+
@@ -66,9 +66,42 @@
{% endblock %}
+{% block css %}
+
+{% endblock %}
+
{% block js %}
+
+
+
{% include "new_security/_scripts.html" %}
{% endblock %}
--
cgit v1.2.3
From 92a47463b73c25a9a5cffc6caaea696d628cca3b Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Sat, 18 Apr 2015 18:43:54 +0300
Subject: allow for attribute table to not exist
---
wqflask/wqflask/show_trait/SampleList.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
(limited to 'wqflask')
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
--
cgit v1.2.3
From 53d8a8bff6418a203e3d2565aaeca4fcb5dc0752 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Thu, 7 May 2015 17:45:07 +0300
Subject: fix CSV export of trait data
---
wqflask/wqflask/show_trait/show_trait.py | 1 +
.../static/new/javascript/show_trait.coffee | 17 +-
.../wqflask/static/new/javascript/show_trait.js | 888 ++++++++++-----------
wqflask/wqflask/views.py | 3 +-
4 files changed, 454 insertions(+), 455 deletions(-)
(limited to 'wqflask')
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('
');
- 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('
');
- 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('
');
+ 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('
');
+ 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 = "
| | ";
- 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 += "" + value + " | ";
- }
- header += "
|---|
";
- console.log("windex header is:", header);
- the_rows = "
";
- for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
- row = Stat_Table_Rows[_i];
- console.log("rowing");
- row_line = "";
- if (row.url != null) {
- row_line += "| " + row.pretty + " | ";
+ 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 += "" + row.pretty + " | ";
+ 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 += "foo | ";
+ 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 += "
";
- console.log("row line:", row_line);
- the_rows += row_line;
- }
- the_rows += "";
- 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 = "
| | ";
+ 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 += "" + value + " | ";
+ }
+ header += "
|---|
";
+ console.log("windex header is:", header);
+ the_rows = "
";
+ for (i = 0, len = Stat_Table_Rows.length; i < len; i++) {
+ row = Stat_Table_Rows[i];
+ console.log("rowing");
+ row_line = "";
+ if (row.url != null) {
+ row_line += "| " + row.pretty + " | ";
+ } else {
+ row_line += "" + row.pretty + " | ";
}
+ 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 += "foo | ";
+ }
+ row_line += "
";
+ 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 "";
- };
- 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 += "";
+ 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 "
";
+ };
+ 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..abd8f05b 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -186,7 +186,8 @@ def environments():
doc = docs.Docs("environments")
return render_template("docs.html", **doc.__dict__)
-@app.route('/export_trait_csv', methods=('POST',))
+# TODO
+@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")
--
cgit v1.2.3
From cd9e120fa77a68f570d615a17071928d0c91aac2 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Thu, 7 May 2015 18:05:57 +0300
Subject: Excel export of trait data
---
misc/requirements.txt | 1 +
wqflask/wqflask/views.py | 19 +++++++++++--------
2 files changed, 12 insertions(+), 8 deletions(-)
(limited to 'wqflask')
diff --git a/misc/requirements.txt b/misc/requirements.txt
index ec02a2c2..3487aa09 100644
--- a/misc/requirements.txt
+++ b/misc/requirements.txt
@@ -32,3 +32,4 @@ scipy==0.11.0
simplejson==3.0.7
wsgiref==0.1.2
yolk==0.4.3
+XlsxWriter=0.7.2
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index abd8f05b..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 +187,6 @@ def environments():
doc = docs.Docs("environments")
return render_template("docs.html", **doc.__dict__)
-# TODO
@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"""
@@ -197,15 +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():
--
cgit v1.2.3
From bf860dd3c6e2c8d32e9d40ae129e33613151fab5 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Fri, 8 May 2015 12:59:38 +0300
Subject: Fix #29
The number of bins was set to 20 for all datasets.
Changed the number to be sqrt(#samples) as suggested on Wikipedia.
