From edea9d9596fdea6d5b41d99a9733bd451957a70b Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Tue, 20 Feb 2018 17:23:03 +0100
Subject: [PATCH] Add export to TSV for summary
---
src/dgenies/static/js/dgenies.result.min.js | 2 +-
.../static/js/dgenies.result.summary.js | 57 +++++++++++--------
2 files changed, 35 insertions(+), 24 deletions(-)
diff --git a/src/dgenies/static/js/dgenies.result.min.js b/src/dgenies/static/js/dgenies.result.min.js
index 25721e0..c8e2b81 100644
--- a/src/dgenies/static/js/dgenies.result.min.js
+++ b/src/dgenies/static/js/dgenies.result.min.js
@@ -2,7 +2,7 @@ if(!dgenies){throw"dgenies wasn't included!"}dgenies.result={};// GLOBAL VARIABL
dgenies.result.id_res=null;dgenies.result.init=function(id_res){dgenies.result.id_res=id_res;dgenies.result.add_to_list();d3.boxplot.init()};dgenies.result.add_to_list=function(){console.log("pass",dgenies.result.id_res);let cookies=$.cookie("results");cookies=cookies!==undefined?cookies.split("|"):[];console.log(cookies);if(cookies.indexOf(dgenies.result.id_res)===-1){console.log("oui");cookies.splice(0,0,dgenies.result.id_res);dgenies.save_cookies(cookies);dgenies.update_results(cookies)}};dgenies.result.remove_job_from_cookie=function(job){let cookies=$.cookie("results");cookies=cookies!==undefined?cookies.split("|"):[];let index=cookies.indexOf(job);let need_update=false;if(index>-1){need_update=true;cookies.splice(index,1)}$.cookie("results",cookies.join("|"),{path:"/"});if(need_update){dgenies.update_results(cookies)}};
if(!dgenies||!dgenies.result){throw"dgenies.result wasn't included!"}dgenies.result.controls={};dgenies.result.controls.init=function(){$("#sort-contigs").click(dgenies.result.controls.launch_sort_contigs);$("#hide-noise").click(dgenies.result.controls.launch_hide_noise);$("#summary").click(dgenies.result.controls.summary);$("#delete-job").click(dgenies.result.controls.delete_job);$("form#select-zone input.submit").click(dgenies.result.controls.select_zone);$("form#export select").change(dgenies.result.export.export)};dgenies.result.controls.summary=function(){dgenies.show_loading("Building...");window.setTimeout(()=>{dgenies.post(`/summary/${dgenies.result.id_res}`,{},function(data){dgenies.hide_loading();if(data["success"]){if(data["status"]==="done"){dgenies.result.summary.show(data["percents"])}else if(data["status"]==="waiting"){dgenies.result.controls.summary()}}else{dgenies.notify(data["message"]||"An error occurred! Please contact us to report the bug","danger")}})},0)};dgenies.result.controls.launch_sort_contigs=function(){d3.boxplot.zoom.reset_scale();window.setTimeout(()=>{dgenies.show_loading("Building...");window.setTimeout(()=>{dgenies.post(`/sort/${dgenies.result.id_res}`,{},function(data){if(data["success"]){dgenies.reset_loading_message();window.setTimeout(()=>{d3.boxplot.launch(data,true)},0)}else{dgenies.hide_loading();dgenies.notify(data["message"]||"An error occurred! Please contact us to report the bug","danger")}})},0)},0)};dgenies.result.controls.launch_reverse_contig=function(){if(d3.boxplot.query_selected!==null){d3.boxplot.zoom.reset_scale();window.setTimeout(()=>{dgenies.show_loading("Building...");window.setTimeout(()=>{dgenies.post(`/reverse-contig/${dgenies.result.id_res}`,{"contig":d3.boxplot.query_selected},function(data){if(data["success"]){dgenies.reset_loading_message();window.setTimeout(()=>{d3.boxplot.launch(data,true)},0)}else{dgenies.hide_loading();dgenies.notify(data["message"]||"An error occurred! Please contact us to report the bug","danger")}})},0)},0)}else{dgenies.notify("Error: no query selected. Please contact us to report the bug","danger")}};dgenies.result.controls.launch_hide_noise=function(){d3.boxplot.zoom.reset_scale();window.setTimeout(()=>{dgenies.show_loading("Building...");window.setTimeout(()=>{dgenies.post(`/freenoise/${dgenies.result.id_res}`,{noise:dgenies.noise?0:1},function(data){if(data["success"]){dgenies.noise=!dgenies.noise;dgenies.reset_loading_message();window.setTimeout(()=>{d3.boxplot.launch(data,true,true)},0)}else{dgenies.hide_loading();dgenies.notify(data["message"]||"An error occurred! Please contact us to report the bug","danger")}})},0)},0)};dgenies.result.controls.select_zone=function(){let contig_select=$("#select-contig").find(":selected");let target_select=$("#select-target").find(":selected");if(contig_select.val()!