From 27d0c86528fdbeaed56a7f5eaa71a950c522f183 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 5 Apr 2013 23:17:02 +0000
Subject: Loading bar now correctly shows the time to completion and the code
seems to run correctly
---
wqflask/other_config/wqflask-nginx.conf | 2 +-
wqflask/utility/temp_data.py | 1 -
.../wqflask/marker_regression/marker_regression.py | 9 +++--
wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 15 ++++----
.../new/javascript/show_trait_mapping_tools.coffee | 42 +++++++++++++++++++---
.../new/javascript/show_trait_mapping_tools.js | 36 ++++++++++++++++---
.../wqflask/templates/show_trait_progress_bar.html | 2 ++
7 files changed, 86 insertions(+), 21 deletions(-)
diff --git a/wqflask/other_config/wqflask-nginx.conf b/wqflask/other_config/wqflask-nginx.conf
index f0076f54..50f9d73c 100644
--- a/wqflask/other_config/wqflask-nginx.conf
+++ b/wqflask/other_config/wqflask-nginx.conf
@@ -36,7 +36,7 @@ server {
proxy_set_header X-Real-IP $remote_addr;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
- proxy_read_timeout 20m;
+ proxy_read_timeout 40m;
}
}
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 0df79e54..004d45c6 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -11,7 +11,6 @@ class TempData(object):
self.key = "tempdata:{}".format(self.temp_uuid)
def store(self, field, value):
- print("Storing...")
self.redis.hset(self.key, field, value)
self.redis.expire(self.key, 60*15) # Expire in 15 minutes
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 5f4f9be8..545c8162 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -71,7 +71,7 @@ class MarkerRegression(object):
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_value_samples=[])
pdb.set_trace()
@@ -90,7 +90,12 @@ class MarkerRegression(object):
self.dataset.group.markers.add_pvalues(p_values)
- self.qtl_results = self.dataset.group.markers.markers
+ self.qtl_results = []
+ for marker in self.dataset.group.markers.markers:
+ if marker['p_value'] < 0.2:
+ self.qtl_results.append(marker)
+
+ #self.qtl_results = self.dataset.group.markers.markers
def gen_human_results(self, pheno_vector, tempdata):
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 4de77173..0e965c8e 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -62,17 +62,18 @@ def run_human(pheno_vector,
plink_input.getSNPIterator()
total_snps = plink_input.numSNPs
-
- count = 0
+
with Bench("snp iterator loop"):
+ count = 0
for snp, this_id in plink_input:
- #if count > 1000:
+ #if count > 5000:
# break
count += 1
+
percent_complete = (float(count) / total_snps) * 100
- print("percent_complete: ", pf(percent_complete))
- temp_data.store("percent_complete", percent_complete)
+ #print("percent_complete: ", percent_complete)
+ temp_data.store("percent_complete", percent_complete)
x = snp[keep].reshape((n,1))
#x[[1,50,100,200,3000],:] = np.nan
@@ -113,11 +114,9 @@ def run_human(pheno_vector,
if refit:
lmm_ob.fit(X=x)
ts, ps, beta, betaVar = lmm_ob.association(x)
-
+
p_values.append(ps)
t_stats.append(ts)
-
- print("p_values: ", pf(p_values))
return p_values, t_stats
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 22427e4f..bc176ab9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -1,3 +1,6 @@
+# http://stackoverflow.com/a/4215132/1175849
+root = exports ? this
+
$ ->
submit_special = ->
# Add submit_special class plus a data-url field to any button
@@ -10,7 +13,29 @@ $ ->
console.log("url is:", url)
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit()
+
+ #update_time_remaining = (percent_complete) ->
+ # seconds_remaining = 1 / (percent_complete - root.previous_percent) * (100 - percent_complete)
+ # minutes_remaining = seconds_remaining / 60
+ # $('#time_remaining').text(Math.round(minutes_remaining) + " minutes remaining")
+ # root.previous_percent = percent_complete
+ update_time_remaining = (percent_complete) ->
+ now = new Date()
+ period = now.getTime() - root.start_time
+ console.log("period is:", period)
+ if period > 8000
+ total_seconds_remaining = (period / percent_complete * (100 - percent_complete))/1000
+ minutes_remaining = Math.round(total_seconds_remaining / 60)
+ #seconds_remaining = Math.round(total_seconds_remaining % 60)