---
.../wqflask/static/new/javascript/histogram.coffee | 5 +-
wqflask/wqflask/static/new/javascript/histogram.js | 223 +++++++++++----------
2 files changed, 117 insertions(+), 111 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 98f89ac6..7adb53f9 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -53,8 +53,9 @@ class Histogram
get_histogram_data: () ->
console.log("sample_vals:", @sample_vals)
+ n_bins = sqrt(@sample_vals.length)
@histogram_data = d3.layout.histogram()
- .bins(@x_scale.ticks(20))(@sample_vals)
+ .bins(@x_scale.ticks(n_bins))(@sample_vals)
console.log("histogram_data:", @histogram_data[0])
create_y_scale: () ->
@@ -131,4 +132,4 @@ class Histogram
return @format_count(d.y)
)
-root.Histogram = Histogram
\ No newline at end of file
+root.Histogram = Histogram
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 561a3068..3ab5eefa 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -1,124 +1,129 @@
-// Generated by CoffeeScript 1.8.0
-var Histogram, root;
+// Generated by CoffeeScript 1.9.2
+(function() {
+ var Histogram, root;
-root = typeof exports !== "undefined" && exports !== null ? exports : this;
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
-Histogram = (function() {
- function Histogram(sample_list, sample_group) {
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.sort_by = "name";
- this.format_count = d3.format(",.0f");
- this.get_sample_vals();
- this.margin = {
- top: 10,
- right: 30,
- bottom: 30,
- left: 30
- };
- this.plot_width = 960 - this.margin.left - this.margin.right;
- this.plot_height = 500 - this.margin.top - this.margin.bottom;
- this.x_buffer = this.plot_width / 20;
- this.y_buffer = this.plot_height / 20;
- this.y_min = d3.min(this.sample_vals);
- this.y_max = d3.max(this.sample_vals) * 1.1;
- this.plot_height -= this.y_buffer;
- this.create_x_scale();
- this.get_histogram_data();
- this.create_y_scale();
- this.svg = this.create_svg();
- this.create_graph();
- }
+ Histogram = (function() {
+ function Histogram(sample_list, sample_group) {
+ this.sample_list = sample_list;
+ this.sample_group = sample_group;
+ this.sort_by = "name";
+ this.format_count = d3.format(",.0f");
+ this.get_sample_vals();
+ this.margin = {
+ top: 10,
+ right: 30,
+ bottom: 30,
+ left: 30
+ };
+ this.plot_width = 960 - this.margin.left - this.margin.right;
+ this.plot_height = 500 - this.margin.top - this.margin.bottom;
+ this.x_buffer = this.plot_width / 20;
+ this.y_buffer = this.plot_height / 20;
+ this.y_min = d3.min(this.sample_vals);
+ this.y_max = d3.max(this.sample_vals) * 1.1;
+ this.plot_height -= this.y_buffer;
+ this.create_x_scale();
+ this.get_histogram_data();
+ this.create_y_scale();
+ this.svg = this.create_svg();
+ this.create_graph();
+ }
- Histogram.prototype.get_sample_vals = function() {
- var sample;
- return this.sample_vals = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sample_list;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- if (sample.value !== null) {
- _results.push(sample.value);
+ Histogram.prototype.get_sample_vals = function() {
+ var sample;
+ return this.sample_vals = (function() {
+ var i, len, ref, results;
+ ref = this.sample_list;
+ results = [];
+ for (i = 0, len = ref.length; i < len; i++) {
+ sample = ref[i];
+ if (sample.value !== null) {
+ results.push(sample.value);
+ }
}
- }
- return _results;
- }).call(this);
- };
+ return results;
+ }).call(this);
+ };
- Histogram.prototype.create_svg = function() {
- var svg;
- svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
- return svg;
- };
+ Histogram.prototype.create_svg = function() {
+ var svg;
+ svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")");
+ return svg;
+ };
+
+ Histogram.prototype.create_x_scale = function() {
+ var x0;
+ console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
+ x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+ return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
+ };
- Histogram.prototype.create_x_scale = function() {
- var x0;
- console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
- x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
- return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
- };
+ Histogram.prototype.get_histogram_data = function() {
+ var n_bins;
+ console.log("sample_vals:", this.sample_vals);
+ n_bins = Math.sqrt(this.sample_vals.length);
+ this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals);
+ return console.log("histogram_data:", this.histogram_data[0]);
+ };
- Histogram.prototype.get_histogram_data = function() {
- console.log("sample_vals:", this.sample_vals);
- this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
- return console.log("histogram_data:", this.histogram_data[0]);
- };
+ Histogram.prototype.create_y_scale = function() {
+ return this.y_scale = d3.scale.linear().domain([
+ 0, d3.max(this.histogram_data, (function(_this) {
+ return function(d) {
+ return d.y;
+ };
+ })(this))
+ ]).range([this.plot_height, 0]);
+ };
- Histogram.prototype.create_y_scale = function() {
- return this.y_scale = d3.scale.linear().domain([
- 0, d3.max(this.histogram_data, (function(_this) {
- return function(d) {
- return d.y;
- };
