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authorZachary Sloan2013-11-22 22:33:22 +0000
committerZachary Sloan2013-11-22 22:33:22 +0000
commit5143738870b8872a915432225acf01508de620ee (patch)
tree451832a079bcd0baa557360753461f7bc1b4fcda /wqflask
parent4cfdad02e5f8ebd4bd347f078999b063041b29d2 (diff)
downloadgenenetwork2-5143738870b8872a915432225acf01508de620ee.tar.gz
Did some work towards getting the interval mapping page working
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/interval_mapping/__init__.py0
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py20
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.coffee25
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.js15
-rw-r--r--wqflask/wqflask/static/new/javascript/box_plot.coffee45
-rw-r--r--wqflask/wqflask/static/new/javascript/box_plot.js83
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.coffee433
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js477
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee26
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js27
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html9
-rw-r--r--wqflask/wqflask/user_manager.py30
-rw-r--r--wqflask/wqflask/views.py16
14 files changed, 307 insertions, 900 deletions
diff --git a/wqflask/wqflask/interval_mapping/__init__.py b/wqflask/wqflask/interval_mapping/__init__.py
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/wqflask/wqflask/interval_mapping/__init__.py
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index aca99cbe..f41ebd2c 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -37,6 +37,8 @@ class IntervalMapping(object):
def __init__(self, start_vars, temp_uuid):
+ print("TESTING!!!")
+
#Currently only getting trait data for one trait, but will need
#to change this to accept multiple traits once the collection page is implemented
helper_functions.get_species_dataset_trait(self, start_vars)
@@ -51,6 +53,8 @@ class IntervalMapping(object):
self.samples.append(str(sample))
self.vals.append(value)
+ print("start_vars:", start_vars)
+
self.set_options(start_vars)
self.gen_qtl_results(tempdata)
@@ -69,24 +73,24 @@ class IntervalMapping(object):
def set_options(self, start_vars):
"""Sets various options (physical/genetic mapping, # permutations, which chromosome"""
- self.plot_scale = start_vars['scale']
+ #self.plot_scale = start_vars['scale']
#if self.plotScale == 'physic' and not fd.genotype.Mbmap:
# self.plotScale = 'morgan'
self.num_permutations = start_vars['num_permutations']
- self.do_bootstrap = start_vars['do_bootstrap']
- self.control_locus = start_vars['control_locus']
- self.selected_chr = start_vars['selected_chr']
- self.weighted_regression = start_vars['weighted']
- self.lrs_lod = start_vars['lrs_lod']
+ #self.do_bootstrap = start_vars['do_bootstrap']
+ #self.control_locus = start_vars['control_locus']
+ self.selected_chr = start_vars['chromosome']
+ #self.weighted_regression = start_vars['weighted']
+ #self.lrs_lod = start_vars['lrs_lod']
def gen_qtl_results(self, tempdata):
"""Generates qtl results for plotting interval map"""
self.dataset.group.get_markers()
- self.dataset.read_genotype_file()
+ self.dataset.group.read_genotype_file()
- samples, values, variances = self.trait.export_informative()
+ samples, values, variances = self.this_trait.export_informative()
if self.control_locus:
if self.weighted_regression:
self.qtl_results = self.dataset.genotype.regression(strains = samples,
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index 749a7dc0..2c60d3ab 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -121,6 +121,10 @@ class Bar_Chart
$('.x.axis').remove()
@add_x_axis(x_scale)
)
+
+ d3.select("#color_by_trait").on("click", =>
+ @color_by_trait()
+ )
get_attr_color_dict: () ->
@attr_color_dict = {}
@@ -299,20 +303,15 @@ class Bar_Chart
.text((d) =>
return d
)
-
-
+
color_by_trait: () ->
- console.log("Before load")
- $('#collections_holder').load('/collections/list #collections_list')
- $.colorbox(
- inline: true
- href: "#collections_holder"
+ $('#collections_holder').load('/collections/list #collections_list', =>
+ $.colorbox(
+ inline: true
+ href: "#collections_holder"
+ )
)
- console.log("After load")
- #$.colorbox({href:"/collections/list"})
- #$.get(
- # url: /collections/list
- #
- #)
+
+
root.Bar_Chart = Bar_Chart \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.js b/wqflask/wqflask/static/new/javascript/bar_chart.js
index 20fab15c..03902741 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -125,6 +125,9 @@
return _this.add_x_axis(x_scale);
