diff options
Diffstat (limited to 'wqflask')
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 @@ <div class="progress active"> <div id="marker_regression_progress" class="bar"></div> </div> + <div id="time_remaining"> + </div> </div> </div>
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