=="###NONE###"&&target_select.val()!=="###NONE###"){d3.boxplot.select_zone(null,null,target_select.val(),contig_select.val(),true)}else{dgenies.notify("Please select zones into zoom!","danger",2000)}};dgenies.result.controls.do_delete_job=function(){dgenies.post(`/delete/${dgenies.result.id_res}`,{},function(data){if(data["success"]){dgenies.notify("Your job has been deleted!","success",1500);window.setTimeout(()=>{dgenies.result.remove_job_from_cookie(dgenies.result.id_res);window.location="/"},1500)}else{dgenies.notify("error"in data?data["error"]:"An error has occurred. Please contact the support","danger")}})};dgenies.result.controls.delete_job=function(){let dialog=$("<div>").attr("id","dialog-confirm").attr("title","Delete job?");let icon=$("<span>").attr("class","ui-icon ui-icon-help").css("float","left").css("margin","12px 12px 20px 0");let body=$("<p>");body.append(icon);body.append("Confirm deletion of this job? This operation is definitive.");dialog.append(body);dialog.dialog({resizable:false,height:"auto",width:500,modal:true,buttons:{"Yes":function(){$(this).dialog("close");dgenies.result.controls.do_delete_job()},"No":function(){$(this).dialog("close")}}})};
if(!dgenies||!dgenies.result){throw"dgenies.result wasn't included!"}dgenies.result.export={};dgenies.result.export.get_svg=function(){return"<svg width='5000px' height='5000px' viewBox='0 0 100 100'>"+$("#draw-in").find(">svg").html()+"</svg>"};dgenies.result.export.save_file=function(blob,format){dgenies.hide_loading();saveAs(blob,`map_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.${format}`)};dgenies.result.export.export_png=function(){dgenies.show_loading("Building picture...",210);window.setTimeout(()=>{let export_div=$("div#export-pict");export_div.html("").append($("<canvas>"));canvg(export_div.find("canvas")[0],dgenies.result.export.get_svg());let canvas=export_div.find("canvas")[0];canvas.toBlob(function(blob){dgenies.result.export.save_file(blob,"png");export_div.html("")},"image/png")},0)};dgenies.result.export.export_svg=function(){dgenies.show_loading("Building picture...",180);window.setTimeout(()=>{let transform=d3.boxplot.container.attr("transform");let after=function(){let blob=new Blob([dgenies.result.export.get_svg()],{type:"image/svg+xml"});d3.boxplot.zoom.restore_scale(transform);dgenies.result.export.save_file(blob,"svg")};d3.boxplot.zoom.reset_scale(true,after)},0)};dgenies.result.export.export_paf=function(){let export_div=$("div#export-pict");export_div.html("");export_div.append($("<a>").attr("href",`/paf/${dgenies.result.id_res}`).attr("download",`map_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.paf`).attr("id","my-download").text("download"));dgenies.hide_loading();document.getElementById("my-download").click()};dgenies.result.export.dl_fasta=function(gzip=false){let export_div=$("div#export-pict");export_div.html("");export_div.append($("<a>").attr("href",`/fasta-query/${dgenies.result.id_res}`).attr("download",d3.boxplot.name_y+(gzip?".fasta.gz":".fasta")).attr("id","my-download").text("download"));dgenies.hide_loading();document.getElementById("my-download").click()};dgenies.result.export.export_fasta=function(compress=false){dgenies.show_loading("Building file...",180);dgenies.post("/get-fasta-query/"+dgenies.result.id_res,{gzip:compress},function(data,success){if(data["status"]===0){window.setTimeout(()=>{dgenies.result.export.export_fasta()},10000)}else if(data["status"]===2){dgenies.result.export.dl_fasta(data["gzip"])}else if(data["status"]===1){dgenies.hide_loading();dgenies.notify("We are building your Fasta file. You will receive by mail a link to download it soon!","info")}else{dgenies.hide_loading();dgenies.notify("An error has occurred. Please contact us to report the bug","danger")}})};dgenies.result.export.ask_export_fasta=function(){let dialog=$("<div>").attr("id","dialog-confirm").attr("title","Gzip?");let icon=$("<span>").attr("class","ui-icon ui-icon-help").css("float","left").css("margin","12px 12px 20px 0");let body=$("<p>");body.append(icon);body.append("Compression