genevalidatorapp 1.4.13 → 1.5.0

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Files changed (41) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +1 -1
  3. data/Rakefile +5 -1
  4. data/bin/genevalidatorapp +227 -73
  5. data/config.ru +1 -1
  6. data/genevalidatorapp.gemspec +7 -6
  7. data/lib/genevalidatorapp.rb +247 -0
  8. data/lib/{GeneValidatorApp → genevalidatorapp}/config.rb +7 -6
  9. data/lib/{GeneValidatorApp → genevalidatorapp}/database.rb +8 -13
  10. data/lib/genevalidatorapp/exceptions.rb +162 -0
  11. data/lib/{GeneValidatorApp → genevalidatorapp}/genevalidator.rb +52 -58
  12. data/lib/{GeneValidatorApp → genevalidatorapp}/logger.rb +0 -0
  13. data/lib/genevalidatorapp/routes.rb +81 -0
  14. data/lib/genevalidatorapp/server.rb +63 -0
  15. data/lib/{GeneValidatorApp → genevalidatorapp}/version.rb +1 -1
  16. data/public/{web_files → src}/css/bootstrap1.min.css +0 -0
  17. data/public/{web_files → src}/css/custom.css +8 -13
  18. data/public/{web_files → src}/css/custom.min.css +0 -0
  19. data/public/{web_files → src}/css/font-awesome.min.css +0 -0
  20. data/public/{web_files → src}/js/bionode-seq.min.js +0 -0
  21. data/public/{web_files → src}/js/bootstrap.min.js +0 -0
  22. data/public/{web_files → src}/js/d3.v3.min.js +0 -0
  23. data/public/{web_files → src}/js/genevalidator.js +44 -49
  24. data/public/{web_files → src}/js/jquery.cookie.min.js +0 -0
  25. data/public/{web_files → src}/js/jquery.min.js +0 -0
  26. data/public/{web_files → src}/js/jquery.tablesorter.min.js +0 -0
  27. data/public/{web_files → src}/js/jquery.validate.min.js +0 -0
  28. data/public/src/js/plots.js +814 -0
  29. data/public/web_files/css/GV_compiled_css.min.css +15 -0
  30. data/public/web_files/js/GV_compiled_js.min.js +34 -0
  31. data/spec/app_spec.rb +1 -1
  32. data/spec/database_spec.rb +2 -2
  33. data/views/index.slim +1 -1
  34. data/views/layout.slim +15 -24
  35. data/views/results.slim +54 -0
  36. metadata +39 -35
  37. data/lib/GeneValidatorApp.rb +0 -321
  38. data/public/web_files/css/bootstrap.min.css +0 -7
  39. data/public/web_files/js/genevalidator.min.js +0 -1
  40. data/public/web_files/js/plots.js +0 -744
  41. data/public/web_files/js/plots.min.js +0 -1
data/public/web_files/css/GV_compiled_css.min.css ADDED
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+ @import url("//fonts.googleapis.com/css?family=Lato:400,700,400italic");/*!
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+ * bootswatch v3.3.1+2
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+ * Homepage: http://bootswatch.com
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+ * Copyright 2012-2014 Thomas Park
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+ * Licensed under MIT
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+ * Based on Bootstrap
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13
+ /*custom*/
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5
+ // Bootstrap
6
+ /*!
7
+ * Bootstrap v3.1.1 (http://getbootstrap.com)
8
+ * Copyright 2011-2014 Twitter, Inc.
9
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
10
+ */
11
+ if("undefined"==typeof jQuery)throw new Error("Bootstrap's JavaScript requires jQuery");+function(a){"use strict";function b(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in b)if(void 0!==a.style[c])return{end:b[c]};return!1}a.fn.emulateTransitionEnd=function(b){var c=!1,d=this;a(this).one(a.support.transition.end,function(){c=!0});var e=function(){c||a(d).trigger(a.support.transition.end)};return setTimeout(e,b),this},a(function(){a.support.transition=b()})}(jQuery),+function(a){"use strict";var b='[data-dismiss="alert"]',c=function(c){a(c).on("click",b,this.close)};c.prototype.close=function(b){function c(){f.trigger("closed.bs.alert").remove()}var d=a(this),e=d.attr("data-target");e||(e=d.attr("href"),e=e&&e.replace(/.*(?=#[^\s]*$)/,""));var 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b=function(b){this.element=a(b)};b.prototype.show=function(){var b=this.element,c=b.closest("ul:not(.dropdown-menu)"),d=b.data("target");if(d||(d=b.attr("href"),d=d&&d.replace(/.*(?=#[^\s]*$)/,"")),!b.parent("li").hasClass("active")){var e=c.find(".active:last a")[0],f=a.Event("show.bs.tab",{relatedTarget:e});if(b.trigger(f),!f.isDefaultPrevented()){var g=a(d);this.activate(b.parent("li"),c),this.activate(g,g.parent(),function(){b.trigger({type:"shown.bs.tab",relatedTarget:e})})}}},b.prototype.activate=function(b,c,d){function e(){f.removeClass("active").find("> .dropdown-menu > .active").removeClass("active"),b.addClass("active"),g?(b[0].offsetWidth,b.addClass("in")):b.removeClass("fade"),b.parent(".dropdown-menu")&&b.closest("li.dropdown").addClass("active"),d&&d()}var f=c.find("> .active"),g=d&&a.support.transition&&f.hasClass("fade");g?f.one(a.support.transition.end,e).emulateTransitionEnd(150):e(),f.removeClass("in")};var c=a.fn.tab;a.fn.tab=function(c){return this.each(function(){var d=a(this),e=d.data("bs.tab");e||d.data("bs.tab",e=new b(this)),"string"==typeof c&&e[c]()})},a.fn.tab.Constructor=b,a.fn.tab.noConflict=function(){return a.fn.tab=c,this},a(document).on("click.bs.tab.data-api",'[data-toggle="tab"], [data-toggle="pill"]',function(b){b.preventDefault(),a(this).tab("show")})}(jQuery),+function(a){"use strict";var b=function(c,d){this.options=a.extend({},b.DEFAULTS,d),this.$window=a(window).on("scroll.bs.affix.data-api",a.proxy(this.checkPosition,this)).on("click.bs.affix.data-api",a.proxy(this.checkPositionWithEventLoop,this)),this.$element=a(c),this.affixed=this.unpin=this.pinnedOffset=null,this.checkPosition()};b.RESET="affix affix-top affix-bottom",b.DEFAULTS={offset:0},b.prototype.getPinnedOffset=function(){if(this.pinnedOffset)return this.pinnedOffset;this.$element.removeClass(b.RESET).addClass("affix");var a=this.$window.scrollTop(),c=this.$element.offset();return this.pinnedOffset=c.top-a},b.prototype.checkPositionWithEventLoop=function(){setTimeout(a.proxy(this.checkPosition,this),1)},b.prototype.checkPosition=function(){if(this.$element.is(":visible")){var c=a(document).height(),d=this.$window.scrollTop(),e=this.$element.offset(),f=this.options.offset,g=f.top,h=f.bottom;"top"==this.affixed&&(e.top+=d),"object"!=typeof f&&(h=g=f),"function"==typeof g&&(g=f.top(this.$element)),"function"==typeof h&&(h=f.bottom(this.$element));var i=null!=this.unpin&&d+this.unpin<=e.top?!1:null!=h&&e.top+this.$element.height()>=c-h?"bottom":null!=g&&g>=d?"top":!1;if(this.affixed!==i){this.unpin&&this.$element.css("top","");var j="affix"+(i?"-"+i:""),k=a.Event(j+".bs.affix");this.$element.trigger(k),k.isDefaultPrevented()||(this.affixed=i,this.unpin="bottom"==i?this.getPinnedOffset():null,this.$element.removeClass(b.RESET).addClass(j).trigger(a.Event(j.replace("affix","affixed"))),"bottom"==i&&this.$element.offset({top:c-h-this.$element.height()}))}}};var c=a.fn.affix;a.fn.affix=function(c){return this.each(function(){var d=a(this),e=d.data("bs.affix"),f="object"==typeof c&&c;e||d.data("bs.affix",e=new b(this,f)),"string"==typeof c&&e[c]()})},a.fn.affix.Constructor=b,a.fn.affix.noConflict=function(){return a.fn.affix=c,this},a(window).on("load",function(){a('[data-spy="affix"]').each(function(){var b=a(this),c=b.data();c.offset=c.offset||{},c.offsetBottom&&(c.offset.bottom=c.offsetBottom),c.offsetTop&&(c.offset.top=c.offsetTop),b.affix(c)})})}(jQuery);
12
+ // jquery.tablesorter
13
+ /*!
