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-rwxr-xr-xwqflask/base/data_set.py12
-rwxr-xr-xwqflask/base/trait.py26
-rw-r--r--wqflask/wqflask/collect.py23
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py93
-rw-r--r--wqflask/wqflask/static/new/css/interval_mapping.css27
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.coffee7
-rw-r--r--wqflask/wqflask/static/new/javascript/bar_chart.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee15
-rw-r--r--wqflask/wqflask/static/new/javascript/get_traits_from_collection.js20
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.coffee293
-rw-r--r--wqflask/wqflask/static/new/javascript/interval_mapping.js272
-rw-r--r--wqflask/wqflask/static/new/javascript/scientific_notation.js13
-rw-r--r--wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js13
-rw-r--r--wqflask/wqflask/templates/base.html2
-rw-r--r--wqflask/wqflask/templates/collections/list.html11
-rw-r--r--wqflask/wqflask/templates/interval_mapping.html104
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html1
-rw-r--r--wqflask/wqflask/views.py13
19 files changed, 890 insertions, 58 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cd8c1ac1..8296adea 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -318,12 +318,17 @@ class DatasetGroup(object):
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- self.genotype = genotype_2
+ #self.genotype = genotype_2
+ genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = genotype_1
+ #self.genotype = genotype_1
+ genotype = genotype_1
- self.samplelist = list(self.genotype.prgy)
+ #self.samplelist = list(self.genotype.prgy)
+ self.samplelist = list(genotype.prgy)
+
+ return genotype
#class DataSets(object):
@@ -1084,6 +1089,7 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
+ print("RETRIEVED RESULTS HERE:", results)
return results
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 731f99eb..74bc07bb 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -154,7 +154,7 @@ class GeneralTrait(object):
result.append(None)
return result
- def export_informative(self, incVar=0):
+ def export_informative(self, include_variance=0):
"""
export informative sample
mostly used in qtl regression
@@ -163,12 +163,12 @@ class GeneralTrait(object):
samples = []
vals = []
the_vars = []
- for sample, value in self.data.items():
- if value.val != None:
- if not incVar or value.var != None:
- samples.append(sample)
- vals.append(value.val)
- the_vars.append(value.var)
+ for sample_name, sample_data in self.data.items():
+ if sample_data.value != None:
+ if not include_variance or sample_data.variance != None:
+ samples.append(sample_name)
+ vals.append(sample_data.value)
+ the_vars.append(sample_data.variance)
return samples, vals, the_vars
@@ -235,11 +235,19 @@ class GeneralTrait(object):
# Todo: is this necessary? If not remove
self.data.clear()
+ if self.dataset.group.parlist:
+ all_samples_ordered = (self.dataset.group.parlist +
+ self.dataset.group.f1list +
+ self.dataset.group.samplelist)
+ elif self.dataset.group.f1list:
+ all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist
+ else:
+ all_samples_ordered = self.dataset.group.samplelist
+
if results:
for item in results:
- #name, value, variance, num_cases = item
+ name, value, variance, num_cases = item
if not samplelist or (samplelist and name in samplelist):
- name = item[0]
self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
#def keys(self):
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index ef7b37df..991d281c 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -23,7 +23,7 @@ Redis = redis.StrictRedis()
from flask import (Flask, g, render_template, url_for, request, make_response,
- redirect, flash)
+ redirect, flash, jsonify)
from wqflask import app
@@ -122,16 +122,18 @@ def create_new():
@app.route("/collections/list")
def list_collections():
+ params = request.args
user_collections = g.user_session.user_ob.user_collections
return render_template("collections/list.html",
+ params = params,
user_collections = user_collections,
)
-
@app.route("/collections/view")
def view_collection():
params = request.args
+ print("params in view collection:", params)
uc_id = params['uc_id']
uc = model.UserCollection.query.get(uc_id)
traits = json.loads(uc.members)
@@ -139,6 +141,7 @@ def view_collection():
print("in view_collection traits are:", traits)
trait_obs = []
+ json_version = []
for atrait in traits:
name, dataset_name = atrait.split(':')