+ #console.log("seconds_remaining:", seconds_remaining)
+ if minutes_remaining < 3
+ $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining")
+ else
+ $('#time_remaining').text(minutes_remaining + " minutes remaining")
+ #else
+ # $('#time_remaining').text("period too small")
+
get_progress = ->
console.log("temp_uuid:", $("#temp_uuid").val())
temp_uuid = $("#temp_uuid").val()
@@ -22,9 +47,16 @@ $ ->
type: "GET"
url: url
success: (progress_data) =>
+ percent_complete = progress_data['percent_complete']
console.log("in get_progress data:", progress_data)
- console.log(progress_data['percent_complete'] + "%")
- $('#marker_regression_progress').css("width", progress_data['percent_complete'] + "%")
+
+ $('#marker_regression_progress').css("width", percent_complete + "%")
+
+ if root.start_time
+ unless isNaN(percent_complete)
+ update_time_remaining(percent_complete)
+ else
+ root.start_time = new Date().getTime()
)
return false
@@ -38,17 +70,19 @@ $ ->
url: url
data: form_data
error: (xhr, ajaxOptions, thrownError) =>
- alert("some error occurred")
+ alert("Sorry, an error occurred")
console.log(xhr)
clearInterval(this.my_timer)
$('#progress_bar_container').modal('hide')
- $("body").html("error")
+ $("body").html("We got an error.")
success: (data) =>
clearInterval(this.my_timer)
$('#progress_bar_container').modal('hide')
$("body").html(data)
)
console.log("settingInterval")
+
+ #root.start_time = new Date().getTime()
this.my_timer = setInterval(get_progress, 1000)
return false
)
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 daf9b273..b017257a 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -1,8 +1,11 @@
// Generated by CoffeeScript 1.4.0
(function() {
+ var root;
+
+ root = typeof exports !== "undefined" && exports !== null ? exports : this;
$(function() {
- var composite_mapping_fields, get_progress, submit_special, toggle_enable_disable,
+ var composite_mapping_fields, get_progress, submit_special, toggle_enable_disable, update_time_remaining,
_this = this;
submit_special = function() {
var url;
@@ -14,6 +17,21 @@
$("#trait_data_form").attr("action", url);
return $("#trait_data_form").submit();
};
+ update_time_remaining = function(percent_complete) {
+ var minutes_remaining, now, period, total_seconds_remaining;
+ now = new Date();
+ period = now.getTime() - root.start_time;
+ console.log("period is:", period);
+ if (period > 8000) {
+ total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000;
+ minutes_remaining = Math.round(total_seconds_remaining / 60);
+ if (minutes_remaining < 3) {
+ return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining");
+ } else {
+ return $('#time_remaining').text(minutes_remaining + " minutes remaining");
+ }
+ }
+ };
get_progress = function() {
var params, params_str, temp_uuid, url,
_this = this;
@@ -29,9 +47,17 @@
type: "GET",
url: url,
success: function(progress_data) {
+ var percent_complete;
+ percent_complete = progress_data['percent_complete'];
console.log("in get_progress data:", progress_data);
- console.log(progress_data['percent_complete'] + "%");
- return $('#marker_regression_progress').css("width", progress_data['percent_complete'] + "%");
+ $('#marker_regression_progress').css("width", percent_complete + "%");
+ if (root.start_time) {
+ if (!isNaN(percent_complete)) {
+ return update_time_remaining(percent_complete);
+ }
+ } else {
+ return root.start_time = new Date().getTime();
+ }
}
});
return false;
@@ -47,11 +73,11 @@
url: url,
data: form_data,
error: function(xhr, ajaxOptions, thrownError) {
- alert("some error occurred");
+ alert("Sorry, an error occurred");
console.log(xhr);
clearInterval(_this.my_timer);
$('#progress_bar_container').modal('hide');
- return $("body").html("error");
+ return $("body").html("We got an error.");
},
success: function(data) {
clearInterval(_this.my_timer);
diff --git a/wqflask/wqflask/templates/show_trait_progress_bar.html b/wqflask/wqflask/templates/show_trait_progress_bar.html
index eff5c391..0c3f0e6e 100644
--- a/wqflask/wqflask/templates/show_trait_progress_bar.html
+++ b/wqflask/wqflask/templates/show_trait_progress_bar.html
@@ -6,5 +6,7 @@
+
+
\ No newline at end of file
--
cgit v1.2.3