14
+ * TableSorter 2.17.7 min - Client-side table sorting with ease!
15
+ * Copyright (c) 2007 Christian Bach
16
+ */
17
+ !function(h){h.extend({tablesorter:new function(){function d(){var a=arguments[0],b=1<arguments.length?Array.prototype.slice.call(arguments):a;if("undefined"!==typeof console&&"undefined"!==typeof console.log)console[/error/i.test(a)?"error":/warn/i.test(a)?"warn":"log"](b);else alert(b)}function q(a,b){d(a+" ("+((new Date).getTime()-b.getTime())+"ms)")}function n(a){for(var b in a)return!1;return!0}function r(a,b,c){if(!b)return"";var g,e=a.config,l=e.textExtraction||"",d="",d="basic"===l?h(b).attr(e.textAttribute)|| b.textContent||b.innerText||h(b).text()||"":"function"===typeof l?l(b,a,c):"function"===typeof(g=f.getColumnData(a,l,c))?g(b,a,c):b.textContent||b.innerText||h(b).text()||"";return h.trim(d)}function v(a){var b,c,g=a.config,e=g.$tbodies=g.$table.children("tbody:not(."+g.cssInfoBlock+")"),l,x,k,h,m,B,u,s,t,n=0,v="",w=e.length;if(0===w)return g.debug?d("Warning: *Empty table!* Not building a parser cache"):"";g.debug&&(t=new Date,d("Detecting parsers for each column"));b=[];for(c=[];n<w;){l=e[n].rows; if(l[n])for(x=g.columns,k=0;k<x;k++){h=g.$headers.filter('[data-column="'+k+'"]:last');m=f.getColumnData(a,g.headers,k);s=f.getParserById(f.getData(h,m,"extractor"));u=f.getParserById(f.getData(h,m,"sorter"));B="false"===f.getData(h,m,"parser");g.empties[k]=f.getData(h,m,"empty")||g.emptyTo||(g.emptyToBottom?"bottom":"top");g.strings[k]=f.getData(h,m,"string")||g.stringTo||"max";B&&(u=f.getParserById("no-parser"));s||(s=!1);if(!u)a:{h=a;m=l;B=-1;u=k;for(var A=void 0,K=f.parsers.length,H=!1,z="",A= !0;""===z&&A;)B++,m[B]?(H=m[B].cells[u],z=r(h,H,u),h.config.debug&&d("Checking if value was empty on row "+B+", column: "+u+': "'+z+'"')):A=!1;for(;0<=--K;)if((A=f.parsers[K])&&"text"!==A.id&&A.is&&A.is(z,h,H)){u=A;break a}u=f.getParserById("text")}g.debug&&(v+="column:"+k+"; extractor:"+s.id+"; parser:"+u.id+"; string:"+g.strings[k]+"; empty: "+g.empties[k]+"\n");c[k]=u;b[k]=s}n+=c.length?w:1}g.debug&&(d(v?v:"No parsers detected"),q("Completed detecting parsers",t));g.parsers=c;g.extractors=b}function w(a){var b, c,g,e,l,x,k,p,m,n,u,s=a.config,t=s.$table.children("tbody"),v=s.extractors,w=s.parsers;s.cache={};s.totalRows=0;if(!w)return s.debug?d("Warning: *Empty table!* Not building a cache"):"";s.debug&&(p=new Date);s.showProcessing&&f.isProcessing(a,!0);for(l=0;l<t.length;l++)if(u=[],b=s.cache[l]={normalized:[]},!t.eq(l).hasClass(s.cssInfoBlock)){m=t[l]&&t[l].rows.length||0;for(g=0;g<m;++g)if(n={child:[]},x=h(t[l].rows[g]),k=[],x.hasClass(s.cssChildRow)&&0!==g)c=b.normalized.length-1,b.normalized[c][s.columns].$row= b.normalized[c][s.columns].$row.add(x),x.prev().hasClass(s.cssChildRow)||x.prev().addClass(f.css.cssHasChild),n.child[c]=h.trim(x[0].textContent||x[0].innerText||x.text()||"");else{n.$row=x;n.order=g;for(e=0;e<s.columns;++e)"undefined"===typeof w[e]?s.debug&&d("No parser found for cell:",x[0].cells[e],"does it have a header?"):(c=r(a,x[0].cells[e],e),c="undefined"===typeof v[e].id?c:v[e].format(c,a,x[0].cells[e],e),c="no-parser"===w[e].id?"":w[e].format(c,a,x[0].cells[e],e),k.push(s.ignoreCase&&"string"=== typeof c?c.toLowerCase():c),"numeric"===(w[e].type||"").toLowerCase()&&(u[e]=Math.max(Math.abs(c)||0,u[e]||0)));k[s.columns]=n;b.normalized.push(k)}b.colMax=u;s.totalRows+=b.normalized.length}s.showProcessing&&f.isProcessing(a);s.debug&&q("Building cache for "+m+" rows",p)}function z(a,b){var c=a.config,g=c.widgetOptions,e=a.tBodies,l=[],d=c.cache,k,p,m,r,u,s;if(n(d))return c.appender?c.appender(a,l):a.isUpdating?c.$table.trigger("updateComplete",a):"";c.debug&&(s=new Date);for(u=0;u<e.length;u++)if(k= h(e[u]),k.length&&!k.hasClass(c.cssInfoBlock)){m=f.processTbody(a,k,!0);k=d[u].normalized;p=k.length;for(r=0;r<p;r++)l.push(k[r][c.columns].$row),c.appender&&(!c.pager||c.pager.removeRows&&g.pager_removeRows||c.pager.ajax)||m.append(k[r][c.columns].$row);f.processTbody(a,m,!1)}c.appender&&c.appender(a,l);c.debug&&q("Rebuilt table",s);b||c.appender||f.applyWidget(a);a.isUpdating&&c.$table.trigger("updateComplete",a)}function D(a){return/^d/i.test(a)||1===a}function E(a){var b,c,g,e,l,x,k,p=a.config; p.headerList=[];p.headerContent=[];p.debug&&(k=new Date);p.columns=f.computeColumnIndex(p.$table.children("thead, tfoot").children("tr"));e=p.cssIcon?'<i class="'+(p.cssIcon===f.css.icon?f.css.icon:p.cssIcon+" "+f.css.icon)+'"></i>':"";p.$headers=h(a).find(p.selectorHeaders).each(function(k){c=h(this);b=f.getColumnData(a,p.headers,k,!0);p.headerContent[k]=h(this).html();l=p.headerTemplate.replace(/\{content\}/g,h(this).html()).replace(/\{icon\}/g,e);p.onRenderTemplate&&(g=p.onRenderTemplate.apply(c, [k,l]))&&"string"===typeof g&&(l=g);h(this).html('<div class="'+f.css.headerIn+'">'+l+"</div>");p.onRenderHeader&&p.onRenderHeader.apply(c,[k]);this.column=parseInt(h(this).attr("data-column"),10);this.order=D(f.getData(c,b,"sortInitialOrder")||p.sortInitialOrder)?[1,0,2]:[0,1,2];this.count=-1;this.lockedOrder=!1;x=f.getData(c,b,"lockedOrder")||!1;"undefined"!==typeof x&&!1!==x&&(this.order=this.lockedOrder=D(x)?[1,1,1]:[0,0,0]);c.addClass(f.css.header+" "+p.cssHeader);p.headerList[k]=this;c.parent().addClass(f.css.headerRow+ " "+p.cssHeaderRow).attr("role","row");p.tabIndex&&c.attr("tabindex",0)}).attr({scope:"col",role:"columnheader"});C(a);p.debug&&(q("Built headers:",k),d(p.$headers))}function F(a,b,c){var g=a.config;g.$table.find(g.selectorRemove).remove();v(a);w(a);I(g.$table,b,c)}function C(a){var b,c,g,e=a.config;e.$headers.each(function(l,d){c=h(d);g=f.getColumnData(a,e.headers,l,!0);b="false"===f.getData(d,g,"sorter")||"false"===f.getData(d,g,"parser");d.sortDisabled=b;c[b?"addClass":"removeClass"]("sorter-false").attr("aria-disabled", ""+b);a.id&&(b?c.removeAttr("aria-controls"):c.attr("aria-controls",a.id))})}function G(a){var b,c,g=a.config,e=g.sortList,l=e.length,d=f.css.sortNone+" "+g.cssNone,k=[f.css.sortAsc+" "+g.cssAsc,f.css.sortDesc+" "+g.cssDesc],p=["ascending","descending"],m=h(a).find("tfoot tr").children().add(g.$extraHeaders).removeClass(k.join(" "));g.$headers.removeClass(k.join(" ")).addClass(d).attr("aria-sort","none");for(b=0;b<l;b++)if(2!==e[b][1]&&(a=g.$headers.not(".sorter-false").filter('[data-column="'+e[b][0]+ '"]'+(1===l?":last":"")),a.length)){for(c=0;c<a.length;c++)a[c].sortDisabled||a.eq(c).removeClass(d).addClass(k[e[b][1]]).attr("aria-sort",p[e[b][1]]);m.length&&m.filter('[data-column="'+e[b][0]+'"]').removeClass(d).addClass(k[e[b][1]])}g.