@@ -146,8 +149,16 @@ def view_collection():
trait_ob = trait.GeneralTrait(name=name, dataset_name=dataset_name)
trait_ob.get_info()
trait_obs.append(trait_ob)
-
- return render_template("collections/view.html",
- trait_obs=trait_obs,
- uc = uc,
+
+ json_version.append(dict(name=trait_ob.name))
+ #dis=trait_ob.description))
+
+ collection_info = dict(trait_obs=trait_obs,
+ uc = uc)
+ if "json" in params:
+ print("json_version:", json_version)
+ return json.dumps(json_version)
+ else:
+ return render_template("collections/view.html",
+ **collection_info
)
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index f41ebd2c..de7a2704 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -64,10 +64,12 @@ class IntervalMapping(object):
for key in self.species.chromosomes.chromosomes.keys():
chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+ #print("self.qtl_results:", self.qtl_results)
+
self.js_data = dict(
- lrs_lod = self.lrs_lod,
chromosomes = chromosome_mb_lengths,
qtl_results = self.qtl_results,
+ #lrs_lod = self.lrs_lod,
)
def set_options(self, start_vars):
@@ -76,10 +78,13 @@ class IntervalMapping(object):
#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.num_permutations = int(start_vars['num_permutations'])
#self.do_bootstrap = start_vars['do_bootstrap']
- #self.control_locus = start_vars['control_locus']
self.selected_chr = start_vars['chromosome']
+ if 'control_locus' in start_vars:
+ self.control_locus = start_vars['control_locus']
+ else:
+ self.control_locus = None
#self.weighted_regression = start_vars['weighted']
#self.lrs_lod = start_vars['lrs_lod']
@@ -88,40 +93,76 @@ class IntervalMapping(object):
"""Generates qtl results for plotting interval map"""
self.dataset.group.get_markers()
- self.dataset.group.read_genotype_file()
+ genotype = self.dataset.group.read_genotype_file()
samples, values, variances = self.this_trait.export_informative()
+
+ trimmed_samples = []
+ trimmed_values = []
+ for i in range(0, len(samples)):
+ if samples[i] in self.dataset.group.samplelist:
+ trimmed_samples.append(samples[i])
+ trimmed_values.append(values[i])
+
+ #if self.weighted_regression:
+ # self.lrs_array = self.genotype.permutation(strains = trimmed_samples,
+ # trait = trimmed_values,
+ # variance = _vars,
+ # nperm=self.num_permutations)
+ #else:
+ self.lrs_array = genotype.permutation(strains = trimmed_samples,
+ trait = trimmed_values,
+ nperm= self.num_permutations)
+ self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)]
+ self.significant = self.lrs_array[int(self.num_permutations*0.95-1)]
+
+ print("samples:", trimmed_samples)
+
if self.control_locus:
- if self.weighted_regression:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- variance = variances,
- control = self.control_locus)
- else:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- control = self.control_locus)
+ #if self.weighted_regression:
+ # self.qtl_results = self.dataset.genotype.regression(strains = samples,
+ # trait = values,
+ # variance = variances,
+ # control = self.control_locus)
+ #else:
+ #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
+ # trait = trimmed_values,
+ # control = self.control_locus)
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = self.control_locus)
else:
- if self.weighted_regression:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values,
- variance = variances)
- else:
- self.qtl_results = self.dataset.genotype.regression(strains = samples,
- trait = values)
+ #if self.weighted_regression:
+ # self.qtl_results = self.dataset.genotype.regression(strains = samples,
+ # trait = values,
+ # variance = variances)
+ #else:
+ print("strains:", trimmed_samples)
+ print("trait:", trimmed_values)
+ #reaper_results = self.dataset.group.genotype.regression(strains = trimmed_samples,
+ # trait = trimmed_values)
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values)
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ self.qtl_results = []
+ for qtl in reaper_results:
+ reaper_locus = qtl.locus
+ locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
+ qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive}
+ self.qtl_results.append(qtl)
#pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
#if self.dataset.group.species == "human":
# p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
#else:
- genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
-
- no_val_samples = self.identify_empty_samples()
- trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
-
- genotype_matrix = np.array(trimmed_genotype_data).T
+ #genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+ #
+ #no_val_samples = self.identify_empty_samples()
+ #trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+ #
+ #genotype_matrix = np.array(trimmed_genotype_data).T
#t_stats, p_values = lmm.run(
# pheno_vector,
diff --git a/wqflask/wqflask/static/new/css/interval_mapping.css b/wqflask/wqflask/static/new/css/interval_mapping.css
new file mode 100644
index 00000000..9d23ba25
--- /dev/null
+++ b/wqflask/wqflask/static/new/css/interval_mapping.css
@@ -0,0 +1,27 @@
+.manhattan_plot .y_axis path,
+.manhattan_plot .y_axis line {
+ fill: none;
+ stroke: black;
+ shape-rendering: crispEdges;
+}
+.manhattan_plot .y_axis text {
+ font-family: sans-serif;
+ font-size: 14px;
+}
+
+.manhattan_plot .x_axis path,
+.manhattan_plot .x_axis line {
+ fill: none;
+ stroke: black;
+ shape-rendering: crispEdges;
+}
+.manhattan_plot .x_axis text {
+ text-anchor: end;
+ font-family: sans-serif;
+ font-size: 8px;
+}
+
+rect {
+ stroke: WhiteSmoke;
+ fill: lightgrey;
+} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/bar_chart.coffee b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
index 2c60d3ab..4921b55e 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.coffee
@@ -276,7 +276,7 @@ class Bar_Chart
.attr("height", 100)
.attr("width", 100)
.attr('transform', 'translate(-20,50)')
-
+
legend_rect = legend.selectAll('rect')
.data(distinct_vals)
.enter()
@@ -305,13 +305,12 @@ class Bar_Chart
)
color_by_trait: () ->
- $('#collections_holder').load('/collections/list #collections_list', =>
+ $('#collections_holder').load('/collections/list?color_by_trait #collections_list', =>
$.colorbox(
inline: true
href: "#collections_holder"
)
)
-
-
+
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 03902741..9c2059c0 100644
--- a/wqflask/wqflask/static/new/javascript/bar_chart.js
+++ b/wqflask/wqflask/static/new/javascript/bar_chart.js
@@ -322,7 +322,7 @@
Bar_Chart.prototype.color_by_trait = function() {
var _this = this;
- return $('#collections_holder').load('/collections/list #collections_list', function() {
+ return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', function() {
return $.colorbox({
inline: true,
href: "#collections_holder"
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
new file mode 100644
index 00000000..6854dda5
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.coffee
@@ -0,0 +1,15 @@
+
+console.log("before get_traits_from_collection")
+
+
+collection_hover = () ->
+ console.log("Hovering over:", $(this))
+ this_collection_url = $(this).find('.collection_name').prop("href")
+ this_collection_url += "&json"
+ console.log("this_collection_url", this_collection_url)
+
+$ ->
+ console.log("inside get_traits_from_collection")
+ $(document).on("mouseover", ".collection_line", collection_hover)
+
+ \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
new file mode 100644
index 00000000..9ef31088
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -0,0 +1,20 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+ var collection_hover;
+
+ console.log("before get_traits_from_collection");
+
+ collection_hover = function() {
+ var this_collection_url;
+ console.log("Hovering over:", $(this));
+ this_collection_url = $(this).find('.collection_name').prop("href");
+ this_collection_url += "&json";
+ return console.log("this_collection_url", this_collection_url);
+ };
+
+ $(function() {
+ console.log("inside get_traits_from_collection");
+ return $(document).on("mouseover", ".collection_line", collection_hover);
+ });
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.coffee b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
new file mode 100644
index 00000000..78265f27
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.coffee
@@ -0,0 +1,293 @@
+$ ->
+
+ class Interval_Map
+ constructor: (@plot_height, @plot_width) ->
+ @qtl_results = js_data.qtl_results
+ console.log("qtl_results are:", @qtl_results)
+ @chromosomes = js_data.chromosomes
+
+ @total_length = 0
+
+ @max_chr = @get_max_chr()
+
+ @x_coords = []
+ @y_coords = []
+ @marker_names = []
+ console.time('Create coordinates')
+ @create_coordinates()
+ console.log("@x_coords: ", @x_coords)
+ console.log("@y_coords: ", @y_coords)
+ console.timeEnd('Create coordinates')
+ [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
+