}
});
+ d3.select("#color_by_trait").on("click", function() {
+ return _this.color_by_trait();
+ });
}
Bar_Chart.prototype.get_attr_color_dict = function() {
@@ -318,13 +321,13 @@
};
Bar_Chart.prototype.color_by_trait = function() {
- console.log("Before load");
- $('#collections_holder').load('/collections/list #collections_list');
- $.colorbox({
- inline: true,
- href: "#collections_holder"
+ var _this = this;
+ return $('#collections_holder').load('/collections/list #collections_list', function() {
+ return $.colorbox({
+ inline: true,
+ href: "#collections_holder"
+ });
});
- return console.log("After load");
};
return Bar_Chart;
diff --git a/wqflask/wqflask/static/new/javascript/box_plot.coffee b/wqflask/wqflask/static/new/javascript/box_plot.coffee
index 562bd1dc..e9035456 100644
--- a/wqflask/wqflask/static/new/javascript/box_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/box_plot.coffee
@@ -5,46 +5,53 @@ class Box_Plot
@get_samples()
@margin = {top: 10, right: 50, bottom: 20, left: 50}
- @plot_width = 120 - @margin.left - @margin.right
+ @plot_width = 200 - @margin.left - @margin.right
@plot_height = 500 - @margin.top - @margin.bottom
@min = d3.min(@sample_vals)
- @max = d3.max(@sample_vals) * 1.1
+ @max = d3.max(@sample_vals)
@svg = @create_svg()
-
@enter_data()
-
+
get_samples: () ->
- @sample_names = (sample.name for sample in @sample_list when sample.value != null)
@sample_vals = (sample.value for sample in @sample_list when sample.value != null)
- @samples = _.zip(@sample_names, @sample_vals)
- create_svg: () -> d3.chart.box()
- .whiskers(@inter_quartile_range(1.5))
- .width(@plot_width)
- .height(@plot_height)
- .domain([@min, @max])
-
+ create_svg: () ->
+ svg = d3.box()
+ .whiskers(@inter_quartile_range(1.5))
+ .width(@plot_width)
+ .height(@plot_height)
+ .domain([@min, @max])
+ return svg
+
enter_data: () ->
d3.select("#box_plot").selectAll("svg")
- .data(@sample_vals)
+ .data([@sample_vals])
.enter().append("svg:svg")
.attr("class", "box")
.attr("width", @plot_width)
.attr("height", @plot_height)
+ .append("svg:g")
.call(@svg)
inter_quartile_range: (k) ->
return (d, i) =>
- q1 = d.quartiles[0],
- q3 = d.quartiles[2],
+ console.log("iqr d:", d)
+ q1 = d.quartiles[0]
+ q3 = d.quartiles[2]
inter_quartile_range = (q3 - q1) * k
- i = -1
+ console.log("iqr:", inter_quartile_range)
+ i = 0
j = d.length
- while (d[++i] < q1 - inter_quartile_range)
- while (d[--j] > q3 + inter_quartile_range)
+ console.log("d[-1]:", d[1])
+ console.log("q1 - iqr:", q1 - inter_quartile_range)
+ i++ while (d[i] < q1 - inter_quartile_range)
+ j-- while (d[j] > q3 + inter_quartile_range)
+ #while (d[++i] < q1 - inter_quartile_range
+ #while d[--j] > q3 + inter_quartile_range
+ console.log("[i, j]", [i, j])
return [i, j]
- \ No newline at end of file
+root.Box_Plot = Box_Plot \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/box_plot.js b/wqflask/wqflask/static/new/javascript/box_plot.js
new file mode 100644
index 00000000..2dd624e1
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/box_plot.js
@@ -0,0 +1,83 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+ var Box_Plot, root;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+ Box_Plot = (function() {
+
+ function Box_Plot(sample_list, sample_group) {
+ this.sample_list = sample_list;
+ this.sample_group = sample_group;
+ this.get_samples();
+ this.margin = {
+ top: 10,
+ right: 50,
+ bottom: 20,
+ left: 50
+ };
+ this.plot_width = 200 - this.margin.left - this.margin.right;
+ this.plot_height = 500 - this.margin.top - this.margin.bottom;
+ this.min = d3.min(this.sample_vals);
+ this.max = d3.max(this.sample_vals);
+ this.svg = this.create_svg();
+ this.enter_data();
+ }
+
+ Box_Plot.prototype.get_samples = 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);
+ };
+
+ Box_Plot.prototype.create_svg = function() {
+ var svg;
+ svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width).height(this.plot_height).domain([this.min, this.max]);
+ return svg;
+ };
+
+ Box_Plot.prototype.enter_data = function() {
+ return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
+ };
+
+ Box_Plot.prototype.inter_quartile_range = function(k) {
+ var _this = this;
+ return function(d, i) {
+ var inter_quartile_range, j, q1, q3;
+ console.log("iqr d:", d);
+ q1 = d.quartiles[0];
+ q3 = d.quartiles[2];
+ inter_quartile_range = (q3 - q1) * k;
+ console.log("iqr:", inter_quartile_range);
+ i = 0;
+ j = d.length;
+ console.log("d[-1]:", d[1]);
+ console.log("q1 - iqr:", q1 - inter_quartile_range);