is recommanded on slow connections. Download Gzip file?");dialog.append(body);dialog.dialog({resizable:false,height:"auto",width:500,modal:true,buttons:{"Use default":function(){$(this).dialog("close");dgenies.result.export.export_fasta(false)},"Use Gzip":function(){$(this).dialog("close");dgenies.result.export.export_fasta(true)},Cancel:function(){$(this).dialog("close")}}})};dgenies.result.export.export_association_table=function(){let export_div=$("div#export-pict");export_div.html("");export_div.append($("<a>").attr("href",`/qt-assoc/${dgenies.result.id_res}`).attr("download",d3.boxplot.name_y+"_"+d3.boxplot.name_x+"_assoc.tsv").attr("id","my-download").text("download"));dgenies.hide_loading();document.getElementById("my-download").click()};dgenies.result.export.export_no_association_file=function(to){window.setTimeout(()=>{dgenies.show_loading("Building file...",180);let on=to==="query"?"target":"query";dgenies.post("/no-assoc/"+dgenies.result.id_res,{"to":to},function(data,success){dgenies.hide_loading();if(!data["empty"]){let blob=new Blob([data["file_content"]],{type:"text/plain"});saveAs(blob,`no_${to}_matches_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.txt`)}else{dgenies.notify(`No contigs in ${to} have None match with any ${on}!`,"success")}})},0)};dgenies.result.export.export_query_as_reference_fasta_webserver=function(){dgenies.post(`/build-query-as-reference/${dgenies.result.id_res}`,{},function(data,success){if(data["success"]){dgenies.notify("You will receive a mail soon with the link to download your Fasta file","success")}else{dgenies.notify(`An error has occurred. Please contact the support`,"danger")}})};dgenies.result.export.export_query_as_reference_fasta_standalone=function(){dgenies.show_loading("Building file...",180);window.setTimeout(()=>{dgenies.post(`/build-query-as-reference/${dgenies.result.id_res}`,{},function(data,success){if(data["success"]){let export_div=$("div#export-pict");export_div.html("");export_div.append($("<a>").attr("href",`/get-query-as-reference/${dgenies.result.id_res}`).attr("download",`as_reference_${d3.boxplot.name_y}.fasta`).attr("id","my-download").text("download"));document.getElementById("my-download").click();dgenies.hide_loading()}else{dgenies.notify(`An error has occurred. Please contact the support`,"danger")}})},0)};dgenies.result.export.export=function(){let select=$("form#export select");let selection=parseInt(select.val());window.setTimeout(()=>{if(selection>0){let async=false;if(selection===1){dgenies.result.export.export_svg();async=true}else if(selection===2){dgenies.result.export.export_png();async=true}else if(selection===3)dgenies.result.export.export_paf();else if(selection===4){dgenies.result.export.ask_export_fasta();async=true}else if(selection===5){dgenies.result.export.export_association_table()}else if(selection===6){dgenies.result.export.export_no_association_file("query");async=true}else if(selection===7){dgenies.result.export.export_no_association_file("target");async=true}else if(selection===8){if(dgenies.mode==="webserver"){dgenies.result.export.export_query_as_reference_fasta_webserver()}else{dgenies.result.export.export_query_as_reference_fasta_standalone();async=true}}else dgenies.notify("Not supported yet!","danger",2000);if(!async)dgenies.hide_loading();select.val("0")}},0)};
-if(!dgenies||!dgenies.result){throw"dgenies.result wasn't included!"}dgenies.result.summary={};dgenies.result.summary.show=function(percents){console.log(percents);let svgcontainer=d3.select("#draw-stats").html("").append("svg:svg").attr("width","500px").attr("height","220px");let container=svgcontainer.append("svg:g");let percents_order=["-1","0","1","2","3"];let x=0;let percent_value=0;for(let i in percents_order){let percent=percents_order[i];let label="";switch(percent){case"-1":label="No match";break;case"0":label="< 25 %";break;case"1":label="< 50 %";break;case"2":label="< 75 %";break;case"3":label="> 75 %";break;}console.log(percent);x+=percent_value;percent_value=percent in