+ # Buffer to allow for the ticks/labels to be drawn
+ @x_buffer = @plot_width/30
+ @y_buffer = @plot_height/20
+
+ #@x_max = d3.max(@x_coords)
+ @x_max = @total_length
+ console.log("@x_max: ", @x_max)
+ console.log("@x_buffer: ", @x_buffer)
+ @y_max = d3.max(@y_coords) * 1.2
+
+ @svg = @create_svg()
+ @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)
+
+ @plot_height -= @y_buffer
+ @create_scales()
+ console.time('Create graph')
+ @create_graph()
+ console.timeEnd('Create graph')
+
+ get_max_chr: () ->
+ max_chr = 0
+ for result in @qtl_results
+ chr = parseInt(result.chr)
+ if not _.isNaN(chr)
+ if chr > max_chr
+ max_chr = chr
+ return max_chr
+
+ get_chr_lengths: () ->
+ ###
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
+ ###
+
+ console.log("@chromosomes: ", @chromosomes)
+
+ cumulative_chr_lengths = []
+ chr_lengths = []
+ total_length = 0
+ for key of @chromosomes
+ this_length = @chromosomes[key]
+ chr_lengths.push(this_length)
+ cumulative_chr_lengths.push(total_length + this_length)
+ total_length += this_length
+
+ console.log("chr_lengths: ", chr_lengths)
+
+ return [chr_lengths, cumulative_chr_lengths]
+
+ create_coordinates: () ->
+ chr_lengths = []
+ chr_seen = []
+ for result in js_data.qtl_results
+ if result.locus.chr == "X"
+ chr_length = parseFloat(@chromosomes[20])
+ else
+ chr_length = parseFloat(@chromosomes[result.locus.chr])
+ if not(result.locus.chr in chr_seen)
+ chr_seen.push(result.locus.chr)
+ chr_lengths.push(chr_length)
+ if result.locus.chr != "1"
+ @total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
+ @x_coords.push(@total_length + parseFloat(result.locus.Mb))
+ @y_coords.push(result.lrs)
+ @marker_names.push(result.locus.name)
+ @total_length += parseFloat(chr_lengths[chr_lengths.length-1])
+ #console.log("chr_lengths: ", chr_lengths)
+
+ create_svg: () ->
+ svg = d3.select("#interval_map")
+ .append("svg")
+ .attr("class", "interval_map")
+ .attr("width", @plot_width+@x_buffer)
+ .attr("height", @plot_height+@y_buffer)
+
+ return svg
+
+ create_graph: () ->
+ @add_border()
+ @add_x_axis()
+ @add_y_axis()
+ @add_chr_lines()
+ @fill_chr_areas()
+ @add_chr_labels()
+ @connect_markers()
+
+ add_border: () ->
+ border_coords = [[@y_buffer, @plot_height, @x_buffer, @x_buffer],
+ [@y_buffer, @plot_height, @plot_width, @plot_width],
+ [@y_buffer, @y_buffer, @x_buffer, @plot_width],
+ [@plot_height, @plot_height, @x_buffer, @plot_width]]
+
+ @svg.selectAll("line")
+ .data(border_coords)
+ .enter()
+ .append("line")
+ .attr("y1", (d) =>
+ return d[0]
+ )
+ .attr("y2", (d) =>
+ return d[1]
+ )
+ .attr("x1", (d) =>
+ return d[2]
+ )
+ .attr("x2", (d) =>
+ return d[3]
+ )
+ .style("stroke", "#000")
+
+ create_scales: () ->
+ @x_scale = d3.scale.linear()
+ .domain([0, d3.max(@x_coords)])
+ .range([@x_buffer, @plot_width])
+
+ @y_scale = d3.scale.linear()
+ .domain([0, @y_max])
+ .range([@plot_height, @y_buffer])
+
+ create_x_axis_tick_values: () ->
+ tick_vals = []
+ for val in [25..@cumulative_chr_lengths[0]] when val%25 == 0
+ tick_vals.push(val)
+
+ for length, i in @cumulative_chr_lengths
+ if i == 0
+ continue
+ chr_ticks = []
+ tick_count = Math.floor(@chr_lengths[i]/25)
+ tick_val = parseInt(@cumulative_chr_lengths[i-1])
+ for tick in [0..(tick_count-1)]
+ tick_val += 25
+ chr_ticks.push(tick_val)
+ Array::push.apply tick_vals, chr_ticks
+
+ #console.log("tick_vals:", tick_vals)
+ return tick_vals
+
+ add_x_axis: () ->
+ xAxis = d3.svg.axis()
+ .scale(@x_scale)
+ .orient("bottom")
+ .tickValues(@create_x_axis_tick_values())
+
+ next_chr = 1
+ tmp_tick_val = 0
+ xAxis.tickFormat((d) =>
+ d3.format("d") #format as integer
+ if d < @cumulative_chr_lengths[0]
+ tick_val = d
+ else
+ next_chr_length = @cumulative_chr_lengths[next_chr]
+ if d > next_chr_length
+ next_chr += 1
+ tmp_tick_val = 25
+ tick_val = tmp_tick_val
+ else
+ tmp_tick_val += 25
+ tick_val = tmp_tick_val
+ return (tick_val)
+ )
+
+ @svg.append("g")
+ .attr("class", "x_axis")
+ .attr("transform", "translate(0," + @plot_height + ")")
+ .call(xAxis)
+ .selectAll("text")
+ .attr("text-anchor", "right")
+ .attr("dx", "-1.6em")
+ .attr("transform", (d) =>
+ return "translate(-12,0) rotate(-90)"
+ )
+ #.attr("dy", "-1.0em")
+
+
+ add_y_axis: () ->
+ yAxis = d3.svg.axis()
+ .scale(@y_scale)
+ .orient("left")
+ .ticks(5)
+
+ @svg.append("g")
+ .attr("class", "y_axis")
+ .attr("transform", "translate(" + @x_buffer + ",0)")
+ .call(yAxis)
+
+ add_chr_lines: () ->