+ while (d[i] < q1 - inter_quartile_range) {
+ i++;
+ }
+ while (d[j] > q3 + inter_quartile_range) {
+ j--;
+ }
+ console.log("[i, j]", [i, j]);
+ return [i, j];
+ };
+ };
+
+ return Box_Plot;
+
+ })();
+
+ root.Box_Plot = Box_Plot;
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 8bcca85d..7d23345f 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -59,373 +59,6 @@ Stat_Table_Rows = [
]
$ ->
- class Bar_Chart
- constructor: (@sample_list, @sample_group) ->
- @get_samples()
- console.log("sample names:", @sample_names)
- if @sample_attr_vals.length > 0
- @get_distinct_attr_vals()
- @get_attr_color_dict()
-
- #Used to calculate the bottom margin so sample names aren't cut off
- longest_sample_name = d3.max(sample.length for sample in @sample_names)
-
- @margin = {top: 20, right: 20, bottom: longest_sample_name * 7, left: 40}
- @plot_width = @sample_vals.length * 15 - @margin.left - @margin.right
- @plot_height = 500 - @margin.top - @margin.bottom
-
- @x_buffer = @plot_width/20
- @y_buffer = @plot_height/20
-
- @y_min = d3.min(@sample_vals)
- @y_max = d3.max(@sample_vals) * 1.1
-
- @svg = @create_svg()
-
- @plot_height -= @y_buffer
- @create_scales()
- @create_graph()
-
- d3.select("#color_attribute").on("change", =>
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Name'
- @svg.selectAll(".bar")
- .data(@sorted_samples())
- .transition()
- .duration(1000)
- .style("fill", (d) =>
- if attribute == "None"
- return "steelblue"
- else
- return @attr_color_dict[attribute][d[2][attribute]]
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- else
- @svg.selectAll(".bar")
- .data(@samples)
- .transition()
- .duration(1000)
- .style("fill", (d) =>
- if attribute == "None"
- return "steelblue"
- else
- return @attr_color_dict[attribute][d[2][attribute]]
- )
- @add_legend(attribute, @distinct_attr_vals[attribute])
- )
-
-
- d3.select("#update_bar_chart").on("click", =>
- if @attributes.length > 0
- attribute = $("#color_attribute").val()
- if $("#update_bar_chart").html() == 'Sort By Value'
- $("#update_bar_chart").html('Sort By Name')
- sortItems = (a, b) ->
- return a[1] - b[1]
-
- @svg.selectAll(".bar")
- .data(@sorted_samples())
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- sorted_sample_names = (sample[0] for sample in @sorted_samples())
- x_scale = d3.scale.ordinal()
- .domain(sorted_sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
- else
- $("#update_bar_chart").html('Sort By Value')
- @svg.selectAll(".bar")
- .data(@samples)
- .transition()
- .duration(1000)
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .style("fill", (d) =>
- if @attributes.length > 0
- return @attr_color_dict[attribute][d[2][attribute]]
- else
- return "steelblue"
- )
- .select("title")
- .text((d) =>
- return d[1]
- )
- x_scale = d3.scale.ordinal()
- .domain(@sample_names)
- .rangeBands([0, @plot_width], .1)
- $('.x.axis').remove()
- @add_x_axis(x_scale)
- )
-
- d3.select("#color_by_trait").on("click", =>
- @color_by_trait()
- )
-
- get_attr_color_dict: () ->
- @attr_color_dict = {}
- console.log("distinct_attr_vals:", @distinct_attr_vals)
- for own key, distinct_vals of @distinct_attr_vals
- this_color_dict = {}
- if distinct_vals.length < 10
- color = d3.scale.category10()
- for value, i in distinct_vals
- this_color_dict[value] = color(i)
- else
- console.log("distinct_values:", distinct_vals)
- if _.every(distinct_vals, (d) =>
- if isNaN(d)
- return false
- else
- return true
- )
- color_range = d3.scale.linear()
- .domain([d3.min(distinct_vals),
- d3.max(distinct_vals)])
- .range([0,4])
- for value, i in distinct_vals
- console.log("color_range(value):", color_range(parseInt(value)))
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)))
- #this_color_dict[value] = "rgb(0, 0, " + color_range(parseInt(value)) + ")"
- @attr_color_dict[key] = this_color_dict
-
- get_samples: () ->
- @sample_names = (sample.name for sample in @sample_list when sample.value != null)
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
- @attributes = (key for key of @sample_list[0]["extra_attributes"])
- console.log("attributes:", @attributes)
- @sample_attr_vals = []
- if @attributes.length > 0
- for sample in @sample_list
- attr_vals = {}
- for attribute in @attributes
- attr_vals[attribute] = sample["extra_attributes"][attribute]
- @sample_attr_vals.push(attr_vals)
- @samples = _.zip(@sample_names, @sample_vals, @sample_attr_vals)
-
- get_distinct_attr_vals: () ->
- @distinct_attr_vals = {}
- for sample in @sample_attr_vals
- for attribute of sample
- if not @distinct_attr_vals[attribute]