percents?percents[percent]:0;container.append("rect").attr("x",x+"%").attr("y",0).attr("width",percent_value+"%").attr("height","50px").attr("stroke","none").attr("fill",d3.boxplot.color_idy[d3.boxplot.color_idy_theme][percent]);container.append("rect").attr("x",5).attr("y",70+i*30).attr("width","10px").attr("height","10px").attr("fill",d3.boxplot.color_idy[d3.boxplot.color_idy_theme][percent]).style("stroke","#000").style("stroke-width","1px");container.append("text").attr("x",30).attr("y",82+i*30).attr("font-family","sans-serif").attr("font-size","12pt").text(label+":");container.append("text").attr("x",110).attr("y",82+i*30).attr("font-family","sans-serif").attr("font-size","12pt").text(percent_value.toFixed(2)+" %")}container.append("rect").attr("x",0).attr("y",0).attr("width","100%").attr("height","50px").style("stroke","#000").style("fill","none").style("stroke-width","1px");$("#modal-stats").dialog({title:"Summary of identity",width:"550px",buttons:[{text:"Export PNG",click:dgenies.result.summary.export_png},{text:"Export SVG",click:dgenies.result.summary.export_svg},{text:"Close",click:function(){$(this).dialog("close")}}]})};dgenies.result.summary.get_svg=function(){return $("#draw-stats").html()};dgenies.result.summary.save_file=function(blob,format){saveAs(blob,`summary_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.${format}`)};dgenies.result.summary.export_svg=function(){let blob=new Blob([dgenies.result.summary.get_svg()],{type:"image/svg+xml"});dgenies.result.summary.save_file(blob,"svg")};dgenies.result.summary.export_png=function(){let export_div=$("div#export-pict");export_div.html("").append($("<canvas>"));canvg(export_div.find("canvas")[0],dgenies.result.summary.get_svg());let canvas=export_div.find("canvas")[0];canvas.toBlob(function(blob){dgenies.result.summary.save_file(blob,"png");export_div.html("")},"image/png")};
+if(!dgenies||!dgenies.result){throw"dgenies.result wasn't included!"}dgenies.result.summary={};dgenies.result.summary.percents={};dgenies.result.summary.show=function(percents){dgenies.result.summary.percents=percents;let svgcontainer=d3.select("#draw-stats").html("").append("svg:svg").attr("width","500px").attr("height","220px");let container=svgcontainer.append("svg:g");let percents_order=["-1","0","1","2","3"];let x=0;let percent_value=0;for(let i in percents_order){let percent=percents_order[i];let label=dgenies.result.summary._get_label(percent);x+=percent_value;percent_value=percent in percents?percents[percent]:0;container.append("rect").attr("x",x+"%").attr("y",0).attr("width",percent_value+"%").attr("height","50px").attr("stroke","none").attr("fill",d3.boxplot.color_idy[d3.boxplot.color_idy_theme][percent]);container.append("rect").attr("x",5).attr("y",70+i*30).attr("width","10px").attr("height","10px").attr("fill",d3.boxplot.color_idy[d3.boxplot.color_idy_theme][percent]).style("stroke","#000").style("stroke-width","1px");container.append("text").attr("x",30).attr("y",82+i*30).attr("font-family","sans-serif").attr("font-size","12pt").text(label+":");container.append("text").attr("x",110).attr("y",82+i*30).attr("font-family","sans-serif").attr("font-size","12pt").text(percent_value.toFixed(2)+" %")}container.append("rect").attr("x",0).attr("y",0).attr("width","100%").attr("height","50px").style("stroke","#000").style("fill","none").style("stroke-width","1px");$("#modal-stats").dialog({title:"Summary of identity",width:"560px",buttons:[{text:"Export TSV",click:dgenies.result.summary.export_tsv},{text:"Export PNG",click:dgenies.result.summary.export_png},{text:"Export SVG",click:dgenies.result.summary.export_svg},{text:"Close",click:function(){$(this).dialog("close")},default:true}],open:function(){$(this).parents().find(".ui-dialog-buttonpane button")[3].focus()}})};dgenies.result.summary._get_label=function(percent_class){switch(percent_class){case"-1":return"No match";case"0":return"< 25 %";case"1":return"< 50 %";case"2":return"< 75 %";case"3":return"> 75 %";}};dgenies.result.summary.get_svg=function(){return $("#draw-stats").html()};dgenies.result.summary.save_file=function(blob,format){saveAs(blob,`summary_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.