$headers.not(".sorter-false").each(function(){var a=h(this),b=this.order[(this.count+1)%(g.sortReset?3:2)],b=a.text()+": "+f.language[a.hasClass(f.css.sortAsc)?"sortAsc":a.hasClass(f.css.sortDesc)?"sortDesc":"sortNone"]+f.language[0===b?"nextAsc":1===b?"nextDesc": "nextNone"];a.attr("aria-label",b)})}function O(a){if(a.config.widthFixed&&0===h(a).find("colgroup").length){var b=h("<colgroup>"),c=h(a).width();h(a.tBodies[0]).find("tr:first").children(":visible").each(function(){b.append(h("<col>").css("width",parseInt(h(this).width()/c*1E3,10)/10+"%"))});h(a).prepend(b)}}function P(a,b){var c,g,e,l,f,k=a.config,d=b||k.sortList;k.sortList=[];h.each(d,function(a,b){l=parseInt(b[0],10);if(e=k.$headers.filter('[data-column="'+l+'"]:last')[0]){g=(g=(""+b[1]).match(/^(1|d|s|o|n)/))? g[0]:"";switch(g){case "1":case "d":g=1;break;case "s":g=f||0;break;case "o":c=e.order[(f||0)%(k.sortReset?3:2)];g=0===c?1:1===c?0:2;break;case "n":e.count+=1;g=e.order[e.count%(k.sortReset?3:2)];break;default:g=0}f=0===a?g:f;c=[l,parseInt(g,10)||0];k.sortList.push(c);g=h.inArray(c[1],e.order);e.count=0<=g?g:c[1]%(k.sortReset?3:2)}})}function Q(a,b){return a&&a[b]?a[b].type||"":""}function L(a,b,c){if(a.isUpdating)return setTimeout(function(){L(a,b,c)},50);var g,e,l,d,k=a.config,p=!c[k.sortMultiSortKey], m=k.$table;m.trigger("sortStart",a);b.count=c[k.sortResetKey]?2:(b.count+1)%(k.sortReset?3:2);k.sortRestart&&(e=b,k.$headers.each(function(){this===e||!p&&h(this).is("."+f.css.sortDesc+",."+f.css.sortAsc)||(this.count=-1)}));e=b.column;if(p){k.sortList=[];if(null!==k.sortForce)for(g=k.sortForce,l=0;l<g.length;l++)g[l][0]!==e&&k.sortList.push(g[l]);g=b.order[b.count];if(2>g&&(k.sortList.push([e,g]),1<b.colSpan))for(l=1;l<b.colSpan;l++)k.sortList.push([e+l,g])}else{if(k.sortAppend&&1<k.sortList.length)for(l= 0;l<k.sortAppend.length;l++)d=f.isValueInArray(k.sortAppend[l][0],k.sortList),0<=d&&k.sortList.splice(d,1);if(0<=f.isValueInArray(e,k.sortList))for(l=0;l<k.sortList.length;l++)d=k.sortList[l],g=k.$headers.filter('[data-column="'+d[0]+'"]:last')[0],d[0]===e&&(d[1]=g.order[b.count],2===d[1]&&(k.sortList.splice(l,1),g.count=-1));else if(g=b.order[b.count],2>g&&(k.sortList.push([e,g]),1<b.colSpan))for(l=1;l<b.colSpan;l++)k.sortList.push([e+l,g])}if(null!==k.sortAppend)for(g=k.sortAppend,l=0;l<g.length;l++)g[l][0]!== e&&k.sortList.push(g[l]);m.trigger("sortBegin",a);setTimeout(function(){G(a);J(a);z(a);m.trigger("sortEnd",a)},1)}function J(a){var b,c,g,e,l,d,k,h,m,r,u,s=0,t=a.config,v=t.textSorter||"",w=t.sortList,y=w.length,z=a.tBodies.length;if(!t.serverSideSorting&&!n(t.cache)){t.debug&&(l=new Date);for(c=0;c<z;c++)d=t.cache[c].colMax,k=t.cache[c].normalized,k.sort(function(c,l){for(b=0;b<y;b++){e=w[b][0];h=w[b][1];s=0===h;if(t.sortStable&&c[e]===l[e]&&1===y)break;(g=/n/i.test(Q(t.parsers,e)))&&t.strings[e]? 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24
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25
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26
+ // genevalidator.min.js
27
+ $(document).ready(function(){"use strict";checkCollapseState(),keepFooterFixedToBottom(),addSeqValidation(),inputValidation(),bindTdClicks(),$(document).bind("keydown",function(G){G.ctrlKey&&13===G.keyCode&&$("#input").trigger("submit")})});var checkCollapseState=function(){"use strict";if($.cookie("GeneValidator_adv_params_status")){var G=$.cookie("GeneValidator_adv_params_status");if("open"===G){var T=document.getElementById("adv_params_btn");T.innerHTML='<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters',$("#adv_params").addClass("in")}}},keepFooterFixedToBottom=function(){"use strict";$("#mainbody").css({"margin-bottom":$("#footer").height()+15+"px"}),$(window).resize(function(){$("#mainbody").css({"margin-bottom":$("#footer").height()+15+"px"})})},addSeqValidation=function(){"use strict";jQuery.validator.addMethod("checkInputType",function(G,T){var A=[],e="";if(">"===G.charAt(0)){for(var C=G.split(">"),t=1;t<C.length;t++){var a=C[t].split("\n");if(0!==a.length){var n=jQuery.grep(a,function(G){return G});if(0!==n.length){n.shift();var r=n.join("");if(e=checkType(r,.9),A.push(e),"protein"!==e&&"dna"!==e&&"rna"!==e)return!1}}}for(var V=A[0],s=0;s<A.length;s++)if(A[s]!==V)return!1;return!0}return e=checkType(G,.9),"protein"!==e&&"dna"!==e&&"rna"!==e?!1:!0},"* The Input must be either DNA or protein sequence(s). 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T=">Insulin\nATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG\n>Insulin (with a duplication)\nATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGACAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG",A=">Methylmalonyl-CoA carboxyltransferase 12S 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+ // jquery.cookie.min.js
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+ !function(a){"function"==typeof define&&define.amd?define(["jquery"],a):"object"==typeof exports?a(require("jquery")):a(jQuery)}(function(a){function c(a){return h.raw?a:encodeURIComponent(a)}function d(a){return h.raw?a:decodeURIComponent(a)}function e(a){return c(h.json?JSON.stringify(a):String(a))}function f(a){0===a.indexOf('"')&&(a=a.slice(1,-1).replace(/\\"/g,'"').replace(/\\\\/g,"\\"));try{return a=decodeURIComponent(a.replace(b," ")),h.json?JSON.parse(a):a}catch(c){}}function g(b,c){var d=h.raw?b:f(b);return a.isFunction(c)?c(d):d}var b=/\+/g,h=a.cookie=function(b,f,i){if(void 0!==f&&!a.isFunction(f)){if(i=a.extend({},h.defaults,i),"number"==typeof i.expires){var j=i.expires,k=i.expires=new Date;k.setTime(+k+864e5*j)}return document.cookie=[c(b),"=",e(f),i.expires?"; expires="+i.expires.toUTCString():"",i.path?"; path="+i.path:"",i.domain?"; domain="+i.domain:"",i.secure?"; secure":""].join("")}for(var l=b?void 0:{},m=document.cookie?document.cookie.split("; "):[],n=0,o=m.length;o>n;n++){var p=m[n].split("="),q=d(p.shift()),r=p.join("=");if(b&&b===q){l=g(r,f);break}b||void 0===(r=g(r))||(l[q]=r)}return l};h.defaults={},a.removeCookie=function(b,c){return void 0===a.cookie(b)?!1:(a.cookie(b,"",a.extend({},c,{expires:-1})),!a.cookie(b))}});
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+ // jquery.validate.min.js
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+ /*! jQuery Validation Plugin - v1.13.0 - 7/1/2014
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+ * http://jqueryvalidation.org/
33
+ * Copyright (c) 2014 Jörn Zaefferer; Licensed MIT */