- @distinct_attr_vals[attribute] = []
- if sample[attribute] not in @distinct_attr_vals[attribute]
- @distinct_attr_vals[attribute].push(sample[attribute])
- #console.log("distinct_attr_vals:", @distinct_attr_vals)
-
- create_svg: () ->
- svg = d3.select("#bar_chart")
- .append("svg")
- .attr("class", "bar_chart")
- .attr("width", @plot_width + @margin.left + @margin.right)
- .attr("height", @plot_height + @margin.top + @margin.bottom)
- .append("g")
- .attr("transform", "translate(" + @margin.left + "," + @margin.top + ")")
-
- return svg
-
- create_scales: () ->
- @x_scale = d3.scale.ordinal()
- .domain(@sample_names)
- .rangeBands([0, @plot_width], .1)
-
- @y_scale = d3.scale.linear()
- .domain([@y_min * 0.75, @y_max])
- .range([@plot_height, @y_buffer])
-
- create_graph: () ->
-
- #@add_border()
- @add_x_axis(@x_scale)
- @add_y_axis()
-
- @add_bars()
-
- add_x_axis: (scale) ->
- xAxis = d3.svg.axis()
- .scale(scale)
- .orient("bottom");
-
- @svg.append("g")
- .attr("class", "x axis")
- .attr("transform", "translate(0," + @plot_height + ")")
- .call(xAxis)
- .selectAll("text")
- .style("text-anchor", "end")
- .style("font-size", "12px")
- .attr("dx", "-.8em")
- .attr("dy", "-.3em")
- .attr("transform", (d) =>
- return "rotate(-90)"
- )
-
- add_y_axis: () ->
- yAxis = d3.svg.axis()
- .scale(@y_scale)
- .orient("left")
- .ticks(5)
-
- @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")
-
- add_bars: () ->
- @svg.selectAll(".bar")
- .data(@samples)
- .enter().append("rect")
- .style("fill", "steelblue")
- .attr("class", "bar")
- .attr("x", (d) =>
- return @x_scale(d[0])
- )
- .attr("width", @x_scale.rangeBand())
- .attr("y", (d) =>
- return @y_scale(d[1])
- )
- .attr("height", (d) =>
- return @plot_height - @y_scale(d[1])
- )
- .append("svg:title")
- .text((d) =>
- return d[1]
- )
-
- sorted_samples: () ->
- #if @sample_attr_vals.length > 0
- sample_list = _.zip(@sample_names, @sample_vals, @sample_attr_vals)
- #else
- # sample_list = _.zip(@sample_names, @sample_vals)
- sorted = _.sortBy(sample_list, (sample) =>
- return sample[1]
- )
- console.log("sorted:", sorted)
- return sorted
-
- add_legend: (attribute, distinct_vals) ->
- legend = @svg.append("g")
- .attr("class", "legend")
- .attr("height", 100)
- .attr("width", 100)
- .attr('transform', 'translate(-20,50)')
-
- legend_rect = legend.selectAll('rect')
- .data(distinct_vals)
- .enter()
- .append("rect")
- .attr("x", @plot_width - 65)
- .attr("width", 10)
- .attr("height", 10)
- .attr("y", (d, i) =>
- return i * 20
- )
- .style("fill", (d) =>
- console.log("TEST:", @attr_color_dict[attribute][d])
- return @attr_color_dict[attribute][d]
- )
-
- legend_text = legend.selectAll('text')
- .data(distinct_vals)
- .enter()
- .append("text")
- .attr("x", @plot_width - 52)
- .attr("y", (d, i) =>
- return i*20 + 9
- )
- .text((d) =>
- return d
- )
-
- color_by_trait: () ->
- $('#collections_holder').load('/collections/list #collections_list', =>
- $.colorbox(
- inline: true
- href: "#collections_holder"
- )
- )
-
- class Box_Plot
- constructor: (@sample_list, @sample_group) ->
- @get_samples()
-
- @margin = {top: 10, right: 50, bottom: 20, left: 50}
- @plot_width = 200 - @margin.left - @margin.right
- @plot_height = 500 - @margin.top - @margin.bottom
-
- @min = d3.min(@sample_vals)
- @max = d3.max(@sample_vals)
-
- @svg = @create_svg()
- @enter_data()
-
-
- get_samples: () ->
- @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
-
- create_svg: () ->
- svg = d3.box()
- .whiskers(@inter_quartile_range(1.5))
- .width(@plot_width)
- .height(@plot_height)
- .domain([@min, @max])
- return svg
-
- enter_data: () ->
- d3.select("#box_plot").selectAll("svg")
- .data([@sample_vals])
- .enter().append("svg:svg")
- .attr("class", "box")
- .attr("width", @plot_width)
- .attr("height", @plot_height)
- .append("svg:g")
- .call(@svg)
-
- inter_quartile_range: (k) ->
- return (d, i) =>
- console.log("iqr d:", d)
- q1 = d.quartiles[0]
- q3 = d.quartiles[2]
- inter_quartile_range = (q3 - q1) * k
- console.log("iqr:", inter_quartile_range)
- i = 0
- j = d.length
- console.log("d[-1]:", d[1])
- console.log("q1 - iqr:", q1 - inter_quartile_range)
- i++ while (d[i] < q1 - inter_quartile_range)
- j-- while (d[j] > q3 + inter_quartile_range)
- #while (d[++i] < q1 - inter_quartile_range
- #while d[--j] > q3 + inter_quartile_range
- console.log("[i, j]", [i, j])
- return [i, j]
-
-
sample_lists = js_data.sample_lists
sample_group_types = js_data.sample_group_types
@@ -504,39 +137,6 @@ $ ->
console.log("Calling change_stats_value")
