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lomereiter/range_fixes.patch

Created July 17, 2015 18:12
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range_fixes.patch
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a572a60..b152357 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -555,12 +555,22 @@ class DataSet(object):
# """ % (query_args))
try:
- self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ if self.type != "ProbeSet":
+ self.datascale = None
+ self.id, self.name, self.fullname, self.shortname = g.db.execute("""
SELECT Id, Name, FullName, ShortName
FROM %s
WHERE public > %s AND
(Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args)).fetchone()
+ """ % (query_args)).fetchone()
+ else:
+ self.id, self.name, self.fullname, self.shortname, self.datascale = g.db.execute("""
+ SELECT Id, Name, FullName, ShortName, DataScale
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args)).fetchone()
+
except TypeError:
print("Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 0247226..05f99a9 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -146,7 +146,9 @@ class ShowTrait(object):
js_data = dict(sample_group_types = self.sample_group_types,
sample_lists = sample_lists,
attribute_names = self.sample_groups[0].attributes,
- temp_uuid = self.temp_uuid)
+ temp_uuid = self.temp_uuid,
+ dataset_type = self.dataset.type,
+ datascale = self.dataset.datascale)
self.js_data = js_data
def get_mapping_methods(self):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 91aa15b..592158c 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -6,7 +6,7 @@ console.log("start_b")
is_number = (o) ->
return ! isNaN (o-0) && o != null
-Stat_Table_Rows = [
+Common_Stat_Table_Rows = [
{
vn: "n_of_samples"
pretty: "N of Samples"
@@ -41,10 +41,13 @@ Stat_Table_Rows = [
vn: "max"
pretty: "Maximum"
digits: 2
- },
+ }
+ ]
+
+Extra_Stat_Table_Rows = [
{
vn: "range"
- pretty: "Range (log2)"
+ pretty: "Range" + (if js_data.datascale == "linear" then "" else " (log2)")
digits: 2
},
{
@@ -62,6 +65,12 @@ Stat_Table_Rows = [
$ ->
+ stat_table_rows = ->
+ rows = Common_Stat_Table_Rows
+ if js_data.dataset_type == "ProbeSet" and js_data.datascale != "z_score"
+ rows = rows.concat(Extra_Stat_Table_Rows)
+ rows
+
add = ->
trait = $("input[name=trait_hmac]").val()
console.log("trait is:", trait)
@@ -136,7 +145,7 @@ $ ->
update_stat_values = (sample_sets)->
show_effects = $(".tab-pane.active").attr("id") == "stats_tab"
for category in ['samples_primary', 'samples_other', 'samples_all']
- for row in Stat_Table_Rows
+ for row in stat_table_rows()
console.log("Calling change_stats_value")
change_stats_value(sample_sets, category, row.vn, row.digits, show_effects)
@@ -152,7 +161,13 @@ $ ->
make_table = ->
header = "<thead><tr><th>&nbsp;</th>"
console.log("js_data.sample_group_types:", js_data.sample_group_types)
- for own key, value of js_data.sample_group_types
+ non_empty_group_types = {}
+ if js_data.sample_lists.length == 1
+ non_empty_group_types['samples_all'] = js_data.sample_group_types['samples_all']
+ else
+ non_empty_group_types = js_data.sample_group_types
+ console.log("non-empty sample_group_types:", non_empty_group_types)
+ for own key, value of non_empty_group_types
console.log("aa key:", key)
console.log("aa value:", value)
the_id = process_id("column", key)
@@ -163,15 +178,15 @@ $ ->
#console.log("rows are:", rows)
the_rows = "<tbody>"
#console.log("length of rows:", rows.length)
- for row in Stat_Table_Rows
+ for row in stat_table_rows()
console.log("rowing")
row_line = """<tr>"""
if row.url?