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+ !function(a){"function"==typeof define&&define.amd?define(["jquery"],a):a(jQuery)}(function(a){a.extend(a.fn,{validate:function(b){if(!this.length)return void(b&&b.debug&&window.console&&console.warn("Nothing selected, can't validate, returning nothing."));var c=a.data(this[0],"validator");return c?c:(this.attr("novalidate","novalidate"),c=new a.validator(b,this[0]),a.data(this[0],"validator",c),c.settings.onsubmit&&(this.validateDelegate(":submit","click",function(b){c.settings.submitHandler&&(c.submitButton=b.target),a(b.target).hasClass("cancel")&&(c.cancelSubmit=!0),void 0!==a(b.target).attr("formnovalidate")&&(c.cancelSubmit=!0)}),this.submit(function(b){function d(){var d;return c.settings.submitHandler?(c.submitButton&&(d=a("<input type='hidden'/>").attr("name",c.submitButton.name).val(a(c.submitButton).val()).appendTo(c.currentForm)),c.settings.submitHandler.call(c,c.currentForm,b),c.submitButton&&d.remove(),!1):!0}return 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a(b).data("msg"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase())||a(b).data("msg")},customMessage:function(a,b){var c=this.settings.messages[a];return c&&(c.constructor===String?c:c[b])},findDefined:function(){for(var a=0;a<arguments.length;a++)if(void 0!==arguments[a])return arguments[a];return void 0},defaultMessage:function(b,c){return this.findDefined(this.customMessage(b.name,c),this.customDataMessage(b,c),!this.settings.ignoreTitle&&b.title||void 0,a.validator.messages[c],"<strong>Warning: No message defined for "+b.name+"</strong>")},formatAndAdd:function(b,c){var d=this.defaultMessage(b,c.method),e=/\$?\{(\d+)\}/g;"function"==typeof d?d=d.call(this,c.parameters,b):e.test(d)&&(d=a.validator.format(d.replace(e,"{$1}"),c.parameters)),this.errorList.push({message:d,element:b,method:c.method}),this.errorMap[b.name]=d,this.submitted[b.name]=d},addWrapper:function(a){return this.settings.wrapper&&(a=a.add(a.parent(this.settings.wrapper))),a},defaultShowErrors:function(){var 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this.settings.success?g.addClass(this.settings.success):this.settings.success(g,b)),this.toShow=this.toShow.add(g)},errorsFor:function(b){var c=this.idOrName(b),d=a(b).attr("aria-describedby"),e="label[for='"+c+"'], label[for='"+c+"'] *";return d&&(e=e+", #"+d.replace(/\s+/g,", #")),this.errors().filter(e)},idOrName:function(a){return this.groups[a.name]||(this.checkable(a)?a.name:a.id||a.name)},validationTargetFor:function(a){return this.checkable(a)&&(a=this.findByName(a.name).not(this.settings.ignore)[0]),a},checkable:function(a){return/radio|checkbox/i.test(a.type)},findByName:function(b){return a(this.currentForm).find("[name='"+b+"']")},getLength:function(b,c){switch(c.nodeName.toLowerCase()){case"select":return a("option:selected",c).length;case"input":if(this.checkable(c))return this.findByName(c.name).filter(":checked").length}return b.length},depend:function(a,b){return this.dependTypes[typeof a]?this.dependTypes[typeof a](a,b):!0},dependTypes:{"boolean":function(a){return a},string:function(b,c){return!!a(b,c.form).length},"function":function(a,b){return a(b)}},optional:function(b){var c=this.elementValue(b);return!a.validator.methods.required.call(this,c,b)&&"dependency-mismatch"},startRequest:function(a){this.pending[a.name]||(this.pendingRequest++,this.pending[a.name]=!0)},stopRequest:function(b,c){this.pendingRequest--,this.pendingRequest<0&&(this.pendingRequest=0),delete this.pending[b.name],c&&0===this.pendingRequest&&this.formSubmitted&&this.form()?(a(this.currentForm).submit(),this.formSubmitted=!1):!c&&0===this.pendingRequest&&this.formSubmitted&&(a(this.currentForm).triggerHandler("invalid-form",[this]),this.formSubmitted=!1)},previousValue:function(b){return a.data(b,"previousValue")||a.data(b,"previousValue",{old:null,valid:!0,message:this.defaultMessage(b,"remote")})}},classRuleSettings:{required:{required:!0},email:{email:!0},url:{url:!0},date:{date:!0},dateISO:{dateISO:!0},number:{number:!0},digits:{digits:!0},creditcard:{creditcard:!0}},addClassRules:function(b,c){b.constructor===String?this.classRuleSettings[b]=c:a.extend(this.classRuleSettings,b)},classRules:function(b){var c={},d=a(b).attr("class");return d&&a.each(d.split(" "),function(){this in a.validator.classRuleSettings&&a.extend(c,a.validator.classRuleSettings[this])}),c},attributeRules:function(b){var c,d,e={},f=a(b),g=b.getAttribute("type");for(c in a.validator.methods)"required"===c?(d=b.getAttribute(c),""===d&&(d=!0),d=!!d):d=f.attr(c),/min|max/.test(c)&&(null===g||/number|range|text/.test(g))&&(d=Number(d)),d||0===d?e[c]=d:g===c&&"range"!==g&&(e[c]=!0);return e.maxlength&&/-1|2147483647|524288/.test(e.maxlength)&&delete e.maxlength,e},dataRules:function(b){var c,d,e={},f=a(b);for(c in a.validator.methods)d=f.data("rule"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase()),void 0!==d&&(e[c]=d);return e},staticRules:function(b){var c={},d=a.data(b.form,"validator");return d.settings.rules&&(c=a.validator.normalizeRule(d.settings.rules[b.name])||{}),c},normalizeRules:function(b,c){return a.each(b,function(d,e){if(e===!1)return void delete b[d];if(e.param||e.depends){var f=!0;switch(typeof e.depends){case"string":f=!!a(e.depends,c.form).length;break;case"function":f=e.depends.call(c,c)}f?b[d]=void 0!==e.param?e.param:!0:delete b[d]}}),a.each(b,function(d,e){b[d]=a.isFunction(e)?e(c):e}),a.each(["minlength","maxlength"],function(){b[this]&&(b[this]=Number(b[this]))}),a.each(["rangelength","range"],function(){var c;b[this]&&(a.isArray(b[this])?b[this]=[Number(b[this][0]),Number(b[this][1])]:"string"==typeof b[this]&&(c=b[this].replace(/[\[\]]/g,"").split(/[\s,]+/),b[this]=[Number(c[0]),Number(c[1])]))}),a.validator.autoCreateRanges&&(b.min&&b.max&&(b.range=[b.min,b.max],delete b.min,delete b.max),b.minlength&&b.maxlength&&(b.rangelength=[b.minlength,b.maxlength],delete b.minlength,delete b.maxlength)),b},normalizeRule:function(b){if("string"==typeof b){var c={};a.each(b.split(/\s/),function(){c[this]=!0}),b=c}return b},addMethod:function(b,c,d){a.validator.methods[b]=c,a.validator.messages[b]=void 0!==d?d:a.validator.messages[b],c.length<3&&a.validator.addClassRules(b,a.validator.normalizeRule(b))},methods:{required:function(b,c,d){if(!this.depend(d,c))return"dependency-mismatch";if("select"===c.nodeName.toLowerCase()){var e=a(c).val();return e&&e.length>0}return this.checkable(c)?this.getLength(b,c)>0:a.trim(b).length>0},email:function(a,b){return this.optional(b)||/^[a-zA-Z0-9.!#$%&'*+\/=?^_`{|}~-]+@[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?(?:\.[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?)*$/.test(a)},url:function(a,b){return this.optional(b)||/^(https?|s?ftp):\/\/(((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:)*@)?(((\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5]))|((([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.)+(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.?)(:\d*)?)(\/((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)+(\/(([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)*)*)?)?(\?((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|[\uE000-\uF8FF]|\/|\?)*)?(#((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|\/|\?)*)?$/i.test(a)},date:function(a,b){return this.optional(b)||!/Invalid|NaN/.test(new Date(a).toString())},dateISO:function(a,b){return this.optional(b)||/^\d{4}[\/\-](0?[1-9]|1[012])[\/\-](0?