change_stats_value(sample_sets, category, row.vn, row.digits)
- edit_data_change = ->
- 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 table in tables
- rows = $("#" + table).find('tr')
- for row in rows
- 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 and is_number(real_value) and 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 not (name of already_seen)
- console.log("haven't seen")
- sample_sets['samples_all'].add_value(real_value)
- already_seen[name] = true
- console.log("towards end:", sample_sets)
- update_stat_values(sample_sets)
-
make_table = ->
header = "<thead><tr><th>&nbsp;</th>"
@@ -585,6 +185,38 @@ $ ->
processed += value
return processed
+ edit_data_change = ->
+ 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 table in tables
+ rows = $("#" + table).find('tr')
+ for row in rows
+ 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 and is_number(real_value) and 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 not (name of already_seen)
+ console.log("haven't seen")
+ sample_sets['samples_all'].add_value(real_value)
+ already_seen[name] = true
+ console.log("towards end:", sample_sets)
+ update_stat_values(sample_sets)
show_hide_outliers = ->
console.log("FOOBAR in beginning of show_hide_outliers")
@@ -613,7 +245,6 @@ $ ->
$('select[name=corr_method]').change(on_corr_method_change)
-
##End Calculate Correlations Code
##Populate Samples Attribute Values Code
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index b562bfe2..718e365a 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -2,7 +2,6 @@
(function() {
var Stat_Table_Rows, is_number,
__hasProp = {}.hasOwnProperty,
- __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; },
__slice = [].slice;
console.log("start_b");
@@ -57,407 +56,7 @@
];
$(function() {
- var Bar_Chart, Box_Plot, 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, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
- Bar_Chart = (function() {
-
- function Bar_Chart(sample_list, sample_group) {
- var longest_sample_name, sample,
- _this = this;
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.get_samples();
- console.log("sample names:", this.sample_names);
- if (this.sample_attr_vals.length > 0) {
- this.get_distinct_attr_vals();
- this.get_attr_color_dict();
- }
- longest_sample_name = d3.max((function() {
- var _i, _len, _ref, _results;
- _ref = this.sample_names;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push(sample.length);
- }
- return _results;
- }).call(this));
- this.margin = {
- top: 20,
- right: 20,
- bottom: longest_sample_name * 7,
- left: 40
- };
- this.plot_width = this.sample_vals.length * 15 - 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.svg = this.create_svg();
- this.plot_height -= this.y_buffer;
- this.create_scales();
- this.create_graph();
- d3.select("#color_attribute").on("change", function() {
- var attribute;
- attribute = $("#color_attribute").val();
- if ($("#update_bar_chart").html() === 'Sort By Name') {
- _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
- return "steelblue";
- } else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- } else {
- _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).style("fill", function(d) {
- if (attribute === "None") {
- return "steelblue";
- } else {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- }
- });
- }
- return _this.add_legend(attribute, _this.distinct_attr_vals[attribute]);
- });
- d3.select("#update_bar_chart").on("click", function() {
- var attribute, sortItems, sorted_sample_names, x_scale;
- if (_this.attributes.length > 0) {
- attribute = $("#color_attribute").val();
- }
- if ($("#update_bar_chart").html() === 'Sort By Value') {
- $("#update_bar_chart").html('Sort By Name');
- sortItems = function(a, b) {
- return a[1] - b[1];
- };
- _this.svg.selectAll(".bar").data(_this.sorted_samples()).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- sorted_sample_names = (function() {
- var _i, _len, _ref, _results;
- _ref = this.sorted_samples();
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push(sample[0]);
- }
- return _results;
- }).call(_this);
- x_scale = d3.scale.ordinal().domain(sorted_sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
- } else {
- $("#update_bar_chart").html('Sort By Value');
- _this.svg.selectAll(".bar").data(_this.samples).transition().duration(1000).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).style("fill", function(d) {
- if (_this.attributes.length > 0) {
- return _this.attr_color_dict[attribute][d[2][attribute]];
