From e71ec85ba3fc7ac45d035c7c1363b36aed709433 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Tue, 12 Mar 2013 22:22:49 +0000
Subject: Got cashing working with pickle
---
wqflask/base/data_set.py | 45 +++++++++++-----------
wqflask/base/species.py | 2 +-
wqflask/utility/helper_functions.py | 4 +-
wqflask/wqflask/show_trait/show_trait.py | 10 ++---
.../static/new/javascript/marker_regression.coffee | 32 +++++++--------
.../static/new/javascript/marker_regression.js | 28 +++++++-------
wqflask/wqflask/templates/marker_regression.html | 11 ++++--
.../templates/show_trait_mapping_tools.html | 18 +--------
wqflask/wqflask/views.py | 29 +++++++-------
9 files changed, 83 insertions(+), 96 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d474302c..10f047f8 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -95,11 +95,14 @@ class DatasetGroup(object):
if self.name == 'BXD300':
self.name = "BXD"
+ self.f1list = None
+ self.parlist = None
+ self.get_f1_parent_strains()
+ print("parents/f1s: {}:{}".format(self.parlist, self.f1list))
+
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
self.incparentsf1 = False
- self.f1list = None
- self.parlist = None
self.allsamples = None
self.markers = Markers(self.name)
@@ -117,6 +120,18 @@ class DatasetGroup(object):
# markers = json.load(json_data)
#
+ def get_f1_parent_strains(self):
+ try:
+ # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
+ f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
+ except KeyError:
+ f1 = f12 = maternal = paternal = None
+
+ if f1 and f12:
+ self.f1list = [f1, f12]
+ if maternal and paternal:
+ self.parlist = [maternal, paternal]
+
def read_genotype_file(self):
'''Read genotype from .geno file instead of database'''
#if self.group == 'BXD300':
@@ -128,38 +143,24 @@ class DatasetGroup(object):
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
genotype_1 = reaper.Dataset()
-
+
# reaper barfs on unicode filenames, so here we ensure it's a string
full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
genotype_1.read(full_filename)
- print("Got to after read")
-
- try:
- # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
- except KeyError:
- f1 = f12 = maternal = paternal = None
-
-
- if genotype_1.type == "group" and maternal and paternal:
- genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1)
+ if genotype_1.type == "group" and self.parlist:
+ genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
else:
genotype_2 = genotype_1
#determine default genotype object
if self.incparentsf1 and genotype_1.type != "intercross":
- self.genotype = genotype_2
+ genotype = genotype_2
else:
self.incparentsf1 = 0
- self.genotype = genotype_1
-
- self.samplelist = list(self.genotype.prgy)
+ genotype = genotype_1
- if f1 and f12:
- self.f1list = [f1, f12]
- if maternal and paternal:
- self.parlist = [maternal, paternal]
+ self.samplelist = list(genotype.prgy)
class DataSet(object):
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 9d4cac4c..689e5c05 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -62,7 +62,7 @@ class Chromosomes(object):
self.chromosomes[item.Name] = IndChromosome(item.Length)
self.set_mb_graph_interval()
- self.get_cm_length_list()
+ #self.get_cm_length_list()
def set_mb_graph_interval(self):
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 56b409e6..28242c27 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -12,7 +12,7 @@ def get_species_dataset_trait(self, start_vars):
self.this_trait = GeneralTrait(dataset=self.dataset.name,
name=start_vars['trait_id'],
cellid=None)
-
+
#if read_genotype:
self.dataset.group.read_genotype_file()
- self.genotype = self.dataset.group.genotype
+ #self.genotype = self.dataset.group.genotype
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 16aec827..12d512b2 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -51,10 +51,10 @@ class ShowTrait(object):
# cellid=None)
#
#
- #self.dataset.group.read_genotype_file()
+ self.dataset.group.read_genotype_file()
- if not self.dataset.group.genotype:
- self.read_data(include_f1=True)
+ #if not self.dataset.group.genotype:
+ # self.read_data(include_f1=True)
# Todo: Add back in the ones we actually need from below, as we discover we need them
@@ -163,8 +163,8 @@ class ShowTrait(object):
#if incf1 == None:
# incf1 = []
- if not self.genotype:
- self.dataset.read_genotype_file()
+ #if not self.genotype:
+ # self.dataset.read_genotype_file()
if not samplelist:
if include_f1:
samplelist = self.f1list + self.samplelist