[1-9]|[12][0-9]|3[01])$/.test(a)},number:function(a,b){return this.optional(b)||/^-?(?:\d+|\d{1,3}(?:,\d{3})+)?(?:\.\d+)?$/.test(a)},digits:function(a,b){return this.optional(b)||/^\d+$/.test(a)},creditcard:function(a,b){if(this.optional(b))return"dependency-mismatch";if(/[^0-9 \-]+/.test(a))return!1;var c,d,e=0,f=0,g=!1;if(a=a.replace(/\D/g,""),a.length<13||a.length>19)return!1;for(c=a.length-1;c>=0;c--)d=a.charAt(c),f=parseInt(d,10),g&&(f*=2)>9&&(f-=9),e+=f,g=!g;return e%10===0},minlength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||e>=d},maxlength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||d>=e},rangelength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||e>=d[0]&&e<=d[1]},min:function(a,b,c){return this.optional(b)||a>=c},max:function(a,b,c){return this.optional(b)||c>=a},range:function(a,b,c){return this.optional(b)||a>=c[0]&&a<=c[1]},equalTo:function(b,c,d){var e=a(d);return this.settings.onfocusout&&e.unbind(".validate-equalTo").bind("blur.validate-equalTo",function(){a(c).valid()}),b===e.val()},remote:function(b,c,d){if(this.optional(c))return"dependency-mismatch";var e,f,g=this.previousValue(c);return this.settings.messages[c.name]||(this.settings.messages[c.name]={}),g.originalMessage=this.settings.messages[c.name].remote,this.settings.messages[c.name].remote=g.message,d="string"==typeof d&&{url:d}||d,g.old===b?g.valid:(g.old=b,e=this,this.startRequest(c),f={},f[c.name]=b,a.ajax(a.extend(!0,{url:d,mode:"abort",port:"validate"+c.name,dataType:"json",data:f,context:e.currentForm,success:function(d){var f,h,i,j=d===!0||"true"===d;e.settings.messages[c.name].remote=g.originalMessage,j?(i=e.formSubmitted,e.prepareElement(c),e.formSubmitted=i,e.successList.push(c),delete e.invalid[c.name],e.showErrors()):(f={},h=d||e.defaultMessage(c,"remote"),f[c.name]=g.message=a.isFunction(h)?h(b):h,e.invalid[c.name]=!0,e.showErrors(f)),g.valid=j,e.stopRequest(c,j)}},d)),"pending")}}}),a.format=function(){throw"$.format has been deprecated. Please use $.validator.format instead."};var b,c={};a.ajaxPrefilter?a.ajaxPrefilter(function(a,b,d){var e=a.port;"abort"===a.mode&&(c[e]&&c[e].abort(),c[e]=d)}):(b=a.ajax,a.ajax=function(d){var e=("mode"in d?d:a.ajaxSettings).mode,f=("port"in d?d:a.ajaxSettings).port;return"abort"===e?(c[f]&&c[f].abort(),c[f]=b.apply(this,arguments),c[f]):b.apply(this,arguments)}),a.extend(a.fn,{validateDelegate:function(b,c,d){return this.bind(c,function(c){var e=a(c.target);return e.is(b)?d.apply(e,arguments):void 0})}})});
data/spec/app_spec.rb CHANGED
@@ -1,4 +1,4 @@
1
- require 'GeneValidatorApp'
1
+ require 'genevalidatorapp'
2
2
  require 'rack/test'
3
3
  require 'w3c_validators'
4
4
 
data/spec/database_spec.rb CHANGED
@@ -1,5 +1,5 @@
1
- require 'GeneValidatorApp'
2
- require 'GeneValidatorApp/database'
1
+ require 'genevalidatorapp'
2
+ require 'genevalidatorapp/database'
3
3
  require 'rspec'
4
4
 
5
5
  module GeneValidatorApp
data/views/index.slim CHANGED
@@ -8,7 +8,7 @@ section#search
8
8
  - if @max_characters != 'undefined'
9
9
  textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false" data-maxCharacters="#{@max_characters}"
10
10
  - else
11
- textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false"
11
+ textarea#seq.form-control autofocus="" name="seq" placeholder="Paste your sequence(s) here..." rows="10" spellcheck="false"
12
12
  .clearfix
13
13
  button#adv_params_btn.btn.btn-primary type="button" onclick="changeAdvParamsBtnText()"
14
14
  i.fa.fa-pencil-square-o
data/views/layout.slim CHANGED
@@ -4,23 +4,14 @@ html lang="en"
4
4
  meta charset="utf-8"
5
5
  meta content="IE=edge" http-equiv="X-UA-Compatible"
6
6
  meta content="width=device-width, initial-scale=1" name="viewport"
7
- meta content="" name="description"
8
- meta content="" name="author"
7
+ meta content="GeneValidator | Identify problems with Gene Predictions" name="description"
8
+ meta content="Wurmlab" name="author"
9
9
  title GeneValidator | Identify problems with Gene Predictions
10
10
 
11
- script type="text/javascript" src="#{uri('web_files/js/jquery.min.js')}"
12
- script type="text/javascript" src="#{uri('web_files/js/bootstrap.min.js')}"
13
- script type="text/javascript" src="#{uri('web_files/js/jquery.tablesorter.min.js')}"
14
- script type="text/javascript" src="#{uri('web_files/js/d3.v3.min.js')}"
15
- script type="text/javascript" src="#{uri('web_files/js/plots.min.js')}"
16
- script type="text/javascript" src="#{uri('web_files/js/genevalidator.min.js')}"
17
- script type="text/javascript" src="#{uri('web_files/js/jquery.cookie.min.js')}"
18
- script type="text/javascript" src="#{uri('web_files/js/jquery.validate.min.js')}"
11
+ script type="text/javascript" src="#{uri('web_files/js/GV_compiled_js.min.js')}"
19
12
 
20
13
  /! Bootstrap core CSS
21
- link href="#{uri('web_files/css/bootstrap1.min.css')}" rel="stylesheet" type="text/css"
22
- link href="#{uri('web_files/css/font-awesome.min.css')}" rel="stylesheet" type="text/css"
23
- link href="#{uri('web_files/css/custom.min.css')}" rel="stylesheet" type="text/css"
14
+ link href="#{uri('web_files/css/GV_compiled_css.min.css')}" rel="stylesheet" type="text/css"
24
15
 
25
16
  /! HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries
26
17
  /![if lt IE 9]
@@ -31,7 +22,7 @@ html lang="en"
31
22
  .navbar.navbar-default.navbar-fixed-top role="navigation"
32
23
  .nav-container
33
24
  .navbar-header
34
- button.navbar-toggle data-target=".navbar-responsive-collapse" data-toggle="collapse" type="button"
25
+ button.navbar-toggle data-target=".navbar-responsive-collapse" data-toggle="collapse" type="button"
35
26
  span.icon-bar
36
27
  span.icon-bar
37
28
  span.icon-bar
@@ -42,17 +33,17 @@ html lang="en"
42
33
  li
43
34
  a href="#" Home
44
35
  li
45
- a href="https://github.com/IsmailM/GeneValidatorApp" target="_blank" Source Code
36
+ a href="https://github.com/wurmlab/genevalidatorapp" target="_blank" Source Code
46
37
  li
47
- a href="https://ismailm.github.io/GeneValidatorApp-API" target="_blank" API
38
+ a href="https://wurmlab.github.io/GeneValidatorApp-API" target="_blank" API
48
39
  /! a href="#" Documentation
49
40
  /! li
50
41
  /! a href="#" Support
51
42
  li
52
- a href="http://yannick.poulet.org" target="_blank" Wurm Lab
43
+ a href="https://wurmlab.github.io" target="_blank" Wurm Lab
53
44
  ul.nav.navbar-nav.navbar-right
54
45
  li
55
- a.nav_github_icon href="https://github.com/IsmailM/GeneValidatorApp" target="_blank"
46
+ a.nav_github_icon href="https://github.com/wurmlab/genevalidatorapp" target="_blank"
56
47
  span.i.fa.fa-2x.fa-github
57
48
  ==yield
58
49
  #spinner.modal aria-hidden="true" aria-labelledby="spinner" role="dialog" tabindex="-1"
@@ -63,14 +54,14 @@ html lang="en"
63
54
  p.results_link This may take some time. Please leave this page open.