- } else {
- return "steelblue";
- }
- }).select("title").text(function(d) {
- return d[1];
- });
- x_scale = d3.scale.ordinal().domain(_this.sample_names).rangeBands([0, _this.plot_width], .1);
- $('.x.axis').remove();
- return _this.add_x_axis(x_scale);
- }
- });
- d3.select("#color_by_trait").on("click", function() {
- return _this.color_by_trait();
- });
- }
-
- Bar_Chart.prototype.get_attr_color_dict = function() {
- var color, color_range, distinct_vals, i, key, this_color_dict, value, _i, _j, _len, _len1, _ref, _results,
- _this = this;
- this.attr_color_dict = {};
- console.log("distinct_attr_vals:", this.distinct_attr_vals);
- _ref = this.distinct_attr_vals;
- _results = [];
- for (key in _ref) {
- if (!__hasProp.call(_ref, key)) continue;
- distinct_vals = _ref[key];
- this_color_dict = {};
- if (distinct_vals.length < 10) {
- color = d3.scale.category10();
- for (i = _i = 0, _len = distinct_vals.length; _i < _len; i = ++_i) {
- value = distinct_vals[i];
- this_color_dict[value] = color(i);
- }
- } else {
- console.log("distinct_values:", distinct_vals);
- if (_.every(distinct_vals, function(d) {
- if (isNaN(d)) {
- return false;
- } else {
- return true;
- }
- })) {
- color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 4]);
- for (i = _j = 0, _len1 = distinct_vals.length; _j < _len1; i = ++_j) {
- value = distinct_vals[i];
- console.log("color_range(value):", color_range(parseInt(value)));
- this_color_dict[value] = d3.rgb("lightblue").darker(color_range(parseInt(value)));
- }
- }
- }
- _results.push(this.attr_color_dict[key] = this_color_dict);
- }
- return _results;
- };
-
- Bar_Chart.prototype.get_samples = function() {
- var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
- this.sample_names = (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.name);
- }
- }
- return _results;
- }).call(this);
- 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);
- this.attributes = (function() {
- var _results;
- _results = [];
- for (key in this.sample_list[0]["extra_attributes"]) {
- _results.push(key);
- }
- return _results;
- }).call(this);
- console.log("attributes:", this.attributes);
- this.sample_attr_vals = [];
- if (this.attributes.length > 0) {
- _ref = this.sample_list;
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- attr_vals = {};
- _ref1 = this.attributes;
- for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
- attribute = _ref1[_j];
- attr_vals[attribute] = sample["extra_attributes"][attribute];
- }
- this.sample_attr_vals.push(attr_vals);
- }
- }
- return this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
- };
-
- Bar_Chart.prototype.get_distinct_attr_vals = function() {
- var attribute, sample, _i, _len, _ref, _results;
- this.distinct_attr_vals = {};
- _ref = this.sample_attr_vals;
- _results = [];
- for (_i = 0, _len = _ref.length; _i < _len; _i++) {
- sample = _ref[_i];
- _results.push((function() {
- var _ref1, _results1;
- _results1 = [];
- for (attribute in sample) {
- if (!this.distinct_attr_vals[attribute]) {
- this.distinct_attr_vals[attribute] = [];
- }
- if (_ref1 = sample[attribute], __indexOf.call(this.distinct_attr_vals[attribute], _ref1) < 0) {
- _results1.push(this.distinct_attr_vals[attribute].push(sample[attribute]));
- } else {
- _results1.push(void 0);
- }
- }
- return _results1;
- }).call(this));
- }
- return _results;
- };
-
- Bar_Chart.prototype.create_svg = function() {
- var svg;
- svg = d3.select("#bar_chart").append("svg").attr("class", "bar_chart").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;
- };
-
- Bar_Chart.prototype.create_scales = function() {
- this.x_scale = d3.scale.ordinal().domain(this.sample_names).rangeBands([0, this.plot_width], .1);
- return this.y_scale = d3.scale.linear().domain([this.y_min * 0.75, this.y_max]).range([this.plot_height, this.y_buffer]);
- };
-
- Bar_Chart.prototype.create_graph = function() {
- this.add_x_axis(this.x_scale);
- this.add_y_axis();
- return this.add_bars();
- };
-
- Bar_Chart.prototype.add_x_axis = function(scale) {
- var xAxis,
- _this = this;
- xAxis = d3.svg.axis().scale(scale).orient("bottom");
- return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").style("text-anchor", "end").style("font-size", "12px").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) {
- return "rotate(-90)";
- });
- };
-
- Bar_Chart.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");
- };
-
- Bar_Chart.prototype.add_bars = function() {
- var _this = this;