- })(this))
- ]).range([this.plot_height, 0]);
- };
+ Histogram.prototype.create_graph = function() {
+ this.add_x_axis();
+ this.add_y_axis();
+ return this.add_bars();
+ };
- Histogram.prototype.create_graph = function() {
- this.add_x_axis();
- this.add_y_axis();
- return this.add_bars();
- };
+ Histogram.prototype.add_x_axis = function() {
+ var x_axis;
+ x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
+ return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
+ };
- Histogram.prototype.add_x_axis = function() {
- var x_axis;
- x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom");
- return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
- };
+ Histogram.prototype.add_y_axis = function() {
+ var yAxis;
+ yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+ return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
+ };
- Histogram.prototype.add_y_axis = function() {
- var yAxis;
- yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
- return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
- };
+ Histogram.prototype.add_bars = function() {
+ var bar;
+ console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
+ bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
+ return function(d) {
+ return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
+ };
+ })(this));
+ bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
+ return function(d) {
+ return _this.plot_height - _this.y_scale(d.y);
+ };
+ })(this));
+ return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
+ return function(d) {
+ var bar_height;
+ bar_height = _this.plot_height - _this.y_scale(d.y);
+ if (bar_height > 20) {
+ return _this.format_count(d.y);
+ }
+ };
+ })(this));
+ };
- Histogram.prototype.add_bars = function() {
- var bar;
- console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
- bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
- return function(d) {
- return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
- };
- })(this));
- bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
- return function(d) {
- return _this.plot_height - _this.y_scale(d.y);
- };
- })(this));
- return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
- return function(d) {
- var bar_height;
- bar_height = _this.plot_height - _this.y_scale(d.y);
- if (bar_height > 20) {
- return _this.format_count(d.y);
- }
- };
- })(this));
- };
+ return Histogram;
- return Histogram;
+ })();
-})();
+ root.Histogram = Histogram;
-root.Histogram = Histogram;
+}).call(this);
--
cgit v1.2.3
From 22903fc679e4dbbd820b2849703d6f41950483b3 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Fri, 8 May 2015 13:37:09 +0300
Subject: fix
---
wqflask/wqflask/static/new/javascript/histogram.coffee | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 7adb53f9..879c0fb8 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -53,7 +53,7 @@ class Histogram
get_histogram_data: () ->
console.log("sample_vals:", @sample_vals)
- n_bins = sqrt(@sample_vals.length)
+ n_bins = Math.sqrt(@sample_vals.length)
@histogram_data = d3.layout.histogram()
.bins(@x_scale.ticks(n_bins))(@sample_vals)
console.log("histogram_data:", @histogram_data[0])
--
cgit v1.2.3
From 4e6c08c51dbd2c4ec3cdf92e10f24c3987675bf8 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Fri, 8 May 2015 14:15:50 +0300
Subject: fix histogram bin width
It was calculated wrongly when bins began from a non-zero value
---
.../wqflask/static/new/javascript/histogram.coffee | 22 +++++++++-----
wqflask/wqflask/static/new/javascript/histogram.js | 35 ++++++++++++----------
2 files changed, 34 insertions(+), 23 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 879c0fb8..b27a389e 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -4,7 +4,6 @@ class Histogram
constructor: (@sample_list, @sample_group) ->
@sort_by = "name"
@format_count = d3.format(",.0f") #a formatter for counts
- @get_sample_vals()
@margin = {top: 10, right: 30, bottom: 30, left: 30}
@plot_width = 960 - @margin.left - @margin.right
@@ -12,21 +11,25 @@ class Histogram
@x_buffer = @plot_width/20
@y_buffer = @plot_height/20
+ @plot_height -= @y_buffer
+
+ @redraw(@sample_list)
+ redraw: (sample_list) ->
+ @get_sample_vals(sample_list)
@y_min = d3.min(@sample_vals)
@y_max = d3.max(@sample_vals) * 1.1
-
- @plot_height -= @y_buffer
+
@create_x_scale()
@get_histogram_data()
@create_y_scale()
+ $("#histogram").empty()
@svg = @create_svg()
-
@create_graph()
- get_sample_vals: () ->
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
+ get_sample_vals: (sample_list) ->
+ @sample_vals = (sample.value for sample in sample_list when sample.value != null)
create_svg: () ->
svg = d3.select("#histogram")
@@ -113,17 +116,20 @@ class Histogram
.attr("class", "bar")
.attr("transform", (d) =>
return "translate(" + @x_scale(d.x) + "," + @y_scale(d.y) + ")")
+
+ rect_width = @x_scale(@histogram_data[0].x + @histogram_data[0].dx) -
+ @x_scale(@histogram_data[0].x)
bar.append("rect")
.attr("x", 1)
- .attr("width", @x_scale(@histogram_data[0].x + @histogram_data[0].dx) - 1)
+ .attr("width", rect_width - 1)
.attr("height", (d) =>
return @plot_height - @y_scale(d.y)
)
bar.append("text")
.attr("dy", ".75em")