+ @svg.selectAll("line")
+ .data(@cumulative_chr_lengths, (d) =>
+ return d
+ )
+ .enter()
+ .append("line")
+ .attr("x1", @x_scale)
+ .attr("x2", @x_scale)
+ .attr("y1", @y_buffer)
+ .attr("y2", @plot_height)
+ .style("stroke", "#ccc")
+
+ fill_chr_areas: () ->
+ @svg.selectAll("rect.chr_fill_area_1")
+ .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
+ return d
+ )
+ .enter()
+ .append("rect")
+ .attr("class", "chr_fill_area_1")
+ .attr("x", (d, i) =>
+ if i == 0
+ return @x_scale(0)
+ else
+ return @x_scale(@cumulative_chr_lengths[i-1])
+ )
+ .attr("y", @y_buffer)
+ .attr("width", (d) =>
+ return @x_scale(d[0])
+ )
+ .attr("height", @plot_height-@y_buffer)
+
+ add_chr_labels: () ->
+ chr_names = []
+ for key of @chromosomes
+ chr_names.push(key)
+ chr_info = _.zip(chr_names, @chr_lengths, @cumulative_chr_lengths)
+ @svg.selectAll("text")
+ .data(chr_info, (d) =>
+ return d
+ )
+ .enter()
+ .append("text")
+ .text((d) =>
+ return d[0]
+ )
+ .attr("x", (d) =>
+ return @x_scale(d[2] - d[1]/2)
+ )
+ .attr("y", @plot_height * 0.1)
+ .attr("dx", "0em")
+ .attr("text-anchor", "middle")
+ .attr("font-family", "sans-serif")
+ .attr("font-size", "18px")
+ .attr("fill", "grey")
+
+ connect_markers: () ->
+ @svg.selectAll("path")
+ .data(@plot_coordinates)
+ .enter()
+ .attr("x1", (d, i) =>
+ if i == 0
+ return @x_buffer
+ else
+ return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * @plot_coordinates[i-1][0]/parseFloat(@x_max))
+ )
+ .attr("y1", (d, i) =>
+ if i == 0
+ return @plot_height
+ else
+ return @plot_height - ((@plot_height-@y_buffer) * @plot_coordinates[i-1][1]/@y_max)
+ )
+ .attr("x2", (d) =>
+ return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * d[0]/parseFloat(@x_max))
+ )
+ .attr("y2", (d) =>
+ return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
+ )
+
+ console.time('Create manhattan plot')
+ new Interval_Map(600, 1200)
+ console.timeEnd('Create manhattan plot') \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/interval_mapping.js b/wqflask/wqflask/static/new/javascript/interval_mapping.js
new file mode 100644
index 00000000..5ae8ffab
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/interval_mapping.js
@@ -0,0 +1,272 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+ var __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; };
+
+ $(function() {
+ var Interval_Map;
+ Interval_Map = (function() {
+
+ function Interval_Map(plot_height, plot_width) {
+ var _ref;
+ this.plot_height = plot_height;
+ this.plot_width = plot_width;
+ this.qtl_results = js_data.qtl_results;
+ console.log("qtl_results are:", this.qtl_results);
+ this.chromosomes = js_data.chromosomes;
+ this.total_length = 0;
+ this.max_chr = this.get_max_chr();
+ this.x_coords = [];
+ this.y_coords = [];
+ this.marker_names = [];
+ console.time('Create coordinates');
+ this.create_coordinates();
+ console.log("@x_coords: ", this.x_coords);
+ console.log("@y_coords: ", this.y_coords);
+ console.timeEnd('Create coordinates');
+ _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
+ this.x_buffer = this.plot_width / 30;
+ this.y_buffer = this.plot_height / 20;
+ this.x_max = this.total_length;
+ console.log("@x_max: ", this.x_max);
+ console.log("@x_buffer: ", this.x_buffer);
+ this.y_max = d3.max(this.y_coords) * 1.2;
+ this.svg = this.create_svg();
+ this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
+ this.plot_height -= this.y_buffer;
+ this.create_scales();
+ console.time('Create graph');
+ this.create_graph();
+ console.timeEnd('Create graph');
+ }
+
+ Interval_Map.prototype.get_max_chr = function() {
+ var chr, max_chr, result, _i, _len, _ref;
+ max_chr = 0;
+ _ref = this.qtl_results;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ result = _ref[_i];
+ chr = parseInt(result.chr);
+ if (!_.isNaN(chr)) {
+ if (chr > max_chr) {
+ max_chr = chr;
+ }
+ }
+ }
+ return max_chr;
+ };
+
+ Interval_Map.prototype.get_chr_lengths = function() {
+ /*
+ #Gets a list of both individual and cumulative (the position of one on the graph
+ #is its own length plus the lengths of all preceding chromosomes) lengths in order
+ #to draw the vertical lines separating chromosomes and the chromosome labels
+ #
+ */
+
+ var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
+ console.log("@chromosomes: ", this.chromosomes);
+ cumulative_chr_lengths = [];
+ chr_lengths = [];
+ total_length = 0;
+ for (key in this.chromosomes) {
+ this_length = this.chromosomes[key];