- return this.svg.selectAll(".bar").data(this.samples).enter().append("rect").style("fill", "steelblue").attr("class", "bar").attr("x", function(d) {
- return _this.x_scale(d[0]);
- }).attr("width", this.x_scale.rangeBand()).attr("y", function(d) {
- return _this.y_scale(d[1]);
- }).attr("height", function(d) {
- return _this.plot_height - _this.y_scale(d[1]);
- }).append("svg:title").text(function(d) {
- return d[1];
- });
- };
-
- Bar_Chart.prototype.sorted_samples = function() {
- var sample_list, sorted,
- _this = this;
- sample_list = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
- sorted = _.sortBy(sample_list, function(sample) {
- return sample[1];
- });
- console.log("sorted:", sorted);
- return sorted;
- };
-
- Bar_Chart.prototype.add_legend = function(attribute, distinct_vals) {
- var legend, legend_rect, legend_text,
- _this = this;
- legend = this.svg.append("g").attr("class", "legend").attr("height", 100).attr("width", 100).attr('transform', 'translate(-20,50)');
- legend_rect = legend.selectAll('rect').data(distinct_vals).enter().append("rect").attr("x", this.plot_width - 65).attr("width", 10).attr("height", 10).attr("y", function(d, i) {
- return i * 20;
- }).style("fill", function(d) {
- console.log("TEST:", _this.attr_color_dict[attribute][d]);
- return _this.attr_color_dict[attribute][d];
- });
- return legend_text = legend.selectAll('text').data(distinct_vals).enter().append("text").attr("x", this.plot_width - 52).attr("y", function(d, i) {
- return i * 20 + 9;
- }).text(function(d) {
- return d;
- });
- };
-
- Bar_Chart.prototype.color_by_trait = function() {
- var _this = this;
- return $('#collections_holder').load('/collections/list #collections_list', function() {
- return $.colorbox({
- inline: true,
- href: "#collections_holder"
- });
- });
- };
-
- return Bar_Chart;
-
- })();
- Box_Plot = (function() {
-
- function Box_Plot(sample_list, sample_group) {
- this.sample_list = sample_list;
- this.sample_group = sample_group;
- this.get_samples();
- this.margin = {
- top: 10,
- right: 50,
- bottom: 20,
- left: 50
- };
- this.plot_width = 200 - this.margin.left - this.margin.right;
- this.plot_height = 500 - this.margin.top - this.margin.bottom;
- this.min = d3.min(this.sample_vals);
- this.max = d3.max(this.sample_vals);
- this.svg = this.create_svg();
- this.enter_data();
- }
-
- Box_Plot.prototype.get_samples = 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);
- };
-
- Box_Plot.prototype.create_svg = function() {
- var svg;
- svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width).height(this.plot_height).domain([this.min, this.max]);
- return svg;
- };
-
- Box_Plot.prototype.enter_data = function() {
- return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg);
- };
-
- Box_Plot.prototype.inter_quartile_range = function(k) {
- var _this = this;
- return function(d, i) {
- var inter_quartile_range, j, q1, q3;
- console.log("iqr d:", d);
- q1 = d.quartiles[0];
- q3 = d.quartiles[2];
- inter_quartile_range = (q3 - q1) * k;
- console.log("iqr:", inter_quartile_range);
- i = 0;
- j = d.length;
- console.log("d[-1]:", d[1]);
- console.log("q1 - iqr:", q1 - inter_quartile_range);
- while (d[i] < q1 - inter_quartile_range) {
- i++;
- }
- while (d[j] > q3 + inter_quartile_range) {
- j--;
- }
- console.log("[i, j]", [i, j]);
- return [i, j];
- };
- };
-
- return Box_Plot;
-
- })();
+ 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, 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;
new Bar_Chart(sample_lists[0]);
@@ -546,43 +145,6 @@
}
return _results;
};
- 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;
- }
- }
- }
- }
- console.log("towards end:", sample_sets);
- return update_stat_values(sample_sets);
- };
make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
header = "<thead><tr><th>&nbsp;</th>";
@@ -645,6 +207,43 @@
}
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;
+ }
+ }
+ }
+ }
+ 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");
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index 3c995441..8571753e 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -52,6 +52,32 @@ $ ->
)
return false
+ $("#interval_mapping_compute").click(() =>
+ $("#progress_bar_container").modal()
+ url = "/interval_mapping"
+ form_data = $('#trait_data_form').serialize()
+ console.log("form_data is:", form_data)
+ $.ajax(
+ type: "POST"
+ url: url
+ data: form_data
+ error: (xhr, ajaxOptions, thrownError) =>
+ alert("Sorry, an error occurred")
+ console.log(xhr)
+ clearInterval(this.my_timer)
+ $('#progress_bar_container').modal('hide')
+ $("body").html("We got an error.")