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index ef56dc99..ebd96b19 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -10,10 +10,11 @@ $ ->
@x_coords = []
@y_coords = []
- @marker_names = []
+ @marker_names = []
+ console.time('Create coordinates')
@create_coordinates()
+ console.timeEnd('Create coordinates')
[@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
- console.log("cumulative_chr_len: ", @cumulative_chr_lengths)
# Buffer to allow for the ticks/labels to be drawn
@x_buffer = @plot_width/30
@@ -25,15 +26,17 @@ $ ->
@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)
- console.log("foo:", chr, typeof(chr))
if not _.isNaN(chr)
if chr > max_chr
max_chr = chr
@@ -56,7 +59,7 @@ $ ->
cumulative_chr_lengths.push(total_length + this_length)
total_length += this_length
- console.log("total length is:", total_length)
+ #console.log("total length is:", total_length)
return [chr_lengths, cumulative_chr_lengths]
@@ -70,13 +73,13 @@ $ ->
chr_lengths.push(chr_length)
if result.chr != "1"
@total_length += chr_lengths[chr_lengths.length - 2]
- console.log("total_length is:", @total_length)
@x_coords.push(@total_length + parseFloat(result.Mb))
@y_coords.push(result.lod_score)
@marker_names.push(result.name)
@total_length += chr_lengths[chr_lengths.length-1]
show_marker_in_table: (marker_info) ->
+ console.log("in show_marker_in_table")
### Searches for the select marker in the results table below ###
if marker_info
marker_name = marker_info[2]
@@ -148,11 +151,10 @@ $ ->
tick_val = parseInt(@cumulative_chr_lengths[i-1])
for tick in [0..(tick_count-1)]
tick_val += 25
- console.log("tick_val is:", tick_val)
chr_ticks.push(tick_val)
Array::push.apply tick_vals, chr_ticks
- console.log("tick_vals:", tick_vals)
+ #console.log("tick_vals:", tick_vals)
return tick_vals
add_x_axis: () ->
@@ -176,7 +178,6 @@ $ ->
else
tmp_tick_val += 25
tick_val = tmp_tick_val
- console.log("tick_val: ", tick_val)
return (tick_val)
)
@@ -242,7 +243,6 @@ $ ->
for key of @chromosomes
chr_names.push(key)
chr_info = _.zip(chr_names, @chr_lengths, @cumulative_chr_lengths)
- console.log("chr_info is", chr_info)
@svg.selectAll("text")
.data(chr_info, (d) =>
return d
@@ -250,7 +250,6 @@ $ ->
.enter()
.append("text")
.text((d) =>
- console.log("d[0] is ", d[0])
return d[0]
)
.attr("x", (d) =>
@@ -263,9 +262,7 @@ $ ->
.attr("font-size", "18px")
.attr("fill", "grey")
-
add_plot_points: () ->
- console.log("x_max is:", @x_max)
@svg.selectAll("circle")
.data(@plot_coordinates)
.enter()
@@ -279,16 +276,21 @@ $ ->
.attr("r", 2)
.classed("circle", true)
.on("mouseover", (d) =>
- d3.select(d3.event.target).classed("d3_highlight", true)
+ console.log("this:", this)
+ console.log("d3.event is:", d3.event)
+ console.log("d is:", d)
+ d3.select(d3.event)
.attr("r", 5)
.attr("fill", "yellow")
.call(@show_marker_in_table(d))
)
.on("mouseout", () =>
- d3.select(d3.event.target).classed("d3_highlight", false)
+ d3.select(d3.event)
.attr("r", 2)
.attr("fill", "black")
.call(@show_marker_in_table())
)
- new Manhattan_Plot(600, 1200)
\ No newline at end of file
+ console.time('Create manhattan plot')
+ new Manhattan_Plot(600, 1200)
+ console.timeEnd('Create manhattan plot')
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index efe6f508..25a8d5b5 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -17,9 +17,10 @@
this.x_coords = [];
this.y_coords = [];
this.marker_names = [];
+ console.time('Create coordinates');
this.create_coordinates();
+ console.timeEnd('Create coordinates');
_ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
- console.log("cumulative_chr_len: ", this.cumulative_chr_lengths);
this.x_buffer = this.plot_width / 30;
this.y_buffer = this.plot_height / 20;
this.x_max = this.total_length;
@@ -28,7 +29,9 @@
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');
}
Manhattan_Plot.prototype.get_max_chr = function() {
@@ -38,7 +41,6 @@
for (_i = 0, _len = _ref.length; _i < _len; _i++) {
result = _ref[_i];
chr = parseInt(result.chr);
- console.log("foo:", chr, typeof chr);
if (!_.isNaN(chr)) {
if (chr > max_chr) {
max_chr = chr;
@@ -65,7 +67,6 @@
cumulative_chr_lengths.push(total_length + this_length);
total_length += this_length;
}
- console.log("total length is:", total_length);
return [chr_lengths, cumulative_chr_lengths];
};
@@ -82,7 +83,6 @@
chr_lengths.push(chr_length);
if (result.chr !== "1") {
this.total_length += chr_lengths[chr_lengths.length - 2];
- console.log("total_length is:", this.total_length);
}
}
this.x_coords.push(this.total_length + parseFloat(result.Mb));
@@ -93,10 +93,11 @@
};
Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
+ var marker_name;