+ chr_lengths.push(this_length);
+ cumulative_chr_lengths.push(total_length + this_length);
+ total_length += this_length;
+ }
+ console.log("chr_lengths: ", chr_lengths);
+ return [chr_lengths, cumulative_chr_lengths];
+ };
+
+ Interval_Map.prototype.create_coordinates = function() {
+ var chr_length, chr_lengths, chr_seen, result, _i, _len, _ref, _ref1;
+ chr_lengths = [];
+ chr_seen = [];
+ _ref = js_data.qtl_results;
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ result = _ref[_i];
+ if (result.locus.chr === "X") {
+ chr_length = parseFloat(this.chromosomes[20]);
+ } else {
+ chr_length = parseFloat(this.chromosomes[result.locus.chr]);
+ }
+ if (!(_ref1 = result.locus.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
+ chr_seen.push(result.locus.chr);
+ chr_lengths.push(chr_length);
+ if (result.locus.chr !== "1") {
+ this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
+ }
+ }
+ this.x_coords.push(this.total_length + parseFloat(result.locus.Mb));
+ this.y_coords.push(result.lrs);
+ this.marker_names.push(result.locus.name);
+ }
+ return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
+ };
+
+ Interval_Map.prototype.create_svg = function() {
+ var svg;
+ svg = d3.select("#interval_map").append("svg").attr("class", "interval_map").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer);
+ return svg;
+ };
+
+ Interval_Map.prototype.create_graph = function() {
+ this.add_border();
+ this.add_x_axis();
+ this.add_y_axis();
+ this.add_chr_lines();
+ this.fill_chr_areas();
+ this.add_chr_labels();
+ return this.connect_markers();
+ };
+
+ Interval_Map.prototype.add_border = function() {
+ var border_coords,
+ _this = this;
+ border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]];
+ return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", function(d) {
+ return d[0];
+ }).attr("y2", function(d) {
+ return d[1];
+ }).attr("x1", function(d) {
+ return d[2];
+ }).attr("x2", function(d) {
+ return d[3];
+ }).style("stroke", "#000");
+ };
+
+ Interval_Map.prototype.create_scales = function() {
+ this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
+ return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+ };
+
+ Interval_Map.prototype.create_x_axis_tick_values = function() {
+ var chr_ticks, i, length, tick, tick_count, tick_val, tick_vals, val, _i, _j, _k, _len, _ref, _ref1, _ref2;
+ tick_vals = [];
+ for (val = _i = 25, _ref = this.cumulative_chr_lengths[0]; 25 <= _ref ? _i <= _ref : _i >= _ref; val = 25 <= _ref ? ++_i : --_i) {
+ if (val % 25 === 0) {
+ tick_vals.push(val);
+ }
+ }
+ _ref1 = this.cumulative_chr_lengths;
+ for (i = _j = 0, _len = _ref1.length; _j < _len; i = ++_j) {
+ length = _ref1[i];
+ if (i === 0) {
+ continue;
+ }
+ chr_ticks = [];
+ tick_count = Math.floor(this.chr_lengths[i] / 25);
+ tick_val = parseInt(this.cumulative_chr_lengths[i - 1]);
+ for (tick = _k = 0, _ref2 = tick_count - 1; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; tick = 0 <= _ref2 ? ++_k : --_k) {
+ tick_val += 25;
+ chr_ticks.push(tick_val);
+ }
+ Array.prototype.push.apply(tick_vals, chr_ticks);
+ }
+ return tick_vals;
+ };
+
+ Interval_Map.prototype.add_x_axis = function() {
+ var next_chr, tmp_tick_val, xAxis,
+ _this = this;
+ xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").tickValues(this.create_x_axis_tick_values());
+ next_chr = 1;
+ tmp_tick_val = 0;
+ xAxis.tickFormat(function(d) {
+ var next_chr_length, tick_val;
+ d3.format("d");
+ if (d < _this.cumulative_chr_lengths[0]) {
+ tick_val = d;
+ } else {
+ next_chr_length = _this.cumulative_chr_lengths[next_chr];
+ if (d > next_chr_length) {
+ next_chr += 1;
+ tmp_tick_val = 25;
+ tick_val = tmp_tick_val;
+ } else {
+ tmp_tick_val += 25;
+ tick_val = tmp_tick_val;
+ }
+ }
+ return tick_val;
+ });
+ return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(xAxis).selectAll("text").attr("text-anchor", "right").attr("dx", "-1.6em").attr("transform", function(d) {
+ return "translate(-12,0) rotate(-90)";
+ });
+ };
+
+ Interval_Map.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").attr("transform", "translate(" + this.x_buffer + ",0)").call(yAxis);
+ };
+
+ Interval_Map.prototype.add_chr_lines = function() {
+ var _this = this;
+ return this.svg.selectAll("line").data(this.cumulative_chr_lengths, function(d) {
+ return d;
+ }).enter().append("line").attr("x1", this.x_scale).attr("x2", this.x_scale).attr("y1", this.y_buffer).attr("y2", this.plot_height).style("stroke", "#ccc");
