!hasProp.call(ref, key)) continue; + attribute_info = ref[key]; + sample_attributes[attribute_info.name] = attribute_info.distinct_values; } + console.log("[visa] attributes is:", sample_attributes); + selected_attribute = $('#exclude_menu').val().replace("_", " "); + console.log("selected_attribute is:", selected_attribute); + ref1 = sample_attributes[selected_attribute]; + results = []; + for (i = 0, len = ref1.length; i < len; i++) { + value = ref1[i]; + results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + } + return results; + }; + if (js_data.attribute_names.length > 0) { + populate_sample_attributes_values_dropdown(); } - return _results; - }; - $('#block_by_index').click(block_by_index); - hide_no_value = function() { - return $('.value_se').each((function(_this) { - return function(_index, element) { - if ($(element).find('.trait_value_input').val() === 'x') { - return $(element).hide(); - } - }; - })(this)); - }; - $('#hide_no_value').click(hide_no_value); - block_outliers = function() { - return $('.outlier').each((function(_this) { - return function(_index, element) { - return $(element).find('.trait_value_input').val('x'); - }; - })(this)); - }; - $('#block_outliers').click(block_outliers); - reset_samples_table = function() { - return $('.trait_value_input').each((function(_this) { - return function(_index, element) { - console.log("value is:", $(element).val()); - $(element).val($(element).data('value')); - console.log("data-value is:", $(element).data('value')); - return $(element).parents('.value_se').show(); - }; - })(this)); - }; - $('#reset').click(reset_samples_table); - get_sample_table_data = function() { - var other_samples, primary_samples, samples; - samples = {}; - primary_samples = []; - other_samples = []; - $('#sortable1').find('.value_se').each((function(_this) { - return function(_index, element) { - var attribute_info, key, row_data, _ref; - row_data = {}; - row_data.name = $.trim($(element).find('.column_name-Sample').text()); - row_data.value = $(element).find('.edit_sample_value').val(); - if ($(element).find('.edit_sample_se').length !== -1) { - row_data.se = $(element).find('.edit_sample_se').val(); + $('#exclude_menu').change(populate_sample_attributes_values_dropdown); + block_by_attribute_value = function() { + var attribute_name, cell_class, exclude_by_value; + attribute_name = $('#exclude_menu').val(); + exclude_by_value = $('#attribute_values').val(); + cell_class = ".column_name-" + attribute_name; + return $(cell_class).each((function(_this) { + return function(index, element) { + var row; + if ($.trim($(element).text()) === exclude_by_value) { + row = $(element).parent('tr'); + return $(row).find(".trait_value_input").val("x"); + } + }; + })(this)); + }; + $('#exclude_group').click(block_by_attribute_value); + block_by_index = function() { + var end_index, error, i, index, index_list, index_set, index_string, j, k, len, len1, ref, ref1, ref2, results, start_index; + index_string = $('#remove_samples_field').val(); + index_list = []; + ref = index_string.split(","); + for (i = 0, len = ref.length; i < len; i++) { + index_set = ref[i]; + if (index_set.indexOf('-') !== -1) { + try { + start_index = parseInt(index_set.split("-")[0]); + end_index = parseInt(index_set.split("-")[1]); + for (index = j = ref1 = start_index, ref2 = end_index; ref1 <= ref2 ? j <= ref2 : j >= ref2; index = ref1 <= ref2 ? ++j : --j) { + index_list.push(index); + } + } catch (_error) { + error = _error; + alert("Syntax error"); + } + } else { + index = parseInt(index_set); + console.log("index:", index); + index_list.push(index); } - _ref = js_data.attribute_names; - for (key in _ref) { - if (!__hasProp.call(_ref, key)) continue; - attribute_info = _ref[key]; - row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_")).text()); + } + console.log("index_list:", index_list); + results = []; + for (k = 0, len1 = index_list.length; k < len1; k++) { + index = index_list[k]; + if ($('#block_group').val() === "primary") { + console.log("block_group:", $('#block_group').val()); + console.log("row:", $('#Primary_' + index.toString())); + results.push($('#Primary_' + index.toString()).find('.trait_value_input').val("x")); + } else if ($('#block_group').val() === "other") { + console.log("block_group:", $('#block_group').val()); + console.log("row:", $('#Other_' + index.toString())); + results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x")); + } else { + results.push(void 0); } - console.log("row_data is:", row_data); - return primary_samples.push(row_data); - }; - })(this)); - console.log("primary_samples is:", primary_samples); - samples.primary_samples = primary_samples; - samples.other_samples = other_samples; - return samples; - }; - export_sample_table_data = function() { - var format, json_sample_data, sample_data; - sample_data = get_sample_table_data(); - console.log("sample_data is:", sample_data); - json_sample_data = JSON.stringify(sample_data); - console.log("json_sample_data is:", json_sample_data); - $('input[name=export_data]').val(json_sample_data); - console.log("export_data is", $('input[name=export_data]').val()); - format = $('#export_format').val(); - if (format === "excel") { - $('#trait_data_form').attr('action', '/export_trait_excel'); - } else { - $('#trait_data_form').attr('action', '/export_trait_csv'); - } - console.log("action is:", $('#trait_data_form').attr('action')); - return $('#trait_data_form').submit(); - }; - $('#export').click(export_sample_table_data); - console.log("before registering block_outliers"); - $('#block_outliers').click(block_outliers); - console.log("after registering block_outliers"); - _.mixin(_.str.exports()); - $('#edit_sample_lists').change(edit_data_change); - console.log("loaded"); - make_table(); - edit_data_change(); - return console.log("end"); -}); + } + return results; + }; + $('#block_by_index').click(block_by_index); + hide_no_value = function() { + return $('.value_se').each((function(_this) { + return function(_index, element) { + if ($(element).find('.trait_value_input').val() === 'x') { + return $(element).hide(); + } + }; + })(this)); + }; + $('#hide_no_value').click(hide_no_value); + block_outliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait_value_input').val('x'); + }; + })(this)); + }; + $('#block_outliers').click(block_outliers); + reset_samples_table = function() { + return $('.trait_value_input').each((function(_this) { + return function(_index, element) { + console.log("value is:", $(element).val()); + $(element).val($(element).data('value')); + console.log("data-value is:", $(element).data('value')); + return $(element).parents('.value_se').show(); + }; + })(this)); + }; + $('#reset').click(reset_samples_table); + get_sample_table_data = function(table_name) { + var samples; + samples = []; + $('#' + table_name).find('.value_se').each((function(_this) { + return function(_index, element) { + var attribute_info, key, ref, row_data; + row_data = {}; + row_data.name = $.trim($(element).find('.column_name-Sample').text()); + row_data.value = $(element).find('.edit_sample_value').val(); + if ($(element).find('.edit_sample_se').length !== -1) { + row_data.se = $(element).find('.edit_sample_se').val(); + } + ref = js_data.attribute_names; + for (key in ref) { + if (!hasProp.call(ref, key)) continue; + attribute_info = ref[key]; + row_data[attribute_info.name] = $.trim($(element).find('.column_name-' + attribute_info.name.replace(" ", "_")).text()); + } + console.log("row_data is:", row_data); + return samples.push(row_data); + }; + })(this)); + return samples; + }; + export_sample_table_data = function() { + var format, json_sample_data, sample_data; + sample_data = {}; + sample_data.primary_samples = get_sample_table_data('samples_primary'); + sample_data.other_samples = get_sample_table_data('samples_other'); + console.log("sample_data is:", sample_data); + json_sample_data = JSON.stringify(sample_data); + console.log("json_sample_data is:", json_sample_data); + $('input[name=export_data]').val(json_sample_data); + console.log("export_data is", $('input[name=export_data]').val()); + format = $('#export_format').val(); + if (format === "excel") { + $('#trait_data_form').attr('action', '/export_trait_excel'); + } else { + $('#trait_data_form').attr('action', '/export_trait_csv'); + } + console.log("action is:", $('#trait_data_form').attr('action')); + return $('#trait_data_form').submit(); + }; + $('#export').click(export_sample_table_data); + console.log("before registering block_outliers"); + $('#block_outliers').click(block_outliers); + console.log("after registering block_outliers"); + _.mixin(_.str.exports()); + $('#edit_sample_lists').change(edit_data_change); + console.log("loaded"); + make_table(); + edit_data_change(); + return console.log("end"); + }); + +}).call(this); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 39004f07..79c1c967 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -5,6 +5,7 @@ import sys print("sys.path is:", sys.path) import csv +import xlsxwriter import StringIO # Todo: Use cStringIO? import gc @@ -186,7 +187,7 @@ def environments(): doc = docs.Docs("environments") return render_template("docs.html", **doc.__dict__) -@app.route('/export_trait_csv', methods=('POST',)) +@app.route('/export_trait_excel', methods=('POST',)) def export_trait_excel(): """Excel file consisting of the sample data from the trait data and analysis page""" print("In export_trait_excel") @@ -196,15 +197,18 @@ def export_trait_excel(): print("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data))) buff = StringIO.StringIO() - writer = csv.writer(buff) - for row in sample_data: - writer.writerow(row) - csv_data = buff.getvalue() + workbook = xlsxwriter.Workbook(buff, {'in_memory': True}) + worksheet = workbook.add_worksheet() + for i, row in enumerate(sample_data): + worksheet.write(i, 0, row[0]) + worksheet.write(i, 1, row[1]) + workbook.close() + excel_data = buff.getvalue() buff.close() - return Response(csv_data, - mimetype='text/csv', - headers={"Content-Disposition":"attachment;filename=test.csv"}) + return Response(excel_data, + mimetype='application/vnd.ms-excel', + headers={"Content-Disposition":"attachment;filename=test.xlsx"}) @app.route('/export_trait_csv', methods=('POST',)) def export_trait_csv(): |