64
55
  i.fa.fa-spinner.fa-5x.fa-spin
65
56
  footer#footer
66
- p.text-muted.text-center
67
- | Please cite "Dragan M, Moghul MI, Priyam A &amp; Wurm Y
68
- em
57
+ p.text-muted.text-center
58
+ | Please cite "Dragan M<sup>&Dagger;</sup>, Moghul MI<sup>&Dagger;</sup>, Priyam A, Bustos C &amp; Wurm Y
59
+ em
69
60
  | (in prep)
70
61
  | GeneValidator: identify problematic gene predictions"
71
62
  br
72
63
  | Developed at
73
- a href="http://yannick.poulet.org" target="_blank" Wurm Lab
64
+ a href="https://wurmlab.github.io" target="_blank" Wurm Lab
74
65
  | ,
75
66
  a href="http://www.sbcs.qmul.ac.uk" target="_blank" QMUL
76
67
  | with funding by
@@ -79,7 +70,7 @@ html lang="en"
79
70
  a href="https://www.google-melange.com/gsoc/homepage/google/gsoc2013" target="_blank" Google Summer of Code 2013
80
71
  br
81
72
  | This page was created by
82
- a href="https://github.com/IsmailM/GeneValidatorApp" target="_blank" GeneValidator Web Application
73
+ a href="https://github.com/wurmlab/genevalidatorapp" target="_blank" GeneValidator Web Application
83
74
  | v#{GeneValidatorApp::VERSION} (using
84
- a href="https://github.com/monicadragan/GeneValidator" target="_blank" GeneValidator
75
+ a href="https://github.com/wurmlab/genevalidator" target="_blank" GeneValidator
85
76
  | v#{@current_gv_version})
data/views/results.slim ADDED
@@ -0,0 +1,54 @@
1
+ h4 Overview
2
+ #overview.text-left
3
+ #overview_text
4
+ button#overview_btn.btn.btn-primary.btn-sm data-toggle="button" onclick="GV.toggleOverviewBtn();"
5
+ br/
6
+ hr/
7
+ h4#results_header Results
8
+ table#sortable_table.table.table-striped.table-collapsed.table-bordered.table-condensed.tablesorter
9
+ thead
10
+ tr#header
11
+ th #
12
+ th Ranking
13
+ th
14
+ | Sequence Definition 
15
+ span data-placement="top" data-toggle="tooltip" title=("Query definition as it apears in the input fasta file.")
16
+ i.fa.fa-question-circle
17
+ th
18
+ | No. Hits 
19
+ span data-placement="top" data-toggle="tooltip" title=("Number of non-identical hits found by BLAST.")
20
+ i.fa.fa-question-circle
21
+ - @json_results[0]['validations'].each do |_short_header, item|
22
+ th.sorter-false
23
+ b= item['header']
24
+ | &nbsp;
25
+ - if item['header'] == "Length Cluster" || item['header'] == "Gene Merge" || item['header'] == "Main ORF" || item['header'] == "Missing/Extra Sequences"
26
+ span data-placement="top" data-toggle="tooltip" title=("Charts available for this validation")
27
+ i.fa.fa-bar-chart-o.chartIcon
28
+ | &nbsp;
29
+ span data-placement="top" data-toggle="tooltip" title="#{item['description']}"
30
+ i.fa.fa-question-circle
31
+ - else
32
+ span data-placement="top" data-toggle="tooltip" title="#{item['description']}"
33
+ i.fa.fa-question-circle
34
+ th.sorter-false.chart-column
35
+ tbody
36
+ - @json_results.each do |query|
37
+ - json_file = "web_files/json/input_file.fa_#{query['idx']}.json"
38
+ tr data-jsonfile="#{uri(json_file)}" data-target="toggle#{query['idx']}"
39
+ td title="idx" = query['idx']
40
+ td data-score="#{query['overall_score']}"
41
+ .ratings
42
+ .empty-stars
43
+ .full-stars style=("width:#{query['overall_score']}%;")
44
+ td title="Definition" = query['definition']
45
+ td title=("No. Hits") = query['no_hits']
46
+ - query['validations'].each do |_short_header, item|
47
+ td class="#{item['status']}" title="#{item['header']}"
48
+ == item['print'].gsub(/\s/, '&nbsp;').gsub(';&nbsp;', '; ')
49
+ - if query['validations'].select{|_short_header, item| item['graphs'] != nil}.map{|_short_header, item| item['graphs'].length}.inject(0){|r, e| r+e } != 0
50
+ td
51
+ button.plot_btn.btn.btn-default title=("Show plots")
52
+ i.fa.fa-bar-chart-o
53
+ - else
54
+ td
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: genevalidatorapp
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.4.13
4
+ version: 1.5.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Ismail Moghul
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2015-05-22 00:00:00.000000000 Z
11
+ date: 2015-07-28 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: bundler
@@ -67,33 +67,33 @@ dependencies:
67
67
  - !ruby/object:Gem::Version
68
68
  version: '0.6'
69
69
  - !ruby/object:Gem::Dependency
70
- name: bio
70
+ name: genevalidator
71
71
  requirement: !ruby/object:Gem::Requirement
72
72
  requirements:
73
73
  - - "~>"
74
74
  - !ruby/object:Gem::Version
75
- version: '1.4'
75
+ version: '1.6'
76
76
  type: :runtime
77
77
  prerelease: false
78
78
  version_requirements: !ruby/object:Gem::Requirement
79
79
  requirements:
80
80
  - - "~>"
81
81
  - !ruby/object:Gem::Version
82
- version: '1.4'
82
+ version: '1.6'
83
83
  - !ruby/object:Gem::Dependency
84
- name: genevalidator
84
+ name: bio
85
85
  requirement: !ruby/object:Gem::Requirement
86
86
  requirements:
87
87
  - - "~>"
88
88
  - !ruby/object:Gem::Version
89
- version: '1.5'
89
+ version: '1.4'
90
90
  type: :runtime
91
91
  prerelease: false
92
92
  version_requirements: !ruby/object:Gem::Requirement
93
93
  requirements:
94
94
  - - "~>"
95
95
  - !ruby/object:Gem::Version
96
- version: '1.5'
96
+ version: '1.4'
97
97
  - !ruby/object:Gem::Dependency
98
98
  name: sinatra
99
99
  requirement: !ruby/object:Gem::Requirement
@@ -156,14 +156,14 @@ dependencies:
156
156
  requirements:
157
157
  - - "~>"
158
158
  - !ruby/object:Gem::Version
159
- version: '4.0'
159
+ version: '3.6'
160
160
  type: :runtime
161
161
  prerelease: false
162
162
  version_requirements: !ruby/object:Gem::Requirement
163
163
  requirements:
164
164
  - - "~>"
165
165
  - !ruby/object:Gem::Version
166
- version: '4.0'
166
+ version: '3.6'
167
167
  - !ruby/object:Gem::Dependency
168
168
  name: thin
169
169
  requirement: !ruby/object:Gem::Requirement
@@ -209,35 +209,37 @@ files:
209
209
  - bin/genevalidatorapp
210
210
  - config.ru
211
211
  - genevalidatorapp.gemspec
212
- - lib/GeneValidatorApp.rb
213
- - lib/GeneValidatorApp/config.rb
214
- - lib/GeneValidatorApp/database.rb
215
- - lib/GeneValidatorApp/genevalidator.rb
216
- - lib/GeneValidatorApp/logger.rb
217
- - lib/GeneValidatorApp/version.rb
212
+ - lib/genevalidatorapp.rb
213
+ - lib/genevalidatorapp/config.rb
214