+ console.log("in show_marker_in_table");
/* Searches for the select marker in the results table below
*/
- var marker_name;
if (marker_info) {
marker_name = marker_info[2];
} else {
@@ -160,12 +161,10 @@
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;
- console.log("tick_val is:", tick_val);
chr_ticks.push(tick_val);
}
Array.prototype.push.apply(tick_vals, chr_ticks);
}
- console.log("tick_vals:", tick_vals);
return tick_vals;
};
@@ -191,7 +190,6 @@
tick_val = tmp_tick_val;
}
}
- console.log("tick_val: ", 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) {
@@ -235,11 +233,9 @@
chr_names.push(key);
}
chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
- console.log("chr_info is", chr_info);
return this.svg.selectAll("text").data(chr_info, function(d) {
return d;
}).enter().append("text").text(function(d) {
- console.log("d[0] is ", d[0]);
return d[0];
}).attr("x", function(d) {
return _this.x_scale(d[2] - d[1] / 2);
@@ -248,22 +244,26 @@
Manhattan_Plot.prototype.add_plot_points = function() {
var _this = this;
- console.log("x_max is:", this.x_max);
return this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
return _this.x_buffer + ((_this.plot_width - _this.x_buffer) * d[0] / _this.x_max);
}).attr("cy", function(d) {
return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
}).attr("r", 2).classed("circle", true).on("mouseover", function(d) {
- return d3.select(d3.event.target).classed("d3_highlight", true).attr("r", 5).attr("fill", "yellow").call(_this.show_marker_in_table(d));
+ console.log("this:", _this);
+ console.log("d3.event is:", d3.event);
+ console.log("d is:", d);
+ return d3.select(d3.event).attr("r", 5).attr("fill", "yellow").call(_this.show_marker_in_table(d));
}).on("mouseout", function() {
- return d3.select(d3.event.target).classed("d3_highlight", false).attr("r", 2).attr("fill", "black").call(_this.show_marker_in_table());
+ return d3.select(d3.event).attr("r", 2).attr("fill", "black").call(_this.show_marker_in_table());
});
};
return Manhattan_Plot;
})();
- return new Manhattan_Plot(600, 1200);
+ console.time('Create manhattan plot');
+ new Manhattan_Plot(600, 1200);
+ return console.timeEnd('Create manhattan plot');
});
}).call(this);
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index fc068d21..afbbb7c9 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -69,18 +69,18 @@
-
+
-
-
+
{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 58174c78..a98a75c7 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -41,23 +41,7 @@
-
-
- {% if dataset.group.genotype.Mbmap %}
-
- {% endif %}
+
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index c8432877..46433430 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -31,6 +31,7 @@ from utility import temp_data
from wqflask.dataSharing import SharingInfo, SharingInfoPage
from base import webqtlFormData
+from utility.benchmark import Bench
from pprint import pformat as pf
@@ -168,25 +169,18 @@ def marker_regression_page():
start_vars[key] = value
version = "v5"
- print("version is:", version)
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
- result = Redis.get(key)
+ with Bench("Loading cache"):
+ result = Redis.get(key)
- print("************************ Starting result *****************")
+ #print("************************ Starting result *****************")
#print("result is [{}]: {}".format(type(result), result))
- print("************************ Ending result ********************")
+ #print("************************ Ending result ********************")
if result:
- with open("/tmp/result", "w") as fh:
- fh.write(result)
print("Cache hit!!!")
- import __builtin__
- import reaper
- __builtin__.Dataset = reaper.Dataset
- #result = yaml.load(result)
- result = pickle.loads(result)
- print("Done loading yaml")
-
+ with Bench("Loading results"):
+ result = pickle.loads(result)
else:
print("Cache miss!!!")
template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid)
@@ -197,14 +191,17 @@ def marker_regression_page():
result = template_vars.__dict__
- for item in template_vars.__dict__.keys():
- print(" ---**--- {}: {}".format(type(item), item))
+ #for item in template_vars.__dict__.keys():
+ # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
#causeerror
Redis.set(key, pickle.dumps(result))
Redis.expire(key, 60*60)
+
+ with Bench("Rendering template"):
+ rendered_template = render_template("marker_regression.html", **result)
- return render_template("marker_regression.html", **result)
+ return rendered_template
@app.route("/corr_compute", methods=('POST',))
--
cgit v1.2.3