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)
- for own key, value of js_data.sample_group_types
+ console.log("box - sample_group_types:", non_empty_group_types)
+ for own key, value of non_empty_group_types
console.log("apple key:", key)
the_id = process_id(key, row.vn)
console.log("the_id:", the_id)
@@ -199,9 +214,9 @@ $ ->
edit_data_change = ->
already_seen = {}
sample_sets =
- samples_primary: new Stats([])
- samples_other: new Stats([])
- samples_all: new Stats([])
+ samples_primary: new Stats([], js_data.datascale)
+ samples_other: new Stats([], js_data.datascale)
+ samples_all: new Stats([], js_data.datascale)
root.selected_samples = # maps: sample name -> value
samples_primary: {}
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 302d5ec..9563d1c 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.8.0
+// Generated by CoffeeScript 1.9.2
(function() {
- var Stat_Table_Rows, is_number,
- __hasProp = {}.hasOwnProperty,
- __slice = [].slice;
+ var Common_Stat_Table_Rows, Extra_Stat_Table_Rows, is_number,
+ hasProp = {}.hasOwnProperty,
+ slice = [].slice;
console.log("start_b");
@@ -10,7 +10,7 @@
return !isNaN((o - 0) && o !== null);
};
- Stat_Table_Rows = [
+ Common_Stat_Table_Rows = [
{
vn: "n_of_samples",
pretty: "N of Samples",
@@ -39,9 +39,13 @@
vn: "max",
pretty: "Maximum",
digits: 2
- }, {
+ }
+ ];
+
+ Extra_Stat_Table_Rows = [
+ {
vn: "range",
- pretty: "Range (log2)",
+ pretty: "Range" + (js_data.datascale === "linear" ? "" : " (log2)"),
digits: 2
}, {
vn: "range_fold",
@@ -56,7 +60,15 @@
];
$(function() {
- var add, 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, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
+ var add, 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, redraw_bar_chart, redraw_histogram, redraw_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stat_table_rows, stats_mdp_change, update_stat_values;
+ stat_table_rows = function() {
+ var rows;
+ rows = Common_Stat_Table_Rows;
+ if (js_data.dataset_type === "ProbeSet" && js_data.datascale !== "z_score") {
+ rows = rows.concat(Extra_Stat_Table_Rows);
+ }
+ return rows;
+ };
add = function() {
var trait;
trait = $("input[name=trait_hmac]").val();
@@ -91,12 +103,12 @@
})(this));
};
hide_tabs = function(start) {
- var x, _i, _results;
- _results = [];
- for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) {
- _results.push($("#stats_tabs" + x).hide());
+ 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;
+ return results;
};
stats_mdp_change = function() {
var selected;
@@ -133,36 +145,37 @@
}
};
update_stat_values = function(sample_sets) {
- var category, row, show_effects, _i, _len, _ref, _results;
+ var category, i, len, ref, results, row, show_effects;
show_effects = $(".tab-pane.active").attr("id") === "stats_tab";
- _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];
+ 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, ref1, results1;
+ ref1 = stat_table_rows();
+ results1 = [];
+ for (j = 0, len1 = ref1.length; j < len1; j++) {
+ row = ref1[j];
console.log("Calling change_stats_value");
- _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects));
+ results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects));
}
- return _results1;
+ return results1;
})());
}
- return _results;
+ return results;
};
redraw_histogram = function() {
var x;
return root.histogram.redraw((function() {
- var _i, _len, _ref, _results;
- _ref = _.values(root.selected_samples[root.histogram_group]);
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- x = _ref[_i];
- _results.push(x.value);
+ var i, len, ref, results;
+ ref = _.values(root.selected_samples[root.histogram_group]);
+ results = [];
+ for (i = 0, len = ref.length; i < len; i++) {
+ x = ref[i];
+ results.push(x.value);
}
- return _results;
+ return results;
})());
};
redraw_bar_chart = function() {
@@ -172,13 +185,19 @@
return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group);
};
make_table = function() {
- var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
+ var header, i, key, len, non_empty_group_types, ref, row, row_line, table, the_id, the_rows, value;