+ - lib/genevalidatorapp/database.rb
215
+ - lib/genevalidatorapp/exceptions.rb
216
+ - lib/genevalidatorapp/genevalidator.rb
217
+ - lib/genevalidatorapp/logger.rb
218
+ - lib/genevalidatorapp/routes.rb
219
+ - lib/genevalidatorapp/server.rb
220
+ - lib/genevalidatorapp/version.rb
218
221
  - public/GeneValidator/.gitkeep
219
- - public/web_files/css/bootstrap.min.css
220
- - public/web_files/css/bootstrap1.min.css
221
- - public/web_files/css/custom.css
222
- - public/web_files/css/custom.min.css
223
- - public/web_files/css/font-awesome.min.css
222
+ - public/src/css/bootstrap1.min.css
223
+ - public/src/css/custom.css
224
+ - public/src/css/custom.min.css
225
+ - public/src/css/font-awesome.min.css
226
+ - public/src/js/bionode-seq.min.js
227
+ - public/src/js/bootstrap.min.js
228
+ - public/src/js/d3.v3.min.js
229
+ - public/src/js/genevalidator.js
230
+ - public/src/js/jquery.cookie.min.js
231
+ - public/src/js/jquery.min.js
232
+ - public/src/js/jquery.tablesorter.min.js
233
+ - public/src/js/jquery.validate.min.js
234
+ - public/src/js/plots.js
235
+ - public/web_files/css/GV_compiled_css.min.css
224
236
  - public/web_files/fonts/FontAwesome.otf
225
237
  - public/web_files/fonts/fontawesome-webfont.eot
226
238
  - public/web_files/fonts/fontawesome-webfont.svg
227
239
  - public/web_files/fonts/fontawesome-webfont.ttf
228
240
  - public/web_files/fonts/fontawesome-webfont.woff
229
241
  - public/web_files/img/gene.png
230
- - public/web_files/js/bionode-seq.min.js
231
- - public/web_files/js/bootstrap.min.js
232
- - public/web_files/js/d3.v3.min.js
233
- - public/web_files/js/genevalidator.js
234
- - public/web_files/js/genevalidator.min.js
235
- - public/web_files/js/jquery.cookie.min.js
236
- - public/web_files/js/jquery.min.js
237
- - public/web_files/js/jquery.tablesorter.min.js
238
- - public/web_files/js/jquery.validate.min.js
239
- - public/web_files/js/plots.js
240
- - public/web_files/js/plots.min.js
242
+ - public/web_files/js/GV_compiled_js.min.js
241
243
  - spec/app_spec.rb
242
244
  - spec/database/funky_ids/funky_ids.fa
243
245
  - spec/database/funky_ids/funky_ids.fa.nhr
@@ -270,7 +272,8 @@ files:
270
272
  - views/500.slim
271
273
  - views/index.slim
272
274
  - views/layout.slim
273
- homepage: https://github.com/wurmlab/GeneValidatorApp
275
+ - views/results.slim
276
+ homepage: https://github.com/wurmlab/genevalidatorapp
274
277
  licenses:
275
278
  - AGPL
276
279
  metadata: {}
@@ -283,7 +286,7 @@ post_install_message: |2+
283
286
 
284
287
  $ genevalidatorapp [options]
285
288
 
286
- Visit https://github.com/wurmlab/GeneValidatorApp for more information.
289
+ Visit https://github.com/wurmlab/genevalidatorapp for more information.
287
290
  ------------------------------------------------------------------------
288
291
 
289
292
  rdoc_options: []
@@ -301,7 +304,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
301
304
  version: '0'
302
305
  requirements: []
303
306
  rubyforge_project:
304
- rubygems_version: 2.4.6
307
+ rubygems_version: 2.4.8
305
308
  signing_key:
306
309
  specification_version: 4
307
310
  summary: A Web App wrapper for GeneValidator.
@@ -335,3 +338,4 @@ test_files:
335
338
  - spec/database/without_parse_seqids/without_parse_seqids.fa.psq
336
339
  - spec/database_spec.rb
337
340
  - spec/empty_config.yml
341
+ has_rdoc:
data/lib/GeneValidatorApp.rb DELETED
@@ -1,321 +0,0 @@
1
- require 'GeneValidatorApp/database'
2
- require 'GeneValidatorApp/genevalidator'
3
- require 'GeneValidatorApp/logger'
4
- require 'GeneValidatorApp/config'
5
- require 'GeneValidatorApp/version'
6
- require 'genevalidator/version'
7
-
8
- require 'pathname'
9
- require 'yaml'
10
- require 'sinatra/base'
11
- require 'sinatra/cross_origin'
12
- require 'slim'
13
- require 'thin'
14
-
15
- module GeneValidatorApp
16
- # Use a fixed minimum version of BLAST+
17
- MINIMUM_BLAST_VERSION = '2.2.30+'
18
-
19
- class << self
20
- attr_reader :public_dir, :tempdir, :config
21
-
22
- # Returns the Rack Environment
23
- def environment
24
- ENV['RACK_ENV']
25
- end
26
-
27
- # Run by the logger method - sets the logger level to verbose if in
28
- # development environment
29
- def verbose?
30
- @verbose ||= (environment == 'development')
31
- end
32
-
33
- # Root dir of the App
34
- def root
35
- Pathname.new(__FILE__).dirname.parent
36
- end
37
-
38
- def logger
39
- @logger ||= Logger.new(STDERR, verbose?)
40
- end
41
-
42
- # Setting up the environment before running the app...
43
- def init(config = {})
44
- @config = Config.new(config)
45
- init_blast_and_mafft_binaries
46
- init_database
47
- load_extension
48
- check_num_threads
49
- check_max_characters
50
- init_gv_tempdir
51
- init_public_dir
52
- self
53
- end
54
-
55
- # Starting the app manually using Thin
56
- def run
57
- check_host
58
- url = "http://#{config[:host]}:#{config[:port]}"
59
- server = Thin::Server.new(config[:host], config[:port], signals: false) do
60
- use Rack::CommonLogger if GeneValidatorApp.environment == 'development'
61
- run GeneValidatorApp
62
- end
63
- server.timeout = 2700 # 45 minutes
64
- server.silent = true
65
- server.backend.start do
66
- puts '** GeneValidatorApp is ready.'
67
- puts " Go to #{url} in your browser and start analysing Genes!"
68
- puts ' Press CTRL+C to quit.'
69
- puts
70
- open_default_browser(url)
71
- [:INT, :TERM].each do |sig|
72
- trap sig do
73
- server.stop!
74
- puts
75
- puts
76
- puts '** Thank you for using GeneValidatorApp :).'
77
- puts ' Please cite: '
78
- puts ' Dragan M., Moghul M.I., Priyam A., Wurm Y (in prep).'
79
- puts ' GeneValidator: identify problematic gene predictions.'
80
- end
81
- end
82
- end
83
- rescue
84
- puts '** Oops! There was an error.'
85
- puts " Is GeneValidatorApp already accessible at #{url}?"
86
- puts ' Try running GeneValidatorApp on another port, like so:'
87
- puts
88
- puts ' genevalidatorapp -p 4570.'
89
- end
90
-
91
- # Set the max characters accepted from the app (for the app templates)
92
- def max_characters
93
- (config[:max_characters]) ? config[:max_characters] : 'undefined'
94
- end
95
-
96
- def [](key)
97
- config[key]
98
- end
99
-
100
- # Rack-interface.