+ };
+
+ Interval_Map.prototype.fill_chr_areas = function() {
+ var _this = this;
+ return this.svg.selectAll("rect.chr_fill_area_1").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+ return d;
+ }).enter().append("rect").attr("class", "chr_fill_area_1").attr("x", function(d, i) {
+ if (i === 0) {
+ return _this.x_scale(0);
+ } else {
+ return _this.x_scale(_this.cumulative_chr_lengths[i - 1]);
+ }
+ }).attr("y", this.y_buffer).attr("width", function(d) {
+ return _this.x_scale(d[0]);
+ }).attr("height", this.plot_height - this.y_buffer);
+ };
+
+ Interval_Map.prototype.add_chr_labels = function() {
+ var chr_info, chr_names, key,
+ _this = this;
+ chr_names = [];
+ for (key in this.chromosomes) {
+ chr_names.push(key);
+ }
+ chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
+ return this.svg.selectAll("text").data(chr_info, function(d) {
+ return d;
+ }).enter().append("text").text(function(d) {
+ return d[0];
+ }).attr("x", function(d) {
+ return _this.x_scale(d[2] - d[1] / 2);
+ }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "grey");
+ };
+
+ Interval_Map.prototype.connect_markers = function() {
+ var _this = this;
+ return this.svg.selectAll("path").data(this.plot_coordinates).enter().attr("x1", function(d, i) {
+ if (i === 0) {
+ return _this.x_buffer;
+ } else {
+ return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * _this.plot_coordinates[i - 1][0] / parseFloat(_this.x_max));
+ }
+ }).attr("y1", function(d, i) {
+ if (i === 0) {
+ return _this.plot_height;
+ } else {
+ return _this.plot_height - ((_this.plot_height - _this.y_buffer) * _this.plot_coordinates[i - 1][1] / _this.y_max);
+ }
+ }).attr("x2", function(d) {
+ return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
+ }).attr("y2", function(d) {
+ return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
+ });
+ };
+
+ return Interval_Map;
+
+ })();
+ console.time('Create manhattan plot');
+ new Interval_Map(600, 1200);
+ return console.timeEnd('Create manhattan plot');
+ });
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/scientific_notation.js b/wqflask/wqflask/static/new/javascript/scientific_notation.js
new file mode 100644
index 00000000..82c55fda
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/scientific_notation.js
@@ -0,0 +1,13 @@
+jQuery.extend( jQuery.fn.dataTableExt.oSort, {
+ "scientific-pre": function ( a ) {
+ return parseFloat(a);
+ },
+
+ "scientific-asc": function ( a, b ) {
+ return ((a < b) ? -1 : ((a > b) ? 1 : 0));
+ },
+
+ "scientific-desc": function ( a, b ) {
+ return ((a < b) ? 1 : ((a > b) ? -1 : 0));
+ }
+} ); \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js b/wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js
new file mode 100644
index 00000000..82c55fda
--- /dev/null
+++ b/wqflask/wqflask/static/new/packages/DataTables/js/dataTables.scientific.js
@@ -0,0 +1,13 @@
+jQuery.extend( jQuery.fn.dataTableExt.oSort, {
+ "scientific-pre": function ( a ) {
+ return parseFloat(a);
+ },
+
+ "scientific-asc": function ( a, b ) {
+ return ((a < b) ? -1 : ((a > b) ? 1 : 0));
+ },
+
+ "scientific-desc": function ( a, b ) {
+ return ((a < b) ? 1 : ((a > b) ? -1 : 0));
+ }
+} ); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index ea6db646..9b98c955 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -198,7 +198,7 @@
<!--</div>-->
</div>
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.10.2/jquery.min.js"></script>
<script src="/static/packages/bootstrap/js/bootstrap.min.js"></script>
<script>
//http://stackoverflow.com/questions/11521763/bootstrap-scrollspy-not-working
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index dce7d41d..ac621a61 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -5,6 +5,7 @@
{{ header("Your Collections",
'You have {}.'.format(numify(user_collections|count, "collection", "collections"))) }}
+
<div class="container">
<div class="page-header">
<h1>Collections owned by {{ g.user_session.user_ob.full_name }}</h1>
@@ -23,8 +24,8 @@
<tbody>
{% for uc in user_collections %}
- <tr>
- <td><a href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
+ <tr class="collection_line">
+ <td><a class="collection_name" href="{{ url_for('view_collection', uc_id=uc.id) }}">{{ uc.name }}</a></td>
<td>{{ timeago(uc.created_timestamp.isoformat() + "Z") }}</td>
<td>{{ timeago(uc.changed_timestamp.isoformat() + "Z") }}</td>
<td>{{ uc.num_members }}</td>
@@ -33,6 +34,10 @@