header = "<thead><tr><th>&nbsp;</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];
+ non_empty_group_types = {};
+ if (js_data.sample_lists.length === 1) {
+ non_empty_group_types['samples_all'] = js_data.sample_group_types['samples_all'];
+ } else {
+ non_empty_group_types = js_data.sample_group_types;
+ }
+ console.log("non-empty sample_group_types:", non_empty_group_types);
+ for (key in non_empty_group_types) {
+ if (!hasProp.call(non_empty_group_types, key)) continue;
+ value = non_empty_group_types[key];
console.log("aa key:", key);
console.log("aa value:", value);
the_id = process_id("column", key);
@@ -187,8 +206,9 @@
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];
+ ref = stat_table_rows();
+ for (i = 0, len = ref.length; i < len; i++) {
+ row = ref[i];
console.log("rowing");
row_line = "<tr>";
if (row.url != null) {
@@ -196,11 +216,10 @@
} 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("box - sample_group_types:", non_empty_group_types);
+ for (key in non_empty_group_types) {
+ if (!hasProp.call(non_empty_group_types, key)) continue;
+ value = non_empty_group_types[key];
console.log("apple key:", key);
the_id = process_id(key, row.vn);
console.log("the_id:", the_id);
@@ -216,13 +235,13 @@
return $("#stats_table").append(table);
};
process_id = function() {
- var processed, value, values, _i, _len;
- values = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
+ 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];
+ for (i = 0, len = values.length; i < len; i++) {
+ value = values[i];
console.log("value:", value);
value = value.replace(" ", "_");
if (processed.length) {
@@ -233,12 +252,12 @@
return processed;
};
edit_data_change = function() {
- var already_seen, checkbox, checked, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
+ var already_seen, checkbox, checked, i, j, len, len1, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables;
already_seen = {};
sample_sets = {
- samples_primary: new Stats([]),
- samples_other: new Stats([]),
- samples_all: new Stats([])
+ samples_primary: new Stats([], js_data.datascale),
+ samples_other: new Stats([], js_data.datascale),
+ samples_all: new Stats([], js_data.datascale)
};
root.selected_samples = {
samples_primary: {},
@@ -247,11 +266,11 @@
};
console.log("at beginning:", sample_sets);
tables = ['samples_primary', 'samples_other'];
- for (_i = 0, _len = tables.length; _i < _len; _i++) {
- table = tables[_i];
+ 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];
+ 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();
@@ -319,26 +338,26 @@
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;
+ 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];
+ 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($('#attribute_values')));
+ ref1 = sample_attributes[selected_attribute];
+ results = [];
+ for (i = 0, len = ref1.length; i < len; i++) {
+ value = ref1[i];
+ results.push($(create_value_dropdown(value)).appendTo($('#attribute_values')));
}
- return _results;
+ return results;
};
if (js_data.attribute_names.length > 0) {
populate_sample_attributes_values_dropdown();
@@ -361,17 +380,17 @@
};
$('#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;
+ var end_index, error, i, index, index_list, index_set, index_string, j, k, len, len1, ref, ref1, ref2, results, start_index;
index_string = $('#remove_samples_field').val();
index_list = [];
- _ref = index_string.split(",");
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- index_set = _ref[_i];
+ ref = index_string.split(",");
+ for (i = 0, len = ref.length; i < len; i++) {
+ index_set = ref[i];
if (index_set.indexOf('-') !== -1) {
try {
start_index = parseInt(index_set.split("-")[0]);
end_index = parseInt(index_set.split("-")[1]);
- for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
+ for (index = j = ref1 = start_index, ref2 = end_index; ref1 <= ref2 ? j <= ref2 : j >= ref2; index = ref1 <= ref2 ? ++j : --j) {
index_list.push(index);
}
} catch (_error) {
@@ -385,22 +404,22 @@
}
}
console.log("index_list:", index_list);
- _results = [];
- for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