${format}`)};dgenies.result.summary.export_tsv=function(){let content="category\tpercent\n";for(let percent in dgenies.result.summary.percents){content+=`${dgenies.result.summary._get_label(percent)}\t${dgenies.result.summary.percents[percent]}\n`}dgenies.result.summary.save_file(new Blob([content],{type:"plain/text"}),"tsv")};dgenies.result.summary.export_svg=function(){let blob=new Blob([dgenies.result.summary.get_svg()],{type:"image/svg+xml"});dgenies.result.summary.save_file(blob,"svg")};dgenies.result.summary.export_png=function(){let export_div=$("div#export-pict");export_div.html("").append($("<canvas>"));canvg(export_div.find("canvas")[0],dgenies.result.summary.get_svg());let canvas=export_div.find("canvas")[0];canvas.toBlob(function(blob){dgenies.result.summary.save_file(blob,"png");export_div.html("")},"image/png")};
if(!d3){throw"d3 wasn't included!"}d3.boxplot={};//GLOBAL VARIABLES:
d3.boxplot.svgcontainer=null;d3.boxplot.container=null;d3.boxplot.svgsupercontainer=null;d3.boxplot.name_x=null;d3.boxplot.name_y=null;d3.boxplot.lines=null;d3.boxplot.x_len=null;d3.boxplot.y_len=null;d3.boxplot.x_zones=null;d3.boxplot.y_zones=null;d3.boxplot.zoom_enabled=true;d3.boxplot.all_disabled=false;d3.boxplot.min_idy=0;d3.boxplot.max_idy=0;d3.boxplot.zone_selected=false;d3.boxplot.query_selected=null;//For translations:
d3.boxplot.translate_start=null;d3.boxplot.posX=null;d3.boxplot.posY=null;d3.boxplot.old_translate=null;//Graphical parameters:
diff --git a/src/dgenies/static/js/dgenies.result.summary.js b/src/dgenies/static/js/dgenies.result.summary.js
index ea5f0ed..db2f9af 100644
--- a/src/dgenies/static/js/dgenies.result.summary.js
+++ b/src/dgenies/static/js/dgenies.result.summary.js
@@ -2,9 +2,10 @@ if (!dgenies || !dgenies.result) {
throw "dgenies.result wasn't included!"
}
dgenies.result.summary = {};
+dgenies.result.summary.percents = {};
dgenies.result.summary.show = function(percents) {
- console.log(percents);
+ dgenies.result.summary.percents = percents;
let svgcontainer = d3.select("#draw-stats").html("").append("svg:svg")
.attr("width", "500px")
.attr("height", "220px");
@@ -14,25 +15,7 @@ dgenies.result.summary.show = function(percents) {
let percent_value = 0;
for (let i in percents_order) {
let percent = percents_order[i];
- let label="";
- switch (percent) {
- case "-1":
- label = "No match";
- break;
- case "0":
- label = "< 25 %";
- break;
- case "1":
- label = "< 50 %";
- break;
- case "2":
- label = "< 75 %";
- break;
- case "3":
- label = "> 75 %";
- break;
- }
- console.log(percent);
+ let label=dgenies.result.summary._get_label(percent);
x += percent_value;
percent_value = percent in percents ? percents[percent] : 0;
container.append("rect")
@@ -75,8 +58,11 @@ dgenies.result.summary.show = function(percents) {
$("#modal-stats").dialog({
title: "Summary of identity",
- width: "550px",
+ width: "560px",
buttons: [{
+ text: "Export TSV",
+ click: dgenies.result.summary.export_tsv
+ },{
text: "Export PNG",
click: dgenies.result.summary.export_png
},{
@@ -86,11 +72,28 @@ dgenies.result.summary.show = function(percents) {
text: "Close",
click: function() {
$(this).dialog("close");
- }
- }]
+ },
+ default: true
+ }],
+ open: function() { $(this).parents().find(".ui-dialog-buttonpane button")[3].focus() }
})
};
+dgenies.result.summary._get_label = function (percent_class) {
+ switch (percent_class) {
+ case "-1":
+ return "No match";
+ case "0":
+ return "< 25 %";
+ case "1":
+ return "< 50 %";
+ case "2":
+ return "< 75 %";
+ case "3":
+ return "> 75 %";
+ }
+};
+
dgenies.result.summary.get_svg = function () {
return $("#draw-stats").html();
};
@@ -99,6 +102,14 @@ dgenies.result.summary.save_file = function (blob, format) {
saveAs(blob, `summary_${d3.boxplot.name_y}_to_${d3.boxplot.name_x}.${format}`);
};
+dgenies.result.summary.export_tsv = function () {
+ let content = "category\tpercent\n";
+ for (let percent in dgenies.result.summary.percents) {
+ content += `${dgenies.result.summary._get_label(percent)}\t${dgenies.result.summary.percents[percent]}\n`;
+ }
+ dgenies.result.summary.save_file(new Blob([content], {type: "plain/text"}), "tsv");
+};
+
dgenies.result.summary.export_svg = function () {
let blob = new Blob([dgenies.result.summary.get_svg()], {type: "image/svg+xml"});
dgenies.result.summary.save_file(blob, "svg");
--
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