101
- #
102
- # Inject our logger in the env and dispatch request to our
103
- # controller.
104
- def call(env)
105
- env['rack.logger'] = logger
106
- App.call(env)
107
- end
108
-
109
- private
110
-
111
- def open_default_browser(url)
112
- return if using_ssh?
113
- if RUBY_PLATFORM =~ /linux/
114
- `xdg-open #{url}` unless command?('xdg-open') || ENV['DISPLAY']
115
- elsif RUBY_PLATFORM =~ /darwin/
116
- `open #{url}`
117
- end
118
- end
119
-
120
- def using_ssh?
121
- true if ENV['SSH_CLIENT'] || ENV['SSH_TTY'] || ENV['SSH_CONNECTION']
122
- end
123
-
124
- def init_blast_and_mafft_binaries
125
- init_binaries(config[:blast_bin], 'NCBI BLAST+')
126
- assert_blast_installed_and_compatible
127
- init_binaries(config[:mafft_bin], 'Mafft')
128
- assert_mafft_installed
129
- end
130
-
131
- def init_binaries(bin_dir, type)
132
- if bin_dir
133
- bin_dir = File.expand_path bin_dir
134
- unless File.exist?(bin_dir) && File.directory?(bin_dir)
135
- fail BIN_DIR_NOT_FOUND, bin_dir
136
- end
137
- logger.debug("Will use #{type} at: #{config[:blast_bin]}")
138
- export_bin_dir bin_dir
139
- else
140
- logger.debug("Will use #{type} at: $PATH")
141
- end
142
- end
143
-
144
- def init_database
145
- fail DATABASE_DIR_NOT_SET unless config[:database_dir]
146
-
147
- config[:database_dir] = File.expand_path(config[:database_dir])
148
- unless File.exist?(config[:database_dir]) &&
149
- File.directory?(config[:database_dir])
150
- fail DATABASE_DIR_NOT_FOUND, config[:database_dir]
151
- end
152
-
153
- assert_blast_databases_present_in_database_dir
154
- logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
155
-
156
- Database.scan_databases_dir
157
- Database.each do |database|
158
- logger.debug("Found #{database.type.chomp} database" \
159
- " '#{database.title.chomp}' at '#{database.name.chomp}'")
160
- end
161
- end
162
-
163
- def check_num_threads
164
- num_threads = Integer(config[:num_threads])
165
- fail NUM_THREADS_INCORRECT unless num_threads > 0
166
- logger.debug "Will use #{num_threads} threads to run BLAST."
167
- if num_threads > 256
168
- logger.warn "Number of threads set at #{num_threads} is unusually high."
169
- end
170
- rescue
171
- raise NUM_THREADS_INCORRECT
172
- end
173
-
174
- def check_max_characters
175
- Integer(config[:max_characters]) if config[:max_characters]
176
- rescue
177
- raise MAX_CHARACTERS_INCORRECT
178
- end
179
-
180
- def load_extension
181
- return unless config[:require]
182
-
183
- config[:require] = File.expand_path config[:require]
184
- unless File.exist?(config[:require]) && File.file?(config[:require])
185
- fail EXTENSION_FILE_NOT_FOUND, config[:require]
186
- end
187
-
188
- logger.debug("Loading extension: #{config[:require]}")
189
- require config[:require]
190
- end
191
-
192
- # Asserts whether mafft is installed.
193
- def assert_mafft_installed
194
- fail MAFFT_NOT_INSTALLED unless command? 'mafft'
195
- end
196
-
197
- def assert_blast_installed_and_compatible
198
- fail BLAST_NOT_INSTALLED unless command? 'blastdbcmd'
199
- version = `blastdbcmd -version`.split[1]
200
- fail BLAST_NOT_COMPATIBLE, version unless version >= MINIMUM_BLAST_VERSION
201
- end
202
-
203
- def assert_blast_databases_present_in_database_dir
204
- cmd = "blastdbcmd -recursive -list #{config[:database_dir]}"
205
- out = `#{cmd}`
206
- errpat = /BLAST Database error/
207
- fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
208
- fail BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) ||
209
- !$?.success?
210
- end
211
-
212
- # Export bin dir to PATH environment variable.
213
- def export_bin_dir(bin_dir)
214
- return unless bin_dir
215
- return if ENV['PATH'].split(':').include? bin_dir
216
- ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
217
- end
218
-
219
- # Creates a Temp directory (starting with 'GeneValidator_') each time
220
- # GVapp is started. Within this Temp folder, sub directories are created
221
- # in which GeneValidator is run.
222
- def init_gv_tempdir
223
- @tempdir = Pathname.new(Dir.mktmpdir('GeneValidator_'))
224
- end
225
-
226
- # Copy the public folder (in the app root) to the web_dir location - this
227
- # web_dir is then used by the app to serve all dependencies...
228
- def init_public_dir
229
- @public_dir = Pathname.new(config[:web_dir]) +
230
- "GeneValidator_#{Time.now.strftime('%Y%m%d-%H%M%S')}"
231
- root_public_dir = GeneValidatorApp.root + 'public'
232
- FileUtils.cp_r(root_public_dir, @public_dir)
233
- end
234
-
235
- # Check and warn user if host is 0.0.0.0 (default).
236
- def check_host
237
- if config[:host] == '0.0.0.0'
238
- logger.warn 'Will listen on all interfaces (0.0.0.0).' \
239
- ' Consider using 127.0.0.1 (--host option).'
240
- end
241
- end
242
-
243
- # Return `true` if the given command exists and is executable.
244
- def command?(command)
245
- system("which #{command} > /dev/null 2>&1")
246
- end
247
- end
248
-
249
- # The Actual App...
250
- class App < Sinatra::Base
251
- register Sinatra::CrossOrigin
252
-
253
- configure do
254
- # We don't need Rack::MethodOverride. Let's avoid the overhead.
255
- disable :method_override
256
-
257
- # Ensure exceptions never leak out of the app. Exceptions raised within
258
- # the app must be handled by the app. We do this by attaching error
259
- # blocks to exceptions we know how to handle and attaching to Exception
260
- # as fallback.
261
- disable :show_exceptions, :raise_errors
262
-
263
- # Make it a policy to dump to 'rack.errors' any exception raised by the
264
- # app so that error handlers don't have to do it themselves. But for it
265
- # to always work, Exceptions defined by us should not respond to `code`
266
- # or http_status` methods. Error blocks errors must explicitly set http
267
- # status, if needed, by calling `status` method.
268
- enable :dump_errors
269
-
270
- # We don't want Sinatra do setup any loggers for us. We will use our own.
271
- set :logging, nil
272
-
273
- # This is the app root...
274
- set :root, lambda { GeneValidatorApp.root }
275
-
276
- # This is the full path to the public folder...
277
- set :public_folder, lambda { GeneValidatorApp.public_dir }
278
- end
279
-
280
- # Set up global variables for the templates...
281
- before '/' do
282
- @default_db = Database.default_db
283
- @non_default_dbs = Database.non_default_dbs
284
- @max_characters = GeneValidatorApp.max_characters
285
- @current_gv_version = GeneValidator::VERSION
286
- end
287
-
288
- get '/' do
289
- slim :index
290
- end
291
-
292
- post '/' do
293
- cross_origin # Required for the API to work...
294
- RunGeneValidator.init(request.url, params)
295
- RunGeneValidator.run
296
- end
297
-
298
- # This error block will only ever be hit if the user gives us a funny
299
- # sequence or incorrect advanced parameter. Well, we could hit this block
300
- # if someone is playing around with our HTTP API too.
301
- error RunGeneValidator::ArgumentError do
302
- status 400
303
- slim :"500", layout: false
304
- end
305
-
306
- # This will catch any unhandled error and some very special errors. Ideally
307
- # we will never hit this block. If we do, there's a bug in GeneValidatorApp
308
- # or something really weird going on.
309
- # TODO: If we hit this error block we show the stacktrace to the user
310
- # requesting them to post the same to our Google Group.
311
- error Exception, RunGeneValidator::RuntimeError do
312
- status 500 # TODO Create another template...
313
- slim :"500", layout: false
314
- end
315
-
316
- not_found do
317
- status 404
318
- slim :"500" # TODO: Create another Template
319
- end
320
- end
321
- end