+ success: (data) =>
+ clearInterval(this.my_timer)
+ $('#progress_bar_container').modal('hide')
+ $("body").html(data)
+ )
+ console.log("settingInterval")
+
+ this.my_timer = setInterval(get_progress, 1000)
+ return false
+ )
+
$('#suggestive').hide()
$('input[name=display_all]').change(() =>
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index b309b167..1153b8ef 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -62,6 +62,33 @@
});
return false;
};
+ $("#interval_mapping_compute").click(function() {
+ var form_data, url;
+ $("#progress_bar_container").modal();
+ url = "/interval_mapping";
+ form_data = $('#trait_data_form').serialize();
+ console.log("form_data is:", form_data);
+ $.ajax({
+ type: "POST",
+ url: url,
+ data: form_data,
+ error: function(xhr, ajaxOptions, thrownError) {
+ alert("Sorry, an error occurred");
+ console.log(xhr);
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html("We got an error.");
+ },
+ success: function(data) {
+ clearInterval(_this.my_timer);
+ $('#progress_bar_container').modal('hide');
+ return $("body").html(data);
+ }
+ });
+ console.log("settingInterval");
+ _this.my_timer = setInterval(get_progress, 1000);
+ return false;
+ });
$('#suggestive').hide();
$('input[name=display_all]').change(function() {
console.log("check");
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 8a19e07b..91e6df42 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -56,6 +56,7 @@
<script type="text/javascript" src="/static/new/javascript/stats.js"></script>
<script type="text/javascript" src="/static/new/javascript/box.js"></script>
<script type="text/javascript" src="/static/new/javascript/bar_chart.js"></script>
+ <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
<script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
<script type="text/javascript" src="/static/new/javascript/validation.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c2d5211f..00301d39 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -30,7 +30,7 @@
<div class="control-group">
<label for="mapping_permutations" class="control-label">Permutations (n)</label>
<div class="controls">
- <input name="num_perm1" value="2000" type="text" />
+ <input name="num_permutations" value="2000" type="text" />
</div>
</div>
@@ -85,7 +85,8 @@
<div class="control-group">
<div class="controls">
- <button class="btn btn-inverse submit_special"
+ <button id="interval_mapping_compute"
+ class="btn btn-inverse submit_special"
data-url="/interval_mapping"
title="Compute Interval Mapping">
<i class="icon-ok-circle icon-white"></i> Compute
@@ -116,12 +117,12 @@
</div>
</div>
- <div class="control-group">
+<!-- <div class="control-group">
<label for="marker_reg_permutations" class="control-label">Permutations (n)</label>
<div class="controls">
<input name="num_perm" value="2000" type="text" />
</div>
- </div>
+ </div> -->
<div class="control-group">
<div class="controls">
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 768415b5..1d0d9846 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -49,7 +49,8 @@ from utility import Bunch, Struct
from base.data_set import create_datasets_list
-
+THREE_DAYS = 60 * 60 * 24 * 3
+#THREE_DAYS = 45
def timestamp():
return datetime.datetime.utcnow().isoformat()
@@ -74,6 +75,27 @@ class UserSession(object):
print("self.redis_key is:", self.redis_key)
self.session_id = session_id
self.record = Redis.hgetall(self.redis_key)
+
+
+ if not self.record:
+ # This will occur, for example, when the browser has been left open over a long
+ # weekend and the site hasn't been visited by the user
+ self.logged_in = False
+
+ ########### Grrr...this won't work because of the way flask handles cookies
+ # Delete the cookie
+ #response = make_response(redirect(url_for('login')))
+ #response.set_cookie(self.cookie_name, '', expires=0)
+ #flash(
+ # "Due to inactivity your session has expired. If you'd like please login again.")
+ #return response
+ return
+
+ if Redis.ttl(self.redis_key) < THREE_DAYS:
+ # (Almost) everytime the user does something we extend the session_id in Redis...
+ print("Extending ttl...")
+ Redis.expire(self.redis_key, THREE_DAYS)
+
print("record is:", self.record)
self.logged_in = True
@@ -225,8 +247,8 @@ class VerificationEmail(object):
)
Redis.set(key, data)
- two_days = 60 * 60 * 24 * 2
- Redis.expire(key, two_days)
+ #two_days = 60 * 60 * 24 * 2
+ Redis.expire(key, THREE_DAYS)
to = user.email_address
subject = self.subject
body = render_template(self.template_name,
@@ -415,7 +437,7 @@ class LoginUser(object):
if self.remember_me:
expire_time = self.remember_time
else:
- expire_time = 60 * 60 * 24 * 2 # two days
+ expire_time = THREE_DAYS
Redis.expire(key, expire_time)
db_session.add(login_rec)
db_session.commit()
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b2f08ca0..50161d41 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,7 +32,7 @@ from base.data_set import create_datasets_list
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.marker_regression import marker_regression
-#from wqflask.interval_mapping import interval_mapping
+from wqflask.interval_mapping import interval_mapping
from wqflask.correlation import show_corr_results
from wqflask.correlation import corr_scatter_plot
from utility import temp_data
@@ -256,7 +256,11 @@ def interval_mapping_page():
wanted = (
'trait_id',
'dataset',
- 'suggestive'
+ 'chromosome',
+ 'num_permutations',
+ 'do_bootstraps',
+ 'default_control_locus',
+ 'control_locus'
)
start_vars = {}
@@ -308,10 +312,10 @@ def corr_scatter_plot_page():
indent=" ")
return render_template("corr_scatter_plot.html", **template_vars.__dict__)
-@app.route("/int_mapping", methods=('POST',))
-def interval_mapping_page():
- template_vars = interval_mapping.IntervalMapping(request.args)
- return render_template("interval_mapping.html", **template_vars.__dict__)
+#@app.route("/int_mapping", methods=('POST',))
+#def interval_mapping_page():
+# template_vars = interval_mapping.IntervalMapping(request.args)
+# return render_template("interval_mapping.html", **template_vars.__dict__)
# Todo: Can we simplify this? -Sam
def sharing_info_page():