</tbody>
</table>
+ {# if "color_by_trait" in params #}
+ <script type="text/javascript" src="/static/new/javascript/get_traits_from_collection.js"></script>
+ {# endif #}
+
</div>
</div>
@@ -41,10 +46,8 @@
{% endblock %}
{% block js %}
-
<script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
<script>
$('body').timeago();
</script>
-
{% endblock %}
diff --git a/wqflask/wqflask/templates/interval_mapping.html b/wqflask/wqflask/templates/interval_mapping.html
new file mode 100644
index 00000000..25de2dc1
--- /dev/null
+++ b/wqflask/wqflask/templates/interval_mapping.html
@@ -0,0 +1,104 @@
+{% extends "base.html" %}
+{% block title %}Interval Mapping{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="/static/packages/jqplot/jquery.jqplot.min.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/interval_mapping.css" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
+ <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+{% endblock %}
+{% block content %} <!-- Start of body -->
+
+ {{ header("Mapping",
+ '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
+ <div class="container">
+ <div>
+ <h2>
+ Whole Genome Mapping
+ </h2>
+ </div>
+ <div id="interval_map" class="interval_map">
+
+ </div>
+ <div>
+ <h2>
+ Results
+ </h2>
+ </div>
+ <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
+ <thead>
+ <tr>
+ <td>Index</td>
+ <td>LRS Score</td>
+ <td>Additive Effect</td>
+ <td>Chr</td>
+ <td>Mb</td>
+ <td>Locus</td>
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in qtl_results %}
+ <tr>
+ <td>{{ loop.index }}</td>
+ <td>{{ marker.lrs|float }}</td>
+ <td>{{ marker.additive|float }}</td>
+ <td>{{ marker.locus.chr|int }}</td>
+ <td>{{ marker.locus.Mb|float }}</td>
+ <td>{{ marker.locus.name }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+
+ </div>
+
+ <!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script>
+ js_data = {{ js_data | safe }}
+ </script>
+
+ <!--[if lt IE 9]>
+ <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>
+ <![endif]-->
+ <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/interval_mapping.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ console.time("Creating table");
+ $('#qtl_results').dataTable( {
+ //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+ "sDom": "lTftipr",
+ "oTableTools": {
+ "aButtons": [
+ "copy",
+ "print",
+ {
+ "sExtends": "collection",
+ "sButtonText": 'Save <span class="caret" />',
+ "aButtons": [ "csv", "xls", "pdf" ]
+ }
+ ],
+ "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+ },
+ "iDisplayLength": 50,
+ "bLengthChange": true,
+ "bDeferRender": true,
+ "bSortClasses": false
+ } );
+ console.timeEnd("Creating table");
+ });
+ </script>
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 91e6df42..ec729e1c 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -57,6 +57,7 @@
<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/get_traits_from_collection.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 00301d39..a835a41b 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -20,6 +20,7 @@
<label for="chromosome" class="control-label">Chromosome</label>
<div class="controls">
<select name="chromosome">
+ <option value="-1">All</option>
{% for name, value in dataset.species.chromosomes.chromosomes.items() %}
<option value="{{ value }}">{{ name }}</option>
{% endfor %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 50161d41..b528f2b1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -213,7 +213,7 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v14"
+ version = "v1"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
@@ -237,8 +237,10 @@ def marker_regression_page():
result = template_vars.__dict__
- #for item in template_vars.__dict__.keys():
- # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+ print("DATASET:", pf(result['dataset']))
+
+ for item in template_vars.__dict__.keys():
+ print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
#causeerror
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
@@ -268,7 +270,7 @@ def interval_mapping_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v1"
+ version = "v7"
key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
@@ -288,6 +290,9 @@ def interval_mapping_page():
result = template_vars.__dict__
+ for item in template_vars.__dict__.keys():
+ print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+
#causeerror
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
Redis.expire(key, 60*60)