- index = index_list[_k];
+ results = [];
+ for (k = 0, len1 = index_list.length; k < len1; k++) {
+ index = index_list[k];
if ($('#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"));
+ 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"));
+ results.push($('#Other_' + index.toString()).find('.trait_value_input').val("x"));
} else {
- _results.push(void 0);
+ results.push(void 0);
}
}
- return _results;
+ return results;
};
$('#block_by_index').click(block_by_index);
hide_no_value = function() {
@@ -437,17 +456,17 @@
samples = [];
$('#' + table_name).find('.value_se').each((function(_this) {
return function(_index, element) {
- var attribute_info, key, row_data, _ref;
+ 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];
+ 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);
diff --git a/wqflask/wqflask/static/new/javascript/stats.coffee b/wqflask/wqflask/static/new/javascript/stats.coffee
index bf79d6c..889d5fa 100755
--- a/wqflask/wqflask/static/new/javascript/stats.coffee
+++ b/wqflask/wqflask/static/new/javascript/stats.coffee
@@ -1,5 +1,5 @@
class Stats
- constructor: (@the_values) ->
+ constructor: (@the_values, @datascale=null) ->
add_value: (value) ->
@the_values.push(value)
@@ -47,9 +47,14 @@ class Stats
range: ->
return @max() - @min()
+ # returns the ratio of maximum and minimum values
range_fold: ->
- return Math.pow(2, @range())
+ if @datascale == "log2"
+ return Math.pow(2, @max() - @min())
+ return @max() / @min()
+ # for linear scale returns the difference between 3rd and 1st quartiles
+ # for log2 scales returns their ratio
interquartile: ->
length = @the_values.length
# Todo: Consider averaging q1 and a3 when the length is odd
@@ -57,8 +62,10 @@ class Stats
console.log("length is:", length)
q1 = @the_values[Math.floor(length * .25)]
q3 = @the_values[Math.floor(length * .75)]
- iq = q3 - q1
- return Math.pow(2, iq)
+ if @datascale == "log2"
+ return Math.pow(2, q3) - Math.pow(2, q1)
+ else
+ return q3 - q1
bxd_only = new Stats([3, 5, 7, 8])
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 203652f..d6e1419 100755
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -1,9 +1,10 @@
-// Generated by CoffeeScript 1.8.0
+// Generated by CoffeeScript 1.9.2
var Stats, bxd_only;
Stats = (function() {
- function Stats(the_values) {
+ function Stats(the_values, datascale) {
this.the_values = the_values;
+ this.datascale = datascale != null ? datascale : null;
}
Stats.prototype.add_value = function(value) {
@@ -15,11 +16,11 @@ Stats = (function() {
};
Stats.prototype.sum = function() {
- var total, value, _i, _len, _ref;
+ var i, len, ref, total, value;
total = 0;
- _ref = this.the_values;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- value = _ref[_i];
+ ref = this.the_values;
+ for (i = 0, len = ref.length; i < len; i++) {
+ value = ref[i];
total += value;
}
return total;
@@ -44,11 +45,11 @@ Stats = (function() {
};
Stats.prototype.std_dev = function() {
- var step_a, step_b, sum, value, _i, _len, _ref;
+ var i, len, ref, step_a, step_b, sum, value;
sum = 0;
- _ref = this.the_values;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- value = _ref[_i];
+ ref = this.the_values;
+ for (i = 0, len = ref.length; i < len; i++) {
+ value = ref[i];
step_a = Math.pow(value - this.mean(), 2);
sum += step_a;
}
@@ -73,18 +74,24 @@ Stats = (function() {
};
Stats.prototype.range_fold = function() {
- return Math.pow(2, this.range());
+ if (this.datascale === "log2") {
+ return Math.pow(2, this.max() - this.min());
+ }
+ return this.max() / this.min();
};
Stats.prototype.interquartile = function() {
- var iq, length, q1, q3;
+ var length, q1, q3;
length = this.the_values.length;
console.log("in interquartile the_values are:", this.the_values);
console.log("length is:", length);
q1 = this.the_values[Math.floor(length * .25)];
q3 = this.the_values[Math.floor(length * .75)];
- iq = q3 - q1;
- return Math.pow(2, iq);
+ if (this.datascale === "log2") {
+ return Math.pow(2, q3) - Math.pow(2, q1);
+ } else {
+ return q3 - q1;
+ }
};
return Stats;
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