.attr("y", 6)
- .attr("x", @x_scale(@histogram_data[0].dx)/2)
+ .attr("x", rect_width / 2)
.attr("text-anchor", "middle")
.style("fill", "#fff")
.text((d) =>
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 3ab5eefa..94144661 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -5,12 +5,11 @@
root = typeof exports !== "undefined" && exports !== null ? exports : this;
Histogram = (function() {
- function Histogram(sample_list, sample_group) {
- this.sample_list = sample_list;
+ function Histogram(sample_list1, sample_group) {
+ this.sample_list = sample_list1;
this.sample_group = sample_group;
this.sort_by = "name";
this.format_count = d3.format(",.0f");
- this.get_sample_vals();
this.margin = {
top: 10,
right: 30,
@@ -21,30 +20,35 @@
this.plot_height = 500 - this.margin.top - this.margin.bottom;
this.x_buffer = this.plot_width / 20;
this.y_buffer = this.plot_height / 20;
+ this.plot_height -= this.y_buffer;
+ this.redraw(this.sample_list);
+ }
+
+ Histogram.prototype.redraw = function(sample_list) {
+ this.get_sample_vals(sample_list);
this.y_min = d3.min(this.sample_vals);
this.y_max = d3.max(this.sample_vals) * 1.1;
- this.plot_height -= this.y_buffer;
this.create_x_scale();
this.get_histogram_data();
this.create_y_scale();
+ $("#histogram").empty();
this.svg = this.create_svg();
- this.create_graph();
- }
+ return this.create_graph();
+ };
- Histogram.prototype.get_sample_vals = function() {
+ Histogram.prototype.get_sample_vals = function(sample_list) {
var sample;
return this.sample_vals = (function() {
- var i, len, ref, results;
- ref = this.sample_list;
+ var i, len, results;
results = [];
- for (i = 0, len = ref.length; i < len; i++) {
- sample = ref[i];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
if (sample.value !== null) {
results.push(sample.value);
}
}
return results;
- }).call(this);
+ })();
};
Histogram.prototype.create_svg = function() {
@@ -97,19 +101,20 @@
};
Histogram.prototype.add_bars = function() {
- var bar;
+ var bar, rect_width;
console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) {
return function(d) {
return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
};
})(this));
- bar.append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - 1).attr("height", (function(_this) {
+ rect_width = this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - this.x_scale(this.histogram_data[0].x);
+ bar.append("rect").attr("x", 1).attr("width", rect_width - 1).attr("height", (function(_this) {
return function(d) {
return _this.plot_height - _this.y_scale(d.y);
};
})(this));
- return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
+ return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", rect_width / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) {
return function(d) {
var bar_height;
bar_height = _this.plot_height - _this.y_scale(d.y);
--
cgit v1.2.3
From 3f3469d007c3e5ff229425911b28f24211c84301 Mon Sep 17 00:00:00 2001
From: Artem Tarasov
Date: Fri, 8 May 2015 14:42:19 +0300
Subject: updating histogram on values' change (#28)
---
wqflask/wqflask/static/new/javascript/histogram.coffee | 6 +++---
wqflask/wqflask/static/new/javascript/histogram.js | 7 ++++---
wqflask/wqflask/static/new/javascript/show_trait.coffee | 1 +
wqflask/wqflask/static/new/javascript/show_trait.js | 1 +
4 files changed, 9 insertions(+), 6 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index b27a389e..68d9b5a2 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -13,10 +13,10 @@ class Histogram
@y_buffer = @plot_height/20
@plot_height -= @y_buffer
- @redraw(@sample_list)
+ @get_sample_vals(@sample_list)
+ @redraw(@sample_vals)
- redraw: (sample_list) ->
- @get_sample_vals(sample_list)
+ redraw: (@sample_vals) ->
@y_min = d3.min(@sample_vals)
@y_max = d3.max(@sample_vals) * 1.1
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 94144661..d872a3ba 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -21,11 +21,12 @@
this.x_buffer = this.plot_width / 20;
this.y_buffer = this.plot_height / 20;
this.plot_height -= this.y_buffer;
- this.redraw(this.sample_list);
+ this.get_sample_vals(this.sample_list);
+ this.redraw(this.sample_vals);
}
- Histogram.prototype.redraw = function(sample_list) {
- this.get_sample_vals(sample_list);
+ Histogram.prototype.redraw = function(sample_vals) {
+ this.sample_vals = sample_vals;
this.y_min = d3.min(this.sample_vals);
this.y_max = d3.max(this.sample_vals) * 1.1;
this.create_x_scale();
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index ee57831f..1d3123ba 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -238,6 +238,7 @@ $ ->
sample_sets['samples_all'].add_value(real_value)
already_seen[name] = true
console.log("towards end:", sample_sets)
+ root.histogram.redraw(sample_sets['samples_primary'].the_values)
update_stat_values(sample_sets)
show_hide_outliers = ->
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c2dc07ee..9323862a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -265,6 +265,7 @@
}
}
console.log("towards end:", sample_sets);
+ root.histogram.redraw(sample_sets['samples_primary'].the_values);
return update_stat_values(sample_sets);
};
show_hide_outliers = function() {
--
cgit v1.2.3